Monday, September 30, 2013

New cool journal

A new open-access journal started mid September and it promises to fill a void in the current publication space. I have written about data release papers before and it seems the perfect outlet for such has just been created from the publishers that are responsible for ZooKeys (the open-access competitor of ZooTaxa):

Biodiversity Data Journal (BDJ) is a community peer-reviewed, open-access, comprehensive online platform, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – will be treated and stored as DATA, in accordance with the Data Publishing Policies and Guidelines of Pensoft Publishers.

The journal will publish papers in biodiversity science containing taxonomic, floristic/faunistic, morphological, genomic, phylogenetic, ecological or environmental data on any taxon of any geological age from any part of the world with no lower or upper limit to manuscript size. For example:

  • single taxon treatments and nomenclatural acts (e.g., new taxa, new taxon names, new synonyms, changes in taxonomic status, re-descriptions, etc.);
  • data papers describing biodiversity-related databases, including ecological and environmental data;
  • any kind of sampling report, local observations or occasional inventories;
  • local or regional checklists and inventories;
  • habitat-based checklists and inventories;
  • ecological and biological observations of species and  communities;
  • any kind of identification keys, from conventional dichotomous to multi-access interactive online keys;
  • descriptions of biodiversity-related software tools.

Friday, September 27, 2013

Caribou diet

Woodland caribou (Rangifer tarandus-caribou) are the largest of all caribou subspecies in North America endemic to boreal forests. As I have detailed before in a different case I am not a big fan of subspecies and therefore I consider the woodland caribou as species but that is not the theme of this post. Actually, The numbers in woodland caribou herds have decreased over the years, their habitats have shrunk too, limiting the areas in which they can be found. Therefore, woodland caribou is considered a threatened species under Canada's Species at Risk Act.

Although there are likely multiple cumulative effects on declining caribou populations, the least studied relate to diet and food quality because these factors have been difficult to study under realistic field conditions This poor understanding of diet, has presented a key uncertainty with respect to understanding nutrition and energetics as response variables to the factors influencing population viability. Winter diet in particular may be a critical factor limiting maintenance of body fat and protein and affecting productivity.

In a new publication colleagues tried to tackle this problem with more recent methods. They compared traditional microhistology methods with DNA Barcoding of fecal samples and with the analysis of videos from collared animals in the wild. Microhistological methods in this context encompass the microscopic search for unique and identifiable plant or lichen pieces from undigested tissues found in a fecal sample. Not only is it difficult to find a lot of undigested material but what ever one finds needs to show enough traits to assign it to a particular species.

Based on more traditional methods such as direct observation and microhistology it was assumed that only a few lichen and woody plant species make up the diet of woodland caribou. It looks like the opposite is true. The researchers retrieved DNA Barcodes for 76 species consumed by woodland caribou, comprising 32 lichen species, 19 tree species, 11 moss species, and 11 species of herbs and grasses. They also present high variability of the proportion of lichen species among the sampled individuals. These results were corroborated by video camera estimates of their winter diet composition.

Overall it becomes clear that these two new technologies, video cameras and DNA Barcoding, can be used to determine the diet of woodland caribou. I would dare to add that only those can actually help to understand the caribou diet to an extend that leads to most effective conservation strategies. Especially DNA Barcoding provides an unprecedented species resolution for this type of samples especially when a reference library of sufficient size and quality is in place as it was in this case (500 species of plants and lichens).

Barcoding provides high species resolution at a fraction of the cost of video estimates, but does not provide the secondary information on habitat types, encounter rates with critical food types, and degree of feeding selectivity provided by animal-borne video technology.

Thursday, September 26, 2013

New electric fish

Akawaio penak (Maldonado-Ocampo,
López-Fernández, Taphorn, Bernard, Crampton & Lovejoy 2013
The bluntnose knifefishes (family hypopomidae) are known from freshwater in Panama and South America. They are so called electric fishes which are known to produce electrical fields from a specialized structure called the electric organ. The electric organ consists of modified muscle or nerve cells, which became specialized for producing bioelectric fields far stronger than those that normal nerve or muscle cells generate. By using this organ the fishes are capable to create a single electrical output which is called electric organ discharge (EOD). Some species can emit an EOD powerful enough to stun prey. The amplitude of the signal can range from 10 to 600 Volts with a current of up to 1 Ampere. However, most electric fish usually generate a discharge that is less than one volt in amplitude. These are too weak to stun prey and instead are used for navigation, object detection and communication with other electric fish that have specific capabilities to detect EOD's. The bluntnose knifefishes belong to the group of weakly electric fishes. 

During a recent expedition to Guyana led by Hernán López-Fernández from the Royal Ontario Museum researchers discovered a new species of bluntnose knifefish. Akawaio penak, was discovered in the shallow, murky waters of the upper Mazaruni River in northern Guyana. The upper Mazaruni River is a hotspot for biological diversity, yet remains largely unexplored because of its remote location. The area contains countless rivers on top of a series of uplands that have remained isolated from the rest of South America for more than 30 million years. 

In their paper the researchers describe the specimens not only as a new species but also as a new genus based on characters of external morphology. The phylogenetic affinities of the new genus were inferred using data from one nuclear (rag2) and two mitochondrial (COI and cyt b) genes. 

Akawaio penak has a long organ running along the base of the body that produces the electric field. The electric field is used to navigate and to communicate with other members of the species. This trait is advantageous given the murky habitats of the habitat. The species is named in honour of the Akawaio Amerindians that populate the upper Mazaruni. The region is increasingly suffering from freshwater habitat degradation as a consequence of gold-mining in the area.

NESCent-EOL-BHL Research Sprint

From the inbox:

Call for proposals for NESCent-EOL-BHL Research Sprint

The National Evolutionary Synthesis Center (NESCent), Encyclopedia of Life (EOL), and Biodiversity Heritage Library (BHL) announce a call for proposals for a research sprint event to take place at NESCent in February 2014.

EOL currently has text and/or multimedia information on more than 1.3 million taxa from more than 250 content providers.  Structured data (species interactions, numeric data, and controlled vocabulary data) are coming soon. BHL has digitized more than 41 million pages of legacy biodiversity literature.  During the research sprint, biologists will use EOL and BHL to address outstanding and novel questions about the ecology and evolution of biodiversity. Successful applicants will be matched with an informatician, in two-person teams, and receive support to travel to and work on-site at the National Evolutionary Synthesis Center for four days.

For more information on the event and to get proposal instructions, please visit

Applications must be submitted no later than 15 November 2013.

Questions regarding the NESCent-EOL-BHL Research Sprint should be directed to Craig McClain ( or Cynthia Parr (

Tuesday, September 24, 2013

Cryptic invasion

Baseodiscus sp. (taken from
Cryptic invasion occurs when native and non-native populations are difficult to distinguish from one another. This presents a challenging set of circumstances, where a non-native invader remains undetected or underestimated. Cryptic invaders can also displace native populations, often forcing difficult management decisions as to which populations to control. (taken from Albert Carbo's course website on Phragmites)

Doesn't that sound like a problem that has been designed for DNA Barcoding? Not convinved? Well, then let's talk about ribbon worms. These animals have their own phylum, Nemertea. They are usually less than 20 cm long,  but you can find several references to a find of one specimen that has been estimated at 54 m! Interesting animals, most of which are marine, but there are a few freshwater species, and even a few species that live in moist tropical habitats on land. Ribbon worms were once classified close to the flatworms, which they superficially resemble but more modern molecular analyses place them more closer to annelids and molluscs .The phylum comprises about 1000 species and they are difficult to tell apart:

Morphology-based nemertean taxonomy is a highly specialised discipline: proper fixation and histological procedures are essential for the correct morphological identification in several groups. Most of the material collected during previous marine expeditions was of poor quality for histological studies, due to differences in fixation and anaesthetisation protocols, and thus, the correct identification of those specimens has been impeded. Within the Nemertea, the taxon Palaeonemertea is a group that often lacks external morphologically discriminant characters; thus, an anatomical analysis is usually essential. Identification of members of the genus Cephalothrix, composed of 28 named species, which we analysed here, is based on very subtle and hard-to-interpret characters.

This is the introductory paragraph of a paper published earlier this year by researchers from the Museo Nacional de Ciencias Naturales in Madrid. Their work which was a combination of morphology and DNA Barcoding unveiled an ongoing invasion of a pacific species, Cephalothrix simula into the Mediterranean Sea:

We consider Cephalothrix simula to be an alien invader whose larvae could have been introduced to their distribution area in the ballast waters of ships. The presence of the same haplotypes in different invaded areas and in its natural distribution range suggests several invasion events. The Mediterranean Sea is one of the world’s regions most affected by biological invasions, mainly since the opening of the Suez Canal. However, the presence of Cephalothrix simula from the eastern Mediterranean Sea has not been reported, and the invasion of Atlantic localities cannot be explained by the hypothesis of a Lessepsian migration to the Mediterranean Sea. In this context, it is possible that environmental changes produced by climate change are currently facilitating the settlement of this species. The presence of developed gonads in one specimen and the presence of juvenile individuals reveal that reproduction is occurring in the invaded areas.

The authors also state that the utility of DNA Barcodes is currently hampered by the fact that there aren't many barcode sequences available for nemerteans. At the time they were writing the paper only about 6% of the species were barcoded. A quick look today on BOLD tells me that we are now at about 13%.

Monday, September 23, 2013

Round gobies

Humans have massively changed many river systems over the last decades. In order to improve ship passages, rivers have been straightened, deepened, and river banks reinforced.  Often the natural river bed has been altered. On top of that water temperatures are rising as a result of climate change. All of those changes actually provide perfect conditions for the round goby (Neogobius melanostomus), a fish traditionally found in the lower stretches of the Danube and along the coasts of the Black Sea. Today, however, Neogobius melanostomus can be found in the headwaters of the Danube as well as in the Rhine, the Baltic Sea and even the Great Lakes in North America.

Scientists at the Technische Universität München have teamed up with the Bavarian State Collection of Zoology to investigate the strategies round gobies use to conquer new stretches of river and the impact on the local ecosystem and existing food webs. The researchers focused on the Danube River especially its headwaters where the species arrived only a few years ago probably as a stowaway in the ballast water of ships.

Founding individuals are usually particularly strong and powerful fish that are able to consume a broad range of food and thereby outperform other species. Gradually this process eliminates native fish species such as the barbel (Barbus barbus) and European chub (Squalius cephalus). Established round goby population already account for over 70 percent of the entire fish stock in some areas. The round goby is also reducing the diversity and abundance of invertebrates. In particular stoneflies, caddisflies and mayflies quickly become the preferred prey of the fish in their new habitat.

The round goby is not the only fish species advancing upstream from the Black Sea. There are currently five different goby species from the lower Danube making their way up the river. And the fish are not the first new settlers. They have already been preceded by many exotic snails, mussels and freshwater amphipods, some even hailing from other continents, e.g. Asia. Like the gobies, a number of these animals dominate the native fauna now. The goby invasion also has led to a 'novel ecosystem' in the headwater of the Danube comprising previously unknown combinations of species. This is not unique to the Danube, however. There are similar developments in the Rhine and in the Great Lakes of North America.

Jürgen Geist  is one of the authors of this publication and he states:  "What we are observing is a very flexible and robust network of different species that adapts itself perfectly to new environments...". "Biodiversity is declining and once the original ecosystem is lost, we can never go back."

Thursday, September 19, 2013

Legless lizards

Legless lizards, represented by more than 200 species worldwide, are well-adapted to life in loose soil. Fascinatingly, lizards on five continents independently lost their limbs in order to burrow more quickly into sand or soil, making them a great textbook example for convergent evolution. Some still have vestigial legs. Though up to 20 cm in length, these reptiles are rarely seen because they live mostly underground, eating insects and larvae, and may spend their lives within an area of one square meter. 

In an earlier genetic study of the California legless lizard (Anniella pulchra) researchers revealed five deep genetic lineages:
These genetic lineages of Anniella are diagnosable with two independently evolving markers (mt and nuDNA), showing that these lineages are, or were historically, independently evolving. Some of the newly discovered lineages are restricted to a few marginal sites in one of the most heavily impacted and degraded regions of California, the San Joaquin Valley. The recognition of several restricted-range lineages of a rare and declining taxon, within a region characterized by intense historical and ongoing habitat destruction, has important conservation implications.

Now, four years later the same researchers describe four new species. Three of the genetic lineages discovered in 2009 can be readily diagnosed through a combination of coloration, scalation, and skeletal characters (trunk vertebra number). A fourth lineage is cryptic, but can be distinguished from the other species by its karyotype, which of course is a bit tedious and makes DNA barcoding more attractive. By the way in the original study a part of COI was also used to determine the lineages. 

The colleagues named the new species after four legendary UC Berkeley scientists: the founder of the  Museum of Vertebrate Zoology at UC Berkeley,  Joseph Grinnell, the paleontologist Charles Camp, philanthropist and amateur scientist Annie Alexander and herpetologist Robert C. Stebbins, at 98 the only one of those still alive.

The former Anniella pulchra, a species of special concern, is now divided into five species. This means A. pulchra has a smaller distribution than previously recognized, thereby enhancing concern about its conservation status. The remaining four species have even smaller ranges, some of which are degraded or threatened by human activities. Whereas much of the range of Anniella stebbinsi is already compromised by urban development, the conservation implications for the other three new species are even more striking because of their very limited distributions. Anniella grinnelli is known from a few sites in the southern San Joaquin Valley, an area that has been greatly modified by urban and agricultural development. Anniella grinnelli persists in small patches within the Bakersfield city limits, but some of the populations we collected were extirpated by development during the course of this study. The type locality at the Sand Ridge Preserve is a secure site that will help ensure the species survival. Anniella alexanderae is known from two sites at the base of the Temblor Mountains, and should be considered rare pending further study. Finally, Anniella campi is known from just three sites. This species may be restricted to the vicinity of potentially fragile springs in canyons that open into the Mojave Desert and so warrants careful monitoring.

Wednesday, September 18, 2013

A handful of feathers and bird poop

The white-winged flufftail (Sarothrura ayresi) is a bird so rare that bird experts believe there are only 250 of them left in the world. In South Africa, the bird has been spotted in only about 15 sites in the 136 years since it was first described in Potchefstroom. The only other country where this small water bird with big feet has been sighted with any regularity is Ethiopia. So little is known about the bird that the question remains whether the two populations, separated by 4 000km, are linked through migration.

The ornithologist Craig Symes from Wits University would like to find out more about the rare bird. He will be using feather samples from Addis Ababa, in Ethiopia and some South African white-winged flufftail samples. By using isotope analysis he intends to work out if the birds have travelled between the two countries. If the isotope signatures of the samples from the different countries prove similar, it could suggest the birds move between South Africa and Ethiopia.
To understand more about the species, Symes also collected white-wing flufftail faeces in Ethiopia. Through DNA Barcoding he hopes to find out what the birds eat. With that information, conservationists believe the bird can be saved as only with a better understanding of its movements and habits effective conservation measures can be implemented.
A few weeks ago, there was a missed opportunity to add to Symes’s feather collection, when a worker at an airport in Durban found a white-winged flufftail near one of the runways. Unfortunately, by the time the bird was identified, it had been released. It was the first time in more than 100 years that a white-winged flufftail had been spotted in Durban. White-winged flufftail numbers are so low that  representatives from BirdLife say this individual could be one of the last of its species in South Africa.

Friday, September 13, 2013

Thursday, September 12, 2013

Life in Toronto

This weekend you will find a lot of us in Toronto as we join the Ontario BioBlitz.

Just in case you don't know - A BioBlitz is a special type of field study, where a group of volunteers conduct an intensive 24-hour biological inventory, attempting to identify and record all species of living organisms in an area, while also educating the public about biodiversity.

The BioBlitz will happen at Rouge National Park which is a rather special kind of park due to it's proximity to the city of Toronto:

A wilderness area in Canada's largest city? That's right! Not too far from the skyscrapers of downtown Toronto, urban dwellers can see a different landscape where historic farms, century-old trees, peaceful meadows and lush wetlands await you at your transit stop.

Rouge Park is over 40 km2, protecting two National Historic Sites and a variety of ecosystems joining the post-glacial Oak Ridges Moraine, roughly 50 km north of Toronto, and the City's biggest wetland, where the Rouge River empties into Lake Ontario.

So, if a few of my readers are in the area, come out and join us for some collecting! 

Wednesday, September 11, 2013

Life in the freezer

Source: climatestate
The possibility that extreme life forms might exist in the lakes beneath the Antarctic ice sheet has fascinated scientists for decades. However, direct sampling of these lakes in the interior of Antarctica continues to present major technological challenges especially some of the them are covered with thick ice sheets. Recognising this, scientists from the British Antarctic Survey, and the Universities of Northumbria and Edinburgh have been searching around the retreating margins of the ice sheet for subglacial lakes that are becoming exposed for the first time since they were buried more than 100,000 years ago. This is because parts of the ice sheet are melting and retreating at unprecedented rates as the temperature rises at the poles due to global warming.

Credit: British Antarctic Survey
The researchers targeted Lake Hodgson on the Antarctic Peninsula which was covered by more than 400 m of ice at the end of the last Ice Age, but is now considered to be an emerging subglacial lake, with a thin layer of just 3-4 metres of ice. By using clean coring technologies they drilled through the ice in order to reach the sediments at the bottom of the lake. Samples were analysed with a variety of methods such as light microscopy, Fluorescence in Situ Hybridization (FISH), SEM, direct culture, and massive parallel sequencing

The lake was thought to be a harsh environment for any form of life but the layers of mud at the bottom of the lake represent a time capsule storing the DNA of the microbes which have lived there throughout the millennia. The top few centimetres of the core contained current and recent organisms which inhabit the lake but once the core reached 3.2 m deep the microbes found most likely date back nearly 100,000 years. Some of the life discovered was in the form of fossil DNA showing that many different types of bacteria live there, including a range of extremophiles which are species adapted to the most extreme environments. 

...the most numerous closest sequence matches were to both marine and soil derived organisms, many of which come from thermophilic environments. Although all were a relatively low fraction of the total, the two most abundant sequence matches were to marine bacteria that are found all over the world: Pirellula staleyi and Rhodopirellula baltica are globally distributed marine bacteria (the former a planctomycete which can also be found in terrestrial habitats). The second group of frequent matches were to the soil bacteria. Spirochaeta aurantia is an aerobe isolated from mud and Conexibacter woesei is a member of the Actinobacteria isolated from forest soil. The third group could be classified as an extremophile: Spirochaeta thermophila which is extremely thermophilic and marine, Thermobaculum terrenum from an extreme thermal soil and Leptospirillum ferrodiazotrophum was isolated from a subsurface acid mine drainage biofilm and is involved in iron oxidation. Further clues about the ecology of the environment could be derived from frequent sequence matches to Frankia—a genus of nitrogen fixing bacteria, Dehalococcoides ethenogenes—which is anaerobic and cannot use inorganic electron acceptors and Methylococcus capsulatus, a thermotolerant obligate methanotroph that is able to oxidize some organic hydrogen containing compounds...

However, only 77% of the DNA sequences identified could be matched to a known sequence, species or type strain, suggesting that a vast amount of biodiversity remains to be discovered. Many of the species are likely to be new to science making clean exploration of the remote lakes isolated under the deeper parts of the ice sheet even more pressing.

Tuesday, September 10, 2013

Life in the deep

The Lukina Jama-Trojama is the deepest cave system in Croatia, extraordinary for its vertical shape, long pits and great depth of -1392 m. From an ecological point of view this cave system is extremely interesting for having three microclimatic layers: first an entrance icy part with temperatures of about 1 °C followed by a middle part with temperatures up to 2 °C. The bottom part of the system shows higher temperatures up to 4 °C. These unusual living conditions make the cave extremely interesting for biodiversity research.

Now my colleague and friend Alexander Weigand has described a new species of the genus Zospeum from this cave system. The new species Zospeum tholussum is a small and fragile snail (1-2 mm), with a dome-like shaped translucent shell. Only one living specimen was found during an expedition around the galleries of the cave system. The animal was found at the remarkable depth of 980 m, in an unnamed chamber full of rocks and sand with a small stream running through it.
The species is related to Zospeum amoenum, but can be distinguished from the latter by some shell features and - as shown in the study as well - by DNA Barcoding.

All known species from the cave-dwelling genus Zospeum have only limited ability to move. Their preference for muddy habitats and the fact that they are usually located near the drainage system of the cave, in a close proximity to running water, however suggest that these animals are not exactly immobile. Scientists hypothesize that dispersal is achieved through passive transportation via water or larger mammals.

Friday, September 6, 2013


Orchids are beautiful, fascinating flowers. There are over 25,000 species of orchids, and many are them are threatened, endangered or extinct, usually due to habitat destruction or poaching. Orchid smuggling is contributing to the loss of many species of orchid in the wild.

It is legal to trade in nursery-produced orchids. Orchid growers use artificial propagation and modern greenhouses that are capable of imitating the temperature, moisture, and wind conditions that orchids thrive upon in the wild. Nursery owners often outdo nature by producing plants superior to those found in the wild, healthier and with flowers that are larger and have more interesting colors.

For two reasons, orchid smuggling continues unabated. First of all, nursery-raised orchids are expensive. This is because it is time-consuming to raise orchids and the technology is not cheap. It is often cheaper, easier, and quicker to obtain orchids illegally from the wild. Because it is so much easier to collect orchids in the wild, smugglers often can undercut the prices of legitimate growers. Secondly, orchid collectors often find nursery-grown orchids to lack the exotic aura and mystery of wild orchids.

In Nepal for example wild orchids are illegally harvested and traded for use in local traditional medicine, horticulture, and international trade. Although the orchid trade has a long tradition, and illegal export to China, India and Hong Kong is rife there was no clear picture on the extend of the issue.

A new study now documents for the first time trade, species diversity, and traditional use of wild-harvested orchids in Nepal. The researchers did field surveys of markets and conducted interviews. Trade volumes and approximate income were estimated based on surveys and current market prices. Orchid samples were identified to species level using a combination of morphology and DNA Barcoding. The results are distressing:

Estimates show that 9.4 tons of wild orchids were illegally traded from the study sites during 2008/2009. A total of 60 species of wild orchids were reported to be used in traditional medicinal practices to cure at least 38 different ailments, including energizers, aphrodisiacs and treatments of burnt skin, fractured or dislocated bones, headaches, fever and wounds. 

That is just one area where illegal harvesting occurs. If one would extrapolate that on a global scale I am sure it would show an alarming picture about the status of orchids on our planet. The researchers in Nepal are taking it to the next level and make recommendations on alternatives that meet the demand and economic needs but still include proper conservation:

Collection of wild orchids was found to be widespread in Nepal, but illegal trade is threatening many species in the wild. Establishment of small-scale sustainable orchid breeding enterprises could be a valuable alternative for the production of medicinal orchids for local communities. Critically endangered species should be placed on CITES Appendix I to provide extra protection to those species. DNA barcoding is an effective method for species identification and monitoring of illegal cross-border trade.