Wednesday, January 31, 2018

Less frogs than expected

DNA barcoding revealed that they all these frogs
belong to one species: Phrynobatrachus auritus
When Smithsonian Conservation Biology Institute (SCBI) conservation biologist Jessica Deichmann joined a project to determine how the construction of a road in Gabon’s Moukalaba-Doudou National Park would affect amphibians in the area, she quickly realized something surprising: the frogs are masters of disguise.

Frogs that showed marked differences in color, pattern and general morphology belonged to the same species. Consequently, Deichmann and her team used DNA barcoding to find out which species populate the area. Based on morphology 48 frog species were counted for the region. DNA barcoding brought this number down to 28 species. When asked what she thinks are potential risks of such an overinflation of existing taxonomy, Jessica Deichmann answered:

In any analysis, results and recommendations can only be as good as the data used to develop them. This leads to inaccurate baselines and makes it impossible to accurately assess changes in amphibian communities. In this instance, one possible repercussion could have been misplacing limited resources for conservation.

It is nice to see that an integrated study utilizing DNA barcodes amongst other means leads to some lumping of inflated estimates. Sometimes DNA barcode studies are suspected to contribute to increases in species counts and taxonomic splitting. 

Tuesday, January 30, 2018

From the inbox - mystery caterpillar

The lab of Walter Carson at the University of Pittsburgh, with the help of Lee Dyer, is currently working on a publication documenting the outbreak of an unknown Lepidoptera in Tena, Ecuador. We are offering co-authorship to anyone that is able to identify this Lepidoptera to family or genus.

The caterpillars, which have aposematic mimicry and non-urticating spines, had completely defoliated an Inga edulisA flock of oropendola was feeding on them and some indigenous women collected them to eat.  The caterpillar is called tupuli kuru in Quichua. Pictures can be accessed through the dropbox link. If you have any questions or can refer anyone to us please contact Samantha Sutton, our undergraduate researcher.

Here some images:

We could barcode it to see if it matches an already collected and identified adult.

Monday, January 29, 2018

Access and benefit-sharing for DNA barcoders

Globalization and the advent of bioinformatics are rapidly changing the landscape of international scientific collaborations, which now often span multiple jurisdictions and increase the volume of international data exchange and transactions of biological materials. At the same time, researchers engaging in such partnerships are often unaware of the complex policy frameworks governing such transactions, which may carry reputational and even legal liabilities.

The United Nations Convention on Biological Diversity (1992) and its supplementary agreement, the Nagoya Protocol (ratified in 2014), are the most prominent international treaties designed to provide a legal framework for ensuring the fair and equitable sharing of the benefits arising from research activities involving genetic resources. Although often challenging and, at times, frustrating, it is important for researchers to understand the ramifications of these international agreements, to ensure that their scientific reputations are not tainted with allegations of unfair or unethical practices.

A new book by Kate Davis, and my colleague Alex Borisenko, provides insights into the ramifications of the CBD and the Nagoya Protocol on molecular biodiversity research. Access and Benefit-Sharing clearly explained from a DNA barcoding point of view and open access - what more do you want?

Friday, January 26, 2018

PhD position in Innsbruck

A new position to pursue a PhD. Check out the announcement below and the site of the Applied and Trophic Ecology Research Group in Innsbruck.
  1. Please send your application and enquiries for further information to assoz. Prof. Dr. Michael Traugott

Thursday, January 25, 2018

Weekend reads

After a long long while some fodder for avid readers. 

Spatial and temporal collections provide important data on the distribution and dispersal of species. Regional-scale monitoring invariably involves hundreds of thousands of samples, the identification of which is costly in both time and money. In this respect, metabarcoding is increasingly seen as a viable alternative to traditional morphological identification, as it eliminates the taxonomic bottleneck previously impeding such work. Here, we assess whether terrestrial arthropods collected from 12 pitfall traps in two farms of a coffee (Coffea arabica L.) growing region of Sao Paulo State, Brazil could differentiate the two locations. We sequenced a portion of the cytochrome oxidase 1 region from minimally processed pools of samples and assessed inter- and intraspecific parameters across the two locations. Our sequencing was sufficient to circumscribe the overall diversity, which was characterized by few dominant taxa, principally small Coleoptera species and Collembola. Thirty-four operational taxonomic units were detected and of these, eight were present in significantly different quantities between the two farms. Analysis of community-wide Beta diversity grouped collections based on farm provenance. Moreover, haplotype-based analyses for a species of Xyleborus beetle showed that there is significant population genetic structuring between the two farms, suggesting limited dispersal. We conclude that metabarcoding can provide important management input and, considering the rapidly declining cost of sequencing, suggest that large-scale monitoring is now feasible and can identify both the taxa present as well as contribute information about genetic diversity of focal species.

Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. By examining templates from more than 5,000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL reduces costs 40-fold from Sanger analysis. Reflecting the capacity of each instrument to recover sequences from more than five million DNA extracts a year, this platform facilitates massive amplicon characterization.

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods. We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.

Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise. The method consists of using a cyclone sampler to acquire fungal spores directly from the air to an Eppendorf tube, and applying DNA barcoding with probabilistic species identification to generate a list of species from the sample. We tested the feasibility of the method by acquiring replicate air samples from different geographical regions within Finland. Our results show that air sampling is adequate for regional-level surveys, with samples collected >100 km apart varying but samples collected <10 km apart not varying in their species composition. The data show marked phenology, and thus that obtaining a representative species list requires aerial sampling that covers the entire fruiting season. In sum, aerial sampling combined with probabilistic molecular species identification offers a highly effective method for generating a species list of air dispersing fungi. The method presented here has the potential to revolutionize fungal surveys, as it provides a highly cost-efficient way to include fungi as a part of large-scale biodiversity assessments and monitoring programs.

Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment.
Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples.
Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer–template mismatches bias the taxonomic profile when using regular and highly degenerate primers.
The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.

Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0.50 per specimen) through Next Generation Sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3290 of 4032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases, and yields precise abundance information.

Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate-derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA. To test whether urban wild mammals can be detected using fly iDNA, we performed DNA metabarcoding of pools of flies captured in Berlin, Germany, using three combinations of blocking primers. Our results show that domestic animal sequences are, as expected, very dominant in urban environments. Nevertheless, wild mammal sequences can often be retrieved, although they usually only represent a minor fraction of the sequence reads. Fly iDNA metabarcoding is therefore a viable approach for quick scans of urban wildlife diversity. Interestingly, our study also shows that blocking primers can interact with each other in ways that affect the outcome of metabarcoding. We conclude that the use of complex combinations of blocking primers, although potentially powerful, should be carefully planned when designing experiments.

Wednesday, January 24, 2018

Posters from the conference

As we all know poster sessions at conferences are always too short and there is no chance to look at the ones that might be of interest let alone all of them. Very often, all that is left after a conference is an abstract somewhere in a thick conference volume unless the work gets published as paper one final day.

It is for this reason that I really like the idea the organizers of the 7th International Barcode of Life conference had. They made all posters available as pdf files on the still functional conference web site. The fact that the conference used digital posters in lieu of printed ones might have made that much easier from a technical standpoint. Both ideas are worth to be pursued in other conferences. It might safe a lot of paper, cost, hassle on airplanes, and makes work, that all too often disappears after one short session, more visible and accessible.

Monday, January 22, 2018

2018 Young Researchers Award

2018 GBIF Young Researchers Award 

15 June nomination deadline for prize recognizing two graduate students whose innovative research relies on biodiversity data accessed through the GBIF network

On behalf of the network of national Participants, the GBIF Secretariat is pleased to invite nominations for the 2018 Young Researchers Award. This annual programme aims to foster innovative research and discovery in biodiversity informatics by graduate students whose master’s and doctoral studies rely on GBIF-mediated data.
The 2018 programme will provide €5,000 prizes recognizing the work of two graduate students—preferably, one master’s and one PhD candidate—nominated by GBIF Participant countries.
Award recipients will be selected from the pool of nominees whose names are received by the GBIF Secretariat by 15 June 2018. The winners will be announced just prior to the 25th GBIF Governing Board meeting, to be held in Kilkenny, Ireland, in October 2018.