Tuesday, January 21, 2020

BIOSCAN - new video

In case you did not come across the new version of the BIOSCAN video - really worth watching!

BIOSCAN 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.



iBOL (International Barcode of Life Consortium) 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.

Monday, January 6, 2020

PostDoc Bioinformatics and Environmental Genomics

A position to work at McGill partly in collaboration with our lab:

Preferred Disciplines: Biology, Bioinformatics (Postdoc position)
Project length: 2 years, renewable for 3rd year 
Approx. start date: February 15, 2020
Location: 
McGill University, Montreal, QC

Summary of Project:
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.

Research Objectives/Sub-Objectives: 1) Develop sensitive metabarcoding bioinformatics protocols to describing aquatic communities; 2) Investigate the impact of multiple stressors on complex aquatic communities. 

Methodology: 1) Use high-throughput sequencing to develop metabarcoding and metagenomics protocols for describing aquatic communities in complex environmental samples; 2) Validate protocols; 3) Apply protocols on highly replicated field experiments.

Expertise and Skills Needed:
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 a PhD in evolution / genetics / computational biology, a good publication record and the ability to work well in a collaborative research environment.
Applicants should send a curriculum vitae, short statements of research interests, and 3 representative publications to melania.cristescu@mcgill.caThe application deadline is January 31, 2020.

McGill University is strongly committed to diversity and equity within its community. McGill University is among Canada’s leading research-intensive universities with students from over 140 countries. The university is located in Montreal, a cosmopolitan city with great cultural and linguistic diversity.

Wednesday, December 11, 2019

Postdoc in Museomics/Ancient DNA Analyses - Oslo

A 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.

The complete text of the job announcement is available here.

More about the position

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.

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).

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.

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 %.
The main purpose of the fellowship is to qualify researchers for work in higher academic positions within their disciplines.

Qualification requirements

The applicants are required to have
- 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
- a strong academic track record
- a strong background and practical experience in cutting edge molecular DNA methodology
- experiences in bioinformatic analyses of big genomic data sets
- team-working and networking skills
- fluent in English (written and spoken). Command of a Scandinavian language is an advantage


Desirable experience

Furthermore, the applicants have/are preferentially
- successfully acquired external funding for research projects
- experienced in having worked with natural history collections
- experienced in working with difficult templates for genetic analyses
- profound knowledge about systematics and taxonomy of invertebrates
Teaching and supervision skills of Master and PhD fellows is an advantage.


Evaluation of candidates will focus on the following:

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.


We offer:

- salary NOK 532 300 - 583 900 per year depending on qualification and seniority as PostDoc Research Fellow (position code 1352)
- challenging research questions and a friendly working environment
- full funding of the project research-related activities, including field work, lab work and presentation of results at international conferences
- membership in the Norwegian Public Service Pension Fund
- attractive welfare benefits


How to apply. 

The application must include (as separate and numbered documents):

1. An informative application/cover letter including a motivation statement for the position
2. A separate one-page statement explaining how this position fits the career plan and interests of the applicant
3. CV (summarizing education, positions and academic work, scientific publications and other relevant experience)
4. Copies of educational certificates and transcripts of records
5. List of publications and academic work that the applicant wishes to be considered by the evaluating committee
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.
7. A one-page research sketch that illustrates the applicant’s prospect of research development in the field
8. Pdf of PhD thesis (or equivalent) and potential publications and academic work that the applicant wishes to be considered by the evaluating committee

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.
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.

Formal regulations

Please see the guidelines and regulations for appointments to Postdoctoral fellowships at the University of Oslo.
No one can be appointed for more than one Postdoctoral Fellow period at the University of Oslo.
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.


Contact information

About the position and project details: FEZ group leader: Professor Lutz Bachmann

About administrative questions and the application procedure: HR advisor Thomas Brånå


Deadline: 15.01.2020.

Friday, September 13, 2019

Online Metabarcoding course January/February 2020

Some shameless self-promotion. I am teaching my online metabarcoding introduction course again:

January 20, 2020 to February 16, 2020



Four weeks learning covering the basics:
  • High-troughput sequencing
  • Environmental DNA (eDNA)
  • Metabarcoding analytics
  • Applications/Recent research




Wednesday, August 21, 2019

Trophic ecology


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. 

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. 

For quite some 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 result of such a decay. 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. Stable isotope ratios are usually measured using stable isotope mass spectrometry and currently the most commonly used isotopes are δ¹³C and δ¹⁵N. 

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. 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. 

A recent study 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.

However, 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.

An earlier study using comparative microbiome analysis showed that adults in contrast to caterpillars were aphytophagous. Now, metabarcoding of caterpillar gut content chloroplast 16S rRNA found a match to the acacia tree (Vachellia drepanolobium) the caterpillars are known to live on. Stable isotope analysis confirmed that Anthene usamba 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.

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).

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.


Friday, August 16, 2019

CSI With DNA

"That’s God’s signature. God’s signature is never a forgery."
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.

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.

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.

Forensic entomology

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 The washing away of wrongs. 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.


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.

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. 

A recent study 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 International Barcoding of Life Project (iBOL) could explore opportunities already today.



Forensic soil analysis

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. 

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 Fitzpatrick 2013).

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 new study now goes further and explores 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. A Danish research group utilized data collected in a nation-wide survey of biodiversity in Denmark 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.

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.

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. Methods for interpreting DNA evidence are inconsistent, 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. 

Wednesday, February 20, 2019

Two research positions on eDNA-based approaches for marine invasive alien species

A research scientist position and a postdoctoral fellowship are available at Galway-Mayo Institute of Technology, Galway, Ireland


Link: https://www.gmit.ie/human-resources/jobs-gmit