Reminder: Conference Registration opens tomorrow

A quick reminder that registration for the 7th International Barcode of Life Conference from 20 - 24 November 2017 at the Nombolo Mdhluli Conference Centre, Skukuza, will open tomorrow Dec 1st.

Please note that space is limited to 500 delegates/attendees due to the high exclusivity of the venue and we therefore strongly encourage to register as soon as possible to avoid potential disappointment.

Here is the direct link to the registration system. It will go live on Dec 1st (in case you just tried and wondered why nothing was working).

Important dates for the Conference 2017

In little less than a year from
now the African Centre for DNA Barcoding, and the University of Johannesburg will be hosting the 7th International Barcode of Life Conference from 20 - 24 November 2017. This is the first time that this event will be held on the African continent and the venue chosen is the Nombolo Mdhluli Conference Centre, Skukuza, located within the heart of African wildlife, the Kruger National Park, South Africa. 

This week registration will open on the conference website. 

Here once again all important dates - please mark your calendars and don't forget to register. 

Registration opens: 01 December 2016

Opening of accommodation booking:
01 December 2016
Call for abstracts: 31 January 2017
Deadline for submission of abstracts:
31 March 2017
Notification of acceptance of abstracts:
30 April 2017
Deadline for early-bird registration:
31 May 2017
Deadline for online registration:
01 November 2017

More details will follow in the days, weeks to come.

Bluebirds as part of viticulture

Bluebirds are one of several groups of birds that catch insects on the wing, but because they're constantly on the move and the animals they eat are tiny and often hard to identify, it's difficult to determine exactly what species make up their diet. 

Researchers from the Missouri Western State University and the University of California, Berkeley tackled this question using molecular scatology, analyzing DNA barcodes found in the birds' feces to determine insect species the Western Bluebirds (Sialia mexicana) were eating. They collected 237 fecal samples from adult and nestling birds living on three vineyards in Napa County, California and did a metabarcoding analysis utilizing a short (250bp) COI fragment sequenced on the Illumina MiSeq platform. Identifications were done using BOLD's ID engine.

They found that the bluebirds in Napa Valley vineyards mostly ate mosquitos and herbivorous insects, likely having only negligible effects on the predaceous insects that benefit vineyard production by eating pests. Even though the authors did not find specific pest species in bluebird diets, they did confirm that bluebirds are mainly eating herbivorous insects, including those in the same families as major pests. This suggests bluebirds may contribute to ecosystem functioning in these systems. The bluebirds' presence is likely a net positive which is why the authors hope that these results encourage more vineyard owners to install bluebird boxes, thereby helping to replace natural tree cavities lost when land is cleared. 

Illegal export of ivory

Some of the Canadian readers of this blog might have come across the following press article a few days ago: 

An Ontario company and its director have been fined $12,500 and sentenced to two years of probation after pleading guilty to unlawfully exporting python skin and elephant ivory. Environment Canada says it began its investigation into 888 Auctions three years ago with help from the U.S. Fish and Wildlife Service. The agency says it found that on one occasion, the company mailed a small elephant ivory tusk and an ivory carving to the U.S. falsely labelled as a gift ornament. The pieces were later determined to be from the African forest elephant. Another time, the agency says 888 Auctions sent a leather case made from python skin to the U.S. Both exports were made without the necessary permits.

You might have guessed that this has something to do with DNA barcoding. Actually, the conviction was successful in part due to DNA barcoding analysis of the elephant ivory tusk mentioned in the article. This was done in our lab here at CBG.

This might not exactly big scientific news but I always like to point out cases were DNA barcoding has made a difference and here it helped to sentence people that deal with illegal wildlife products. Unfortunately, it happens not often enough but every time it does there is hope.

'Monday' reads

Monday reads on a Tuesday? Well, I was a little busy yesterday and just managed to get a job ad out. As a result here my reading suggestions with a slight delay:

Exploring Canadian Echinoderm Diversity through DNA Barcodes

DNA barcoding has proven an effective tool for species identification in varied groups of marine invertebrates including crustaceans, molluscs, polychaetes and echinoderms. In this study, we further validate its utility by analyzing almost half of the 300 species of Echinodermata known from Canadian waters. COI sequences from 999 specimens were assigned to 145 BINs. In most cases, species discrimination was straightforward due to the large difference (25-fold) between mean intra- (0.48%) and inter- (12.0%) specific divergence. Six species were flagged for further taxonomic investigation because specimens assigned to them fell into two or three discrete sequence clusters. The potential influence of larval dispersal capacity and glacial events on patterns of genetic diversity is discussed for 19 trans-oceanic species. Although additional research is needed to clarify biogeographic patterns and resolve taxonomic questions, this study represents an important step in the assembly of a DNA barcode library for all Canadian echinoderms, a valuable resource for future biosurveillance programs.

DNA barcoding of crickets, katydids, and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany, and Switzerland

We present a DNA barcoding study on the insect order Orthoptera that was generated in collaboration between four barcoding projects in three countries, viz. Barcoding Fauna Bavarica (Germany), German Barcode of Life, Austrian Barcode of Life, and Swiss Barcode of Life. Our dataset includes 748 COI sequences from 127 of the 162 taxa (78.4%) recorded in the three countries involved. 93 of these 122 species (76.2%, including all Ensifera), can be reliably identified using DNA barcodes. The remaining 26 caeliferan species (families Acrididae and Tetrigidae) form ten clusters that share barcodes among up to five species, in three cases even across different genera, and in six cases even sharing individual barcodes. We discuss incomplete lineage sorting and hybridization as most likely causes of this phenomenon, as the species concerned are phylogenetically young and hybridization has been previously observed. We also highlight the problem of nuclear mitochondrial pseudogenes (numts), a known problem in the barcoding of orthopteran species, and the possibility of Wolbachia infections. Finally, we discuss the possible taxonomic implications of our barcoding results and point out future research directions.

The importance of taxonomic resolution for additive beta diversity as revealed through DNA barcoding

Additive diversity partitioning (α, β, and γ) is commonly used to study the distribution of species-level diversity across spatial scales. Here, we first investigate whether published studies of additive diversity partitioning show signs of difficulty attaining species-level resolution due to inherent limitations with morphological identifications. Second, we present a DNA barcoding approach to delineate specimens of stream caddisfly larvae (order Trichoptera) and consider the importance of taxonomic resolution on classical (additive) measures of beta (β) diversity. Caddisfly larvae were sampled using a hierarchical spatial design in two regions (subarctic Churchill, Manitoba, Canada; temperate Pennsylvania, USA) and then additively partitioned according to Barcode Index Numbers (molecular clusters that serve as a proxy for species), genus, and family levels; diversity components were expressed as proportional species turnover. We screened 114 articles of additive diversity partitioning and found that a third reported difficulties with achieving species-level identifications, with a clear taxonomic tendency towards challenges identifying invertebrate taxa. Regarding our own study, caddisfly BINs appeared to show greater subregional turnover (e.g., proportional additive β) compared to genus or family levels. Diversity component studies failing to achieve species resolution due to morphological identifications may therefore be underestimating diversity turnover at larger spatial scales.

Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes

Species diversity in most protistan groups has been underestimated. Many morpho-species are in fact complexes that require detailed morphometric studies to be discriminated. However, which traits can be used for species descriptions remains in many cases unclear. The testate amoeba genus Quadrulella produces self-secreted, siliceous plates with a very characteristic square shape—such plates were assumed to be synapomorphic of the genus. Here we demonstrate that Quadrulella symmetrica (the most common Holarctic species) is not monophyletic. Square plate size and arrangement, test size and general shape are efficient criteria for species discrimination. Based on morphology and sequence data, we describe Quadrulella variabilis sp. nov. from Switzerland, and Quadrulella madibai sp. nov. from South Africa, and confirm the validity of Q. alata. The former species Q. subcarinata does not belong to the genus Quadrulella. We therefore transfer this species to the new genus Mrabella gen. nov. Our results show that hyalosphenids presenting siliceous square shell plates do not form a monophyletic clade. Several possible hypotheses about the origins of square plates are discussed. Additionally, this comprehensive phylogenetic analysis of the family Hyalospheniidae confirms that the genus Nebela is paraphyletic and needs to be divided into genera based on general shell shape: Nebela sensu stricto, Longinebela gen. nov., Planocarina gen. nov., Gibbocarina gen. nov., Cornutheca gen. nov. and Mrabella gen. nov.

Not DNA barcoding per se but a very interesting conceptual study:

Deconstructing the relationships between phylogenetic diversity and ecology: a case study on ecosystem functioning

Recent studies have supported a link between phylogenetic diversity and various ecological properties including ecosystem function. However, such studies typically assume that phylogenetic branches of equivalent length are more or less interchangeable. Here we suggest that there is a need to consider not only branch lengths but also their placement on the phylogeny. We demonstrate how two common indices of network centrality can be used to describe the evolutionary distinctiveness of network elements (nodes and branches) on a phylogeny. If phylogenetic diversity enhances ecosystem function via complementarity and the representation of functional diversity, we would predict a correlation between evolutionary distinctiveness of network elements and their contribution to ecosystem process. In contrast, if one or a few evolutionary innovations play key roles in ecosystem function, the relationship between evolutionary distinctiveness and functional contribution may be weak or absent. We illustrate how network elements associated with high functional contribution can be identified from regressions between phylogenetic diversity and productivity using a well-known empirical data set on plant productivity from the Cedar Creek Long-Term Ecological Research. We find no association between evolutionary distinctiveness and ecosystem functioning, but we are able to identify phylogenetic elements associated with species of known high functional contribution within the Fabaceae. Our perspective provides a useful guide in the search for ecological traits linking diversity and ecosystem function, and suggests a more nuanced consideration of phylogenetic diversity is required in the conservation and biodiversity–ecosystem-function literature.

From the inbox: Rebanks Postdoctoral Research Fellowship

Rebanks Postdoctoral Research Fellowship

Cetacean Genomics and Mammalian Bioinformatics

The Royal Ontario Museum in Toronto invites applications for a Rebanks Postdoctoral Research Fellowship in the Department of Natural History starting ideally in February 2017. The successful candidate will work full time in the lab of Dr. Mark Engstrom developing a program on whale genomics and bioinformatics of mammals.

This is a two-year fellowship with an annual salary of $50,000 that provides Canadian citizens or Canadian landed immigrants who have obtained their doctorate degree in the last five years the opportunity to pursue their research with the support of one of Canada’s leading research institutions. The ROM is a superlative showcase of the world’s cultural and natural history – a place of discovery, learning, inspiration and imagination for visitors and staff alike.

With the salvaging of two blue whales from Newfoundland by the ROM in 2014, we have the unprecedented opportunity to sequence the first complete genome of this endangered species, to investigate questions concerning their evolution, phylogeny, historical demography, and conservation in relation to other cetaceans and mammals in general. The candidate will be able to interact with various collaborating labs and will be part of the active and diverse community of evolutionary biologists at the ROM and the University of Toronto.

We seek applicants with excellent skills in de novo next-generation genome assembly and analysis of genomic data with strong programming experience with R, Perl, or Phython, and statistical skills. Other required experience includes molecular laboratory skills such as primer design, PCR optimization, DNA sequencing, and sequence editing and alignment. Familiarity with theoretical phylogenetics, including current developments in tree reconstruction methods and experience with phylogenetic analysis software is needed for the position.

Candidates should electronically submit a letter of application detailing their research experience, interest in the position, preferred start date, curriculum vitae, and names with contact details of three references to: Dr. Mark Engstrom, Deputy Director of Collections & Research and Senior Curator of Mammalogy, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, M5S 2C6, Canada. Application materials must be received by January 6, 2017 for consideration. We especially encourage applications from women and members of minority groups.

From the inbox: Assistant Researcher position, University of Minho, Braga, Portugal

Assistant Researcher position at the Centre of Molecular and Environmental Biology, University of Minho, Braga, Portugal

SCOPE: The NextSea: Next generation monitoring of coastal ecosystems in a scenario of global change (operação NORTE-01-0145-FEDER-000032) wants to fill one (1) Assistant Researcher position in the field of Marine Biology/Ecology. For this purpose, the Centre of Molecular and Environmental Biology at the University of Minho expresses its interest in the collection of personal, academic and professional information of potential candidates to perform duties in the above-mentioned area. For project summary see here. 

ADMISSION REQUIREMENTS: Candidates holding a Ph.D. in the area of Marine Biology or closely related fields, and with a minimum of two (2) years of proven post-doctoral research in the same area; be author or co-author of at least five (5) articles published in Q1 scientific journals "ISI Journal Citation Index”; good communication skills, the ability to work in an autonomous way and within the scope of a multidisciplinary team, including biologists, civil and electronics engineers; experience in biological sampling in marine and estuarine environments is desirable (familiarity with molecular tools in this context will be also valued).

WORK PLAN: The researcher will be involved in the global supervision of the tasks and integration of activities among the project research lines. Coordination of sampling activities (biological and oceanographic sampling), assessment of benthic assemblages and substrate colonization by classical and molecular methods, as well as active collaboration in the development of new generation physical and biological sensors. The fellow is expected to be involved in applications for research grants, graduate student’s supervision, lecturing advanced courses in the scope of the Do*Mar PhD programme, as well as in the public dissemination of the project activities.

WHAT WE OFFER: Opportunity to have a central role in one of a few strategic projects granted to the University of Minho by the North 2020 programme, with a total budget of 1,2M€. The project involves a multidisciplinary team, linking biologists, biochemists, electronic and civil engineers, in a quest for novel integrated approaches for oceanographic and biological monitoring. The fellow will be hosted by the CBMA - Centre of Molecular and Environmental Biology, University of Minho, Campus de Gualtar, Braga, Portugal and will have access to recently inaugurated facilities, at the Institute of Science and Innovation for Bio-Sustainability.

CONTRACT DURATION: The contract will last 12 months, starting on January 2017, with the possibility of renewal, based on mutual agreement, up to the project end. The annual salary corresponds to a gross income of 35,218.64 Euros.

HOW TO APPLY: By email with the subject CBMA/N2020 – INV/04/2016 and with the following information:

- Identification of the candidate (copy of the passport)

- Curriculum Vitae/resume (indicating the URLs for 5 selected articles)

- Motivation letter

- 2 Reference letters

DEADLINE: The invitation to applicants is open from 17 November to 11 December 2016.

Monday reads

And another Monday with some interesting reads I came along. That being said, please have a look at last Friday's post providing links to another special conference issue.

Molecular identification and phylogenetic analysis of the forensically important family Piophilidae (Diptera) from different European locations.

Species identification plays an important role in forensic entomology and is mandatory for an accurate calculation of the minimum post-mortem interval. Many important Diptera and Coleoptera taxa of the cadaver community can already be identified by common barcoding approaches, i.e., by sequencing a 658bp region in the mitochondrial cytochrome c oxidase subunit I (coI) gene. Nevertheless, there is still a lack of reference barcodes for species, in particular, that can be found on cadavers at later decomposition stages. Flies of the family Piophilidae illustrate this gap of knowledge perfectly. Due to the fact that a reliable morphological identification key for the immature stages of this flies is still missing and the immature stages of many piophilids cannot be assigned to a certain species, there is need for additional tools to identify forensically relevant taxa. We collected adult piophilid specimens at 10 locations in five European countries: Spain (n=3 locations), Germany (n=3), Portugal (n=2), Poland (n=1) and Switzerland (n=1). Apart from the coI barcoding region, we additionally analyzed a 398bp long region of the nuclear elongation factor 1 alpha (ef1a) and subsequently established the molecular identifier for nine piophilid species. In addition, we present the molecular phylogeny of the examined taxa.

Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding.

Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecological scales. Our data and analyses suggest that dinoflagellate diversity has been largely underestimated, representing overall ∼ 1/2 of protistan rDNA metabarcode richness assigned at ≥ 90% to a reference sequence in the world's surface oceans. Dinoflagellate metabarcode diversity and abundance display regular patterns across the global scale, with different order-level taxonomic compositions across organismal size fractions. While the pico to nano-planktonic communities are composed of an extreme diversity of metabarcodes assigned to Gymnodiniales or are simply undetermined, most micro-dinoflagellate metabarcodes relate to the well-referenced Gonyaulacales and Peridiniales orders, and a lower abundance and diversity of essentially symbiotic Peridiniales is unveiled in the meso-plankton. Our analyses could help future development of biogeochemical models of pelagic systems integrating the separation of dinoflagellates into functional groups according to plankton size classes.

Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi.

Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293bp and 69,505bp with G+C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as "supergenes" (16 concatenated coding genes), using Shimodaira-Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis 'species complex'.

How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus (Chlorophyceae).

Microalgae identification is extremely difficult. The efficiency of DNA barcoding in microalgae identification involves ideal gene markers and approaches employed, which however, is still under the way. Although Scenedesmus has obtained much research in producing lipids its identification is difficult. Here we present a comprehensive coalescent, distance and character-based DNA barcoding for 118 Scenedesmus strains based on rbcL, tufA, ITS and 16S. The four genes, and their combined data rbcL + tufA + ITS + 16S, rbcL + tufA and ITS + 16S were analyzed by all of GMYC, P ID, PTP, ABGD, and character-based barcoding respectively. It was apparent that the three combined gene data showed a higher proportion of resolution success than the single gene. In comparison, the GMYC and PTP analysis produced more taxonomic lineages. The ABGD generated various resolution in discrimination among the single and combined data. The character-based barcoding was proved to be the most effective approach for species discrimination in both single and combined data which produced consistent species identification. All the integrated results recovered 11 species, five out of which were revealed as potential cryptic species. We suggest that the character-based DNA barcoding together with other approaches based on multiple genes and their combined data could be more effective in microalgae diversity revelation.

Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant's foot tubers.

BACKGROUND:

Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or "elephant's foot" structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal.

RESULTS:

The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet.

CONCLUSIONS:

Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.

Barcodes to Biomes (Part 2)

Two months ago the Canadian journal Genome published the first of two volumes of a special issue derived from presentations at the 6th International Barcode of Life conference for which I was one of the guest associate editors. The second volume has been published now. All articles are Open Access and there is one headed by yours truly (see if you can spot it). 

Enjoy reading:

The multiple applications of DNA barcodes in avian evolutionary studies

Ana S. Barreira, Darío A. Lijtmaer, Pablo L. Tubaro

Fungal DNA barcoding

Jianping Xu

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Muhammad Ashfaq, Paul D.N. Hebert

Barcoding the food chain: from Sanger to high-throughput sequencing

Joanne E. Littlefair, Elizabeth L. Clare

Linking adults and immatures of South African marine fishes

Dirk Steinke, Allan D. Connell, Paul D.N. Hebert

Rates and patterns of molecular evolution in freshwater versus terrestrial insects

T. Fatima Mitterboeck, Jinzhong Fu, Sarah J. Adamowicz

The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data

Elizabeth L. Clare, Frédéric J.J. Chain, Joanne E. Littlefair, Melania E. Cristescu

Improving herpetological surveys in eastern North America using the environmental DNA method

Anaïs Lacoursière-Roussel, Yohann Dubois, Eric Normandeau, Louis Bernatchez

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

Ping-Shin Lee, Han Ming Gan, Gopalasamy Reuben Clements, John-James Wilson

DNA-based identification of invasive alien species in relation to Canadian federal policy and law, and the basis of rapid-response management

Vernon G. Thomas, Robert H. Hanner, Alex V. Borisenko

DNA barcoding for biosecurity: case studies from the UK plant protection program

Jennifer Hodgetts, Jozef C. Ostojá-Starzewski, Thomas Prior, Rebecca Lawson, Jayne Hall, Neil Boonham

Closed-Tube Barcoding

Nicky M. Sirianni, Huijun Yuan, John E. Rice, Ronit S. Kaufman, John Deng, Chandler Fulton, Lawrence J. Wangh

Bushmeat hunting

People have harvested the diverse vertebrate community of Central African forests for millennia, depending on wild meat for protein and to improve their livelihoods; however, recently human population growth, more efficient weapons and greater access to forests have yielded unprecedented rates of modern bushmeat hunting. Hunting alters the vertebrate community by selecting against prey species, resulting in some species ‘losing’ (decreasing in abundance) and others ‘winning’ (increasing in abundance). Large-bodied, tropical mammal species with low reproductive rates, such as primates, are particularly sensitive to hunting pressures and are often ‘losers’ in this process. On the other hand, smaller-bodied sympatric species such as rodents are often ‘winners’ and can come to dominate communities with release from predation and competition for resources.

A new study shows that hunting has dramatically reduced wildlife biodiversity in forests near rural villages in Gabon. The colleagues surveyed wildlife populations along 24 straight sampling lines running between 60 small villages in the Ogooue-Ivindo province of northeastern Gabon. Survey sites were located at distances from 2 kilometers to 30 kilometers outside the nearest village. At each survey location, the team documented the diversity and abundance of all large vertebrate animal species they observed, along with any evidence of hunting - such as discarded shotgun shells, campfire sites or sightings of hunters themselves.

We observed a sharp decline in species diversity and a change in species composition the closer we got to any village. Conversely, the richness of mammal species increased by roughly 1.5 species for every 10 kilometers we traveled away from the village. That's a much steeper gradient of change than we had anticipated. It presents new evidence that bushmeat-hunting by rural communities is drastically shaping the wildlife community, an effect that could cascade through entire ecosystems and alter forest composition and diversity across the entire region. And this problem is only going to grow worse as the human population in the region increases.

The concentrated small-scale hunting occurring around the villages likely is also having an impact on plant diversity in the region. As the number of seed-dispersing species such as monkeys and apes decreases with proximity to villages and the number of seed-eating rodents rises, the relative abundance of large fruiting trees, which are food sources for both animal and human populations, could be reduced across the landscape.

The researchers suggest that near villages, resource management should focus on sustainable community-led hunting programs that provide long-term supplies of wild meat to rural people. Resource management far from villages should focus on law enforcement and promoting industry practices that maintain remote tracts of land to preserve ecosystem services like carbon storage and biodiversity.

The not so common octopus

Madako, which means 'common octopus,' is a name well known in Japan and, for over a century it referred to the species Octopus vulgaris. The name Octopus vulgaris was first used for the European common octopus, which was long thought to be cosmopolitan with a global distribution.

Molecular studies showed that Octopus vulgaris is actually a mixture of several distinct, though closely related, species. One of these is now recognized as Octopus sinensis, which is found throughout warm seas on the continental shelf of East Asia, including the main islands of Japan which means Madako is not Octopus vulgaris after all.

A new study used morphology and DNA barcoding and the results allow a clear distinction of the two species. The impact of this finding is significant because the growing popularity of octopus as food resource is putting intense pressure on marine resources.

A steady decline in catches of common octopuses around the world is causing concern. Imports of Octopus vulgaris have been masking the decline in Octopus sinensis catches in Japan. And off Europe and Africa, Octopus vulgaris is in trouble, too. The Moroccan octopus fishery collapsed several years ago, while stocks off Mauritania continue to be heavily exploited.

Until recently, the declining numbers caused little concern, as it was assumed that all common octopuses belong to a widely available global species. But now that it's been proven that there are several independent species of common octopus within the Octopus vulgaris group, and that the numbers are limited, researchers are calling for more focus on local fisheries management policies, in order to make sure that each species can be fished sustainably.

Monday reads

Monday morning is my time for going through all my RSS feeds and read some of the more recent publications. A number of very interesting reads for me this morning which made me think that I might as well share a slection with all the blog readers. So, in case you haven't come across them, here are some:

DNA barcoding and health

Detection of Theileria orientalis in mosquito blood meals in the United Kingdom.

Theileria spp. are tick-borne protozoan parasites that infect a wide range of wild and domestic animals. In this study, the utility of xenosurveillance of blood-fed specimens of Culiseta annulata for detecting the presence of piroplasms in livestock was investigated. Blood-fed mosquitoes were collected at Elmley National Nature Reserve, Kent, United Kingdom. All specimens were morphologically identified, and DNA barcoding was used to confirm the morphological identification. Both the vertebrate host species and Theileria genome was detected within the bloodmeal by real-time PCR. Sequencing was used to confirm the identity of all amplicons. In total, 105 blood-fed mosquitoes morphologically identified as Cs. annulata were collected. DNA barcoding revealed that 102 specimens were Cs. annulata (99%), while a single specimen was identified as Anopheles messeae. Two specimens could not be identified molecularly due to PCR amplification failure. Blood meal analysis revealed that Cs. annulata fed almost exclusively on cattle at the collection site (n = 100). The application of a pan-piroplasm PCR detected 16 positive samples (15.2%) and sequence analysis of the amplicons demonstrated that the piroplasms present in the blood meal belonged to the Theileria orientalis group. This study demonstrates how xenosurveillance can be applied to detecting pathogens in livestock and confirms the presence of Theileria species in livestock from the United Kingdom.

Use of DNA barcoding to distinguish the malaria vector Anopheles neivai in Colombia.

A reference 535 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI), acquired from specimens of An. neivai Howard, Dyar & Knab, 1913 from its type locality in Panama, was used as a tool for distinguishing this species from others in the subgenus Kerteszia. Comparisons with corresponding regions of COI between An. neivai and other species in the subgenus (An. bellator Dyar & Knab 1906, An. homunculus Komp 1937, An cruzii Dyar & Knab, 1908 and An. laneanus Corrêa & Cerqueira, 1944) produced K2P genetic distances of 8.3–12.6%, values well above those associated with intraspecific variation. In contrast, genetic distances among 55 specimens from five municipalities in the Colombian Pacific coastal state of Chocó were all within the range of 0–2.5%, with an optimized barcode threshold of 1.3%, the limit for unambiguous differentiation of An. neivai. Among specimens from the Chocó region, 18 haplotypes were detected, two of which were widely distributed over the municipalities sampled. The barcode sequence permits discrimination of An. neivai from sympatric species and indicates genetic variability within the species; aspects key to malaria surveillance and control as well as defining geographic distribution and dispersion patterns.

Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification

Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.

High-Throughput Sequencing

Evaluating and Optimizing the Performance of Software Commonly Used for the Taxonomic Classification of DNA Metabarcoding Sequence Data
The taxonomic classification of DNA sequences has become a critical component of numerous ecological research applications; however, few studies have evaluated the strengths and weaknesses of commonly used sequence classification approaches. Further, the methods and software available for sequence classification are diverse, creating an environment in which it may be difficult to determine the best course of action and the tradeoffs made using different classification approaches. Here, we provide an in silico evaluation of three DNA sequence classifiers, the RDP Naïve Bayesian Classifier, RTAX and UTAX. Further, we discuss the results, merits and limitations of both the classifiers and our method of classifier evaluation. Our methods of comparison are simple, yet robust, and will provide researchers a methodological and conceptual foundation for making such evaluations in a variety of research situations. Generally, we found a considerable trade-off between accuracy and sensitivity for the classifiers tested, indicating a need for further improvement of sequence classification tools.

Invertebrates that impact human well-being

DNA barcoding for biosecurity: case studies from the UK plant protection program.
Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.

The diversity of arthropods in homes across the United States as determined by environmental DNA analyses

We spend most of our lives inside homes, surrounded by arthropods that impact our property as pests and our health as disease vectors and producers of sensitizing allergens. Despite their relevance to human health and well-being, we know relatively little about the arthropods that exist in our homes and the factors structuring their diversity. Since previous work has been limited in scale by the costs and time associated with collecting arthropods and the subsequent morphological identification we used a DNA-based method for investigating the arthropod diversity in homes via high-throughput marker gene sequencing of home dust. Settled dust samples were collected by citizen scientists from both inside and outside more than 700 homes across the United States, yielding the first continental-scale estimates of arthropod diversity associated with our residences. We were able to document food webs and previously unknown geographic distributions of diverse arthropods-from allergen producers to invasive species and nuisance pests. Home characteristics, including the presence of basements, home occupants, and surrounding land-use, were more useful than climate parameters at predicting arthropod diversity in homes. These non-invasive, scalable tools and resultant findings not only provide the first continental-scale maps of household arthropod diversity, our analyses also provide valuable baseline information on arthropod allergen exposures and the distributions of invasive pests inside homes. This article is protected by copyright. All rights reserved.

Quantifying biodiversity

I stumbled across an interesting paper in PNAS these days but I am afraid I have to complain a little:

Over a series of three- to six-month field sessions across 10 years, a research team hiked across the hilly tropical agricultural landscape of Coto Brus, an area in Costa Rica. In an ecological gradient from protected forest to treeless pasture, the team made a total of 67,737 observations of 908 species, comprised of understory plants, non-flying mammals, bats, birds, reptiles and amphibians.

They plotted their plant and animal observations on fine-scale maps from Google Earth aerial photographs. The perhaps not so surprising find was that tree cover is very important. More surprising was the fact that for four of the six species groups (plants, non-flying mammals, bats and birds), the colleagues saw a significant increase in the number of species with increasing tree cover visible on Google Earth maps. The models they developed were able to predict biodiversity in the region within a 30- to 70-meter radius and also demonstrated how the number and kind of species change as trees are added to plots of land.

So far so good but I think this study lacks a lot of species that make up the majority of the local diversity - the team did not include any invertebrate species although they make up most of the diversity and are of crucial importance for agriculture. I am not saying their idea was a bad one or the results are flawed. On the contrary, their analysis is great but I think the study is incomplete. One of the main messages "trees are good" could be even stronger if they had started to count  e.g. arthropod taxa as well which would have taken them much longer and they already worked for 10 years. 

My main problem with this study is not the study itself but the claim that this way of looking at diversity (remote sensing through aerial photography) could be used by policymakers to help protect biodiversity and endangered species. For such a statement they haven't done enough which might sound harsh given the years of work that were put into this. However, I am always critical of shortcuts which leave out a very large portion of live and its role in the respective ecosystems. I am afraid it ain't that easy. Most of our current estimates, assessments, policies are based on very few key indicator species selected for their alleged role in an ecosystem. This has been rightfully criticized by many scientists and even policy experts. If we as humans are really serious about protecting biodiversity we have to go through the pains of understanding it properly and in its entirety. Bad news for policymakers but who said that live is easy?