Tuesday, December 6, 2016

"Monday" reads

Another post Monday issue on new DNA barcoding articles. Once again my Monday was too busy to find a few minutes to assemble the post. Nevertheless, here we go - some interesting reads for the week:

While pollinators are widely acknowledged as important contributors to seed production in plant communities, we do not yet have a good understanding of the importance of pollinator specialists for this ecosystem service. Determination of the prevalence of pollinator specialists is often hindered by the occurrence of cryptic species and the limitations of observational data on pollinator visitation rates, two areas where DNA barcoding of pollinators and pollen can be useful. Further, the demonstrated adequacy of pollen DNA barcoding from historical records offers opportunities to observe the effects of pollinator loss over longer timescales, and phylogenetic approaches can elucidate the historical rates of extinction of specialist lineages. In this Viewpoint article, we review how advances in DNA barcoding and metabarcoding of plants and pollinators have brought important developments to our understanding of specialization in plant-pollinator interactions. We then put forth several lines of inquiry that we feel are especially promising for providing insight on changes in plant-pollinator interactions over space and time. Obtaining estimates of the effects of reductions in specialists will contribute to forecasting the loss of ecosystem services that will accompany the erosion of plant and pollinator diversity.

Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.

Plants are colonized various microorganisms including endophytes. These microbes can play an important role in agricultural production as they promote plant growth and/or enhance the resistance of their host plant against diseases and environmental stress conditions. Although culture-independent molecular approaches such as DNA barcoding have greatly enhanced our understanding of bacterial and fungal endophyte communities, there are some methodical problems when investigating endophyte diversity. One main issue are sequence contaminations such as plastid-derived rRNA gene sequences which are co-amplified due to their high homology to bacterial 16S rRNA genes. The same is true for plant and fungal ITS sequences. The application of highly specific-primers suppressing co-amplification of these sequence contaminations is a good solution for this issue. Here, we describe a detailed protocol for assessing bacterial and fungal endophyte diversity in plants using these primers in combination with next-generation sequencing.

BACKGROUND:
DNA barcoding has demonstrated that many discrete phenotypes are in fact genetically distinct (pseudo)cryptic species. Genetically identical, isogenic individuals, however, can also express similarly different phenotypes in response to a trigger condition, e.g. in the environment. This alternative explanation to cryptic speciation often remains untested because it requires considerable effort to reject the hypothesis that the observed underlying genetic homogeneity of the different phenotypes may be trivially caused by too slowly evolving molecular markers. The widespread squat lobster Munida gregaria comprises two discrete ecotypes, gregaria s. str. and subrugosa, which were long regarded as different species due to marked differences in morphological, ecological and behavioral traits. We studied the morphometry and genetics of M. gregaria s. l. and tested (1) whether the phenotypic differences remain stable after continental-scale sampling and inclusion of different life stages, (2) and whether each phenotype is underpinned by a specific genotype.
RESULTS:
A total number of 219 gregaria s. str. and subrugosa individuals from 25 stations encompassing almost entire range in South America were included in morphological and genetic analyses using nine unlinked hypervariable microsatellites and new COI sequences. Results from the PCA and using discriminant functions demonstrated that the morphology of the two forms remains discrete. The mitochondrial data showed a shallow, star-like haplotype network and complete overlap of genetic distances within and among ecotypes. Coalescent-based species delimitation methods, PTP and GMYC, coherently suggested that haplotypes of both ecotypes forms a single species. Although all microsatellite markers possess sufficient genetic variation, AMOVA, PCoA and Bayesian clustering approaches revealed no genetic clusters corresponding to ecotypes or geographic units across the entire South-American distribution. No evidence of isolation-by-distance could be detected for this species in South America.
CONCLUSIONS:
Despite their pronounced bimodal morphologies and different lifestyles, the gregaria s. str. and subrugosa ecotypes form a single, dimorphic species M. gregaria s. l.. Based on adequate geographic coverage and multiple independent polymorphic loci, there is no indication that each phenotype may have a unique genetic basis, leaving phenotypic plasticity or localized genomic islands of speciation as possible explanations.

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.