Barcodes to validate mitogenomic data

Mitogenomic data are increasingly used in many fields of biology especially since new sequencing technology enabled us to retrieve them rather easy and at low cost. However, very often with increasing numbers the chance for the occurrence of erroneous data increases as well. Over the years I came across a couple of fish mitogenomes that were assigned to the wrong species likely due to initial mis-identification. 

A new paper in Mitochondrial DNA - the journal that probably publishes most of the current papers on newly sequences mitogenomes - shows another case of such a erroneous assignment, this time for a bat sequence. However, the authors don't stop there, they actually propose some best practices for future studies to implement some sort of quality control. Some of the proposed standards are pretty common withing the DNA barcoding community and others actually suggest to use DNA barcoding to confirm the identity of a species.

Here is what the authors propose:

Proposed guidelines for accurately reporting new mitogenomes

(1) Provide detailed information on the origin of the sample used for mitogenome sequencing.

(2) Conduct a phylogenetic analysis of the new mitogenome in the context of closely related species.

(3) Provide a barcoding identification assessment of the sample thanks to a ML tree based on the closest available sequences.

There is much more detail on each of the three points in the paper and I hope it will be used as quality control standard for Mitogenome Announcement publications in Mitochondrial DNA and elsewhere. 

What's in fish feed?

One of today's most popular sources of protein is seafood. The demand is constantly increasing and as a consequence almost half of the seafood we eat comes from aquaculture. In fact seafood farming is the fastest growing food production system in the world. It is expected to exceed the production of beef, pork or poultry within the next decades. Aquaculture is also portrait as a method to harvest seafood without further impact on biodiversity probably even reducing the pressure on natural populations. However, the industry heavily depends on marine captured fishes as main nutrient source, e.g. fishmeal.

Fishmeal is a commercial product made from both the whole fishes and their bones and offal from processed fish in order to provide the farmed fish species with natural high quality proteins. The fishmeal industry relies greatly on a “hunting-and-gathering” technique. Cooking, pressing, drying and grinding the fish make fishmeal. As a result, about one-fourth of the seafood harvested from the wild is consumed in fishmeal or other products, not for human consumption. It seems to be a global trend to produce fishmeal using fish processing waste; for example, in Spain and in United Kingdom accounted for 100 and 84% of total fishmeal production respectively. Currently about 25% of the world's fishmeal is generated from fish processing wastes. The proportion is expected to increase, given the growth of aquaculture.

The future expansion of aquaculture may be constrained by the dependence on such low value/trash fish and the impact on natural populations of fish. Therefore, it is very important to have tools in place to monitor fishmeal composition. Obviously, DNA Barcoding lends itself to such investigations but the product in question has been heavily processed which would exclude a conventional Sanger-based sequencing approach.

This is why a group of Egyptian researchers used the metabarcoding approach, applying the Roche/454 platform, to determine fish species composition of fish feeds used in local aquaculture. Their results are concerning as about 46% of all fish species detected are either overexploited or populations are in strong decline. In addition all products contained iridescent shark (Pangasianodon hypophthalmus), an endangered species. 

Interestingly, there are fishmeal products that are incorporated into the diet of herbivorous fishes such as tilapia and carp. The study shows that these products differ in species composition from the those used in fish feed for carnivorous species. However, my first question would be why we are feeding fishmeal to herbivorous species in the first place?

In this scenario, an aquaculture regulatory framework in the countries concerned with fish feed production and trading, including Egypt, should be established in order to regulate fisheries and aquaculture sustainability and to protect biodiversity. Finally, we strongly recommend the introduction of NGS technologies as a tool for fish feed inspections in order to balance/regulate the fish feed productions for sustaining both animal and human life.

A virus and its carrier on their way northward

Early this week, the World Health Organization announced that the Zika virus, a mosquito-borne illness that in the past year has swept quickly throughout equatorial countries, is expected to spread across the Americas and into the United States.

The disease, which was discovered already back in 1947 but had since been seen in only small, short-lived outbreaks, causes symptoms including a rash, headache and small fever. However, a May 2015 outbreak in Brazil led to nearly 3,500 reports of birth defects linked to the virus, even after its symptoms had passed, as well as an increase in cases of the immune disorder Guillain-Barre syndrome. 

Zika virus is transmitted by the mosquito species Aedes aegypti, which is also a carrier of two other tropical diseases, dengue fever and chikungunya. This mosquito species is not native to North America and restricted to tropical and subtropical regions of the world and not found farther north in the United States than Alabama, Mississippi, Georgia and South Carolina.

Researchers at the University of Notre Dame who study the species have now reported a discovery of a population of the mosquitoes in a Capitol Hill neighborhood in Washington, D.C.

Analysis of a 441-bp fragment of the mitochondrial cytochrome oxidase I gene sequence identified the same two haplotype sequences during 2011–2014, and placed these within two discrete groups known to be derived from lineages resident in the Americas. Analysis of 10 microsatellite loci for specimens collected during 2011–2014 revealed no evidence for introgression of new alleles across years. 

These findings are evidence that these mosquitoes not only occur in more northern areas of the USA but also that they have overwintered for at least the past four years, meaning they are adapting for persistence in a northern climate well out of their normal range.

The Washington population is currently disease-free but the fact that some mosquito species are finding ways to survive in normally restrictive environments by taking advantage of underground refugia means that there is a real potential for active transmission of mosquito-borne tropical diseases in the future.

Taxonomic resolution matters when studying stress responses of indicator taxa

Most freshwater ecosystems are subject to multiple anthropogenic stressors, which commonly reduce biodiversity across all levels. Existing freshwater bioassessment programmes aim at identifying responses of aquatic biota to stressors. For practical reasons, higher-level taxonomic groups (e.g. genus or family) are often used in these programmes. This approach, however, may bias assessment results as different species can differ substantially in their biological traits, thus emphasising the need for species-level data. 

Animal species have been used as indicators for decades to collect information about particular regions and/or habitats. In freshwater environments many taxa are strongly associated with natural habitats with good water quality and are therefore used as indicator species as opposed to other species which can thrive in highly modified waterbodies with poor water quality. 

For example in New Zealand Single Gill Mayflies of the genus Deleatidium indicate good habitat and water quality conditions, especially if other mayfly or stonefly groups are abundant as well. Sixteen species are known, however, the distribution range of many species is unknown and identification of both adults and larvae is anything but easy. This is clearly a case where molecular methods such as DNA Barcoding could be of great help. In fact there are a number of colleagues who claim that species identification using DNA Barcodes may allow assessing biodiversity and degradation of freshwater ecosystems in greater detail than classical approaches.

A new study by researchers from Germany and New Zealand represents a very good example for the validity of this claim. The colleagues compared stress–response patterns of bioindicator taxa (Deleatidium spp.) using both traditional morphology-based methods and DNA Barcoding.

As it turns out their Deleatidium sample consisted of twelve distinct clades that likely represent distinct cryptic species. Morphological analysis did not allow for further identification than genus. Finally, In a subsequent step they compared stressor responses assessed at genus and species level. 

While overall Deleatidium abundance was unrelated to stressor levels, some of the individual clades differed clearly in the magnitude and direction of their responses to nutrient and sediment stress...These contrasting patterns indicate that individual freshwater invertebrate species, often merged to a higher taxonomic level for biomonitoring purposes, can differ substantially in their tolerance to stressors and respond in more complex ways than observed at genus level.

Hand sanitizer to preserve DNA

Prevention of DNA degradation is essential to conducting molecular analyses of field-captured specimens. This is especially important for projects that incorporate participation of non-specialists in research, such as agency monitoring of pests, or citizen science, where standard methods of preservation may be inaccessible. 

The commonly used 95 percent ethanol or pure propylene glycol are expensive and hard to access for everyone outside a professional lab. However, collecting and preserving samples and the DNA in them even if it is only for short-term storage and shipment requires appropriate chemicals. 

A new study, published in the journal Invertebrate Systematics, presents the results of a study by researchers from Florida in which they tested several commonly available products for their ability to preserve the DNA in ambrosia beetles. They preserved 33 ambrosia beetles under experimental conditions in ethanol (control), hand sanitizer, pure propylene glycol and automobile antifreeze and coolant.

Each sample was left for two or seven days under direct outdoor exposure and the colleagues assessed the relative quantity of intact DNA by performing RT-PCR. Successful amplification of the target gene was then verified by sequencing. 

They found that alcohol-based hand sanitizer, and propylene and ethylene glycol-based automobile antifreeze can preserve DNA at least for a short-term and thereby serve as effective substitutes for laboratory-grade preservatives.

This finding opens the door for much broader participation in citizen science, Now, there is an easy way for anyone who is interested in preserving insects for a project to get the materials themselves. It also means that professionals can sample more widely, at a lower cost and with fewer concerns about safety. This also offers a big boost for scientists who collect samples in remote locations, where accessing laboratory-grade materials can be difficult or impossible. We hope this encourages many more projects to incorporate a citizen science component without worrying about cost of or access to preservation materials.

eDNA to measure fish abundance in a lake

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

As a consequence an increasing number of studies applies methods using eDNA to identify and track organisms in various aquatic ecosystems, such as lakes/ponds, rivers, and oceans. However, a major challenge is to develop a technique to quantify eDNA concentrations and thereby determine not only an organisms presence but also its abundance.

A team of researchers of the Université Laval and supervised by an old friend, Louis Bernatchez, tested the capability of eDNA techniques to measure abundance with some lake trout populations in 12 southern Quebec lakes. For comparisons with traditional methods the colleagues used lake trout population estimates obtained by their colleagues at Quebec's Ministry of Forests, Wildlife and Parks. This method consists of estimating entire lake populations by extrapolating from the number of fish captured using nets deployed in different parts of the body of water. This method is often time and labor intensive, in addition to having a potentially negative effect on fish populations.

To measure the concentration of lake trout eDNA, the researchers took approximately 10 one-liter samples of water from different areas of each lake studied. They then filtered the water and subjected the particles retained to qPCR analysis of a small COI Barcode fragment in order to accurately measure the quantity of lake trout DNA.

The results showed a strong correlation between population estimates obtained using the traditional approach and those based on eDNA concentration. Variations in eDNA abundance in different parts of each lake are also similar to those reported for net catches.

Our results indicate that eDNA may additionally be used to quantify fish relative abundance in lakes. From a fisheries management perspective, such eDNA analyses represent a new step towards improving spatial and temporal coverage of population assessment and monitoring while being less invasive, less time-consuming and less expensive. While resources generally support the survey of only a few lakes per year using the gillnet method, here eDNA sampling covering southern Québec was achieved in seven sampling days and required two technicians working on average <2 h to cover an entire lake.

The colleagues are continuing their work to extend their method to other target species that are of interest for fishing, such as walleye, sauger, brook trout, Arctic char, and northern pike, but also for a number of rare or threatened species as well as invasive exotic species.

Special Issue on Fungal DNA Barcoding

A special issue of Fungal Biology titled Barcoding - Species Concepts and Species Recognition in Medical Mycology was just published. Very interesting focus on fungi that cause infections in humans and animals. Here we go, all articles and DOI links to them:

DNA barcoding of fungi causing infections in humans and animals

Laszlo Irinyi, Michaela Lackner, G. Sybren de Hoog, Wieland Meyer

The ‘species complex’ issue in clinically relevant fungi: A case study in Scedosporium apiospermum

Min Chen, Jingsi Zeng, G. Sybren De Hoog, Benjamin Stielow, A.H.G. Gerrits Van Den Ende, Wanqing Liao, Michaela Lackner

Intra- and interspecific diversity of ultrastructural markers in Scedosporium

Amaliya A. Stepanova, G. Sybren de Hoog, Nataliya V. Vasilyeva

Discriminative potential of some PCR-based and biochemical methods at Scedosporium strains

Lucia Kraková, Domenico Pangallo, Elena Piecková, Mária Majorošová

Towards proteomic species barcoding of fungi – An example using Scedosporium/Pseudallescheria complex isolates

Mareike Bernhard, Andreas Erich Zautner, Joerg Steinmann, Michael Weig, Uwe Groß, Oliver Bader

Prospective evaluation of the chromogenic medium CandiSelect 4 for differentiation and presumptive identification of non-Candida albicans Candida species

Liang Zhao, G. Sybren de Hoog, Akke Cornelissen, Qian Lyu, Lili Mou, Taohua Liu, Yu Cao, Mansoureh Vatanshenassan, Yingqian Kang

DNA barcoding revealed Nematodospora valgi gen. nov., sp. nov. and Candida cetoniae sp. nov. in the Lodderomyces clade

Dilnora E. Gouliamova, Roumen A. Dimitrov, Maudy Th. Smith, Marizeth Groenewald, Margarita M. Stoilova-Disheva, Borislav V. Guéorguiev, Teun Boekhout

Barcoding markers for Pneumocystis species in wildlife

Patrizia Danesi, Graziana da Rold, Annapaola Rizzoli, Heidi C. Hauffe, Stefano Marangon, Kittipan Samerpitak, Cristine Demanche, Jacques Guillot, Gioia Capelli, Sybren G. de Hoog

Arthrocladium, an unexpected human opportunist in Trichomeriaceae (Chaetothyriales)

Mariana M.F. Nascimento, Laura Selbmann, Somayeh Sharifynia, Abdullah M.S. Al-Hatmi, Hermann Voglmayr, Vania A. Vicente, Shuwen Deng, Alexandra Kargl, Tarek A.A. Moussa, Hassan S. Al-Zahrani, Omar A. Almaghrabi, G. Sybren de Hoog

Barcoding and species recognition of opportunistic pathogens in Ochroconis and Verruconis

Kittipan Samerpitak, Bert H.G. Gerrits van den Ende, J. Benjamin Stielow, Steph B.J. Menken, G. Sybren de Hoog

Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium

Abdullah M.S. Al-Hatmi, A.H.G. Gerrits Van Den Ende, J. Benjamin Stielow, Anne D. Van Diepeningen, Keith A. Seifert, Wayne McCormick, Rafik Assabgui, Tom Gräfenhan, G. Sybren De Hoog, C. André Levesque

Sporothrix chilensis sp. nov. (Ascomycota: Ophiostomatales), a soil-borne agent of human sporotrichosis with mild-pathogenic potential to mammals

Anderson Messias Rodrigues, Rodrigo Cruz Choappa, Geisa Ferreira Fernandes, G. Sybren de Hoog, Zoilo Pires de Camargo

DNA barcoding, MALDI-TOF, and AFLP data support Fusarium ficicrescens as a distinct species within the Fusarium fujikuroi species complex

Abdullah M.S. Al-Hatmi, Mansoureh Mirabolfathy, Ferry Hagen, Anne-Cécile Normand, J. Benjamin Stielow, Rouhollah Karami-Osbo, Anne D. van Diepeningen, Jacques F. Meis, G. Sybren de Hoog

Identification of fungal pathogens in Formalin-fixed, Paraffin-embedded tissue samples by molecular methods

Volker Rickerts

Galleria mellonella: An invertebrate model to study pathogenicity in correctly defined fungal species

Ulrike Binder, Elisabeth Maurer, Cornelia Lass-Flörl

Enjoy reading.

From the inbox: High-Throughput Sequencing in Limnology Session at SIL2016

Found this today in my inbox and thought there might be some readers that are interested:

XXXIII Congress of the International Society of Limnology

Special Session 25

High-Throughput Sequencing in Limnology

The advances in high-throughput sequencing provide a very interesting possibility to study eukaryotic as well as prokaryotic genes in freshwater system. The sequencing depth allows us to face fundamental ecological questions in important topics such as temporal and spatial successions, community ecology, metabolic redundancies, and evolution, to only name a few of them. This sessions intends to provide an overview on work that is currently conducted in aquatic sciences using high-throughput sequencing as well as give an outlook on the possibilities opened up by this methodology. If you are part of the community of limnologist that advance the field by the use of high-throughput sequencing, we kindly invite you to submit your abstract to our special session.

Deadline for submission of abstract: February 1st

Reminder: Distance Education course

Just a little reminder in between - coming up soon:

February 8th - April 1st, 2016

Marine Ostracods

Ostracods are often called seed shrimp which is in reference to their body shape. Their bodies are flattened from side to side and protected by a mussel-like, chitinous or calcareous valve or "shell". The hinge of the two valves is in the upper region of the body. 

Planktonic ostracods are thought to play an important role in the cycling of organic carbon below the thermocline and they are also sensitive to water temperature and salinity changes, making them potential indicators of climate change.

Some 40,000 species have been described but the majority of them is long extinct and known only through the fossil record. Species numbers vary greatly in the literature and the true diversity of extant ostracods is - as in many other groups - unknown. There are more than 200 described species of marine planktonic ostracods, many of which (especially conspecific species) can be identified only by microscopic examination and dissection of fragile morphological characters. 

On top of the problems of morphological identifications there is a dramatic lack of taxonomic expertise for the group -  only two or three active researchers currently have sufficient expertise for species identification and description .Given all these problems, DNA Barcodes seemed particularly useful and necessary. 

An international group of colleagues now adds DNA Barcodes of 78 species of marine planktonic ostracods to the global reference library, including two novel species, and 51 species for which DNA Barcodes have not been previously published. Specimens were collected back in 2006 to 2008 from the Atlantic, Indian, and Southern Oceans, Greenland Sea and Gulf of Alaska. Samples were collected from surface to 5,000 m using various collection devices. This number might not sound very impressive and large but given the difficulties to obtain these species it is certainly a great accomplishment.

Not surprisingly they researchers concluded:

Based on taxonomically and geographically extensive sampling and analysis (albeit with small sample sizes), the COI barcode region was shown to be a valuable character for discrimination, recognition, identification, and discovery of species of marine planktonic ostracods.

Impact assessments with DNA Barcoding

Mining operations are supposed to track the impact of their activities on biodiversity and demonstrate the effectiveness of their site restoration programs. As soon as profitable mining comes to an end it is the responsibility of the mining company to recreate conditions allowing biota to develop on previously mined substrate to function within a natural, self-sustaining ecosystem. 

In reality however, mine sites often leave a legacy, including perpetually altered plant communities elevated contaminants in surface and groundwater, thin, compact soils, altered soil function, and magnification of contaminants within the food chain .

Government regulations on mining operations usually set guidelines for such reclamation projects but such regulations do not exist in every country. In fact I think it is fair to say that only a minority of countries have sufficient legislation in place. But even if they are in place we know little about the ideal way to properly restore former mining sites:

Despite pervasive efforts to meet and improve upon regulatory guidelines for ecosystem services at previously mined sites, there is a large degree of uncertainty in mine land restoration. Consistent application of revegetation,soil amendments, and regrading treatments can lead to very different results, even on the same site. 

There are many potential reasons for this. The authors of a new review published in the journal Restoration Ecology e.g. list variability in starting conditions, slope, aspect, and many hitherto unmeasured or insufficiently measured factors. The latter includes measures of local biodiversity which will be at the end of the day one key measure of how well a site has been restored.

Our institute has partnered with the mining company New Gold Inc. to explore the potential of DNA Barcoding for expediting environmental impact assessments. My colleagues here conducted a pilot study at New Gold’s New Afton site near Kamloops, BC. It investigated the addition of mass arthropod sampling and DNA Barcoding to evaluate the success of site remediation efforts. The pilot program involved four sites: two grassland sites (disturbed and undisturbed) and two wetland sites (disturbed and undisturbed). Between 294 and 5,560 individual invertebrates were captured in Malaise traps each week, and 51,264 specimens were identified representing 3,956 species.

The volume of taxonomic and functional data collected for arthropods at the New Afton site is unprecedented for the mining industry, owing to the successful application of DNA Barcoding. New Afton managers intend to continue monitoring with this approach on a 4–5 year time scale. Such baseline data will provide a comprehensive understanding of the trajectory arthropod communities take as this mine site develops and is reclaimed.

Guest post: Sample size estimation for DNA barcoding: Are current sampling levels enough?

Today a guest post by Jarrett Philips. He writes about a project of his Masters studies in Bioinformatics which he also presented as a poster contribution at the 6th International Barcode of Life Conference last August. Enjoy and many thanks to Jarrett for his contribution.

The ability of DNA barcodes to detect meaningful genetic variation within and between species is strongly influenced by the scale of specimen sampling. Unfortunately, global barcoding efforts have only been partially successful in this regard due to the majority of studies forgoing deep taxon sampling in favour of optimizing the number of taxa sampled. 

A practical sample size of five individuals per species is common in barcoding studies, but such a strategy is by no means sufficient. This has led to sampling schemes in which many more specimens per species are collected.

A group of researchers from the University of Guelph wished to test whether current sampling efforts are adequate to document standing genetic variation at the species level.

To do this, they developed a simple quantitative model to predict total sample sizes given estimates of observed specimen as well as observed COI haplotype numbers and total haplotype diversity for a species. In creating their model, one very important assumption was made: that haplotypes occur at equal frequency within species populations. Such an assumption is not biologically realistic since species abundances are often skewed geographically.

The authors found wide-ranging sample sizes (between 150-5400 individuals/species) are likely needed to uncover all haplotype diversity across 18 selected species comprising freshwater, marine and migratory ray-finned fishes (Chordata: Actinopterygii). This is a far cry from sampling intensities currently employed in many barcoding initiatives; however such numbers may not be practical and further investigation will be required to fully probe the extent of sampling necessary to gauge existing species genetic diversity in this group and others. 

Haplotype accumulation curves and frequency histograms for four species selected to show a range of sample sizes and haplotype diversity. Those species whose curves show rapid saturation indicate that much of the intraspecific haplotype diversity may have been sampled. Species curves showing little to no indication of asymptotic behavior suggest further sampling is necessary. 

The final paragraph of their study is particularly motivating:

We recognize that estimates of N* calculated from our model likely represent underestimates of the true number of individuals of a given species which should be sampled. Many more specimens should therefore be sampled in order to ensure a sufficient number of haplotypes have been recovered. Equal haplotype frequencies are rarely observed in natural populations, and we suggest the development of more sophisticated models should explore the use of data simulations to evolve models that explicitly account for variation in species haplotype frequencies.

DNA Barcoding for pollen detectives

I have to admit that I knew little about today's topic before. The term 'forensic palynology' was unknown to me. Forensic palynology has been a law enforcement tool for over 60 years. It is the application of pollen and spores in solving legal issues, either civil or criminal. Pollen can be a critical forensic marker in cases where determining geographic origin is important, including investigative leads, missing persons cases, and intelligence applications. Pollen and spores can be obtained from an extremely wide range of items, including bodies and thereby providing clues as to the source of the items and the characteristics of the environments from which the material on them was sourced. 

Despite these clear advantages, the use of palynology has been rather limited in forensic studies and this has likely to do with that fact that you need highly trained, specialized experts to reliably identify pollen via microscopy. The process is slow which in some criminal cases or in the field of intelligence might be crucial. In addition the taxonomic resolution is rather poor (family or genus level at most) even if done by experts. In recent years automated analysis of pollen samples has been developed and the most prominent idea was image processing of microscope images combined with a statistical or machine learning classifier. Other microscopy technologies have been tested as well but what all of them have in common is a general limitation: the lack of morphological characters in pollen for species-level taxonomic resolution in many plant groups.

In a recent review paper colleagues discuss the utility of DNA Barcoding for the identification of pollen. The paper discusses some key challenges that might have prevented DNA Barcoding from being used much wider but the authors also highlight recent progress.

Based on these recent methodological developments in pollen DNA barcoding, we believe that now is the time to start applying these techniques in forensic palynology. In this article, we discuss the potential for these methods, and outline directions for future research to further improve on the technology and increase its applicability to a broader range of situations.

Overall a very nice read and the take home message is that DNA Barcoding is very close to being feasible for routine analysis in forensics, and improvements on technical issues are occurring so rapidly that there is no more excuse to not start using it already. 

Finding the Goby

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

Many colleagues think that eDNA monitoring approaches could considerably improve our ability to detect of rare, endangered and invasive species but because this methodology is rather new we need more studies in which new approaches are compared with traditional techniques.

And here is a new one: The primary objective of this research was to use a multimethod occupancy modelling framework to compare method-specific detection probabilities between eDNA techniques and traditional seining for monitoring tidewater goby.

The tidewater goby (Eucyclogbobius newberryi) is a small fish that occurs in patches along a large stretch of California's coastline. It is a low dispersal species that was already listed as endangered in 1994. About 1/6 of the historically documented populations have disappeared and an estimated 50% of the remaining populations are considered vulnerable to extinction because of habitat loss.

Using eDNA as a monitoring approach for tidewater goby was conceived as an alternative to traditional field methods primarily because of the difficulty of using traditional field monitoring approaches (e.g. seines and minnow traps) in sloughs and estuaries along California's northern coast. Also, tidewater goby populations vary considerably in annual abundance and may be unevenly distributed throughout a site. Thus, eDNA techniques may provide an efficient and noninvasive means of detection at low abundance.

The colleagues used eDNA approaches and traditional seining methods at 29 sites, including multiple paired subsampling locations at each site. In addition they applied eDNA methods only at a total of 39 sites and analysed the data using a hierarchical occupancy model to evaluate three levels of uncertainty associated with collecting spatial replicate water samples within study sites and performing replicate qPCRs.

Analysis using a multimethod occupancy modelling framework indicated that the probability of detection using eDNA was nearly double (0.74) the rate of detection for seining (0.39). The higher detection rates afforded by eDNA allowed determination of tidewater goby occupancy at two locations where they have not been previously detected and at one location considered to be locally extirpated. Additionally, eDNA concentration was positively related to tidewater goby catch per unit effort, suggesting eDNA could potentially be used as a proxy for local tidewater goby abundance.

Where is the damned collection?

Charles Davies Sherborn (30 June 1861 – 22 June 1942) was an English taxonomist who described himself as '’a magpie” with a “card-index mind'. Sherborn wrote the famous Index Animalium, an 11 volume, 9,000 page work that catalogued the 444,000 names of every living and extinct animal discovered between 1758 and 1850. This work is considered the bibliographic foundation for current zoological nomenclature and he single-handedly worked 43 years on it. 

Until now, Sherborn’s contribution has been recognized and relied upon by professional taxonomists worldwide but he has escaped the celebration of his accomplishment that is his due. This changed on 28 October 2011, with a symposium held in his honour at the Natural History Museum (NHM), London, on the 150th year of his birth. 

The symposium included an international panel of experts on bibliography and biodiversity bioinformatics who linked a view of the past with an active debate on the future of these related fields. All talks were recorded and online material includes slides and poster downloads. The resulting papers were published last week in ZooKeys and here they are. The papers in this volume fall into three general areas. In the first section, seven papers present different facets of Sherborn as a man, scientist and bibliographer, and describe the historical context for taxonomic indexing from the 19th century to today. In the second section, five papers (with a major appendix) discuss current tools and innovations for bringing legacy information into the modern age. The final section, with three papers, tackles the future of biological nomenclature, including innovative publishing models and the changing tools and sociology needed for communicating taxonomy.

Ellinor Michel

Anchoring Biodiversity Information: From Sherborn to the 21st century and beyond

Neal Evenhuis

Charles Davies Sherborn and the “Indexer’s Club”

Karolyn Shindler

A magpie with a card-index mind – Charles Davies Sherborn 1861–1942

Gordon McOuat

Naming and Necessity: Sherborn’s Context in the 19th Century

Giles Miller

Sherborn’s foraminiferal studies and their influence on the collections at the Natural History Museum, London

Michael A. Taylor

‘Where is the damned collection?’ Charles Davies Sherborn’s listing of named natural science collections and its successors

Edward C. Dickinson

Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn’s and Richmond’s historical legacy of bibliographic exploration

Christian Thompson, Thomas Pape

Sherborn’s influence on Systema Dipterorum

Suzanne C. Pilsk, Martin R. Kalfatovic, Joel M. Richard

Unlocking Index Animalium: From paper slips to bytes and bits

Francisco Welter-Schultes, Angela Görlich , Alexandra Lutze

Sherborn’s Index Animalium: New names, systematic errors and availability of names in the light of modern nomenclature

Christopher Lyal

Digitising legacy zoological taxonomic literature: Processes, products and using the output

David Remsen

The use and limits of scientific names in biological informatics

Miguel Alonso-Zarazaga, Daphne Fautin, Ellinor Michel
The List of Available Names (LAN): A new generation for stable taxonomic names in zoology?

Lyubomir Penev, Alan Paton, Nicola Nicolson, Paul Kirk, Richard Pyle, Robert Whitton, Teodor Georgiev, Christine Barker, Christopher Hopkins, Vincent Robert, Jordan Bisserkov, Pavel Stoev

A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index, IPNI), fungi (Index Fungorum, MycoBank) and animals (ZooBank)

Roderic Page

Surfacing the deep data of taxonomy

Richard Pyle

Towards a Global Names Architecture: The future of indexing scientific names

Miguel Alonso-Zarazaga, Philippe Bouchet, Richard Pyle, Nikita Kluge, Daphne Fautin
Manual for proposing a Part of the List of Available Names (LAN) in Zoology

Very interesting reads and a nice combination of history and contemporary thoughts on naming in the digital age. I particularly liked Rod Page's quote: DNA barcoding may give a new lease of life to old names.

Haptophyte diversity in the Skagerrak

(Coccolithus pelagicus)

Haptophyta is a division of algae with a few unique features such as two flagella, both of which are smooth, and a unique organelle called a haptonema, which is superficially similar to a flagellum but differs in the arrangement of microtubules and in its use. Probably the best-known haptophytes are coccolithophores, which have an exoskeleton of calcareous plates called coccoliths (see image).

Marine haptophytes occur in all seas as major components of the smallest plankton and carry out key processes in global biogeochemical cycles. Some of the colony forming representatives can form toxic blooms that are harmful to marine biota in general, farmed fish in particular, and to fisheries and tourism through the production of scum and acrylic acid. On the other hand some haptophytes are economically important (e.g. Pavlova lutheri and Isochrysis sp.) as they are widely used as food source in the aquaculture industry.

Despite their importance haptophyte species are difficult to identify using microscopy only because they are small and fragile. They may change form drastically upon fixation for microscopy, and may lose appendages and scales essential for morphological identification. 

About 300 species have been described so far but investigations of environmental water samples using molecular methods have revealed a large diversity of novel haptophyte sequences which suggests that the total number of species is much higher, particularly among the pico-haptophytes. Currently, ca. 650 unique, full-length or partial 18S rDNA haptophyte sequences are included in the Protist Ribosomal Reference Database (PR2). Some of these environmental sequences may represent novel deep-branching haptophyte lineages.

Researchers from the University of Oslo were interested in the diversity of haptophytes in the Skagerrak and they used 454 pyrosequencing of the 18S ribosomal DNA V4 region (= metabarcoding), and supplemented it with electron microscopy. 

The work revealed higher species richness of haptophytes than previously observed in the Skagerrak by microscopy. From ca. 400,000 reads we obtained 156 haptophyte operational taxonomic units (OTUs) after rigorous filtering and 99.5% clustering. The majority (84%) of the OTUs matched environmental sequences not linked to a morphological species, most of which were affiliated with the order Prymnesiales. Phylogenetic analyses including Oslofjorden OTUs and available cultured and environmental haptophyte sequences showed that several of the OTUs matched sequences forming deep-branching lineages, potentially representing novel haptophyte classes. Pyrosequencing also retrieved cultured species not previously reported by microscopy in the Skagerrak. Electron microscopy revealed species not yet genetically characterised and some potentially novel taxa. 

According to the authors some closely related species have identical 18S V4 rDNA regions, which in turn means that the true richness may be even higher. What strikes me is the fact that new lineages range from species to class level once again highlighting how little we know about the large group of diverse eukaryotic, mainly unicellular microorganisms called protists. 

ICURE

The traditional undergraduate program of study incorporates a selection of classes that represent a broad spectrum of subdisciplines. Unfortunately, few curricula successfully integrate concepts in all subdisciplines, giving undergraduates the misconception that there is a lack of application or connectedness between class subjects.

Perhaps the most common model of non-professionals engaging in research is the tradition of undergraduate students working in a university research lab. A student conducts an independent research project in a faculty member’s laboratory. These apprentice-style projects have large benefits and are usually well received by the students. However, the demand for more hands-on student research is much larger and universities and colleges are asked to provide more of such meaningful and authentic research experiences to their undergrad students. As opposed to the independent research project course-based undergraduate research experiences (CUREs) target all students enrolled in a particular course. Research is conducted as part of the course, in the classroom and teaching labs. 

A new study published in Life Science Education goes a step further and describes the successful application of a course-embedded research project that bridges undergraduate courses across subdisciplines by integrating laboratory research experiences (ICURE). In this case two biology course laboratories focused on a common laboratory outcome: the identification of insects. The authors explain their choice:

• First, insects represent the vast majority of organismal biodiversity, a foundational concept in biology. 
• Second, though methods used to evaluate insect biodiversity are well developed, the methods used to identify insects are currently undergoing revision due to advances in molecular technology. DNA barcoding is a relatively new molecular technique that uses DNA sequence data to identify insects and other organisms and has standardized protocols easily adapted to undergraduate laboratory courses. 
• Third, the act of insect identification allows students to apply alternative techniques for a common research goal, emphasizing the holistic nature of scientific research.

Students were involved in the collection of specimens (Malaise traps), identification (morphological and via DNA barcoding in a lab component of the course), and the analysis of the results. One of the end results of the course was a functioning database containing species identifications, DNA Barcodes, and basic ecological data. Research data collected were maintained and supplemented each semester and year. 

Guess what, the students liked it:

Taken together, the experimental ICURE showed significant positive attitudinal changes for all areas assessed except for attitudes regarding the statement “I am likely to choose a STEM career.” This contrasts with control sections that only showed significant positive attitudinal changes for one area associated with the understanding of how to conduct a research project in one course. The open-ended nature of the biodiversity/DNA barcoding ICURE design along with experimental troubleshooting appears to have had positive attitudinal effects.

DNA Barcodes and Nomenclature

The purpose of this application, under Article 75.6 of the Code, is to conserve the universal usage of Tipula contaminata Linnaeus, 1758 by setting aside all previous type fixations and designating a neotype. Tipula contaminata is the type species of the genus Ptychoptera Meigen, 1803, itself the type genus of the family PTYCHOPTERIDAE Osten Sacken, 1862. This species is found over much of Europe, and all authors subsequent to Meigen (1803) have utilized his concept of the species. However, the holotype of Tipula contaminata Linnaeus, 1758 represents a species of TIPULIDAE. It is proposed that a neotype be designated for Tipula contaminata to preserve two hundred years of common usage and ensure nomenclatural stability at the genus and family rank.

IUZN Case 3664

A recently published comment on the above case by Gunnar Kvifte used almost exclusively DNA Barcoding information to strengthen the application. Gunnar and I agree that this is most likely the first time a DNA barcode data set is used as the main argument for or against a nomenclatoral proposal in the International Commission of Zoological Nomenclature (ICZN). The comment is brief and to the point and uses publicly available data on BOLD as evidence. 

The colleagues show that all their Ptychoptera contaminata sequences form a distinct cluster separate from all other species providing further evidence that it is a valid species well delimited from other species of Ptychoptera in the Palearctic region. Case closed :-)

What's in your tea?

Herbal infusions, commonly referred to as herbal teas, are among the most widely consumed hot beverages. The popularity of herbal teas is mainly due to their claimed health-related properties and consumers’ preference for their specific taste and aroma. Herbal teas are sold in the market mainly as tea bags and ground or fragmented loose products. Because it is difficult to identify the botanical origin of a ground or processed product by its appearance, herbal products such as teas, spices, and dietary supplements are vulnerable to accidental contamination, deliberate substitution, or admixing with a less commercially valuable herbal species and undeclared fillers.

Researchers from turkey now developed a DNA assay to authenticate the botanical origin of herbal teas. They tested the efficiency of a PCR-capillary electrophoresis (PCR-CE) approach on commercial herbal tea samples using two noncoding plastid markers, the trnL intron and the intergenic spacer between trnL and trnF. The authors call these markers DNA Barcodes which is incorrect as none of them is a community-wide accepted DNA region. Nevertheless, it is not the first time trnL was used in a study related to DNA-based species identification and the results are quite promising. 

Single ingredient teas and different admixtures of pairs of herbal species were tested (linden/peppermint; sage/anise; rose hip/chamomile; sage/linden) and the researchers were able to identify deviations from standards (listed ingredients) which were further investigated by isolation of the alien fragments for sequencing. In one case a chamomile tea sample clearly contained other non-listed ingredients and a search in public databases revealed that it contained rosemary and was mislabeled as a single-ingredient product.

It is important to note that the utility of the PCR-CE barcode assays proposed in this work is not limited to herbal teas but can be extended to authenticate all types of processed herbal products or raw material. When an appropriate genomic region with sufficient interspecific size variation is selected as the analyte, capillary electrophoresis analysis is a faster, more cost-efficient, less equipment and labor/expertise demanding, and relatively simple alternative to sequencing for herbal product authenticity analyses. PCR-CE assays can be standardized for individual products by employing references based on the ingredients list and applied as routine tests for the verification of botanical origin. PCR-CE assays can also be coupled with sequencing any time adulteration is suspected in a sample.

Happy New Year

A happy, healthy and prosperous year 2016 to all readers!

I am back after a two-week hiatus. A badly needed break to refresh the mind and reload the creative batteries. 

The first post of the year is a reminder - the next run of our DNA Barcoding Intro Course will start February 8th and the early bird registration ends on January 11th:

I am also happy to announce that together with our Open Education department I am currently developing a new 4-week online course called Metabarcoding and eDNA. The first offering is slated for this fall. Here is the course description:

Metabarcoding is a rapidly evolving method for assessing biodiversity from environmental DNA. It has a wide range of applications: biodiversity monitoring, animal diet assessment, reconstruction of paleo communities, among others. DNA metabarcoding relies on molecular techniques such as PCR and next generation sequencing, and requires bioinformatics and biostatistics competence to analyze sequencing results. This approach integrates several scientific areas and requires a broad range of skills in addition to the basic knowledge related to the considered research topic. This program will provide an overview of the state of current technology and the various platforms used. The course consist of a series of online lectures and research exercises introducing different aspects of metabarcoding and environmental DNA research. It also touches on the suite of bioinformatics tools available for sequence analysis and data interpretation.