Thursday, March 26, 2015

News from the DNA Barcoding intro course

Posting has been light these days as there is a lot going on at the institute and because I am teaching the online DNA Barcoding Introduction course. This course is one for the record books with 44 participants from 30 nations:

Such a large international group is a great resource for information and interesting stories especially when it spreads across almost all continents. The course has a number of interactive elements such as discussion forums one of which started this week. Participants get to exchange ideas and experiences. It is great to see how wide DNA Barcoding has spread within the last 11 years and very helpful to see how it is perceived and used in other parts of the world.

We are currently setting up another offering for June/July. If you are interested or know somebody who could benefit from participating please stay tuned for the official announcement which will hopefully come out next week.

Tuesday, March 24, 2015

Discoveries of the week #31

The small-range millipedes Tasmaniosoma anubis sp. n., T. interfluminum sp. n. and T. nicolaus sp. n. are described, and the colour of live T. barbatulum Mesibov, 2010 is documented.

One of these tiny new millipedes (Tasmaniosoma anubis) is only known to occur within the city of Launceston, Tasmania, Australia. The 1 cm-long species was discovered in a city park by two local naturalists. Its name Anubis is taken from the jackal-headed god of ancient Egypt, and the top of the genitalia of male T. anubis have branches which resemble the snout and ears of a jackal.
no DNA Barcodes

Hallodapomimus antennatus sp. n. (Hemiptera: Heteroptera, Miridae, Phylinae, Hallodapini) is described from a macropterous female found in Eocene Baltic amber. The new species can be recognized readily from the other species of the genus, mainly due to its unusual second antennal segment. A key for the identification of all known fossil Hallodapini is presented.

Don't expect a DNA barcode anytime soon from this new hemipteran species. This is not Jurassic Park. This specimen has been discovered in a piece of amber. Its name refers to the unusual flattened and widened second antennal segment.
no DNA Barcodes

Recent molecular genetic work, combined with morphological comparisons, on Malagasy members of the bat genus Miniopterus (Family Miniopteridae), has uncovered a number of cryptic species. Based on recently collected specimens and associated tissues, we examine patterns of variation in M. aelleni, the holotype of which comes from Ankarana in northernMadagascar. Using molecular genetic (mitochondrial cytochrome b) and morphological characters we describe a new species, M. ambohitrensis sp. nov. In northern Madagascar, M. ambohitrensis and M. aelleni are allopatric, but occur in relatively close geographical contact (approximately 40 km direct line distance) with M. ambohitrensis found at Montagne d’Ambre in montane humid forest and M. aelleni sensu stricto at Ankarana in dry deciduous forest. Morphologically, this new taxon is differentiated from M. aelleni based on pelage coloration, external measurements, craniodental differences, and tragus shape. Comparisons using 725 bp of cytochrome b found a divergence of 1.1% within M. aelleni sensu stricto, 0.8% within M. ambohitrensis, and 3.3% between these two clades. The two sister species do not demonstrate acoustical differences based on recordings made in a flight cage. Miniopterus ambohitrensis is known from four localities in the northern and central portions of Madagascar, all from montane regions and across an elevational range from about 800 to 1600 m; its calculated “Extent of occurrence” is 15,143 km2 . It is possible that this species is at least partially migratory.

The species name is derived from the geographical name of the type locality, which in
Malagasy is Ambohitra. In the Malagasy language, the root word of Ambohitra is vohitra meaning mountain or highlands, also providing an ecological context as the bat occurs at higher elevations. No barcodes unfortunately as the authors decided to sequence cyt b despite the fact that about 800 species of bats already have a proper COI barcode. 
no DNA Barcodes

Macrobrachium indianum new species is described from the Pambar River, Kerala, S. India. The species shares certain characters with M. gurudeve Jayachandran & Raji, 2004, M. bombayense Almelker & Sankolli, 2006 and M. kulkarnii Almelker & Sankolli, 2006, while it differs remarkably from these three species in distinctive diagnostic characters: rostral formula 7–8/3–4 with 1 postorbital teeth, one tooth above orbit; carapace smooth with distal end of rostrum directed downwards; cephalothorax longer than rostrum; in second chelate leg, proximal cutting edge of movable finger with two weak denticles, one weak denticle in immovable finger, carpus longer than merus, merus shorter than propodus and longer than ischium; dactylus the shortest podomere. Five thick and a few thin reddish brown bands of chromatophores are seen on carapace. Pigmentation is found mid and ventro-laterally on abdominal segments, pereiopods have chromatophores at the distal part of podomeres.

A new species pf prawn named after India, the native country of both species and authors.
no DNA Barcodes

The genus Platytenerus Miyatake, 1985 (Coleoptera: Cleridae) is redescribed and classified into the subfamily Neorthopleurinae Opitz, 2009. A phylogenetic tree is supplementally provided for Platytenerus based on twenty morphological and two geographical characters. A new species of the genus, Platytenerus iriomotensis sp. n. is described from Iriomote Island, Okinawa, Japan.

A new species of checkered beetles from Japan. The genus so far had only one representative in Japan. This descritions adds another one to that. The species name is derived from its type locality, Iriomote Island.
no DNA Barcodes

Dysphania geoffreyi is described as a new species, with records in China (Xizang and Yunnan provinces) and Bhutan. It differs from morphologically similar taxa by virtue of the clustered flowers in the inflorescence, indumentum set on the perianth, terminally concave pericarp papillae, and smaller seeds 0.5–0.6 mm in diameter. In total eight native Dysphania species are identified in Himalaya and Tibet, and revised distribution patterns of D. bhutanica, D. himalaica and D. tibetica are presented. The most significant reproductive features of all native Dysphania taxa are summarized. 

A new member of the goosefoot family. The species is named after Dr. Geoffrey Harper a former developmental physiologist at Royal Botanic Garden Edinburgh.
no DNA Barcodes

Monday, March 23, 2015

DNA Barcode Conference Plenary - Louis Bernatchez

Today's DNA Barcoding conference plenary sneak preview comes from a fellow fish researcher who I know since my time as doctoral student. He came as visiting researcher to our lab in Konstanz and shared a lot of his experience in population genetics and the back then brand new methods such as AFLP

Louis Bernatchez is an evolutionary biologist specialised in genomics, conservation, and evolution of fishes in the Department of Biology at Laval University, Québec. He holds a Canadian Research Chair in genomics and conservation of aquatic resources and has received several prestigious awards, including the Prix du Québec Marie-Victorin, elected member of the Royal Society of Canada, and the American Association for the Advancement of Science, the E.W.R. Steacie award (NSERC), the Michel-Jurdant Award (ACFAS), and the Stevenson Lecturer of the Canadian Conference for Fisheries Research. He co-founded and is currently the chief-editor of the journal Evolutionary Applications and has also been Associate Editor with Molecular Ecology for the last 15 years. He is a co-founder of the Canadian Society for Ecology and Evolution and served this Society as Treasurer for its first 5 years of existence. He has published over 300 research articles, with several important contributions to DNA barcoding of North American freshwater fishes.

The majority of the research projects conducted in my laboratory is integrated into the research program of the Canada Research Chair Genomics and Conservation of Aquatic Resources.  We aim to accomplish three general objectives. The first objective is to acquire fundamental knowledge on evolutionary processes responsible for generating and maintaining genetic diversity within and among populations. This will in turn stimulate the long term economic viability and social value of aquatic species in three complementary domains of activity : recreational and commercial exploitation (fisheries), biodiversity conservation, and aquaculture. The second general objective is to foster the training of highly qualified biologists, researchers, and research professionals in areas of high priority for Canada. A third objective is to increase the public awareness of the usefulness university scientific research (both basic and applied) regarding the improvement of management and conservation practices of natural populations. The most distinctive character of our research projects lies in the integrative approach that combines the fields of quantitative and functional genomics, population genomics, bioinformatics, physiology and ecology within an evolutionary framework. The integrative nature of these projects is also reflected by the diversity of their topics. For instance, the current issues surrounding fisheries, aquaculture and biodiversity conservation are generally considered distinct with few common links between them. Such a view has most often been a source of conflict among the people that work or research these areas. In contrast, the view that we are promoting through the research chair program lies on the assumption that these three sectors are facing a common problem, which is the genetic erosion of genetic diversity, as well as incomplete knowledge of the fundamental processes that generate and maintain genetic diversity.  A main research area of our current research projects focuses on the comprehension of genotype-environment interactions, particularly in cases of reproductively isolated populations that have diverged to exploit distinct ecological resources. Our principal study systems include lacustrine fish populations (whitefish, genus Coregonus, Salmonidae) that have recently diverged and vary with respect to their level of reproductive isolation in relation to their level of specialization towards distinct ecological niches. A second main area is to comprehend the respective roles and impact of historical, contemporary and anthropogenic factors (such as exploitation, stocking, translocation, domestication and habitat disturbances) on the genetic diversity of animal populations, as well as the genetic basis of local adaptation. We have also contributed to the Canadian Barcode of Life Network initiative. A new exciting field of application that is currently being investigated pertains to the analysis of environmental DNA (eDNA) towards keeping track of biological invasion, monitor community diversity in aquatic habitats, as well as quantifying biomass in a fishery management context.

From the inbox: NEAT

Just found this letter in my email inbox and thought it is worth to be shared:

Dear colleagues and friends, 
Most of you have already heard about this new academic network on arctic terrestrial/ freshwater arthropods, which we will from now on refer to as:
NEAT – NEtwork on Arthropods of the Tundra.

It has taken a while to get back to you all. One reason for this is that CBMP – the Circumpolar Biodiversity Monitoring Program asked us to form the official network on invertebrates for the CBMP and I have been discussing this with colleagues for the past weeks.

While it makes sense for our network to contribute to such processes as the CBMP, I have decided to propose that we start out as an independent network and work towards our own goals of learning about each other’s study organisms, sites, methods and results with no formal obligations and expectations. This can obviously be changed at a later date.

With this e-mail I would like to ask you to provide input to a short survey, so we can add information to the web site we are about to construct.

We are also planning a newsletter to be sent out twice a year (probably in May and October). Tentatively, the newsletter will include information about field work and meetings taking place as well as a way to distribute job adverts etc. The newsletter would also be an outlet for requests for sample or data collection at multiple sites. Finally, we are considering highlighting recent findings in the research field.

We hope you will take an active role in the network and please send us any suggestions or ideas for ways to make the most of it.
Please pass on this e-mail to others who you think could be interested.

Best wishes to you all,
Toke T. Høye
on behalf of the steering group:
Derek Sikes, Chris Buddle, Terry Wheeler, Steve Coulson, Peter Convey, Tomas Roslin, Joe Bowden, Toke T. Høye

h/t Torbjørn Ekrem

Friday, March 20, 2015

DNA Barcode Conference Plenary - Bridget Stutchbury

Today another guest post by a conference plenary speaker:

Bridget Stutchbury is an ornithologist and professor in the Department of Biology at York University, Toronto. Bridget completed her M.Sc. at Queen’s University and her Ph.D. at Yale, and was a postdoctoral fellow at the Smithsonian Institution where she studied the ‘winter’ ecology of migrants in the tropics. As a Canada Research Chair at York U, Bridget studied migratory songbirds to investigate extra-pair mating systems, off-territory movements, and demographics in fragmented landscapes. She also published a series of papers, and a book, on the behavioural ecology of tropical birds and why it differs from typical temperate zone models. Her current research focusses on tracking the incredible long distance migration journeys of songbirds to understand their migration strategies and population declines. She serves on the board of Wildlife Preservation Canada and is the author of Silence of the Songbirds (2007) and The Bird Detective (2010).

Making the connection between Wood Thrush declines and tropical deforestation

Wood Thrushes are seldom seen but their flute-like song is bold, beautiful, and full of life. Summer evenings can bring a refreshing and ringing dusk chorus of “ee-oh-lay” from the thrushes in nearby forests but this once common bird is well on its way to becoming a rarity. According to the Breeding Bird Survey this species has declined by over 50% since the late 1960s. The Wood Thrush is an ambassador for the forest birds of eastern North America, and a modern day ‘canary in the coal mine’. 

I first wrote about the demise of the Wood Thrush in Silence of the Songbirds (2007) and began a large research project to track the migration of individual birds and map out their core wintering sites in Central America. My students and I used newly miniaturized tracking devices called ‘geolocators’ which the birds carry as a little backpack, and which must be retrieved and downloaded when the bird returns back to its breeding site the next year.  

In May 2008, my graduate students caught the very first Wood Thrush to be tracked for its entire migration. The migration  maps showed that at the same time that its breeding site in Pennsylvania had been buried under 18 inches of fresh snow, the Wood Thrush had been in Nicaragua and completely at home in a world of strangler figs, howler monkeys, and toucans.  I was stunned to see that in spring this bird had flown 3,700 kilometers in only two weeks, including a non-stop flight across the Gulf of Mexico. We have now tracked over 70 Wood Thrushes that bred in the central- and northeastern US, or Ontario, and discovered that the vast majority travel to E. Honduras, Nicaragua or western Costa Rica to escape winter.

This part of Central America is a Wood Thrush hotspot, but the tragedy is that it is also a deforestation hotspot and is losing its tropical forests at one of the highest rates in the world. According to the Food and Agriculture Organization 2011 State of the World’s Forests report, since 1990 Honduras has lost 27% of its forest, and Nicaragua 31%, to agriculture.  It should come as no surprise, then, that Wood Thrushes who depend on those forests are disappearing quickly. 

What can the average person do to make sure that our Wood Thrushes, and other forest songbirds, remain common and serenade future generations for years to come? We must support organizations that work to protect migratory birds, like Bird Studies Canada. But we can also help every morning by drinking coffee that was grown in a forest-like habitat. Bird Friendly® certified shade coffee farms provide tropical forest habitat for dozens of species of migratory songbirds, as well as tropical birds that there live year round.  Saving the traditional heavily shaded coffee farms throughout this region of Central America would protect tens of thousands of hectares of habitat for Wood Thrush and other migrants. But coffee farmers need your help and support!

Thursday, March 19, 2015

New Barcode Bulletin

Our newest edition of the iBOL Barcode Bulletin is out. Lots of very interesting and good reads:

Wednesday, March 18, 2015

The cost to avoid extinction

Falco punctatus
It seems to me that today every discussion on biodiversity or conservation revolves around costs and monetary benefits. The question is if we can put realistic values on biodiversity, e.g. can we put a price tag on, lets say, the efforts to save a species from becoming extinct? 

An international team of researchers was asking this question and they were able to calculate such a value for a subset of species. They computed the cost of, and opportunities for, conserving 841 species of mammals, reptiles, birds and amphibians listed by the Alliance for Zero Extinction (AZE) as restricted to single sites and categorized as Endangered or Critically Endangered on the IUCN Red List.

The  colleagues developed a "conservation opportunity index" using measurable indicators to quantify the possibility of achieving successful conservation of a species, both in its natural habitat and by establishing insurance populations in zoos. 

The total cost: only $1.3 billion per year to safeguard all 841 species, which translates into $1.3 million per species per year, but only if conservation efforts are put in place immediately to ensure habitat protection and management. Of the total, a little over $1.1 billion per year would go towards conserving the species in their natural habitats and the rest for complementary management in zoos. 

Although the cost seems high, safeguarding these species is essential if we want to reduce the extinction rate by 2020. When compared to global government spending on other sectors (such as U.S. defense spending, which is more than 500 times greater), an investment in protecting high biodiversity value sites is minor.

While the study indicated that 39 % of the species scored high for conservation opportunities, it also showed that at least 15 of the species are in imminent danger of extinction given their low conservation opportunity index. This low index is due to one or a combination of different factors such as: high probability of its habitat becoming urbanized, political instability in the site and/or high costs of habitat protection and management. Additionally, the opportunity of establishing an insurance population in zoos for these 15 species is low, either due to high costs or lack of breeding expertise for the species.

Conservation opportunity evaluations like ours show the urgency of implementing management actions before it is too late. It is imperative to rationally determine actions for species that we found to have the lowest chances of successful habitat and zoo conservation actions.

The question is not one of protecting a species in the wild or in zoos. The One Plan approach - effective integration of planning, and the optimal use of limited resources, across the spectrum of management from wild to zoo - is essential if we are to have a hope of achieving the Aichi Biodiversity Targets