Abstract Deadline Extended - Sixth International Barcode of Life Conference

The Sixth International Barcode of Life Conference will be held in Guelph, Canada from August 18-21, 2015. The abstract submission deadline has been extended to April 30th. Note that abstracts associated with an application for a Travel Award must be submitted by the original due date (April 15th).

Themed "Barcodes to Biomes", conference sessions will reflect the ongoing expansion of DNA barcoding research -- in geographic and taxonomic scope, in disciplinary breadth, and in the diversity of socio-economic applications. This conference will feature: 

• publication of all accepted abstracts in a special conference issue of the journal Genome
• an exciting line-up of internationally renowned plenary speakers 
• sessions on systematics, ecology, evolution, conservation, and whole biome analysis 
• sessions on the diverse applications of DNA barcoding including education; international development; protection of endangered species; detection of invasive species, agricultural pests, and species within natural health products; and food safety & authenticity
• poster session 
• diverse opportunities for networking at meals, breaks, and gala dinner 
• 13 prizes for excellent oral and poster presentations by students and post-doctoral fellows
• pre-conference training workshops 
• post-conference excursions to scenic sites such as Niagara Falls 

Submit your abstract by April 30th to ensure its full consideration for inclusion in the scientific program and in the special conference journal issue. We look forward to welcoming you to Guelph for a stimulating and productive meeting. 

Essential Biodiversity Variables in Reporting

Political commitment and policy instruments to halt biodiversity loss require robust data and a diverse indicator set to monitor and report on biodiversity trends. Gaps in data availability and narrow-based indicator sets are significant information barriers to fulfilling these needs.

The Essential Biodiversity Variables (EBVs) which were previously developed by ecology experts in GEO BON, is a list of the most essential elements that need to be monitored worldwide, if we want to know how biodiversity is really changing. Example of essential variables are the population abundances of species (used in the WWF's Living Planet Index ) or the extent of habitat fragmentation.

In a newly published study, researchers used the EBVs as a framework to analyse the gaps between the biodiversity objectives stated in international policy instruments, the indicators used to develop the related policy reports and the data actually available to quantify indicators and proxies.

Results of the study show:

1) that not all aspects of biodiversity are actually being part of policy relevant reporting which means that policy makers are unlikely to receive information on them. For example information on changes in the EBV class "Genetic Composition," is often not required for reporting, nor are there any defined indicators and consequently little data is directly available.

2) which of these biodiversity variables actually end up in CBD reports as quantifiable indicators. For example, information on Ecosystem function is often asked for, but not represented by many useful indicators.

3) that for some EBVs data seems to be already available in order to improve current reporting efforts, a good example are indicators on Ecosystem structure.

Additionally, the study identified potentially available data that could be used to improve existing indicators by adding more taxa or spatial or temporal coverage.

EBVs certainly won't cover all the information needed for policy reporting. This is because the policy objectives also include things related to public awareness building and the implementation of protection measures - aspects which are not within the scope of EBVs.

However, using Essential Biodiversity Variables (EBVs) as a tool, theory-driven comparisons could be made between the biodiversity information gaps in reporting and indicator sets. Analytical properties, such as an identification of which data and indicator(s) are relevant per EBV, will need to be addressed before EBVs can actually become operational and facilitate the integration of data flows for monitoring and reporting. In the meantime, a first analysis shows that existing indicators and available data offer considerable potential for bridging the identified information gaps.

Measuring eDNA concentrations

Evaluations of species distribution and biomass are fundamental in studies on the population dynamics and community structure of an ecosystem. Recently, methods using eDNA were used to identify and track organisms in various aquatic ecosystems, such as lakes/ponds, rivers, and oceans. However, no quantitative eDNA technique has been fully established, because there are methodological limitations to quantifying eDNA concentrations.

A group of Japanese researchers now claim that they used a recently developed new PCR technology to quantify eDNA concentration in eDNA studies. 

Droplet digital PCR (ddPCR), also known as a “third-generation” PCR, is an emerging DNA detection method that provides absolute quantification of target DNA without a standard curve of the reference. DNA is partitioned into approximately 20,000 droplets, some of which ideally contain one or few copies of the target DNA. The PCR occurs in each droplet, and end-point PCR amplification is detected using fluorescence probes.

The colleagues used eDNA from mesocosm experiments with different numbers of common carp to evaluate the quantification accuracy of qPCR and ddPCR when estimating species abundance and biomass. They found that ddPCR quantified the concentration of carp eDNA relative to carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were relatively lower with ddPCR than with qPCR. 

The researchers conclude that in the future this technique could be applied for habitat research on rare or non-native species in the field, because the eDNA recovered for target species from field samples typically occurs in very low concentrations. 

We showed that the relationship between carp abundance and eDNA concentration was higher than that between biomass and eDNA using both ddPCR and qPCR. Therefore, ddPCR can be used to quantify eDNA concentration in water. However, ddPCR is currently more expensive and time consuming compared to qPCR and in natural habitats, eDNA estimation for organism abundance is more complex. Therefore, by using multiple technologies, we can develop better eDNA methods to evaluate the distribution and abundance/biomass of species and communities.

Not one and not the right one

Ecotoxicology combines the methods of ecology and toxicology in studying the effects of toxic substances and especially pollutants on the environment. It employs standardized test procedures that work with model organisms to assess the potentially harmful impact of anthropogenic substances on ecosystems. In order to guarantee the compatibility of these tests on a global scale, the laboratories use model species specified by international guidelines.

Earthworms have been chosen for soil toxicity tests. They are ubiquitous and abundant in most soils, and members of the common family Lumbricidae can reach very high densities. Earthworms play a significant role in soil formation, aeration, and nutrient cycling. Eisenia fetida has been chosen as the standard species for soil toxicity tests. It is widely available, easily reared in laboratory cultures, reproduces quickly and steadily under optimal conditions, and there was baseline data on the ecotoxicology of these worms available. However, ever since these worms have been used in standard testing there were discussions whether the animals used belonged to one species or two. 

An international consortium of five laboratories, led by my former supervisor Markus Pfenninger and Jörg Römbke, closely examined the earthworm species used in ecotoxicology tests and tried to verify its assumed species identity by means of DNA Barcoding . In a broadly designed comparative test, conducted by 28 ecotoxicological laboratories from 15 countries and four continents, they were able to show that only 17 of the 28 labs actually worked with the earthworm species of the genus Eisenia that they had specified. However, at eleven institutes, the tests were conducted de facto with other members of this genus. Since it is not known to what extent the species in questions differ in their reactions to the tested substances, the results and the compatibility of tests are controversial if they were not uniformly conducted with identical species.

In addition, the study also confirmed the existence of a cryptic species in the laboratories, which, although it does not differ morphologically from one of the described Eisenia species, nonetheless constitutes a distinct genetic species. 

The results of this study are now being presented to standardizing organizations such as the Organization for Economic Cooperation and Development (OECD) and the International Standardization Organization (ISO) in order to include this information in their further standardization work, e.g., by modifying existing individual guidelines or by preparing a Guidance Document which describes the DNA Barcoding procedure independently from the individual guidelines. 

Discoveries of the week #33

Uromunna naherba

Uromunna naherba sp. nov. is described from eelgrass beds (Zostera marina and Z. noltii) of the NW Iberian Peninsula. This is the second species of the genus reported from the NE Atlantic, after U. petiti. The new species was more abundant on rhizomes than on the leaves of the plants. Seasonal samples show that ovigerous females are present throughout the year, but become more abundant in late spring and summer, when adult males decrease in frequency. Ovigerous females appear in only one size class. Owing to the yearly productivity cycle of the eelgrasses, these data suggest that the species is semelparous and completes its lifecycle within 1 year. The taxonomic characters of the genus are discussed.

This new isopod species was discovered in eelgrass beds in Spanish waters. The expression Na herba is Galician for “in the grass”.

no DNA Barcodes

Enyalioides sophiarothschildae

Enyalioides altotambo, Enyalioides anisolepis, Enyalioides sophiarothschildae

The discovery of three new species of Enyalioides from the tropical Andes in Ecuador and northern Peru is reported. Enyalioides altotambo sp. n. occurs in northwestern Ecuador and differs from other species of Enyalioides in having dorsal scales that are both smooth and homogeneous in size, a brown iris, and in lacking enlarged, circular and keeled scales on the flanks. Enyalioides anisolepis sp. n. occurs on the Amazonian slopes of the Andes in southern Ecuador and northern Peru and can be distinguished from other species of Enyalioides by its scattered, projecting large scales on the dorsum, flanks, and hind limbs, as well as a well-developed vertebral crest, with the vertebrals on the neck at least three times higher than those between the hind limbs. Enyalioides sophiarothschildae sp. n. is from the Amazonian slopes of the Cordillera Central in northeastern Peru; it differs from other species of Enyalioides in having caudal scales that are relatively homogeneous in size on each caudal segment, a white gular region with a black medial patch and several turquoise scales in males, as well as immaculate white labials and chin. A molecular phylogenetic tree of 18 species of hoplocercines is presented, including the three species described in this paper and E. cofanorum, as well as an updated identification key for species of Hoplocercinae.

Finding three new species of woodlizards is quite unusual given that they are among the largest and most colorful lizards in South American forests. This discovery increases the number of species of woodlizards to 15. The first name refers to the type locality, the second to some unusual scales on the animal, and the third honors a financial supporter (Sophia Rothschild). The authors did some DNA work but unfortunately they did not include the DNA Barcode region. In fact they sequenced a longer mtDNA fragment stretching over some NADH subunites and tRNAs but end right at the very beginning of COI.

no DNA Barcodes

Eadmuna guianensis

The genus Eadmuna Schaus, 1928 is revised to include four species. Eadmuna guianensis sp. n., is described from French Guiana and Guyana. The holotype of Perophora pulverula Schaus, 1896, currently placed in Cicinnus Blanchard, 1852, is determined to be a previously unrecognized female Eadmuna, and is transferred accordingly as E. pulverula comb. n.. Eadmuna paloa Schaus, 1933, rev. status, is removed from synonymy with the type species E. esperans (Schaus, 1905). Eadmuna esperans, E. paloa, and E. pulverula may be of conservation concern due to their limited extent of occurrence and endemicity to the highly imperiled Brazilian Atlantic forest.

A new species of Sackbearer Moth named for the Guianas from where all the specimens were collected.

no DNA Barcodes

Eresus hermani

According to the most recent taxonomic literature, three species of the genus Eresus are known in Central Europe, E. kollari, E. sandaliatus and E. moravicus. We recognized a fourth distinctive species from Hungary, which is described as Eresus hermani sp. n. Eresus hermani has an early spring copulation period, females have a light grey (grizzled) cephalothorax due to a heavy cover of lightly colored setae, and an epigyne with large flat areas posterior to the epigynal pit, while males are distinguished by a broad and blunt terminal tooth of the conductor. An updated and modified comparative table of Řezáč et al. (2008) to include all four Central European Eresus species, and a simple key to the species group’s species are given. Habitus, epigyne, vulva and conductor of E. kollari, E. moravicus and E. sandaliatus are also illustrated. An annotated list of papers illustrating E. hermani due to misidentifications is presented.

The velvet spiders (family Eresidae) are among the most attractive spiders (yes, spiders can be beautiful) with 96 described species. A new species was found in Hungary and named after Ottó Herman (1835–1914), Hungarian arachnologist and polymath, who first recognized color variants within Hungarian Eresus forms, to commemorate the 100th anniversary of his passing.

no DNA Barcodes

Psephellus vanensis

A new species, Psephellus vanensis A.Duran, Behçet & B.Dogan (Asteraceae) from Anatolia, Turkey, is described and illustrated. The species grows on the serpentine stony field of the village of Çaldıran in the district of Başkale (Van province) in eastern Anatolia. It is morphologically similar to Psephellus pyrrhoblepharus (Boiss.) Wagenitz. Diagnostic characters are discussed, and a key to the most similar species is provided. Ecology, conservation status and notes on biogeography of the species are also presented. In addition, the geographical distribution of the new species and other related species in Turkey is mapped.

Today two new plant species from Turkey. For the new member of the Asteracea no information on the Etymology was provided.

no DNA Barcodes

Dianthus aticii

During the taxonomic revision of the Turkish Dianthus species, specimens collected from Bilecik, Seben (Bolu), and Nallıhan (Ankara) were discovered that represent a new species. Its description, images, chorology, ecology, and threat category are provided. It was compared with a closely related species, D. zonatus, and differences are based on its general morphology and seed micromorphology.

Carnations are well known although there are about 300 species in this genus. The new species from Turkey was named in honour of the hydrobiologist Tahir Atıcı.

no DNA Barcodes

DNA Barcode Conference Plenary - Laurence Packer

Another guest post by a conference plenary speaker. Without much further ado the stage is Laurence Packer's:

Laurence Packer is a melittologist (one who studies wild bees) and has been at York University since 1988.  He received his PhD from the University of Toronto in 1986. He runs one of the largest and most diverse bee research laboratories in the world. In addition to training undergraduate and graduate students in matters entomological, he is also very active in outreach, giving numerous talks to diverse audiences each year.  His book: Keeping the Bees (HarperCollins), was well received –being referred to as “a love affair with bees” as well as a humorous romp through matters melittological.

Bees are all the rage these days, everyone wants to know about them.  There is a lot to be learned.  I have at least one hundred species waiting for me to have the time to describe them….

My research career has taken numerous twists and turns.  I started out as a sociobiologist with a side interest in phylogenetic approaches to answering questions about the origins of eusociality in bees.  It turned out that the bees that seemed closest to any recent origin of queen and worker castes are those that nest in the ground.  Consequently, I spent a lot of time digging holes.  In order to assess the evolutionary pattern of social evolution in these bees; I started developing phylogenies for them. Progress on these morphology-based phylogenies was interrupted by the discovery that nobody had looked seriously at the morphological richness to be found in the sting apparatus (see above figure on the right) – a part of bee anatomy most people are well aware of, but which systematists had generally ignored.  That encouraged me to look at other understudied parts of the anatomy of bees, but then….. along came DNA barcoding.  

Starting in 2004, I transferred much of my research effort into either developing the DNA barcode database for bees, or working on a weird group of primarily Chilean bees (Image on the left – and that’s another story, but the current career twist concerns bee biogeography and barcoding in the world’s driest desert - see below).

My laboratory has since generated most of the bee barcodes available on BOLD, with records from all over the world (over 32,000 records from approximately 90 countries so far).

In combination with my ongoing interests in bee biodiversity and taxonomy, the DNA barcode library has yielded a large number of interesting findings.  One is that the commonest and one of the most easily identified wild bee species in North America, the “species” I had studied for my sociobiological PhD turns out to be at least 3 species with large genetic distances (whether based on Neolithic era technologies of allozymes, nuclear gene sequences or DNA barcodes) but with seemingly no consistent morphological differences among them.  This background put me in a good position to evaluate some of the early criticisms of DNA barcoding levelled by “traditional” taxonomists.
It was quite easy to demonstrate that, when the same criticisms were turned on their heads, traditional approaches were rarely any better, and usually worse, than DNA barcoding. This was particularly the case when applied to the issues barcoding was aimed at addressing: discrimination of closely related species.

Having built up a world class collection, I am now working towards a retirement to be spent curating morphological and barcode databases for the world’s bees.

The Vanishing Chocolate Trees

Cacao swollen-shoot virus (CSSV) is a plant virus that primarily infects cacao trees (Theobroma cacao) and has a major effect on crop yields. Within one year of infection yields decrease by 25%, and within two years by 50%. The trees are usually killed within 3 to 4 years. The virus is currently endemic in Togo, Ghana and Nigeria but it has claimed already over 200 million trees in this region that ranks among the top cacao producers in the world. Mealybugs (Pseudococcidae) are the key vectors transmitting the virus from tree to tree. 

The extend of viral transmission is mealybug species specific of mealybugs as virus vectors is species specific and varies depending to their favoured feeding sites on the cacao plant and with respect to the age of the plant. There are 61 species of mealybugs found on cacao, 19 of them have been reported in West Africa, where CSSV occurs.  Of those, 16 are thought to act as vectors.

Morphological keys for mealybugs require a high degree of expertise depending as they do upon characterisation of microscopic structures that are, in vivo, often obscured by filamentous wax exudates. The keys cannot be definitive as some species are known to exhibit misleading phenotypic plasticity and, with few exceptions, morphological keys for mealybugs describe only adult females leaving the peripatetic and therefore more pathogenically important juveniles largely anonymous. 

This calls for DNA-based identification methods and in a newly published study a group of researchers from the UK tested the utility of DNA Barcoding in this context. 

In this work we describe the use of a mitochondrial cytochrome c oxidase 1 (CO1)-based DNA barcoding approach to mealybug identification that circumvents many of these problems... In order to make a DNA barcoding approach a practical tool to support in situ breeding for improved pest resistance of tropical crops such as cacao we have also tested High Resolution Melt Analysis (HRMA) for CO1-based mealybug identification. 

Indeed HRMA allowed them to differentiate the mealybug species that affect cacao and which usually can not be identified by conventional morphological analysis. This find has important implications for research in the affected regions and the authors see its potential to facilitate breeding for resistance to CSSV and even other mealybug transmitted diseases.

HRMA allied to morphological characterisation of mealybug exemplars has immediate utility for the support of CSSV resistance screening in cacao. Once exemplar haplotypes have been established for all species found on West African cacao, reference DNA will be made available so that only HRMA will be necessary at remote sites for the identification of potential CSSV vectors. The approach makes dependence on access to DNA sequencing superfluous and its sensitivity means that samples can be characterised regardless of developmental stage thereby also benefitting quarantine applications.