tag:blogger.com,1999:blog-51177665367838875402024-03-10T23:23:05.829-04:00Biodiversity ScienceDirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.comBlogger1058125tag:blogger.com,1999:blog-5117766536783887540.post-45263102464612347862023-01-23T12:49:00.003-05:002023-01-23T12:49:38.939-05:00Conference PISCeS - 18-20 June 2023 at Guelph<div class="separator" style="clear: both; text-align: center;"><a href="http://www.uoguelph.ca/ib/pisces" imageanchor="1" style="margin-left: 1em; margin-right: 1em;" target="_blank"><img border="0" data-original-height="1207" data-original-width="679" height="640" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEi79MPv-2EYr3j8hcj5qnibZasYi4RjJYskueRi7t6ww2zsr0JQrDzHzYNRzwaEX718HutveHL4Jgffli17kK8T5Kmabg3ye6MsgtVAwGn-uKsf0z6hWEWTgJ6MAGKdlDstJQdoQj13UMIz4nVN56NngzwpP7ns8pc8aaEARIOtqCrEjuR77x-B8Haj0g/w360-h640/PISCeS.jpg" width="360" /></a></div><div class="separator" style="clear: both; text-align: center;"><a href="http://www.uoguelph.ca/ib/pisces" target="_blank"><span style="font-size: large;">for more info</span></a><br /></div><br /><p><br /></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-38003209003152201702022-12-14T14:41:00.004-05:002022-12-14T14:42:39.850-05:00Online Metabarcoding Course - March 6 to 31, 2023<div style="text-align: center;"><img alt="DNA bar code sequence" height="382" src="https://courses.opened.uoguelph.ca/srs/upload/06_DestinyPageBannerMetabarcoding.jpg" style="text-align: left;" width="640" /></div><div style="text-align: justify;"><span style="font-family: inherit;"><br /></span></div><div style="text-align: justify;"><span style="font-family: inherit;">It is time again for my online Metabarcoding course:</span></div><div style="text-align: justify;"><span style="font-family: inherit;"><br /></span></div><div style="text-align: justify;"><span style="font-family: inherit;">This course provides an overview of the state of current technology and the various sequencing platforms used. It consists of a series of online lectures and research exercises and will go over 4 weeks but is designed in a fashion that you can go through course content at your own pace and according to your own schedule with work worth 4-8h per week. The course is fully asynchronous to accommodate for participants from various time zones. We still strive to make it as interactive as possible.</span></div><div><p style="text-align: justify;"><span style="font-family: inherit;">I have updated course content to include the newest HTS technology and methods such as metagenomics and transcriptomics. </span></p><p style="caret-color: rgb(34, 34, 34); color: #222222; line-height: 20px; margin: 10px 0px; padding: 0px; text-align: justify;"><span style="font-family: inherit;">Throughout the course, we will explore:</span></p><ul style="caret-color: rgb(34, 34, 34); color: #222222;"><li style="text-align: justify;"><span style="font-family: inherit;">High throughput sequencing</span></li><li style="text-align: justify;"><span style="font-family: inherit;">Metabarcoding/Metagenomics</span></li><li style="text-align: justify;"><span style="font-family: inherit;">Metabarcoding analytics</span></li><li style="text-align: justify;"><span style="font-family: inherit;">Recent applications</span></li></ul><span style="font-family: inherit;"><span style="background-color: white; caret-color: rgb(34, 34, 34); color: #222222;"><span><div style="text-align: justify;">The course consists of a series of online lectures, research exercises, and group discussions where you have a chance to review the state of current technology, the various platforms used and the suite of bioinformatics tools available for sequence analysis and data interpretation.</div><div style="text-align: justify;"><br /></div></span></span><div style="text-align: justify;"><span style="font-family: inherit;">For more information please go on <a href="https://courses.opened.uoguelph.ca/search/publicCourseSearchDetails.do?method=load&courseId=18146&selectedProgramAreaId=16994&selectedProgramStreamId=12732257">the course enrolment page at the University of Guelph</a>.</span></div></span></div>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-36416895981777531302022-11-08T12:41:00.004-05:002022-11-08T12:45:12.247-05:00Post-Doctoral Fellowship in Bioinformatics and Ecological Genomics, University of Guelph, Canada<div><span style="font-family: helvetica;">I am looking for a new Postdoctoral Fellow. </span><span style="font-family: helvetica;">Here the official posting:</span></div><div><span style="font-family: helvetica;"><br /></span><b><span><span style="font-family: helvetica;">Land Acknowledgement<br /></span></span></b><span><span style="font-family: helvetica;">The University of Guelph resides on the treaty lands and territory of the Mississaugas of the Credit. We recognize this gathering place where we work and learn is home to many past, present, and future First Nations, Inuit, and Métis peoples. Our acknowledgement of the land is our declaration of our collective responsibility to this place and its peoples’ histories, rights, and presence.<br /></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">General Information (Six PDF Positions Available)<br /></span></span></b><span style="font-family: helvetica;"><span>This post-doctoral position will be part of the Food from Thought initiative funded through a Canada First Research Excellence Award: </span><a href="https://foodfromthought.ca/" style="color: #954f72; text-decoration: underline;"><span>https://foodfromthought.ca/</span></a><span>. Contributing to this large endeavour to improve food security and sustainability, our goal is to generate bioinformatics strategies for the prediction of biodiversity and ecosystem services from diverse data types, such as -omics data, digital photographs, and/or environmental data. Data analysis has begun to catch up with the pace of data generation, and in these times where understanding and mitigating the effects of climate change and feeding a growing human population is of utmost importance, we need to turn our sights on connecting different sources of data and extracting actionable meaning from them. The successful applicants will utilize existing and new biological and environmental datasets, along with additional external data, with the goal of predicting ecosystem services, ecosystem health status, and biodiversity metrics using approaches such as statistical learning, machine learning, and network analysis. This may include such important factors as pollination, invasive species resistance, pest control, trophic interactions, water quality, and others. Successful applicants will be part of a cohort of six postdoctoral scholars focused on bioinformatics and ecosystem services, who will work together with a multidisciplinary team of Principal Investigators, students, staff, industry members, and communities.<br /><o:p></o:p></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">What We Offer<br /></span></span></b><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>The opportunity to engage in creative and impactful research relevant for sustainability and </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>food security<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>The opportunity to collaborate with researchers in a variety of fields, including computer </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>science, statistics, ecology, evolutionary biology, and genomics<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Guidance to build valuable skills and to be well prepared for diverse future careers (skills </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>include scientific research; collaboration; communication with diverse stakeholders; </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>technical skills relating to coding, data analysis, graphics, code review, and publishing of </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>bioinformatics tools)<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Access to unique data sets and participation in collaborative partnerships with academics, </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>industry, and governmental agencies<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Regular, inclusive, and supportive mentorship from multiple PIs with diverse expertise to </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>support your research, career, and impact/outreach goals<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Participation in a collaborative working group of PDFs, workshops, and conferences<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Some monetary support for professional development, workshop participation, and </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>conference attendance as well as open-access publishing<br /><o:p></o:p></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">Specific Information (PDF in Bioinformatics and Ecological Genomics)<br /></span></span></b><span style="font-family: helvetica;"><span>We are seeking candidates interested in developing bioinformatics tools for taxonomic and functional annotation of multi-kingdom samples. Data are generated from amplicon-based approaches and/or metagenomics/totalRNA. We want to </span><span lang="EN-US">estimate and potentially forecast how local biodiversity is shaped by regional diversity, functional shifts within communities, spatial gradients of biotic and abiotic factors, seasonal climatic constraints, local habitat heterogeneity, and anthropogenic stressors. <br /><o:p></o:p></span></span><span><span style="font-family: helvetica;">Anticipated deliverables from the research include: one or more scientific publication(s), well-commented and documented code that is made publicly available by the end of the project such that that it is user friendly and can respond to future data availability. The successful PDFs will also be expected to participate in a PDF Working Group (which may include collegial discussion, collaboration, and/or reciprocal code reviews prior to publication), in annual Knowledge Mobilization Working Group Meetings, as well as in at least one relevant scientific conference. The successful applicant will also play a role in co-mentoring undergraduate or graduate students.<br /></span></span><span><span style="font-family: helvetica;">The selected candidate will be based in the research group of Dr. Dirk Steinke (Adjunct Professor of Integrative Biology & Bioinformatics) and will also benefit from working closely with a co-advisor with complementary expertise in statistics or computer science as well as other collaborators.<br /></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">Required Qualifications & Attributes<br /></span></span></b><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Must hold a PhD in bioinformatics, evolutionary biology, molecular ecology, genomics, or a <span> <span> </span></span></span></span></div><div><span style="font-family: helvetica;"><span><span><span> <span> </span></span>r</span>elated discipline<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Published at least one first-authored paper in a peer-reviewed journal <br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Experience with coding in at least one computer language (intermediate to advanced level </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>required; skills must include: data formatting and filtering, data exploration and quality </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>checking, graphics, data analysis; prior experience in usage of high-performance </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>computing resources an asset; prior experience in software development and code testing </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>an asset)<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Experience with at least two of the following: statistical analysis, analysis of DNA </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>sequencing data, genome assembly, machine learning, and/or statistical learning, <br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Commitment to transparent and reproducible science (evidence of this commitment could </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>include prior publication of code and/or a thorough methods section in your prior </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>publication(s))<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Commitment to respectful interactions with others and to equity, diversity & inclusion </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>(evidence of this attribute could include: prior or planned mentorship activities or </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>collaborations; participation in relevant committees or working groups; your personal </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>communication practices, etc.)<br /><o:p></o:p></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span></b><b><span><span style="font-family: helvetica;">Application Requirements<br /></span></span></b><span><span style="font-family: helvetica;">A completed application will consist of:<br /></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Cover letter describing your interest in the position and also highlighting how you meet the </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>required qualifications and attributes<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Curriculum vitae (including education history, experience and skills, publications, </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>conference presentations, outreach or leadership activities, interests)<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>Names and contact information for three referees (You may feel to include academic </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>advisors, collaborators, and/or an individual you have mentored.)<br /><o:p></o:p></span></span><span style="font-family: helvetica;"><span style="mso-list: Ignore;">·<span style="font-stretch: normal; font-style: normal; font-variant-caps: normal; font-weight: normal; line-height: normal;"> </span></span><!--[endif]--><span>PDF reprint of 1-3 publications (should be first author of at least one work published or in </span></span></div><div><span style="font-family: helvetica;"><span><span> <span> </span></span>press; pre-prints are welcome among the selected submissions)<br /><o:p></o:p></span></span><span><span style="font-family: helvetica;"><br /></span></span></div><div><span><span style="font-family: helvetica;">Please combine all of the above components into a <b>single PDF</b> and email to:<br /></span></span><span><span style="font-family: helvetica;"><b>Dr. Dirk Steinke: dsteinke@uoguelph.ca<br /></b></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">Length of Appointment & Salary<br /></span></span></b><span><span style="font-family: helvetica;">The PDF position is available for two years. Goal setting will be completed collaboratively early in the position, and progression will be discussed through regular meetings and reviewed at the one-year mark. The salary is $47,000 Canadian dollars annually, plus 17.2% value in benefits. The selected candidate will also benefit through access to $5,000 in travel funds for workshops and conferences and at least $3,000 to publish in open-access venues.<br /></span></span><b><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span></b><b><span><span style="font-family: helvetica;">Deadline<br /></span></span></b><span><span style="font-family: helvetica;">Review of applications will commence on December 15 and proceed until the position is filled. The start date will be as soon as possible thereafter (subject to discussion with the successful applicant).<br /></span></span><span><o:p><span style="font-family: helvetica;"> <br /></span></o:p></span><b><span><span style="font-family: helvetica;">Equity, Diversity & Inclusion<br /></span></span></b><span style="background-color: white; color: #2c2727; line-height: 15.693334px;"><span style="font-family: helvetica;">The <a href="https://ecologicalgenomics.ca" target="_blank">Steinke lab</a> strongly supports diversity in science, and applicants from under-represented racial, cultural, gender-identity, physical ability, and/or neurological spectrums are particularly encouraged to apply. Applications can be received immediately; however, evaluation of the applications will not commence until December 15, 2022 in order to allow for a diverse applicant pool to be evaluated.</span></span></div><p class="MsoListParagraphCxSpFirst" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpLast" style="mso-list: l2 level1 lfo1; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpFirst" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="margin-left: 18pt; mso-add-space: auto; mso-list: l0 level1 lfo2; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpFirst" style="mso-list: l1 level1 lfo3; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l1 level1 lfo3; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpMiddle" style="mso-list: l1 level1 lfo3; text-indent: -18pt;"><!--[if !supportLists]--></p><p class="MsoListParagraphCxSpLast" style="mso-list: l1 level1 lfo3; text-indent: -18pt;"><!--[if !supportLists]--></p><p style="text-align: justify;"><style class="WebKit-mso-list-quirks-style">
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</style></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-70188570674258675992022-09-16T11:16:00.000-04:002022-09-16T11:16:08.593-04:00Research support program La Tribuna in Colombia.<p>Great video about the research support program La Tribuna in Colombia.</p><p style="text-align: center;"><iframe allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/MmfU3bmeGlU" title="YouTube video player" width="560"></iframe></p><p>An exemplary participatory science exercise: This video shows how the inhabitants of this region become 'biomonitors', people from the local community who, by sharing their expertise, generate a dialogue of traditional knowledge with students from different universities in Colombia. In turn, they learn about modern research methods.</p><p>The video is in Spanish but that's no problem. It is not a problem to understand the message.</p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-65267643646365821292022-08-16T08:24:00.001-04:002022-08-16T08:24:14.335-04:00Job announcement - NINA, Norway: Bioinformatician with focus on eDNA and DNA-metabarcoding<p> <a href="http://www.nina.no/ninaenglish/Start.aspx" style="border: 0px; box-sizing: content-box; color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 20px; font-stretch: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">NINA </a><span style="background-color: white; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 20px;">is among Norway’s largest applied ecology research institutes with approximately 300 employees. NINA´s staff conducts natural and social science research related to interactions between humans and nature. The company’s head office is located in Trondheim, adjacent to the Norwegian University for Science and Technology (NTNU) Gløshaugen campus. NINA also has satellite offices in Oslo, Lillehammer, Bergen and Tromsø, and a salmonid research station at Ims in Rogaland County. The position will be based in NINA´s Department for Aquatic Biodiversity in Trondheim.</span></p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">NINA conducts high quality, applied research that is directly relevant to real world applications. Our projects are financed by a broad variety of private and public sector clients, including environmental managers, industry, and national and international research councils. NINA is a leading research institute in ecological genetics both nationally and internationally, hosting well-equipped modern lab facilities at our Trondheim location. We increasingly use genetic methods for mapping and monitoring of biodiversity on landscape to population levels, and for the detection and monitoring of invasive species, and threatened species. <a href="https://www.nina.no/miljo-DNA" style="border: 0px; box-sizing: content-box; color: #425563; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">NINA runs several national monitoring projects involving eDNA</a> from water, soil, and scat samples, analyzing diversity of fungi, plants, insects, fish, mammals and more. NINA therefore sees a strategic need for bioinformatic expertise in the genetic group in Trondheim, and wishes to expand the group with a permanent, full-time research technician in bioinformatics. </p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">Key tasks in the position will be bioinformatic processing of sequence data and database management, particularly in relation to environmental DNA applications. However, other types of biological data collected in NINA are also relevant for the position. Depending on their skills and preferences, the successful candidate may also be involved in writing of scientific reports and papers, statistical analyses, and graphic presentations of results.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">The successful candidate will be independent and an initiative taker, preferably holding an MSc degree or equivalent in bioinformatics or biology, and with practical qualifications and experience with bioinformatic analyses, R, Bash, Python and SQL/database management. Experience with eDNA and DNA-metabarcoding data is an advantage. Competence within population genetics is a plus, but not a requirement for the position. You are proactive, a good communicator, and like to work in interdisciplinary teams. You like scripting and programming using large datasets and you can handle working with several projects at the same time. You are prepared for challenging and variable work and are flexible to meet the variation of tasks included in applied research.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">The position will be based at the Department of Aquatic biodiversity in Trondheim, but the successful candidate is expected to work on a broad array of projects across all departments in NINA.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">NINA has an international working environment, with employees from more than 25 nationalities. The working language in NINA is Norwegian and it is expected that the successful candidate for this position will learn Norwegian after starting in NINA, if the candidate is not already familiar with a Scandinavian language.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;"><strong style="border: 0px; box-sizing: content-box; color: inherit; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">NINA offers</strong></p><ul style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; list-style-image: initial; list-style-position: outside; margin-block-start: 1em; padding: 0px 0px 0px 15px; vertical-align: baseline;"><li style="border: 0px; box-sizing: content-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; list-style-type: inherit; margin: 0px 0px 2px; padding: 0px; vertical-align: baseline;">Permanent position in one of Europe’s strongest environmental research institutes</li><li style="border: 0px; box-sizing: content-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; list-style-type: inherit; margin: 0px 0px 2px; padding: 0px; vertical-align: baseline;">Payment according to scientific merits and experiences</li><li style="border: 0px; box-sizing: content-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; list-style-type: inherit; margin: 0px 0px 2px; padding: 0px; vertical-align: baseline;">Flexible working hours</li><li style="border: 0px; box-sizing: content-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; list-style-type: inherit; margin: 0px 0px 2px; padding: 0px; vertical-align: baseline;">Obligatory, attractive group pension scheme and insurance</li><li style="border: 0px; box-sizing: content-box; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; list-style-type: inherit; margin: 0px 0px 2px; padding: 0px; vertical-align: baseline;">Attractive work environment in modern offices of high standard</li></ul><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">Applications may be submitted on e-mail to <a href="mailto:siri.svendsen@nina.no" style="border: 0px; box-sizing: content-box; color: #425563; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">siri.svendsen@nina.no</a>. It must include a CV with information on education, relevant work experience, references, and, if relevant, list of scientific publications.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">Competitive candidates will be invited for interview.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">NINA works actively to create a more diverse and inclusive work environment, as well as to recruit more women into research positions. Researchers with a minority background, women, and candidates who contribute to a wider diversity are therefore encouraged to apply.</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;"><strong style="border: 0px; box-sizing: content-box; color: inherit; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">Enquiries about the positions can be made to:</strong></p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">Senior Scientist Frode Fossøy (<a href="mailto:frode.fossoy@nina.no" style="border: 0px; box-sizing: content-box; color: #425563; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">frode.fossoy@nina.no</a>, tel: +47 99692303)</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;">Research Director Ingeborg Palm Helland (<a href="mailto:ingeborg.helland@nina.no" style="border: 0px; box-sizing: content-box; color: #425563; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; vertical-align: baseline;">ingeborg.helland@nina.no</a>, tel: +47 97654820)</p><p style="border: 0px; box-sizing: content-box; caret-color: rgb(66, 85, 99); color: #425563; font-family: "Open Sans", Helvetica, Arial; font-size: 18px; font-stretch: inherit; line-height: 27px; margin: 0px 0px 17px; padding: 0px; vertical-align: baseline;"><strong style="border: 0px; box-sizing: content-box; color: inherit; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">Application deadline is 15 of September 2022.</strong></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-82733565206318544902021-12-09T08:14:00.001-05:002021-12-09T08:15:04.422-05:00PhD position on pond turtles and metabarcoding<p><span style="font-family: ArialMT; font-size: 11pt; text-align: justify;">The </span><a href="https://tbg.senckenberg.de/" style="font-family: ArialMT; font-size: 11pt; text-align: justify;">LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG)</a><span style="font-family: ArialMT; font-size: 11pt; text-align: justify;"> aims at making the genomic basis of biological diversity accessible for basic and applied research. Building on genome sequencing and analysis, LOEWE-TBG research topics range from comparative genomics, natural products genomics, and genomic biomonitoring to functional environmental genomics. LOEWE-TBG is based in Frankfurt am Main, Germany, and is a joint venture of the Senckenberg Gesellschaft für Naturforschung (SGN), Goethe-University Frankfurt, Justus-Liebig-University Giessen and Fraunhofer Institute for Molecular Biology and Applied Ecology.</span></p><div class="page" title="Page 1"><div class="layoutArea"><div class="column"><p style="text-align: justify;"><span style="font-family: ArialMT; font-size: 11pt;">Subject to funding approval LOEWE-TBG and the Senckenberg Gesellschaft für Naturforschung invite applications for a</span></p><p style="text-align: center;"><span style="font-family: Arial; font-size: 13pt; font-weight: 700;">PhD Position (m/f/d; 65%) in the EU-project</span></p><p style="text-align: justify;"><span style="font-family: Arial; font-size: 11pt; font-weight: 700;">EMYS-R: A socio-ecological evaluation of wetlands restoration and reintroduction programs in favor of the emblematic European pond turtle and associated biodiversity: a pan-European approach</span></p><p style="text-align: justify;"><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">Project background: </span><span style="font-family: ArialMT; font-size: 10pt;">Over the last 3 decades, the EU has funded numerous projects for wetland restoration in favor of the European pond turtle. Yet the results of these measures need to be more intensely promoted. A key question remains unanswered: what are the most effective wetland restoration methods suitable for sustainable maintenance and recovery of the European pond turtle and associated wildlife throughout Europe?</span></p><p style="text-align: justify;"><span style="font-family: ArialMT; font-size: 10pt;">EMYS-R consolidates an existing international network of researchers and stakeholders to share complementary knowledge on past, present and future wetlands, biodiversity and their management. It is a 3-year participatory action-oriented research project based on seminal theories in humanities, social and natural sciences. It aims at testing the hypothesis that higher degrees of wetland restoration can compensate for limited capabilities of captive bred turtles to settle in the wild, and assess how specifically such conservation actions benefit society by bringing together people and nature.</span></p><p><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">Your tasks:</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">The successful PhD candidate will be involved in the ecological assessment of wetland restoration, turtle reintroduction and consequences on local biodiversity including non-target species. While based in Frankfurt am Main, Germany, the candidate will spend a substantial amount of time at the German and French field sites, and will also be traveling to trainings and meetings in Poland and Latvia, contributors of the EMYS-R consortium. More specifically, the successful candidate will conduct the following tasks:</span></p><ul><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Data collection: behavioral (animal-borne data loggers including GPS and time-depth-acceleration recorders), biometric/demographic (capture-mark-recapture protocols) and ecological (water, sediment, turtle-centered prey-predators feces samples) on the German study site in Neuburg am Rhein</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">eDNA Metabarcoding of environmental (water and sediment) and ecological (turtle prey-predator feces) samples</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">bioinformatic analyses of metabarcoding sequences for genomic biodiversity monitoring and food web analyses</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Data analyses of existing and formerly collected time series on turtle behavior, biometry and demography</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Support and then lead field sessions in Neuburg am Rhein</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Support with public perception seminars and workshops in Neuburg am Rhein</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Literature review on German-written grey literature about wetland renaturations and turtle reintroductions</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Writing scientific publications, contributing to national and international conferences, as well as to internal</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">reports and international guidelines</span></p></li></ul></div></div></div><div class="page" title="Page 2"> <div class="layoutArea"><div class="column"><p><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">Your profile:</span></p><ul style="text-align: left;"><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Master degree in Biology, Ecology, Environmental Sciences, or equivalent</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Programming experience with manipulating large database (Metabarcoding sequences, behavioral long time</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">series)</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">knowledge in R, MatLab and Linux desirable</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Experience in the molecular genetic lab</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Experience with Metabarcoding desirable</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Mastering multivariate statistics</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Interest in interdisciplinary approaches</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Proven capabilities in implementing field protocols in remote places in autonomy and within a team</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Able to team up within a large international consortium</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Professional communication skills within the scientific consortium, but also with local stakeholders</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Fluent (speech and writing/reading) in German and English</span></p></li><li style="font-family: SymbolMT; font-size: 10pt;"><p><span style="font-family: ArialMT; font-size: 10pt;">Ideally you are owner of the driving license B, are easy with wetlands and are able to swim</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">Salary and benefits are according to a full-time public service position in Germany (TV-H E 13, 65%). The contract should start as soon as possible </span><span style="font-family: ArialMT; font-size: 10pt;">– </span><span style="font-family: ArialMT; font-size: 10pt;">but no later than April 1</span><span style="font-family: ArialMT; font-size: 6pt; vertical-align: 3pt;">st</span><span style="font-family: ArialMT; font-size: 10pt;">, 2022 - and will initially be limited for 3 years.</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">The Senckenberg Research Institutes support equal opportunity of men and women and therefore strongly invites women to apply. Equally qualified handicapped applicants will be given preference. The place of employment is in Frankfurt am Main, Germany.</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">Please send your application, mentioning the reference of this job offer (</span><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">ref. #12-21008</span><span style="font-family: ArialMT; font-size: 10pt;">) before </span><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">14.01.2022 </span><span style="font-family: ArialMT; font-size: 10pt;">by e-mail (attachment in a single pdf document) and including a cover letter detailing research interests and experience, a detailed CV and a copy of your certification to:</span></p><p><span style="font-family: ArialMT; font-size: 10pt;">Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25<br />60325 Frankfurt am Main</span></p><p><span style="font-family: Arial; font-size: 10pt; font-weight: 700;">E-Mail: </span><span style="color: blue; font-family: ArialMT; font-size: 10pt;">recruiting@senckenberg.de<br /></span><span style="font-family: ArialMT; font-size: 10pt;">For more information contact Dr. Kathrin Theissinger (</span><span style="color: blue; font-family: ArialMT; font-size: 10pt;">kathrin.theissinger@senckenberg.de</span><span style="font-family: ArialMT; font-size: 10pt;">).</span></p></li></ul></div></div></div>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-68496291338766253752021-12-07T15:43:00.001-05:002021-12-07T15:43:15.061-05:00Course: Introduction to DNA Barcoding<p> Instructor - yours truly.</p><p style="text-align: center;"><img align="center" alt="Blue samples of DNA across a dark blue background." class="mcnImage" src="https://mcusercontent.com/4a93dfac0538f9300b5765ce4/images/0c1d846c-4fe2-c554-9008-02b39cd38c13.jpg" style="border: 0px; display: inline !important; height: auto; max-width: 1200px; outline: none; padding-bottom: 0px; vertical-align: bottom;" width="600" /></p><p><br /></p><table border="0" cellpadding="0" cellspacing="0" class="mcnTextBlock" style="border-collapse: collapse; color: black; min-width: 100%; width: 100%px;"><tbody class="mcnTextBlockOuter"><tr><td class="mcnTextBlockInner" style="padding-top: 9px;" valign="top"><table align="left" border="0" cellpadding="0" cellspacing="0" class="mcnTextContentContainer" style="border-collapse: collapse; max-width: 100%; min-width: 100%; width: 100%px;"><tbody><tr><td class="mcnTextContent" style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; line-height: 20px; padding: 0px 18px 9px; word-break: break-word;" valign="top"><h1 class="null" style="font-size: 22px; line-height: 27.5px; margin: 0px; padding: 0px; text-align: center;">Early bird deadline - register soon!</h1></td></tr></tbody></table></td></tr></tbody></table><table border="0" cellpadding="0" cellspacing="0" class="mcnTextBlock" style="border-collapse: collapse; color: black; min-width: 100%; width: 100%px;"><tbody class="mcnTextBlockOuter"><tr><td class="mcnTextBlockInner" style="padding-top: 9px;" valign="top"><table align="left" border="0" cellpadding="0" cellspacing="0" class="mcnTextContentContainer" style="border-collapse: collapse; max-width: 100%; min-width: 100%; width: 100%px;"><tbody><tr><td class="mcnTextContent" style="line-height: 20px; padding: 0px 18px 9px; word-break: break-word;" valign="top"><p style="line-height: 20px; margin: 10px 0px; padding: 0px;"></p><div style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; text-align: justify;">The use of DNA Barcoding continues to enhance species identification and biodiversity conservation. Stay up-to-date with the latest research and join the growing industry with <a href="https://courses.opened.uoguelph.ca/search/publicCourseSearchDetails.do?method=load&courseId=18560&selectedProgramAreaId=16994&selectedProgramStreamId=12732257" style="color: #c20430;" target="_blank">Introduction to DNA Barcoding</a>.</div><div style="text-align: justify;"><span style="caret-color: rgb(34, 34, 34); color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif;"><br /></span></div><span style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif;"><div style="text-align: justify;">Take advantage of the opportunity to learn from prominent DNA researcher Dirk Steinke as he guides you through a variety of topics that showcase the different applications of DNA Barcoding.</div></span><br /><strong style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;">Course dates</strong><span style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif;">: January 17 to March 13, 2022</span><br /><strong style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;">Don't forget</strong><span style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif;"> to register by </span><strong style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px;">December 18, 2021</strong><span style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif;"> and save on tuition with our early bird pricing!</span><p></p><table border="0" cellpadding="0" cellspacing="0" class="mcnTextBlock" style="border-collapse: collapse; color: black; min-width: 100%; width: 100%px;"><tbody class="mcnTextBlockOuter"><tr><td class="mcnTextBlockInner" style="padding-top: 9px;" valign="top"><table align="left" border="0" cellpadding="0" cellspacing="0" class="mcnTextContentContainer" style="border-collapse: collapse; max-width: 100%; min-width: 100%; width: 100%px;"><tbody><tr><td class="mcnTextContent" style="color: #222222; font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 16px; line-height: 20px; padding: 0px 18px 9px; word-break: break-word;" valign="top"><p style="line-height: 20px; margin: 10px 0px; padding: 0px;"></p></td></tr></tbody></table></td></tr></tbody></table><table border="0" cellpadding="0" cellspacing="0" class="mcnButtonBlock" style="border-collapse: collapse; color: black; min-width: 100%; width: 100%px;"><tbody class="mcnButtonBlockOuter"><tr><td align="center" class="mcnButtonBlockInner" style="padding: 0px 18px 18px;" valign="top"><table border="0" cellpadding="0" cellspacing="0" class="mcnButtonContentContainer" style="background-color: #c20430; border-bottom-left-radius: 6px; border-bottom-right-radius: 6px; border-top-left-radius: 6px; border-top-right-radius: 6px;"><tbody><tr><td align="center" class="mcnButtonContent" style="font-family: Roboto, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 18px; padding: 15px;" valign="middle"><a class="mcnButton " href="https://courses.opened.uoguelph.ca/search/publicCourseSearchDetails.do?method=load&courseId=18560&selectedProgramAreaId=16994&selectedProgramStreamId=12732257" style="color: white; display: block; font-weight: bold; line-height: 18px; text-decoration: none;" target="_blank" title="Sign me up!">Sign me up!</a></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table></td></tr></tbody></table>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-65280078303177974032021-10-28T08:07:00.002-04:002021-10-28T08:07:14.106-04:00PhD positions at LIB, Bonn<p><span style="font-family: Calibri, sans-serif; font-size: 12pt;"><b>From the Inbox:</b></span></p><p><span style="font-family: Calibri, sans-serif; font-size: 12pt;"><br /></span></p><p><span style="font-family: Calibri, sans-serif; font-size: 12pt;">Dear colleagues,</span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;">I'm currently offering two PhD positions in my recently started SAW-funded junior research group on "Hybrid swarm evolution of native and invasive <i>Phoxinus</i> spp. to the river Sieg, Germany" at the ZMB and ZTM. For those wondering: it's vertebrates --> <u>fish</u>.<o:p></o:p></span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;">The exciting thing is that I am looking for i) one person specialising on ecology and morphology of the fishes and ii) the other person focusing on the genomics. So I'd say the project encompasses a large bouquet for different interests and abilities that jointly venture to understand the hybridisation processes and the invasiveness of hybrids in locally endangered minnow populations.<o:p></o:p></span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;">Deadline is Nov. 7 2021, apply here <a href="https://leibniz-lib.de/en/karriere/" id="LPlnk512565" style="color: purple;" title="https://leibniz-lib.de/en/karriere/"><span style="color: windowtext;">https://leibniz-lib.de/en/karriere/</span></a>!<o:p></o:p></span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;">Thanks and best wishes,<o:p></o:p></span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;">Madlen<o:p></o:p></span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><p style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><div id="Signature"><div id="divtagdefaultwrapper"><div id="divtagdefaultwrapper"><p class="MsoNormal" style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="color: #888888; font-family: Arial, sans-serif; font-size: 10pt;"><img alt="1628580065501" border="0" height="35" id="_x0000_i1025" src="blob:https://www.blogger.com/783e743c-5add-44f8-ac65-dab505bb5dc4" width="306" /></span><span style="font-family: Calibri, sans-serif;"><o:p></o:p></span></p></div><div><p class="MsoNormal" style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p></div><div><p class="MsoNormal" style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><span style="font-family: Calibri, sans-serif;"> </span></p><div><p class="MsoNormal" style="font-family: "Times New Roman", serif; font-size: 12pt; margin: 0cm 0cm 0.0001pt;"><b><span style="font-family: "Source Sans Pro", sans-serif; font-size: 10pt;"> </span></b><b><span lang="DE-CH" style="font-family: "Source Sans Pro", sans-serif; font-size: 10pt;">Dr. Madlen Stange</span></b></p></div></div></div></div>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-59030660677810934112021-02-02T15:38:00.001-05:002021-02-02T15:38:46.346-05:00MSc position, Bees@School project – Fall 2021<p> <b style="font-family: Calibri, sans-serif; text-align: justify;"><span style="font-family: "Times New Roman", serif;">Changing wild bee species distributions and pollination service shifts</span></b></p><p class="MsoNormal" style="margin: 0cm; text-align: justify;"><span style="font-family: Times New Roman, serif;">A MSc graduate student position is available in </span><a href="http://steinkelab.uoguelph.ca/" style="font-family: "Times New Roman", serif;" target="_blank">my research group</a><span style="font-family: Times New Roman, serif;"> in the </span><a href="https://www.uoguelph.ca/ib/" style="font-family: "Times New Roman", serif;" target="_blank">Department of Integrative Biology</a><span style="font-family: Times New Roman, serif;"> at the </span><a href="https://www.uoguelph.ca/cbs/" style="font-family: "Times New Roman", serif;" target="_blank">College of Biological Sciences</a> -<span style="font-family: Times New Roman, serif;"> <a href="https://www.uoguelph.ca" target="_blank">University of Guelph</a>. Research in our group focusses on biodiversity genomics and the development of metabarcoding and metagenomic approaches for biodiversity research. </span><span lang="EN-US" style="font-family: "Times New Roman", serif;">We seek not only information on how communities are composed but also how its members are interconnected and interdependent. In addition to simply counting and registering we explore relationships between community members, to better understand the functional competence of communities, and to model responses to changes in the environment. </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span lang="EN-US" style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">I am looking for an enthusiastic MSc graduate student who wants to work on a research project that is done in close collaboration with schools across Canada and the <a href="http://biodiversitygenomics.net" target="_blank">Centre for Biodiversity Genomics</a>. Each year the <a href="https://beesatschools.ca/" target="_blank">Bees@School project</a> teams up with 200 school classrooms to provide critical information on the changing geographic distributions of plant-pollinator interactions across Canada, and be of considerable benefit to everyone as pollinator-dependent foods already make up a third of our diet. By combining state-of-the-art DNA metabarcoding of bees, and the pollen they carry, with distribution and climate change data, we explore how distributions of Canada’s bee species are changing along with climate. The project also determines how pollination services shift across Canada, with impacts on food production and landscape management advice to improve vital species chances of persisting in agricultural landscapes and alleviating pollination deficits.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">Desired qualifications include excellent communication and strong writing skills (interactions with both school teachers and students are part of the project). The project involves extensive molecular laboratory work (metabarcoding), computational approaches that include some programming and the use of high performance computing infrastructure, as well as GIS modelling. No extensive prior experience is required, but applicants must be willing to learn. Attention to detail and an aptitude towards sometimes tedious manual labour is an asset. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">Highly motivated students with a BSc degree and honours research experience (or equivalent) will be considered. Candidates with strong background in Ecology, Molecular Biology, or Environmental Biology are preferred. This position is open to Canadian citizens or permanent residents. Other strong candidates are also welcome to apply. To learn more about this project and the application process, contact me (<a href="mailto:dsteinke@uoguelph.ca">dsteinke@uoguelph.ca</a>) with your CV, transcript (unofficial is fine), and contact information for two references. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">Dr. Dirk Steinke<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">Department of Integrative Biology | Centre for Biodiversity Genomics<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">University of Guelph<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;">E-mail: <a href="mailto:dsteinke@uoguelph.ca" style="color: #954f72;">dsteinke@uoguelph.ca</a><o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; margin: 0cm; text-align: justify;"><span style="font-family: "Times New Roman", serif;"><a href="http://steinkelab.uoguelph.ca/" style="color: #954f72;">http://steinkelab.uoguelph.ca</a><o:p></o:p></span></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-77307561772108487742021-01-21T12:12:00.000-05:002021-01-21T12:12:02.145-05:00Online Metabarcoding Course - March 1 to 28, 2021<div class="separator" style="clear: both; text-align: center;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiB8d-EuEdFFQ8NtI-XYdfY8qo7qE5oMNzW9lm7ppBqlZvktOYhBQ4nP089gtEU7rGSwHG9yRoadeHjBW-Ry5G0q00XAHWVZEx6X3kDcPr1Jm4teojB4gG_B9l0R8u8a8ZlxojCL69cDqZt/s629/47f2a186-e91d-4488-b065-25fa7ec27920.jpg" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="260" data-original-width="629" height="165" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiB8d-EuEdFFQ8NtI-XYdfY8qo7qE5oMNzW9lm7ppBqlZvktOYhBQ4nP089gtEU7rGSwHG9yRoadeHjBW-Ry5G0q00XAHWVZEx6X3kDcPr1Jm4teojB4gG_B9l0R8u8a8ZlxojCL69cDqZt/w400-h165/47f2a186-e91d-4488-b065-25fa7ec27920.jpg" width="400" /></a></div><br /><p><br /></p><p style="text-align: justify;"><span style="font-family: helvetica;">A reminder that <a href="https://courses.opened.uoguelph.ca/search/publicCourseSearchDetails.do?method=load&courseId=18146&selectedProgramAreaId=16994&selectedProgramStreamId=12732257">this course will start in a little over a month</a>. The deadline for Early bird registration is January 31st to receive a discount. </span></p><p style="text-align: justify;"><span style="font-family: helvetica;">I have updated course content to include the newest HTS technology and methods such as metagenomics and transcriptomics. </span></p><p style="caret-color: rgb(34, 34, 34); color: #222222; line-height: 20px; margin: 10px 0px; padding: 0px; text-align: justify;"><span style="font-family: helvetica;">Throughout the course, we will explore:</span></p><ul style="caret-color: rgb(34, 34, 34); color: #222222;"><li style="text-align: justify;"><span style="font-family: helvetica;">High throughput sequencing</span></li><li style="text-align: justify;"><span style="font-family: helvetica;">Metabarcoding/Metagenomics</span></li><li style="text-align: justify;"><span style="font-family: helvetica;">Metabarcoding analytics</span></li><li style="text-align: justify;"><span style="font-family: helvetica;">Recent applications</span></li></ul><span style="background-color: white; caret-color: rgb(34, 34, 34); color: #222222;"><span style="font-family: helvetica;"><div style="text-align: justify;">The course consists of a series of online lectures, research exercises, and group discussions where you have a chance to review the state of current technology, the various platforms used and the suite of bioinformatics tools available for sequence analysis and data interpretation.</div><div style="text-align: justify;"><br /></div><div style="text-align: justify;">Would be great to meet you there!</div></span></span>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-81721397886782443322020-11-12T15:19:00.000-05:002020-11-12T15:19:18.196-05:00Metabarcoding remote learning course - March 01, 2021 to March 28, 2021<p style="text-align: justify;"><br />I will be teaching our Metabarcoding course again coming March (March 01, 2021 to March 28, 2021).</p><div class="separator" style="clear: both; text-align: left;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgR1_Z8rT7sVI09bo_GkAVUIcV9P7ps6tkq0UP2Q68Dj_LCgHfXP6l_au1RCXlbJSAJvCKsANO1rEHEnY2u-h8YsBt6f_x51B-uf2Dbx24KZ0dEZ7f24fnsO0pe6N6PnSVaCNnFTbaOh3v-/s2048/Screen+Shot+2019-09-13+at+2.45.37+PM.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="1575" data-original-width="2048" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgR1_Z8rT7sVI09bo_GkAVUIcV9P7ps6tkq0UP2Q68Dj_LCgHfXP6l_au1RCXlbJSAJvCKsANO1rEHEnY2u-h8YsBt6f_x51B-uf2Dbx24KZ0dEZ7f24fnsO0pe6N6PnSVaCNnFTbaOh3v-/s320/Screen+Shot+2019-09-13+at+2.45.37+PM.png" width="320" /></a></div><p></p><p style="text-align: justify;">This course will provide an overview of the state of current technology and the various sequencing platforms used. The course consists of a series of online lectures and research exercises introducing different aspects of metabarcoding and metagenomics. We will also touch on the suite of bioinformatics tools available for sequence analysis and data interpretation. The course goes over 4 weeks but is designed in a fashion that you can go through course content at your own pace and according to your own schedule with work worth 4-8h per week. The course is fully asynchronous to accommodate for participants from various time zones. We still strive to make it as interactive as possible.</p><p style="text-align: justify;">For more information please go on the <a href="https://courses.opened.uoguelph.ca/search/publicCourseSearchDetails.do?method=load&courseId=18146">course enrolment page at the University of Guelph.</a></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-14602564119173759682020-08-20T09:08:00.001-04:002020-08-20T09:08:38.281-04:00Important message from the World Register of Marine Species (WoRMS)<p> <b style="font-family: Calibri, sans-serif; font-size: 11pt;"><span lang="EN-US">WoRMS needs YOU! </span></b></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><i><span lang="EN-US">WoRMS is a highly collaborative effort of over 500 involved experts, but we need all users – taxonomists, ecologists and non-scientists – to help us to keep WoRMS up-to-date and correct. If you find an error or an omission, please get in touch with us directly. Direct contact can fix errors a lot faster and more efficient than the WoRMS Team having to learn about these through peer-reviewed publications.<o:p></o:p></span></i></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">The World Register of Marine Species is a community driven effort to provide an authoritative and comprehensive list of names of marine organisms. The only way to achieve this goal is through broad-scale collaboration between taxonomic experts from a wide range of disciplines, regions and backgrounds. The past thirteen years have been a story of success, with more than 500 taxonomic and thematic editors volunteering their time to participate in the creation of this unique and freely available resource.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">WoRMS is truly collaborative and does not rely on the taxonomic editors alone to improve its content and functionality. The input of its users is critical to the work of WoRMS, to provide feedback, spot omissions and errors, and in making suggestions for improved tools and new features the community needs. The support of the Data Management Team, in processing the numerous enquiries from users, answering or directing them to the right editor, and ensuring they are dealt with swiftly, is also key to the success of the database.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">We write this plea for direct contact with the WoRMS team in response to a number of publications written with the aim of highlighting errors and omissions in WoRMS, but without contacting the WoRMS team to inform us of the issues . Although the WoRMS team can fix omissions and errors quite rapidly – on average within a few days – we do need to be aware of them.<o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">With over 500 editors making edits on the database on a daily and voluntary basis – the Steering Committee and the Data Management Team cannot 'police' everything that is being edited, and thus we rely on trust, expertise and goodwill of users and experts to inform us of problems that we can then look into. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">If you notice any errors or omissions in WoRMS we ask that you please simply contact us at <a href="mailto:info@marinespecies.org" style="color: #0563c1;">info@marinespecies.org</a>, rather than writing editorials or blogs or publishing about them. Once the WoRMS Data Management Team have been alerted to the issue then the feedback can be logged and dealt with swiftly and efficiently by either addressing it directly or rerouting it to the responsible editor and/or the WoRMS Steering Committee. It would be most useful if you can also provide relevant documents/research papers together with your feedback to help us processing your feedback quickly. <o:p></o:p></span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US"> </span></p><p class="MsoNormal" style="font-family: Calibri, sans-serif; font-size: 11pt; margin: 0cm 0cm 0.0001pt;"><span lang="EN-US">If we do not know about the problem, we cannot fix it – but we do promise to work to solve issues once we are informed of them. <a href="http://www.marinespecies.org/news.php?p=show&id=8481" target="_blank">Working together, we can improve WoRMS for all users</a>.</span></p>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-55990063150992728892020-05-15T09:47:00.002-04:002020-05-15T09:47:49.440-04:00Weekend reads - Week 20/2020<div class="separator" style="clear: both; text-align: center;">
<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPGXZvTTMmA6xqKMtWVuRsOwnMxf_56pf0S6FY-VMU7-EcIc4dk69vpksg82QlIjpJFSSFSP5JS8PZgkDkw9UbyJmSO_yddYAiTM6-SP1NgOrJ3-RJSr2cTs2K8WlqmcZjHfP44lB1MzHz/s1600/cat.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em; text-align: justify;"><img border="0" data-original-height="177" data-original-width="284" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjPGXZvTTMmA6xqKMtWVuRsOwnMxf_56pf0S6FY-VMU7-EcIc4dk69vpksg82QlIjpJFSSFSP5JS8PZgkDkw9UbyJmSO_yddYAiTM6-SP1NgOrJ3-RJSr2cTs2K8WlqmcZjHfP44lB1MzHz/s1600/cat.jpg" /></a></div>
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Here in Canada we are having a long weekend which means for some there is even more time to read. No worries, I won't add more than usual to this blog post although there have been quite a few new papers that were published over the past two weeks. Here we go: </div>
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<a href="https://doi.org/10.1371/journal.pone.0233189"><b>Large-scale metabarcoding analysis of epipelagic and mesopelagic copepods in the Pacific.</b></a></div>
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<i>A clear insight into the large-scale community structure of planktonic copepods is critical to understanding the mechanisms controlling diversity and biogeography of marine taxa in terms of their high abundance, ubiquity, and sensitivity to environmental changes. Here, we applied a 28S metabarcoding approach to large-scale communities of epipelagic and mesopelagic copepods at 70 stations across the Pacific Ocean and three stations in the Arctic Ocean. Major patterns of community structure and diversity, influenced by water mass structures, agreed with results from previous morphology-based studies. However, a large-scale metabarcoding approach could detect community changes even under stable environmental conditions, including changes in the north/south subtropical gyres and east/west areas within each subtropical gyre. There were strong effects of the epipelagic environment on mesopelagic communities, and community subdivisions were observed in the environmentally stable mesopelagic layer. In each sampling station, higher operational taxonomic unit (OTU) numbers and lower phylogenetic diversity were observed in the mesopelagic layer than in the epipelagic layer, indicating a recent rapid increase in species numbers in the mesopelagic layer. The phylogenetic analysis utilizing representative sequences of OTUs revealed trends of recent emergence of cold-water OTUs, which are mainly distributed at high latitudes with low water temperatures. Conversely, the high diversity of copepods at low latitudes was suggested to have been formed through long evolution under high water temperature conditions. The metabarcoding results suggest that evolutionary processes have strong impacts on current patterns of copepod diversity, and support the "out of the tropics" theory explaining latitudinal diversity gradients of copepods. Diversity patterns in both epipelagic and mesopelagic copepods was highly correlated to sea surface temperature; thus, predicted global warming may have a significant impact on copepod diversity in both layers.</i></div>
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<b><a href="https://doi.org/10.1139/gen-2019-0206">coil: an R package for cytochrome c oxidase I (COI) DNA barcode data cleaning, translation, and error evaluation</a></b></div>
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<i>Biological conclusions based on DNA barcoding and metabarcoding analyses can be strongly influenced by the methods utilized for data generation and curation, leading to varying levels of success in the separation of biological variation from experimental error. The 5' region of cytochrome c oxidase subunit I (COI-5P) is the most common barcode gene for animals, with conserved structure and function that allows for biologically informed error identification. Here, we present coil ( https://CRAN.R-project.org/package=coil ), an R package for the pre-processing and frameshift error assessment of COI-5P animal barcode and metabarcode sequence data. The package contains functions for placement of barcodes into a common reading frame, accurate translation of sequences to amino acids, and highlighting insertion and deletion errors. The analysis of 10 000 barcode sequences of varying quality demonstrated how coil can place barcode sequences in reading frame and distinguish sequences containing indel errors from error-free sequences with greater than 97.5% accuracy. Package limitations were tested through the analysis of COI-5P sequences from the plant and fungal kingdoms as well as the analysis of potential contaminants: nuclear mitochondrial pseudogenes and Wolbachia COI-5P sequences. Results demonstrated that coil is a strong technical error identification method but is not reliable for detecting all biological contaminants.</i></div>
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<b><a href="https://doi.org/10.3897/BDJ.8.e51813">Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding</a></b></div>
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<i>The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm3 sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.</i></div>
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<b><a href="https://doi.org/10.1073/pnas.1918741117">DNA metabarcoding reveals metacommunity dynamics in a threatened boreal wetland wilderness</a></b></div>
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<i>The complexity and natural variability of ecosystems present a challenge for reliable detection of change due to anthropogenic influences. This issue is exacerbated by necessary trade-offs that reduce the quality and resolution of survey data for assessments at large scales. The Peace–Athabasca Delta (PAD) is a large inland wetland complex in northern Alberta, Canada. Despite its geographic isolation, the PAD is threatened by encroachment of oil sands mining in the Athabasca watershed and hydroelectric dams in the Peace watershed. Methods capable of reliably detecting changes in ecosystem health are needed to evaluate and manage risks. Between 2011 and 2016, aquatic macroinvertebrates were sampled across a gradient of wetland flood frequency, applying both microscope-based morphological identification and DNA metabarcoding. By using multispecies occupancy models, we demonstrate that DNA metabarcoding detected a much broader range of taxa and more taxa per sample compared to traditional morphological identification and was essential to identifying significant responses to flood and thermal regimes. We show that family-level occupancy masks high variation among genera and quantify the bias of barcoding primers on the probability of detection in a natural community. Interestingly, patterns of community assembly were nearly random, suggesting a strong role of stochasticity in the dynamics of the metacommunity. This variability seriously compromises effective monitoring at local scales but also reflects resilience to hydrological and thermal variability. Nevertheless, simulations showed the greater efficiency of metabarcoding, particularly at a finer taxonomic resolution, provided the statistical power needed to detect change at the landscape scale.</i></div>
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<b><a href="https://doi.org/10.3390/insects11050294">DNA Metabarcoding as a Tool for Disentangling Food Webs in Agroecosystems</a></b></div>
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<i>Better knowledge of food webs and related ecological processes is fundamental to understanding the functional role of biodiversity in ecosystems. This is particularly true for pest regulation by natural enemies in agroecosystems. However, it is generally difficult to decipher the impact of predators, as they often leave no direct evidence of their activity. Metabarcoding via high-throughput sequencing (HTS) offers new opportunities for unraveling trophic linkages between generalist predators and their prey, and ultimately identifying key ecological drivers of natural pest regulation. Here, this approach proved effective in deciphering the diet composition of key predatory arthropods (nine species.; 27 prey taxa), insectivorous birds (one species, 13 prey taxa) and bats (one species; 103 prey taxa) sampled in a millet-based agroecosystem in Senegal. Such information makes it possible to identify the diet breadth and preferences of predators (e.g., mainly moths for bats), to design a qualitative trophic network, and to identify patterns of intraguild predation across arthropod predators, insectivorous vertebrates and parasitoids. Appropriateness and limitations of the proposed molecular-based approach for assessing the diet of crop pest predators and trophic linkages are discussed.</i></div>
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<b>PREPRINTS</b></div>
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<b><a href="https://www.biorxiv.org/content/10.1101/2020.04.19.048918v1">Efficient assessment of nocturnal flying insect communities by combining automatic light traps and DNA metabarcoding</a></b></div>
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<i>Increasing evidence for global insect declines is prompting a renewed interest in the survey of whole insect communities. DNA metabarcoding can contribute to assessing diverse insect communities over a range of spatial and temporal scales, but efforts are still needed to optimise and standardise procedures, from field sampling, through laboratory analysis, to bioinformatic processing.</i></div>
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<i>Here we describe and test a methodological pipeline for surveying nocturnal flying insects, combining a customised automatic light trap and DNA metabarcoding. We optimised laboratory procedures and then tested the methodological pipeline using 12 field samples collected in northern Portugal in 2017. We focused on Lepidoptera to compare metabarcoding results with those from morphological identification, using three types of bulks produced from each sample (individuals, legs and the unsorted mixture).</i></div>
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<i>The customised trap was highly efficient at collecting nocturnal flying insects, allowing a small team to operate several traps per night, and a fast field processing of samples for subsequent metabarcoding with low contamination risks. Morphological processing yielded 871 identifiable individuals of 102 Lepidoptera species. Metabarcoding detected a total of 528 taxa, most of which were Lepidoptera (31.1%), Diptera (26.1%) and Coleoptera (14.7%). There was a reasonably high matching in community composition between morphology and metabarcoding when considering the ‘individuals’ and ‘legs’ bulk samples, with few errors mostly associated with morphological misidentification of small microlepidoptera. Regarding the ‘mixture’ bulk sample, metabarcoding identified nearly four times more Lepidoptera species than morphological examination.</i></div>
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<i>Our study provides a methodological metabarcoding pipeline that can be used in standardised surveys of nocturnal flying insects, showing that it can overcome limitations and potential shortcomings of traditional methods based on morphological identification. Our approach efficiently collects highly diverse taxonomic groups such as nocturnal Lepidoptera that are poorly represented when using Malaise traps and other widely used field methods. To enhance the potential of this pipeline in ecological studies, efforts are needed to test its effectiveness and potential biases across habitat types and to extend the DNA barcode databases for important groups such as Diptera.</i></div>
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<b><a href="https://www.biorxiv.org/content/10.1101/2020.05.11.089029v1">CommDivMap: Modelling and mapping species richness at different spatial scales</a></b></div>
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<i>Modern ecosystem models have the potential to greatly enhance our capacity to predict community responses to change, but they demand comprehensive spatial distribution information, creating the need for new approaches to gather and synthesize biodiversity data. Metabarcoding or metagenomics can generate comprehensive biodiversity data sets at species-level resolution but they are limited to point samples. CommDivMap contains a number of functions that can be used to turn OTU tables resulting from metabarcoding runs of bulk samples into species richness maps. We tested the method on a series of arthropod bulk samples obtained from various experimental agricultural plots. The script runs smoothly and is reasonably fast. We hope that our assemble first, predict later approach to statistical modelling of species richness will set the stage for the transition from data-rich but finite sets of point samples to spatially continuous biodiversity maps.</i></div>
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<b><a href="https://dx.doi.org/10.21203/rs.3.rs-26532/v1">Recognition of arthropod species names using bigram-based classification</a></b></div>
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<i>The task of recognizing species names in scientific articles is a quintessential step for a large number of applications in high-throughput text mining and data analytics, such as species-specific information collection, construction of species food networks and trophic relationship extraction. These tasks become even more important in fast-paced species-discovery areas such as entomology, where an impressive number of new arthropod species are discovered each year. This article explores the use of twocharacter n-grams (bigrams) in machine learning models for arthropod species name recognition. This particular method has been previously applied successfully to the task of language identification but the application to species name identification had yet to be explored.</i></div>
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<i>Arthropod species names, regular English words used in scientific publications and person names were collected from the public domain and bigrams were extracted and used as classifier features. A number of learning classifiers spanning 7 algorithmic categories (tree-based, rule-based, artificial neural network, Bayesian, boosting, lazy and kernel-based) were tested and the highest accuracies were consistently obtained with LIBLINEAR, Bayesian Logistic Regression, the Multilayer Perceptron, Random Forest, and the LIBSVM classifiers. When compared with dictionary-based external software tools such as GNRD and TaxonFinder, our top-3 classifiers were insensitive to words capitalization and were able to correctly classify novel species names that are absent in dictionary-based approaches with accuracies between 88.6% and 91.6%.</i></div>
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<i>Our results suggest that character bigram-based classification is a suitable method for distinguishing arthropod species names from regular English words and person names commonly found in scientific literature. Moreover, our method can also be used to reduce the number of false positives produced by dictionary-based methods. </i></div>
Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-79466894980996351832020-05-01T14:50:00.001-04:002020-05-01T14:52:22.893-04:00Weekend reads -- Week 18/2020<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: justify;"><tbody>
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I am revitalizing an older tradition of this blog. A weekly (very subjective) collection of papers relating to DNA barcoding, metabarcoding and everything related:</div>
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<b><a href="https://peerj.com/articles/8496/?utm_source=TrendMD&utm_campaign=PeerJ_TrendMD_0&utm_medium=TrendMD">DNA barcoding reveals incorrect labelling of insects sold as food in the UK</a></b></div>
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<i>Insects form an established part of the diet in many parts of the world and insect food products are emerging into the European and North American marketplaces. Consumer confidence in product is key in developing this market, and accurate labelling of content identity is an important component of this. We used DNA barcoding to assess the accuracy of insect food products sold in the UK. </i><i>We purchased insects sold for human consumption from online retailers in the UK and compared the identity of the material ascertained from DNA barcoding to that stated on the product packaging. To this end, the COI sequence of mitochondrial DNA was amplified and sequenced, and compared the sequences produced to reference sequences in NCBI and the Barcode of Life Data System (BOLD). </i><i>The barcode identity of all insects that were farmed was consistent with the packaging label. In contrast, disparity between barcode identity and package contents was revealed in two cases of foraged material (mopane worm and winged termites). One case of very broad family-level description was also highlighted, where material described as grasshopper was identified as Locusta migratoria from DNA barcode. </i><i>Overall these data indicate the need to establish tight protocols to validate product identity in this developing market. Maintaining biosafety and consumer confidence rely on accurate and consistent product labelling that provides a clear chain of information from producer to consumer.</i></div>
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<a href="https://doi.org/10.1002/jsfa.10241"><b>DNA barcoding coupled with high‐resolution melting analysis for nut species and walnut milk beverage authentication</b></a></div>
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<i>Walnut (Juglans regia L.) is one of the most widely cultivated nuts. Walnut milk beverage is very popular in China due to its nutritional value. However, adulterated walnut milk ingredients have been detected in the Chinese market. Peanut and soybean are sold at much lower prices than walnut and are reported to be commonly used for adulteration in the industrial chain of walnut milk production. The purpose of this study is therefore to develop an accurate and efficient method for detecting the authenticity of the raw materials used in walnut milk beverage. </i><i>DNA barcoding and high‐resolution melting (HRM) analyses were used to identify common adulterated raw ingredients such as peanut and soybean in commercial walnut milk beverage samples. The chloroplast psbA‐trnH gene was used for sequencing, and HRM analysis was performed. We also prepared experimental mixtures, in the laboratory, with different quantities of walnut, peanut, and soybean. High‐resolution melting analysis of the experimental mixtures clearly distinguished all of them. The results revealed that most of the walnut milk beverage samples fell in the same cluster of walnut species. Several samples fell in the peanut cluster, confirming that they were adulterated products. </i><i>The results revealed that HRM analysis based on the psbA‐trnH barcode sequence can be used to identify raw ingredients in walnut milk beverages. </i></div>
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<b><a href="https://doi.org/10.3390/insects11010046">A DNA Barcoding Survey of an Arctic Arthropod Community: Implications for Future Monitoring</a></b></div>
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<i>Accurate and cost-effective methods for tracking changes in arthropod communities are needed to develop integrative environmental monitoring programs in the Arctic. To date, even baseline data on their species composition at established ecological monitoring sites are severely lacking. We present the results of a pilot assessment of non-marine arthropod diversity in a middle arctic tundra area near Ikaluktutiak (Cambridge Bay), Victoria Island, Nunavut, undertaken in 2018 using DNA barcodes. A total of 1264 Barcode Index Number (BIN) clusters, used as a proxy for species, were recorded. The efficacy of widely used sampling methods was assessed. Yellow pan traps captured 62% of the entire BIN diversity at the study sites. When complemented with soil and leaf litter sifting, the coverage rose up to 74.6%. Combining community-based data collection with high-throughput DNA barcoding has the potential to overcome many of the logistic, financial, and taxonomic obstacles for large-scale monitoring of the Arctic arthropod fauna.</i></div>
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<b><a href="https://doi.org/10.1111/1755-0998.13056">A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding</a></b></div>
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<i>Improved taxonomic methods are needed to quantify declining populations of insect pollinators. This study devises a high‐throughput DNA barcoding protocol for a regional fauna (United Kingdom) of bees (Apiformes), consisting of reference library construction, a proof‐of‐concept monitoring scheme, and the deep barcoding of individuals to assess potential artefacts and organismal associations. A reference database of cytochrome oxidase c subunit 1 (cox1) sequences including 92.4% of 278 bee species known from the UK showed high congruence with morphological taxon concepts, but molecular species delimitations resulted in numerous split and (fewer) lumped entities within the Linnaean species. Double tagging permitted deep Illumina sequencing of 762 separate individuals of bees from a UK‐wide survey. Extracting the target barcode from the amplicon mix required a new protocol employing read abundance and phylogenetic position, which revealed 180 molecular entities of Apiformes identifiable to species. An additional 72 entities were ascribed to nuclear pseudogenes based on patterns of read abundance and phylogenetic relatedness to the reference set. Clustering of reads revealed a range of secondary operational taxonomic units (OTUs) in almost all samples, resulting from traces of insect species caught in the same traps, organisms associated with the insects including a known mite parasite of bees, and the common detection of human DNA, besides evidence for low‐level cross‐contamination in pan traps and laboratory procedures. Custom scripts were generated to conduct critical steps of the bioinformatics protocol. The resources built here will greatly aid DNA‐based monitoring to inform management and conservation policies for the protection of pollinators.</i></div>
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<b><a href="https://doi.org/10.3389/fevo.2020.00081">Using Environmental DNA to Monitor the Reintroduction Success of the Rhine Sculpin (Cottus rhenanus) in a Restored Stream</a></b></div>
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<i>Freshwaters face some of the highest rates of species loss, caused by strong human impact. To decrease or even revert this strong impact, ecological restorations are increasingly applied to restore and maintain the natural ecological status of freshwaters. Their ecological status can be determined by assessing the presence of indicator species (e.g., certain fish species), which is called biomonitoring. However, traditional biomonitoring of fish, such as electrofishing, is often challenging and invasive. To augment traditional biomonitoring of fish, the analysis of environmental DNA (eDNA) has recently been proposed as an alternative, sensitive approach. The present study employed this modern approach to monitor the Rhine sculpin (Cottus rhenanus), a fish species that has been reintroduced into a recently restored stream within the Emscher catchment in Germany, in order to validate the success of the applied restorations and to monitor the species’ dispersal. We monitored the dispersal of the Rhine sculpin using replicated 12S end-point nested PCR eDNA surveillance at a fine spatial and temporal scale. In that way, we investigated if eDNA analysis can be applied for freshwater assessments. We also performed traditional electrofishing in one instance to validate our eDNA-based approach. We could track the dispersal of the Rhine sculpin and showed a higher dispersal potential of the species than we assumed. eDNA detection indicated the species’ dispersal across a potential dispersal barrier and showed a steep increase of positive detections once the reintroduced population had established. In contrast to that, false negative eDNA results occurred at early reintroduction stages. Our results show that eDNA detection can be used to confirm and monitor reintroductions and to contribute to the assessment and modeling of the ecological status of streams.</i></div>
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<b><a href="https://doi.org/10.1016/j.dib.2020.105553">Dataset of foraminiferal sedimentary DNA (sedDNA) sequences from Svalbard</a></b></div>
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<i>Environmental DNA (eDNA) is usually defined as genetic material obtained directly from environmental samples, such as soil, water, or ice. Coupled to DNA metabarcoding, eDNA is a powerful tool in biodiversity assessments. Results from eDNA approach provided valuable insights to the studies of past and contemporary biodiversity in terrestrial and aquatic environments. However, the state and fate of eDNA are still investigated and the knowledge about the form of eDNA (i.e., extracellular vs. intracellular) or the DNA degradation under different environmental conditions is limited. Here, we tackle this issue by analyzing foraminiferal sedimentary DNA (sedDNA) from different size fractions of marine sediments: >500 µm, 500-100 µm, 100-63 µm, and < 63 µm. Surface sediment samples were collected at 15 sampling stations located in the Svalbard archipelago. Sequences of the foraminifera-specific 37f region were generated using Illumina technology. The presented data may be used as a reference for a wide range of eDNA-based studies, including biomonitoring and biodiversity assessments across time and space.</i></div>
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<i><b>PREPRINTS</b></i></div>
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<b><a href="https://www.biorxiv.org/content/10.1101/2020.04.27.063990v1">A validation scale to determine the readiness of environmental DNA assays for routine species monitoring</a></b></div>
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<i>Environmental DNA (eDNA) analysis utilises trace DNA released by organisms into their environment for species detection and is revolutionising non-invasive species monitoring. The use of this technology requires rigorous validation - from field sampling to interpretation of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Their general applicability, uncertainties and limitations often remain undetermined. The absence of clear guidelines prevents targeted eDNA assays from being incorporated into species monitoring and policy, thus their establishment will be key for the future implementation of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled and consolidated into a scale to assess the validation status of individual assays. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. The 122 variables representing assay validation status were classified into 14 thematic blocks, such as "in silico analysis", and arranged on a 5-level validation scale from "incomplete" to "operational". Additionally, minimum validation criteria were defined for each level. The majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The total number of reported variables ranged from 20% to 76% and deviated both between and within levels. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.</i></div>
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<b><a href="https://www.biorxiv.org/content/10.1101/2020.04.27.063685v1?rss=1&utm_source=dlvr.it&utm_medium=twitter">Relating network analyses to phylogenetic relatedness to infer protistan co-occurrences and co-exclusions in marine and terrestrial environments</a></b></div>
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<i>We used two large-scale metabarcoding datasets to evaluate phylogenetic signals at global marine and regional terrestrial scales using co-occurrence and co-exclusion networks. Phylogenetic relatedness was estimated using either global pairwise sequence distance or phylogenetic distance and the significance of observed patterns relating networks and phylogenies were evaluated against two null models. In all datasets, we found that phylogenetically close OTUs significantly co-occurred more often, and OTUs with intermediate phylogenetic relatedness co-occurred less often, than expected by chance. Phylogenetically close OTUs co-excluded less often than expected by chance in the marine datasets only. Simultaneous excess of co-occurrences and co-exclusions were observed in the inversion zone between close and intermediate phylogenetic distance classes in marine surface. Similar patterns were observed by using either pairwise sequence or phylogenetic distances, and by using both null models. These results suggest that environmental filtering and dispersal limitation are the preponderant forces driving co-occurrence of protists in both environments, while signal of competitive exclusion was only detected in the marine surface environment. The discrepancy in the co-exclusion pattern is potentially linked to the individual environments: water bodies are more homogeneous while tropical forest soils contain a myriad of nutrient rich micro-environment reducing the strength of mutual exclusion.</i></div>
Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-5374044757379812892020-05-01T14:27:00.002-04:002020-05-01T14:27:20.002-04:00The Bees@Schools Program<div style="text-align: justify;">
Some years after the last run of our successful School Malaise Trap Program we started thinking about new ways to involve citizen scientists at schools in our research. We pitched an idea to the Natural Sciences and Engineering Research Council of Canada (NSERC) and were granted some funds to set it up and start with a few runs.</div>
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The <a href="https://beesatschools.ca/">Bees@School project</a> initially involved 100 school classrooms in discerning critical information on the changing geographic distributions of plant-pollinator interactions across Canadat. By combining state-of-the-art DNA barcoding of bees, and the pollen they carry, with distribution and climate change data, we are collecting data to show how distributions of Canada’s bee species are changing along with climate. The project will also help to determine how pollination services shift across Canada, with impacts on food production. The ultimate hope is to provide landscape management advice to improve vital species' chances of persisting in agricultural landscapes and alleviating pollination deficits. </div>
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Each participating school receives a wild bee nest box (perhaps better known as bee hotel) in the spring that is installed throughout the summer. In the fall, nest boxes are sent back to our <a href="https://biodiversitygenomics.net/">institute</a>. Here, the contents of the nest boxes will be analyzed using DNA barcoding of the larvae we found and metabarcoding of the pollen that was provisioned for them. </div>
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The <a href="https://beesatschools.ca/">project</a> is run by one of my grad students, Sage Handler. She is doing pretty much everything from communication with schools and the public to the laboratory work and data analysis. As you can imagine, her planning for this year's run was thrown into chaos once the COVID-19 pandemic caused major lockdowns including the closure of schools here in Canada. However, we were able to shift gears and run the the program regardless. Thanks to the support of so many teachers 200 traps are currently deployed across Canada. You'll find them in teacher's backyards, school yards or public spaces and now we are developing material (videos, activities for kids at home etc.) to keep this as educational as possible amidst the school closures. This video is just an example on how kids can learn and interact with the program. </div>
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-40552832907043784682020-04-30T12:49:00.000-04:002020-04-30T12:49:11.728-04:0018 Million Euros to explore biodiversity <div style="text-align: justify;">
Our friends at <a href="https://www.naturalis.nl/en">Naturalis</a> in Leiden, Netherlands released this piece of great news today: </div>
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An organized overview of all multicellular flora and fauna in the Netherlands and the infrastructure to identify them semi-automatically. This is what the ARISE megaproject wants to achieve in five to ten years’ time. The Dutch Research Council (NWO), Naturalis Biodiversity Center, the University of Amsterdam, the University of Twente and the Westerdijk Fungal Biodiversity Institute are investing a combined total of over 18 million euros. Koos Biesmeijer, leader of the consortium, is very pleased: "ARISE will give a big boost to our understanding of food webs and ecosystems and in the status and trends of our biodiversity."</div>
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The ARISE project aims to construct an infrastructure, the only one of its kind in the world, in order to identify and monitor every species of multicellular flora and fauna in the Netherlands. This infrastructure will combine information from DNA, visual/audio recognition and radar data to yield a comprehensive picture of the country's biodiversity. The international community is following the project with great interest as well. </div>
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The ARISE project may prove highly valuable as a means to supply policymakers, water authorities, provinces and other stakeholders with more reliable input in the field of biodiversity.</div>
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<strong>A new era in species identification</strong></div>
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Edwin van Huis, General manager of Naturalis Biodiversity Center, views this as an important step. “The loss of biodiversity is one of the chief threats to humanity's survival. For this reason, we urgently need better instruments for species identification and for monitoring biodiversity. Because only if we know what is, we can make an effort to preserve it.”</div>
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According to Annemarie van Wezel, scientific director of the Institute for Biodiversity and Ecosystem Dynamics (IBED/UvA), ARISE will lay the foundation for a new era of systematic ecological research into biodiversity. “Together with scientific partners, we will be demonstrating the added value of this infrastructure at demo sites. We'll be able to better understand patterns of biodiversity and changes in those patterns, which in turn will help us improve efforts to manage that biodiversity.”</div>
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Joost Kok, dean at the Faculty of Electrical Engineering, Mathematics and Computer Science at the University of Twente, is enthusiastic about the unprecedented opportunities this project offers. “The proposed infrastructure brings together many new insights in the fields of artificial intelligence and data science. This wouldn't have been feasible even ten years ago.” Pedro Crous, director of the Westerdijk Fungal Biodiversity Institute, adds: “ARISE will make it possible for researchers to identify every species they come across, even if it's one that was previously undiscovered.”</div>
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<strong>Unique combination: multidisciplinary collaboration and integration of expertise</strong></div>
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The Netherlands has long had a leading role in international collaborative partnerships relating to species identification and biodiversity. Because ARISE integrates a variety of techniques, the project is extremely advanced and the only one of its kind in the world. The ARISE project will make it possible to identify species quickly and semi-automatically based on the reference collections of Naturalis and the Westerdijk Institute. The University of Amsterdam is supplying expertise with regard to how ecosystems function and the University of Twente is contributing knowledge of state-of-the-art data science and artificial intelligence. Each of these parties was already exploring the use of sensors, DNA, image recognition, radar, audio and data science for the purpose of species identification.</div>
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<strong>Access to the most advanced near-real-time identification service</strong></div>
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This integrated infrastructure and facility will provide Dutch researchers, nature conservation organizations, government bodies and the business community with access to the most advanced near-real-time identification service for monitoring biodiversity and species detection. This, in turn, will yield new opportunities for understanding how ecosystems function, identifying trends and better integrating attention to biodiversity into solutions for major societal challenges such as the circular economy, nature-inclusive cities and the agricultural cycle. </div>
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-56096843043972505212020-04-09T15:19:00.003-04:002020-04-09T15:19:41.549-04:00The Centre for Biodiversity Genomics: a look inside the world's leading DNA barcoding facility<div style="text-align: justify;">
A new video showing what our institute was busily doing not too long ago. Great way to spend six minutes of your home office time. A tour through the institute by the "Father of DNA Barcoding" himself:</div>
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-60485838462360614862020-03-26T16:33:00.002-04:002020-03-26T16:33:34.670-04:00From the inbox: Looking for a project coordinator in CaBOL<span style="font-family: Helvetica; font-size: 12px;">Dear fellow barcoders,</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">we plan to extend our ongoing barcoding efforts in the Caucasus region by a new project, CaBOL. We submitted the CaBOL proposal a while ago and recently received very positive signals from the funder, although not yet the official grant notification.</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">In order to be ready to start the project soon after COVID loosens its grip, I would like to circulate the job offer for a CaBOL project coordinator (based at ZFMK, Bonn, Germany, but with frequent visits to Georgia and Armenia), please get in touch or forward this:</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">--></span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;"><b>The Zoological Research Museum A. Koenig in Bonn, Germany, is looking for a full-time project coordinator (m/f/d)</b></span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">within the project "CaBOL: <b><i>A Georgian-Armenian-German Initiative to establish a joint Caucasian Biodiversity Research Platform</i></b>". Conditional on the funding of the CaBOL project through BMBF, the position can be filled for three years.</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">Your tasks:</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Coordinating the network of CaBOL partner institutes (in Germany, Georgia, and Armenia), monitoring schedules and project funds, reporting, organization of project meetings</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• PR, dissemination of results, representing CaBOL</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Coordinating web page development, curating content of web page</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Managing the CaBOL subproject at Museum Koenig</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Guest liaison and supervision of students</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Maintaining contact and procuring samples to taxon experts for species identification</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Data analysis</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">Your profile:</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• University degree in biology or related life science, in the organismic domain</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Especially outstanding organizational skills and bargaining strength</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Very good knowledge of the English language and experience with composing scientific texts and reports</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Basic skills in DNA barcoding, in working with databases, and entomological expertise of advantage</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Intercultural competence</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">• Readiness to travel frequently (esp. into the Caucasus)</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">We offer a highly motivating environment at a renowned and pioneering research facility and the possibility to work independently. Salary and benefits are according to a public service position in Germany, TV-L E 13.</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">Equally qualified severely disabled applicants will be given preference. Qualified women are strongly encouraged to apply.</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">Please send your application by e-mail attachment, including a detailed CV, until April 19, 2020 to Mrs. Heike Lenz at Stiftung Zoologisches Forschungsmuseum Alexander Koenig, Leibniz-Institut für Biodiversität der Tiere, Adenauerallee 160, 53113 Bonn or via E-Mail as a summarized PDF to: </span><a href="mailto:h.lenz@leibniz-zfmk.de" style="font-family: Helvetica; font-size: 12px;">h.lenz@leibniz-zfmk.de</a><span style="font-family: Helvetica; font-size: 12px;">. In case of questions concerning the position please send an email to Jonas Astrin: </span><a href="mailto:j.astrin@leibniz-zfmk.de" style="font-family: Helvetica; font-size: 12px;">j.astrin@leibniz-zfmk.de</a><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">For more information about our institution see </span><a href="http://www.leibniz-zfmk.de/en" style="font-family: Helvetica; font-size: 12px;">http://www.leibniz-zfmk.de/en</a><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;"><--</span><br style="font-family: Helvetica; font-size: 12px;" /><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;">Best wishes</span><br style="font-family: Helvetica; font-size: 12px;" /><span style="font-family: Helvetica; font-size: 12px;"> Jonas Astrin</span>Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-84779423315352166832020-02-26T11:49:00.001-05:002020-02-26T11:49:59.325-05:005 Million Specimens at the CBG collectionOver the past decade and a half our Natural History collection here at the Centre for Biodiversity Genomics continuously grew and today our media team publicly announced that we surpassed the 5 Million Specimen mark. Mind you all of those are digitized (and barcoded).<br />
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Here the official press release:<br />
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<span style="background-color: white; color: #666666; font-family: "open sans" , "helveticaneue" , "helvetica neue" , "helvetica" , "arial" , sans-serif; font-size: 13px;">February 2020 marks an important milestone for the Centre for Biodiversity Genomics (CBG) at the University of Guelph. CBG’s in-house natural history collection (</span><a href="http://biodiversitygenomics.net/units/collections/" style="border: 0px; caret-color: rgb(102, 102, 102); color: #666666; font-family: "Open Sans", HelveticaNeue, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px; font-stretch: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;">CBG Collections</a><span style="background-color: white; color: #666666; font-family: "open sans" , "helveticaneue" , "helvetica neue" , "helvetica" , "arial" , sans-serif; font-size: 13px;">) has reached five million barcode voucher specimens. Each specimen is fully digitized, sequenced and available online through the Barcode of Life Data System platform (</span><a href="http://www.boldsystems.org/" rel="noopener noreferrer" style="border: 0px; caret-color: rgb(102, 102, 102); color: #666666; font-family: "Open Sans", HelveticaNeue, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px; font-stretch: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">BOLD</a><span style="background-color: white; color: #666666; font-family: "open sans" , "helveticaneue" , "helvetica neue" , "helvetica" , "arial" , sans-serif; font-size: 13px;">).</span><span style="background-color: white; color: #666666; font-family: "open sans" , "helveticaneue" , "helvetica neue" , "helvetica" , "arial" , sans-serif; font-size: 13px;"></span><br />
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Since its inception in 2006, the barcode reference collection at CBG has grown steadily. The development of DNA barcoding high-throughput workflows has enabled the rapid collection, processing and sequencing of millions of specimens from across the globe. In the last five years, CBG has sorted, prepared and DNA barcoded 800,000 specimens per year before archiving in this unique reference collection. With the recent addition of the <a href="http://biodiversitygenomics.net/news/press-releases/canadas-first-sequel-ii-dna-sequencer-arrives-at-the-centre-for-biodiversity-genomics/" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;">PacBio Sequel sequencing platform</a> and launch of the <a href="https://ibol.org/bioscan/major-scientific-program-bioscanaims-to-provide-data-to-address-biodiversity-loss/" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">BIOSCAN program</a>, the CBG aspires to grow the collection by one to two million specimens each year.</div>
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The final specimen array of 95 specimens added to CBG Collections to reach five million were collected in a Malaise trap located in Guanacaste, Costa Rica as part of the ongoing BIOSCAN project <a href="https://news.uoguelph.ca/2020/01/u-of-gs-centre-for-biodiversity-genomics-awarded-4-million-to-catalogue-life-in-costa-rica/" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">BioAlfa</a>. The array was very diverse, and included some of the following insects:</div>
<ul style="border: 0px; caret-color: rgb(102, 102, 102); color: #666666; font-family: "Open Sans", HelveticaNeue, "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 13px; font-stretch: inherit; line-height: inherit; list-style-image: initial; list-style-position: initial; margin: 0px; padding: 0px 0px 10px 30px; vertical-align: baseline;">
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206743" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Hawk moth</a> (Sphingidae: <span style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: italic; line-height: inherit; margin: 0px; padding: 0px; vertical-align: baseline;">Xylophanes hannemanni</span>) – these strong-flying moths have been recorded year-round in Costa Rica and have multiple generations per year.</li>
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206770" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Spider wasp</a> (Pompilidae) – attack and paralyze spiders to lay their eggs on and feed their young; the adults feed on nectar.</li>
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206779" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Tortoise beetle</a> (Chrysomelidae: Hybosa) – a common beetle that can be encountered in your own backyard; they feed on plant tissues and some are agricultural pests.</li>
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206786" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Lanternfly</a> (Fulgoridae) – a colourful true-bug found throughout the tropics; despite their name, they do not emit light like a lantern.</li>
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206791" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Robber fly or assassin fly</a> (Asilidae) – are ambush predators that target other insects for a meal.</li>
<li style="border: 0px; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: 18px; margin: 0px; padding: 0px; vertical-align: baseline;"><a href="http://v4.boldsystems.org/index.php/MAS_DataRetrieval_OpenSpecimen?selectedrecordid=11206803" rel="noopener noreferrer" style="border: 0px; color: #169fe6; font-family: inherit; font-size: inherit; font-stretch: inherit; font-style: inherit; font-variant-caps: inherit; line-height: inherit; margin: 0px; outline: 0px; padding: 0px; text-decoration: none; transition: color 0.1s ease-in-out; vertical-align: baseline;" target="_blank">Leafhopper</a> (Cicadellidae: Erythrogonia) – come in a variety of colours and patterns and are found worldwide; leafhoppers are small insects with over 20,000 species described.</li>
</ul>
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-16098789283703667132020-01-21T09:31:00.002-05:002020-01-21T09:31:24.197-05:00BIOSCAN - new video<div style="text-align: justify;">
In case you did not come across the new version of the BIOSCAN video - really worth watching!</div>
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<a href="https://ibol.org/programs/bioscan/">BIOSCAN</a> is iBOL's new seven-year, $180 million global research program that aims to revolutionize our understanding of biodiversity and our capacity to manage it. Involving scientists, research organizations, and citizens, BIOSCAN will explore three major research themes: Species Discovery, Species Interactions, Species Dynamics.</div>
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<iframe allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="" frameborder="0" height="315" src="https://www.youtube.com/embed/K1AchBQHnw4" width="560"></iframe>
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<a href="https://ibol.org/">iBOL (International Barcode of Life Consortium)</a> involves researchers in 30+ nations who share a mission to transform biodiversity science through DNA-based approaches with DNA barcoding at its core. iBOL works in partnership with academic, government, and private sector organizations.</div>
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-8552154601130537452020-01-06T06:35:00.001-05:002020-01-06T06:35:16.524-05:00PostDoc Bioinformatics and Environmental GenomicsA position to work at McGill partly in collaboration with our lab:<br />
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Preferred Disciplines:</span></b><span style="font-size: 10pt; letter-spacing: 0.15pt;"> Biology, Bioinformatics (Postdoc position)<br /><b><span style="border: 1pt none windowtext; padding: 0cm;">Project length:</span></b> 2 years, renewable for 3<sup>rd</sup> year <o:p></o:p></span></div>
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Approx. start date: </span></b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">February 15, 2020<b><br />Location: </b></span><span style="font-size: 10pt; letter-spacing: 0.15pt;">McGill University, Montreal, QC<o:p></o:p></span></div>
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Summary of Project:</span></b><span style="font-size: 10pt; letter-spacing: 0.15pt;"><o:p></o:p></span></div>
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<span style="font-size: 10pt; letter-spacing: 0.15pt;">The Postdoctoral Fellow will be involved in long-term and highly replicated laboratory and field experiments on the effect of multiple stressors on the structure and function of aquatic communities. The research will involve developing and implementing bioinformatic tools for analysing metabarcoding, metagenomics and transcriptomics data sets and assessing biodiversity trends for broad taxonomic groups (bacterial, phytoplankton, zooplankton). The fellow will compare biodiversity estimates obtained from traditional sampling techniques with estimates based on refined metabarcoding approaches to describe the biodiversity of contaminated aquatic habitats. The project involves the biodiversity group at McGill University and collaborators from the Centre for Biodiversity Genomics (CBG), University of Guelph, University of Quebec at Montreal and University of Montreal.<o:p></o:p></span></div>
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Research Objectives/Sub-Objectives: </span></b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">1) Develop sensitive metabarcoding bioinformatics protocols to describing aquatic communities; 2) Investigate the impact of multiple stressors on complex aquatic communities. <o:p></o:p></span></div>
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Methodology:</span></b><span style="font-size: 10pt; letter-spacing: 0.15pt;"> 1) Use high-throughput sequencing to <span style="border: 1pt none windowtext; padding: 0cm;">develop metabarcoding and metagenomics protocols for describing aquatic communities in complex environmental samples; </span>2) </span><span style="font-size: 10pt;">Validate protocols;<span style="letter-spacing: 0.15pt;"> 3) </span>Apply protocols on highly replicated field experiments.<span style="letter-spacing: 0.15pt;"><o:p></o:p></span></span></div>
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<b><span style="border: 1pt none windowtext; font-size: 10pt; letter-spacing: 0.15pt; padding: 0cm;">Expertise and Skills Needed:<o:p></o:p></span></b></div>
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<span style="font-size: 10pt; letter-spacing: 0.15pt;">Experience with next generation sequencing or large sequence data and related bioinformatics / computational / programming skills is required. Familiarity with one or more of the following would be an advantage: genomics, transcriptomics, phylogenetic analyses, genome evolution / programming language (R/Unix/Python or Perl). Experience working with aquatic organisms would be an asset. The candidate should have </span><span lang="EN-US" style="font-size: 10pt;">a PhD in evolution / genetics / computational biology,</span><span style="font-size: 10pt; letter-spacing: 0.15pt;"> a good publication record and the ability to work well in a collaborative research environment.<b><span style="border: 1pt none windowtext; padding: 0cm;"><o:p></o:p></span></b></span></div>
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<span lang="EN-US" style="font-size: 10pt;">Applicants should send a curriculum vitae, short statements of research interests, and 3 representative publications to <a href="mailto:melania.cristescu@mcgill.ca">melania.cristescu@mcgill.ca</a>. <u>The application deadline is January 31, 2020</u>.<o:p></o:p></span></div>
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<span lang="EN-US" style="font-size: 10pt;">McGill University is strongly committed to diversity and equity within its community. McGill University is among Canada</span><span lang="EN-US" style="font-family: Helvetica; font-size: 10pt;">’s leading research-intensive universities with students from over 140 countries. The</span><span lang="EN-US" style="font-size: 10pt;"> university is located in Montreal, a cosmopolitan city with great cultural and linguistic diversity.</span><span lang="EN-US" style="font-size: 10pt;"><o:p></o:p></span></div>
Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-15834090377715565602019-12-11T08:30:00.000-05:002019-12-11T08:29:59.975-05:00Postdoc in Museomics/Ancient DNA Analyses - OsloA Postdoctoral Research fellow position in museomics/ancient DNA analyses is available at the Natural History Museum (NHM), University of Oslo, Norway. The position is part of the research group ‘Frontiers in Evolutionary Zoology (FEZ)‘. The appointment is a full time position and is made for a period of up to four years (25 % of which is devoted to required duties) with a starting date no later than 31.08.2020.<br />
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The complete text of the job announcement <a href="https://www.jobbnorge.no/en/available-jobs/job/179037/postdoc-in-museomics-ancient-dna-analyses">is available here</a>.<br />
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<i>More about the position</i><br />
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The research group ‘Frontiers in Evolutionary Zoology (FEZ)‘ at the NHM currently includes three senior scientists with curatorial responsibilities for invertebrate collections, two PhD students, as well as several Master students.<br />
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The Natural History Museum Oslo houses the largest natural history collections in Norway, and has the strategic goal of strengthening cutting edge research on collection material. To further strengthen NHM position in the field we seek a young and dynamic early stage researcher who implements and develops strategies and protocols for molecular approaches to analyze difficult collection material (e.g., samples that have been preserved in either formalin or other fixatives disadvantageous for DNA survival).<br />
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The successful candidate shall have a strong publication record and potential for collaboration with current NHM curators, especially from the FEZ research group. Senior scientists within FEZ focus on various topics including systematics, taxonomy, and molecular evolution of selected marine invertebrate groups, staphylinid beetles, and parasitic flatworms. Given the general topic of the position, the successful candidate is expected to also cooperate with other researchers at the institution. The position offers also the opportunity to actively develop own research projects. Hence, dedication to attract external funding is expected. The museum also plays a leading role in postgraduate education in biodiversity and systematics through ForBio – Research School in Biosystematics and the candidate will help strengthening our profile through teaching and supervision of PhD students.<br />
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Postdoctoral fellows who are appointed for a period of four years are expected to acquire basic pedagogical competency in the course of their fellowship period within the duty component of 25 %.<br />
The main purpose of the fellowship is to qualify researchers for work in higher academic positions within their disciplines.<br />
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<i>Qualification requirements</i><br />
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The applicants are required to have<br />
- a degree equivalent to a Norwegian doctoral degree in biology or equivalent. For candidates not having finished their doctoral degree the doctoral dissertation must be submitted for evaluation by the closing date of the call. An appointment is dependent on the defense of the doctoral thesis being approved<br />
- a strong academic track record<br />
- a strong background and practical experience in cutting edge molecular DNA methodology<br />
- experiences in bioinformatic analyses of big genomic data sets<br />
- team-working and networking skills<br />
- fluent in English (written and spoken). Command of a Scandinavian language is an advantage<br />
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<i>Desirable experience</i><br />
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Furthermore, the applicants have/are preferentially<br />
- successfully acquired external funding for research projects<br />
- experienced in having worked with natural history collections<br />
- experienced in working with difficult templates for genetic analyses<br />
- profound knowledge about systematics and taxonomy of invertebrates<br />
Teaching and supervision skills of Master and PhD fellows is an advantage.<br />
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<i>Evaluation of candidates will focus on the following:</i><br />
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Applications will be assessed with respect to the required qualifications. Candidates for the position will be selected in accordance with the NHM strategic goal of strengthening collection-based research, and are expected to be in the upper segment of their research field. Interviews will be used in the assessment and appointment process. In addition to scientific qualifications particular emphasis will be put on personal capacities, such as collaboration, communication and networking skills as well as potential for scientific leadership.<br />
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<i>We offer:</i><br />
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- salary NOK 532 300 - 583 900 per year depending on qualification and seniority as PostDoc Research Fellow (position code 1352)<br />
- challenging research questions and a friendly working environment<br />
- full funding of the project research-related activities, including field work, lab work and presentation of results at international conferences<br />
- membership in the Norwegian Public Service Pension Fund<br />
- attractive welfare benefits<br />
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<i>How to apply. </i><br />
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The application must include (as separate and numbered documents):<br />
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1. An informative application/cover letter including a motivation statement for the position<br />
2. A separate one-page statement explaining how this position fits the career plan and interests of the applicant<br />
3. CV (summarizing education, positions and academic work, scientific publications and other relevant experience)<br />
4. Copies of educational certificates and transcripts of records<br />
5. List of publications and academic work that the applicant wishes to be considered by the evaluating committee<br />
6. Names and contact details of 2-3 references (name, affiliation, relation to candidate, e-mail and telephone number). The references will be contacted if necessary. Letters of recommendation are therefore not required for the initial application.<br />
7. A one-page research sketch that illustrates the applicant’s prospect of research development in the field<br />
8. Pdf of PhD thesis (or equivalent) and potential publications and academic work that the applicant wishes to be considered by the evaluating committee<br />
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Applicants should deliver the application with the requested attachments (numbered as above) through our electronic recruiting system. Foreign applicants are advised to include an explanation of their University’s grading system. Please remember that all documents should be in English or a Scandinavian language.<br />
In assessing applications, particular emphasis will be placed upon educational and scientific merits and the maturity and potential of the candidates to complete the project successfully within the given time frame. Interviews with selected candidates will be arranged.<br />
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<i>Formal regulations</i><br />
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Please see the guidelines and regulations for appointments to Postdoctoral fellowships at the University of Oslo.<br />
No one can be appointed for more than one Postdoctoral Fellow period at the University of Oslo.<br />
According to the Norwegian Freedom of Information Act (Offentleglova) information about the applicant may be included in the public applicant list, also in cases where the applicant has requested non-disclosure. The University of Oslo has an agreement for all employees, aiming to secure rights to research results etc. The University of Oslo aims to achieve a balanced gender composition in the workforce and to recruit people with ethnic minority backgrounds.<br />
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<i>Contact information</i><br />
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About the position and project details: FEZ group leader: <a href="http://www.nhm.uio.no/english/about/organization/research-collections/people/bachmann/index.html">Professor Lutz Bachmann</a><br />
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About administrative questions and the application procedure: HR advisor <a href="http://www.nhm.uio.no/english/about/organization/administration/people/thombraa/index.html">Thomas Brånå</a><br />
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Deadline: 15.01.2020.<br />
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-79231762755932306712019-09-13T14:49:00.001-04:002019-09-13T14:49:13.346-04:00Online Metabarcoding course January/February 2020Some shameless self-promotion. I am teaching my online metabarcoding introduction course again:<br />
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<b>January 20, 2020 to February 16, 2020</b></div>
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Four weeks learning covering the basics:</div>
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<li>High-troughput sequencing</li>
<li>Environmental DNA (eDNA)</li>
<li>Metabarcoding analytics</li>
<li>Applications/Recent research</li>
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<br />Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-50112014831343538162019-08-21T11:42:00.002-04:002019-08-21T11:42:16.316-04:00Trophic ecology<div class="separator" style="clear: both; text-align: center;">
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEmaaTS0s_f92PQWdPgGOuSEGsZM8E5U2X1_1l1dXB03rt8YXArYoveiMYwyIhmvUXOA2qprVj3NDsCVbMIbwJo1WTKPFLz0fUt1nwwXQUQaVxStP9cp7Xkmy0LCGKozfJqqOOS1xTOzm4/s1600/Leaves-Animal.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em; text-align: justify;"><span style="font-family: inherit;"><img border="0" data-original-height="853" data-original-width="1280" height="213" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhEmaaTS0s_f92PQWdPgGOuSEGsZM8E5U2X1_1l1dXB03rt8YXArYoveiMYwyIhmvUXOA2qprVj3NDsCVbMIbwJo1WTKPFLz0fUt1nwwXQUQaVxStP9cp7Xkmy0LCGKozfJqqOOS1xTOzm4/s320/Leaves-Animal.jpg" width="320" /></span></a><br />
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Understanding the trophic structure of a community is indispensable to understanding the underlying ecosystem in its entirety. Unfortunately, basic information on animal diet is often incomplete or simply missing. This is not a surprise as the assessment of animal diet is rather difficult. Very often direct observation of feeding is not possible. Species are elusive, small, rare or live in regions that are inaccessible. Another issue is variability of diets within species, populations or even between life stages. And to add more complexity to that, diet is dynamic, i.e. it fluctuates with seasons, day time, geography, and ecosystems. </div>
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<span lang="EN-US" style="font-family: inherit; line-height: 18.399999618530273px;">As usual, our knowledge about diet is far more detailed when it comes to vertebrates, specifically larger predators. However, once the focus shifts toward e.g. the trophic ecology of many arthropod species one quickly finds out that not much is covered by the literature, because it has not yet been studied as a consequence of the difficulties described above. </span></div>
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<span style="font-family: inherit;"><span lang="EN-US" style="line-height: 18.399999618530273px;">For quite so</span><span style="font-family: inherit;"><span lang="EN-US" style="line-height: 18.399999618530273px;">me years stable isotope analysis has been used to reconstruct diets, to characterize trophic relationships, to elucidate patterns of resource allocation, and for construction of food webs. Isotopes of a given element differ in the number of neutrons they contain. Everybody might have heard about radioactive isotopes which are those that spontaneously decay into other element isotopes. Stable isotopes are those which do not, but they might be the r</span><span lang="EN-US" style="line-height: 18.399999618530273px;">esult of such a decay. </span><span lang="EN-US" style="line-height: 18.399999618530273px;">Nonradiogenic stable isotopes are most useful for ecological studies, and particularly those of the light elements: H, C, N, O and S, as those are the major constituents of organic materials, and for which there are large relative mass differences between isotopes of the same element. </span>Stable isotope ratios are usually measured using stable isotope mass spectrometry and currently the most commonly used isotopes are δ¹³C and δ¹⁵N. </span></span></div>
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<span style="font-family: inherit;"><span lang="EN-US" style="line-height: 18.399999618530273px;"><span style="font-family: inherit;">Similarly, DNA barcodes have much utility in revealing trophic interactions among organisms and determining diet items although they often can only provide a snapshot of mostly local, present-day interactions. </span></span>Thus, stable isotope analysis can complement DNA barcoding techniques by adding coarser but more integrated averages of food web structure across space and time. In addition it allows for tracing nutrient fluxes in changing organismal communities. In other words, DNA barcodes allow us to pinpoint the exact composition of a species’ diet while both δ¹³C and δ¹⁵N isotopes can be used to trace the structure (and its change over time) of the underlying food webs, with δ¹⁵N showing enrichment between trophic levels and δ¹³C distinguishing between prey groups. </span></div>
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<span style="font-family: inherit;"><a href="https://doi.org/10.1371/journal.pone.0219070">A recent study</a> on a particular butterfly group shows how stable isotope analysis and DNA metabarcoding can be combined to better assess diet and trophic position. The family Lycaenidae (Gossamer-winged butterflies) is the second largest of all butterflies (about 6000 species) with various life histories and diets. About 75% of the species in this group are known to associate with ants and these associations can be mutualistic, parasitic, or predatory. In some cases caterpillars produce nutritious secretions from specialized organs to reward ants in exchange for their protection against predators and parasitoids.</span><br />
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<span style="font-family: inherit;">However, <i>the larval diets of many lycaenid butterflies remain poorly characterized, likely because the caterpillars are camouflaged, difficult to rear in captivity and often live in inaccessible microhabitats such as flower buds or subterranean ant nests. For many species, no records exist for direct observations of feeding behaviors, leaving researchers to rely on indirect evidence to infer larval diets. One such species is Anthene usamba (previously A. hodsoni), a lycaenid butterfly found in the savannas of eastern Africa.</i></span><br />
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<span style="font-family: inherit;"><a href="https://doi.org/10.3389/fmicb.2016.01920">An earlier study</a> using comparative microbiome analysis showed that adults in contrast to caterpillars were aphytophagous. Now, metabarcoding of caterpillar gut content </span>chloroplast <span style="font-family: inherit;">16S rRNA found a match to the acacia tree (</span><i>Vachellia drepanolobium</i>)<span style="font-family: inherit;"> the caterpillars are known to live on. </span>Stable isotope analysis confirmed that <i>Anthene usamba</i> gets most of its carbon directly or indirectly from its host plant, rather than from surrounding grasses. Although the feeding behaviour of the larvae remains unknown it can be clearly stated that they feed on their host tree.<br />
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There is a lot that speaks for the complementary use of stable isotope analysis and DNA barcoding in some dietary studies. There are individual limitations to both methods, e.g. analysis of diets with stable isotope analysis requires prior knowledge of the isotopic signatures of potential food sources. They also are not useful when the number of potential food sources exceeds the number of isotopes available. DNA-based methods such as metabarcoding are subject to various biases especially when PCR is involved. They highly depend on well-parameterized reference libraries and it is not possible to quantify individual contributions to complex DNA mixtures especially in a sample with different levels of degradation (here through differential digestion).<br />
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As there are so many species for which we have no clue on what they are feeding on it is reassuring to know that there are a number of methods available that can help us to learn more.<br />
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Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0tag:blogger.com,1999:blog-5117766536783887540.post-34994998112395839672019-08-16T11:54:00.002-04:002019-08-16T12:03:30.051-04:00CSI With DNA<div style="text-align: justify;">
<i>"That’s God’s signature. God’s signature is never a forgery."</i></div>
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<span style="font-size: x-small;">Eddie Joe Lloyd, quoted in the New York Times (26 August 2002). Lloyd had been sent to prison 17 years before and was released in 2002 when DNA testing showed a mismatch between his DNA profile and the profile developed from evidence at the crime scene.</span></div>
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The first DNA profiling techniques were developed in the mid-1980s. The technology was named DNA fingerprinting in reference to the well-established forensic method that was rarely questioned in the courts. Over the years methodologies changed and were refined. By the mid-1990s criminal justice systems started using short tandem repeat (STR) technology, which is based on hypervariable DNA sequences of relatively short length. The STR system became the new gold standard in DNA profiling. It is widely used to compare criminal suspects' profiles stored in massive databases (e.g. the FBI's Combined DNA Index System - CODIS) with DNA trace evidence to assess the likelihood of their involvement in a crime.</div>
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As technology has progressed, forensic scientists are exploring other applications of DNA-based methods in crime scene investigation. Especially DNA barcoding and metabarcoding are about to revolutionize other aspects of forensic science.</div>
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<b>Forensic entomology</b></div>
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<i>The first recorded incident where insects were used in a criminal investigation was in 13th-century China as described in Sung Tzu's book called <b>The washing away of wrongs</b>. When a farmer was found murdered in a field with a sharp weapon, all the suspects were told to place their sickles on the ground. Only one sickle attracted blow flies to the trace amount of blood hidden to the naked eye which resulted in the confession by the murderer.</i></div>
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<span style="font-size: x-small;"><a href="https://dx.doi.org/10.4103%2F0975-1475.92154">Joseph et al 2011</a></span></div>
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The study of insects in criminal investigation is called forensic entomology. It is mostly known for its use to estimate the time of death. A plethora of insect species are attracted to a decomposing body and may lay eggs in it. The succession waves in which different insect species colonize a corps depend on its state of decomposition which in turn means that the identification of an insect obtained on a decomposing body will allow for a relative precise estimate of the time of death. Insects colonize a corps in successive waves, and each has its own unique life cycle. Many kinds of insects will flock to a decomposing body, but the most common found on a corpse are flies and beetles. Flies, particularly blow flies, can find dead flesh within minutes. Their maggots do the majority of the eating and are responsible for much of a corpse's decay. Beetles, on the other hand, will typically move in once a corpse has dried out. But there is more. Forensic scientists can sometimes determine if a corpse has been moved simply by studying the insect population and their larval stages.</div>
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All these methods require accurate species identification which is not as easy at it would seem. Forensic entomologists are often confronted with large amounts of partial insect remains or impossible to identify early life stages, such as eggs and larvae. In the latter case a scientist would try to incubate and raise insects until distinguishable features become apparent. Aside from the fact that this is not always possible criminal investigations are loosing valuable time during the wait for an insect to mature. </div>
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<a href="https://doi.org/10.1111/1556-4029.13869">A recent study</a> shows very clearly that with a proper reference library and the right technology DNA barcoding enables forensic entomologists to rapidly analyze hundreds of bulk samples obtained from corpses and provide precise and reliable species assignments. In collaboration with the Bavarian State Criminal Police Office, colleagues at the Bavarian State Collection of Zoology used an insect reference library they build over years (together with our institute) to identify the content of 30 metabarcoded bulk samples obtained from the morgue. Given today's cost for high throughput sequencing and the fact that all samples can be done in a single run I am estimating costs of about US$80 per bulk sample in this particular case. All of a sudden regular DNA-based identification of massive amounts of insect remains becomes feasible and applicable in criminal investigations. The only caveat in many parts of the world is the incompleteness of local DNA barcode reference libraries. However, it seems rather feasible to build dedicated datasets based on expert identified material. That being said, countries with very active insect barcoding programs such as Canada, Finland, Germany, Norway and other members of the <a href="https://ibol.org/">International Barcoding of Life Project (iBOL)</a> could explore opportunities already today.</div>
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<b>Forensic soil analysis</b></div>
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<a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2diD6toj2CnXsnG3Xa4T7pCxiYR_HV7pz8V8xM1ztIoV0FCLcfhe5tPjk11T_UMz6QreyLL8mihekRgSqLPIHKpb27OWo9YbVDK5pIB6KVLSZHAuFC89WDNN1eJJ-xj9GuJgHVb3enjPG/s1600/A-systematic-approach-to-discriminate-soils-for-forensic-soil-examinations-where-FTIR-is.png" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" data-original-height="509" data-original-width="579" height="281" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj2diD6toj2CnXsnG3Xa4T7pCxiYR_HV7pz8V8xM1ztIoV0FCLcfhe5tPjk11T_UMz6QreyLL8mihekRgSqLPIHKpb27OWo9YbVDK5pIB6KVLSZHAuFC89WDNN1eJJ-xj9GuJgHVb3enjPG/s320/A-systematic-approach-to-discriminate-soils-for-forensic-soil-examinations-where-FTIR-is.png" width="320" /></a><i>Soil is commonly encountered as trace evidence in criminal cases, i.e. mud sticking to footwear, tires and shovels, soil splash marks on vehicles, and traces left on clothes, the floor or in the trunk of vehicles. Those soil samples can be compared to samples from known locations, where an offence is thought to have occurred, thereby establishing a link between a suspect or a victim and a crime scene. In an investigative process, where for example the crime scene is unknown, soil trace evidence can also give valuable information on geographic origin or provenance and help narrow the search for a location. </i></div>
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<span style="font-size: x-small;"><a href="https://doi.org/10.1371/journal.pone.0202844">Fløjgaard et al 2019</a></span></div>
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Forensic scientists often use inorganic soil properties such as colour, consistency, structure, texture, segregations/coarse fragments (charcoal, ironstone or carbonates), and abundance of roots/pores to aid the identification of soil materials. They are following strict conventions and sophisticated systematic procedures (see figure on the left from <a href="http://onlinelibrary.wiley.com/book/10.1002/9780470061589">Fitzpatrick 2013</a>).<br />
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However, soil contains a lot of DNA from the living organisms that populate it but also in form of environmental DNA (eDNA). Consequently, forensic scientists have begun considering biological material for the characterization of soil types. Pollen grains and grass spores are preserved in soil samples over a longer period of time and can be used to identify surrounding flora. Newer forensic studies also show that a DNA profile of the soil bacterial community DNA in small samples of soil recovered from crime scenes can be matched with representative profiles of a suspect. <a href="https://doi.org/10.1371/journal.pone.0202844">A new stud</a>y now goes further and explores <i>whether soil eDNA could be used to predict a sample’s origin along environmental gradients (light, soil moisture, pH and nutrient status), origin in terms of habitat types (e.g., forest, heathland and rotational field), and in terms of geographic origin</i>. A Danish research group utilized data collected in a <a href="http://bios.au.dk/om-instituttet/organisation/biodiversitet/projekter/biowide/">nation-wide survey of biodiversity in Denmark</a> to establish Ellenberg Indicator Values (EIV). EIVs are based on an ordinal classification of plants according to the position of their ecological niche along an environmental gradient. They were initially applied to the flora of Germany as a model of bioindication. Each plant species is assigned an EIV and the community or site EIV is calculated as an average of all the indicator values. The only issue is that EIVs are only available for Central Europe and the UK. Work elsewhere would require the use of species scores from ordination of large and representative vegetation datasets. The study investigated the potential for constructing predictive models of environmental properties, habitat types and geographic origin based on soil eDNA. The colleagues found that variation in soil eDNA can predict environmental conditions and most habitat types but not geographic provenance. Model predictions for two mock crime scenes corresponded well with the actual EIVs at the site. This shows that an eDNA approach can become be a useful investigative tool in crime scene cases, however, at this point in time only for those without the need for the strict and validated procedures necessary to be used as evidence in court. There is still a lot of work left to be done.</div>
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DNA-based forensics science has come a long way from the first profiles developed in the 1980's and it has matured into a powerful tool for both catching criminals and exonerating innocent people. Nevertheless, it has not reached its full potential as new technologies provide applications in trace evidence analysis.<br />
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Countless CSI TV series might make us believe that solving a crime is only a matter of having the best high-tech at your fingertips and that catching a culprit is only a DNA sequence away. Nothing could be further from the truth. One risk lies in the complexity of the statistical methods used to analyze DNA samples and their interpretation. Attorneys and judges, who must understand how they work to reliably assess their validity in court are facing a challenge. <a href="https://doi.org/10.1016/j.scijus.2015.11.007">Methods for interpreting DNA evidence are inconsistent</a>, potentially leading to biased verdicts on the identities of DNA donors. Therefore, it is paramount to ensure that the science underlying the analysis used to make decisions in court remains transparent and validated by the broader scientific community.
Dirkhttp://www.blogger.com/profile/05686023489012728029noreply@blogger.com0