Friday, December 2, 2016

A glimpse into the Global Malaise Trap Program

from original publication
These results illustrate how a comprehensive DNA barcode reference library can identify unknown specimens, but also reveal how this potential is constrained by gaps in the quantity and quality of records in BOLD, especially for Hymenoptera and Diptera. As voucher specimens are available for morphological study, we invite taxonomic experts to assist in the identification of unnamed BINs.

This is taken from an abstract of a new paper that came out yesterday in the Biodiversity Data Journal. It involves data collected as part of the so called Global Malaise Trap program which is an international collaboration between the Centre for Biodiversity Genomics and a number of international partners. The program started in 2012 and represents the a first attempt at the acquisition of detailed temporal and spatial information on terrestrial arthropod communities across the globe. Malaise traps are deployed over an entire season in order to obtain tissue material and subsequently determine species diversity using DNA barcoding.

The number of arthropod specimens such surveys produce are quite impressive, e.g. the study done at two sites in Germany in 2012 and 2013 resulted in 37,274 specimens that were DNA barcoded. In total they found 5301 different BINs which represent about 63% of the total diversity collected in a single experiment. The Global Malaise Trap Program has partnered with 30 different sites across the planet. There is a lot of data to look forward to.

Wednesday, November 30, 2016

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).

Monday, November 28, 2016

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.

Friday, November 25, 2016

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. 

Thursday, November 24, 2016

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.

Tuesday, November 22, 2016

'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:

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.

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.

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.

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:

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.

Monday, November 21, 2016

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.