Sunday, August 30, 2015

An all taxa inventory

In partnership with the Biodiversity Institute of Ontario and the 6th International Barcode of Life conference, over 100 participants from over 31 institutions and 17 countries searched the rare Charitable Research Reserve -  a 900+ acre land trust located at the confluence of the Grand and Speed Rivers in Cambridge - for all forms of life including birds, bats, spiders, insects, fish, plants, and mushrooms, counting and identifying what was found. Over 1100 species were discovered on the reserve for the first time, including 775 insects, 181 spiders, and even one mammal, a Hoary Bat, never before observed. While more charismatic species like birds and butterflies have been well documented at rare through monitoring and citizen sightings, this BioBlitz shows the magnitude of species existing in front of our eyes and under our feet that we easily miss, e.g. three of the nearly 200 spiders found are new records for the province.

I was one of the participants at the BioBlitz and helped to identify a few fish, some of which belonged to species that were not previously recorded at rare. However, most of my time I spend following colleagues with our video camera and the result is an about 4:00 min long video. Warning! I am not a professional documentary filmmaker. Don't expect BBC or Discovery channel quality.

The BioBlitz spanned nearly 12 hours, covered a variety of different habitats found at rare, and included a BBQ dinner for all participants, but it did not stop there. In the days that followed, over 100 collaborators drafted and published a data release manuscript in the Biodiversity Data Journal that summarizes the findings on the reserve and highlighted the advantages of a rapid blitz approach to species surveys like this one. The paper was published today.

In May of this year the species count for the reserve was at 2 268 species. Now the count is at more than 3 500.

Thursday, August 27, 2015

Protein evolution in Arachnids

Opiliones (Cosmetidae) | by Sidclay Dias
Just at the conference last week it was announced that BOLD, the world's workbench for DNA Barcode data, surpassed the 500 000 species mark. Some 420 000 of those are animal species. With so much information now available for a single gene region (cytochrome c oxidase 1 or COI) we are in a very good position to probe patterns of mitochondrial evolution.

Colleagues here at BIO (Monica Young and Paul Hebert) did just that. In their brand new study they examined levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids. 

Arachnids are the second most diverse group of arthropods with about 100 000 described species but there are colleagues that estimate the real diversity of the group to be at least ten times larger. Certainly a large group to tackle but the with representatives from all 16 orders and 43% of its families (267/625) the dataset studied is equally impressive. 

The colleagues examined divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration.

Indels are an interesting phenomenon especially in animal COI, where they seldom occur.Even more interesting is the relationship between a higher substitution rate and the occurrence of indels and other dramatic changes such as genomic rearrangements. Earlier work has shown that mitochondrial strand-specific nucleotide composition bias in some arachnid groups was among other things caused by an inversion of a fragment containing the COI gene. 

Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa.

Wednesday, August 26, 2015

Water quality assessment

Caloneis amphisbaena
Diatoms are microscopic algae living in both fresh and salt water.  They are unicellular organisms with silica impregnated cell walls. Living diatoms are among the most abundant forms of plankton and represent an essential part of the food chain in the ocean. Diatoms are responsible for at least 25% of global carbon dioxide fixation. Once dead, their shells accumulate on the seabed and eventually form siliceous sediment deposits.

Given that diatoms are photosynthetic algae, they are restricted to the sunlight zone, i.e. the depth of the water in a lake or ocean that is exposed to sufficient quantities of sunlight to allow for survival. They are highly sensitive to any environmental changes such as light availability, temperature, salinity etc.  In general, diatoms prefer cold, nutrient rich waters. This is what makes them so valuable as indicators for water quality. The specific composition of diatom communities is a very sensitive instrument to measure changes in aquatic environments.

Diatoms have been regularly used as bioindicators to assess water quality of surface waters, especially in developed countries. Many of the widely used diatom indices have been developed as part of studies of European rivers.

Jonas Zimmermann, a German PhD student, developed a reliable DNA Barcoding system for freshwater diatoms which can be used for above mentioned water quality assessments. His protocols and suggestions for extended metadata will likely become part of the methods used to comply with the European Water Framework Directive. He not only provided protocol and tests for optimal marker systems but also discovered four new species in water samples of the nation's capital (Berlin) waterways. His results not only confirmed the utility of the proposed DNA Barcode 18S (V4 region) for protists but he was also able to show that it provided good results for both cultivated samples as well as environmental samples.

For his work he was honored with the Horst-Wiehe Price of the German Botanical Society. This scholarship honors young researchers for exceptional scientific work in the field of botany.

Tuesday, August 25, 2015

Species loss through deforestation

There remains a widespread assumption that concentrating conservation efforts on the protection of isolated reserves is the best way we can safeguard biodiversity. But our work shows that in areas of private land that have already been disturbed -- which dominate much of the tropics -- we need to maintain and protect a wide network of forest areas. Without such a landscape-scale approach we can expect many species to go regionally extinct.

As one of the most comprehensive surveys of the impacts of disturbance on tropical forest biodiversity ever conducted, an international team conducted a detailed analysis of nearly 2,000 species of plants, birds, beetles, ants and bees that were found across more than 300 diverse sites in the Brazilian Amazon. 

The researchers found, where forests had been cleared for cattle ranching and agriculture, plant and animal life was impoverished and remaining species invariably consisted of the same subset of the original flora and fauna, overall irrefutable evidence that biodiversity is declining across the tropics. 

According to their observations, to preserve maximum species diversity, reserves should not be concentrated in one part of a region, but as a widespread network of forest reserves. These should include secondary forests where no primary forests remain. The colleagues emphasize how remaining areas of undisturbed and recovering forest provided the last refuge for many species unable to withstand the impact of human activity.

There remains a widespread assumption that concentrating conservation efforts on the protection of isolated reserves is the best way we can safeguard biodiversity. But our work shows that in areas of private land that have already been disturbed -- which dominate much of the tropics -- we need to maintain and protect a wide network of forest areas. Without such a landscape-scale approach we can expect many species to go regionally extinct.

To preserve maximum species diversity, reserves should not be concentrated in one part of a region, but as a widespread network of forest reserves. These should include secondary forests where no primary forests remain. Over time this would not only help to conserve the local biodiversity but also save money.

These findings are timely as Brazil recently revised its environmental laws regulating forests, allowing a trading system for private reserves and designing plans for environmental restoration. For example, the high variation in biodiversity found in secondary forests indicates the role these ecosystems play in regional conservation. For many areas of the Amazon, conserving existing secondary forests may be much cheaper and even more efficient than planting trees

Monday, August 24, 2015

...and now we're back to meat

Although extensive meat species testing has been carried out in Europe in light of the 2013 horsemeat scandal, there has been limited research carried out on this topic in the United States. To our knowledge, the most recent U.S. meat survey was published in 1995.

Researchers from Chapman University have just published two separate studies on meat mislabeling in commercial products in the US. One study focused on identification of species found in ground meat products, and the other focused on game meat species labeling. Both studies used DNA Barcoding for species identification.

In the first study 48 samples were analyzed and 10 were found to be mislabeled. Of those, nine were found to contain additional meat species and one sample was mislabeled in its entirety. Additionally, horse meat, which is illegal to sell in the United States, was detected in two of the samples. The colleagues think that the presence of multiple species suggests the possibility of cross-contamination at the processing facility. Unintentional mislabeling may occur when several species are ground on the same manufacturing equipment, without proper cleaning in between samples. Another trend observed in the study indicates the possibility of lower-cost species being intentionally mixed in with higher-cost species for economic gain.

The second study, focusing on game meat species labeling, used a total of 54 game meat products collected from online retail sources in the United States. Of these, a total of 22 different types of game meat were represented based on the product label. The results showed 10 products to be potentially mislabeled. Two products labeled as bison and one labeled as yak were identified as domestic cattle. Other mislabeling included a product labeled as black bear that was identified as American beaver, and a product labeled as pheasant that was identified as helmeted guinea fowl.

Game meats represent an important specialty market in the United States with an estimate value of $39 billion. According to the U.S. Food and Drug Administration (FDA), game meats are defined as exotic meats, animals and birds, which are not in the Meat and Poultry Act. Game meats produced in the United States are regulated by the U.S. Department of Agriculture, while game meats imported into the U.S. are regulated by the FDA. The latter is already using DNA Barcoding on a regular basis for seafood and species of their dirty 22 list.

Overall, mislabeling was found to be most common in products purchased from online specialty meat distributors (versus supermarkets), showing a 35% rate of mislabeling.

Friday, August 21, 2015


We are done! The 6th International Barcode of Life Conference is over. A moving and humorous last session with wonderful speakers brought it to a great finish. 

Did you like the drone video? Here is a long version of it:

We'd like to thank everyone for coming to Guelph and for making this conference such a success!

Conference post - afternoon session

Some of our afternoon sessions will be on Periscope again. Here is the broadcast schedule:

@dnabarcodes2015   Responses of Biodiversity to Environmental Change
@ATGCdesign         Molecular Evolution
@dirch3                    Education and DNA Barcoding

Check them out between 2:00 pm and 3:30 pm Eastern time.

Thursday, August 20, 2015

Conference post - Second set Parallel sessions live

Here the next set of broadcasts of live sessions:

@dnabarcodes2015  Large-Scale Understanding of Terrestrial Biodiversity
@ATGCdesign Food Authenticity and Safety 2
@dirch3 Next Generation Platforms and Analysis Pipelines 1

Conference post - Periscope broadcast

We have some live broadcasts of selected session up and running. All you need is the Periscope app.
You'll find those by using the twitter handle:


Right now you can watch in respective order:
Food safety

Enjoy and by the way - those sessions are also recorded and will be posted later.

Conference post - Group photo

Because this conference is hosting such a large crowd (500+) we needed to rethink the usual group photo and hired a photographer with his drone. Here is the result, three cool photos (click on them for higher resolution:

Wednesday, August 19, 2015

Conference Post - Formation of the International Society for the Barcode of Life

A message:

Dear Barcoding Colleagues,

This message invites all members of the DNA barcoding community to participate in an online discussion about forming an international society for DNA Barcoding.

This was discussed at a pre-Conference workshop (Monday, 17 August) at the Sixth International Barcode Conference that is taking place in Guelph. 

We invite you to read the document, share your thoughts directly by talking to us at the conference, emailing your views to, or participating online at Connect, and contributing to the Friday morning plenary session. 


David Castle, Bob Hanner, Pete Hollingsworth, Li De Zhu

Periscope Live Broadcasting

We started to live broadcast and record some parallel sessions. Periscope is a free application that works through the twitter system. All you need is the Periscope app for your platform and a twitter account and you can watch live broadcasts from some of our sessions. I will also prepare recordings of the broadcasted sessions later this week.

Tuesday, August 18, 2015

Conference Post - State of Biodiversity

The first 'real' day of conference is almost over with a ton of very interesting contributions. Participants are very enthusiastic - a happy crowd that had a lot of fun with our drone-supported group photo. As soon as I have the first images, I'll post them. Promise!

I am a little sad that I didn't had as much time for all of today's sessions as I had hoped to. The national media picked this first conference day for their interviews and filming. We will see the outcome tomorrow in various news shows across Canada. I'll make sure to share that as well.

Credit: Angela Telfer
In case you belong to the group of people that see Twitter as a trend monitoring tool the hit of the conference is: The Barcode beer.

There is  really active Twitter community on the conference. Friends, keep them coming and don't forget the hashtag #dnabarcodes2015 .

Day 2 tomorrow will end with a big public event which is also open to the public:

Summary: Chaired by Dr. Brock Fenton, this public event features a distinguished panel of leading scientists who will discuss the diversity of species on our planet, the challenges they face, and measures needed to protect them. Presentations will cover threats to birds and bees, as well as more difficult to study species from the arctic and marine biomes. They will also explore the value of DNA-based approaches for bio-literacy. From an examination of extinction rates to emerging perspectives on how to monitor and conserve biodiversity, this session will be of broad interest to those concerned with understanding the changing status of the natural world.

Welcome Reception Hosted by the Guelph Chamber of Commerce and Visit Guelph
Featuring the local flavours, sights and sounds of Guelph

Introduction & Opening Remarks
Kithio Mwania, President and CEO, Guelph Chamber of Commerce
Karl Tibelius, Vice-President, Genomics Programs, Genome Canada
Brock Fenton, Professor Emeritus, University of Western Ontario

Plenary Speakers:
Laurence Packer, Professor of Biology, York University
Monte Hummel, President Emeritus, WWF Canada
Stuart Pimm, Doris Duke Professor of Conservation Ecology, Duke University


Plenary Speakers Continued:
Bridget Stutchbury, Professor of Biology & Canada Research Chair in Ecology and Conservation Biology, York University
Paul Snelgrove, Professor of Biology & Canada Research Chair in Boreal and Cold Ocean Systems, Memorial University of Newfoundland
David Hik, Professor of Biology, University of Alberta
Brock Fenton

Closing Remarks

Monday, August 17, 2015

ResMed, iBOL and BIO

Here a video demonstrating a great collaboration of a large company in the health care sector, ResMed and iBOL and BIO. A Malaise Trap on the grounds of the company, a great way to engage with biodiversity.

Conference post - International Society for the Barcode of Life

Today is pre-conference workshop day. Participants will learn about BOLD and Next Generation Sequencing, get tours of our institute and in the afternoon will be about the formation of ISBOL, the International Society for the Barcode of Life. For all of you who couldn't make it to the conference, this session is scheduled to be broadcasted via YouTube

During the 5th Conference in Kunming, delegates discussed the desirability of establishing an International Society for the Barcode of Life (ISBOL). Because this plan was strongly supported, the Kunming Declaration included it as a key action item. Signatories to this Declaration and members of iBOL’s International Scientific Collaboration Committee have worked to ensure that ISBOL can be activated at the 6th Conference. A not-for-profit corporation (International Barcode of Life Corp.) has been acquired to provide a formal home for ISBOL. The pre-conference workshop will address other matters required to activate ISBOL, including its relationship with the International Union of Biological Sciences (IUBS), a possible umbrella organization.

As a result, Peter Kevan, IUBS Executive Committee Member, will deliver a plenary lecture to workshop participants on this organization. His presentation will be followed by a panel discussion involving key participants in the Kunming Declaration. The workshop will lead to the establishment of ISBOL, a decision on its committee structure, the recruitment of officers and members, and the investigation of a linkage with the IUBS.

Friday, August 14, 2015

Three more days

A few more days and the 6th International Barcode of Life Conference starts and everybody here is busy preparing for over 500 guests from at least 58 nations. This will likely be the largest Barcode of Life conference ever which you easily tell from the large number of jam-packed parallel sessions.

Posting on other topics than the conference will be fairly light. I will be running around for most of the time doing my share to make this conference a success. We will live broadcast the plenary sessions and the pre-conference International Society session over the university's YouTube channel. I will share the links with you on Monday. A few parallel sessions will also be streamed using Twitter's Periscope App. Again, I'll have account names for you on Monday. This will give everybody who couldn't make it this time a chance to listen to some of the many great speakers.

I am sure a lot of people will use Twitter, Facebook and other social media systems to send out the latest news from the conference. All we like to ask them is to make sure they checked with a presenter if tweeting about the talk is fine, and that they use the hashtag #dnabarcodes2015. 

I am looking forward meeting a lot of my readers at the conference and learn about all their work. Everybody else should take the opportunity to enjoy some of the live feeds or recordings which will also be posted once available.

By the way, during the conference this blog will celebrate its 3rd anniversary. 660 posts and still going.

Thursday, August 13, 2015

Brooding as response to ocean acidification

Platynereis massiliensis
Anthropogenic atmospheric carbon dioxide (CO2) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought to have largely deleterious effects on marine invertebrates, primarily impacting early life stages and consequently, their recruitment and species’ survival.

Researchers at Plymouth University have found that polychaete worms located around volcanic vents in the Mediterranean grow and develop their eggs within the protection of the family unit - in contrast to closely-related species that release them into the water column to fend for themselves.

The team found that 12 of the 13 species that had colonized the vent area exhibited brooding characteristics, most notably producing fewer and larger eggs that were usually retained within some form of protective sac. Ten of those species were in higher abundance around the vents than in the ambient areas surrounding them -- some by a ratio as high as nine-to-one.

The observation that brooding worms dominated the CO2 vent areas, and existing evidence of physiological and genetic adaptation in vent-inhabiting species, prompted the researchers to take immature adult Platynereis dumerilii specimens and attempt to cross breed them in the laboratory. A male - taken from the ambient control area - and a female - from the vent zone - almost immediately began to breed. But instead of the typical broadcast pattern, the eggs produced were five times larger than the average and were laid in a complex tube structure or brooding pouch.

DNA Barcoding revealed that worms from inside the CO2 vents were from a sibling species, Platynereis massiliensis, one that has diverged from Platynereis dumerilii relatively recently.

One of the most interesting annelid worms here typically grows to around 3cm in length and is found on the seafloor. It was previously thought that their breeding is triggered by a full moon, when they swim up to the surface and release - or 'broadcast' - their eggs. But our studies at the CO2 vents off Ischia have found something very different: those species living near the volcanic vents, in waters rich in carbon dioxide, seem to have adapted to the harsher conditions by brooding their offspring.

The study confirms the idea that some marine organisms have evolved brooding characteristics in response to environmental stresses, such as ocean acidification:

This study brings us one step closer to understanding which marine species will be more resilient to climate changes. In fact, our work helps in establishing a fundamental principle to be used to guide decisions on the conservation of marine ecosystems and to help better manage the fisheries and aquaculture industries.

Wednesday, August 12, 2015

Fast ploidy assessment in carps

Grass carp (Ctenopharyngodon idella), have been introduced throughout the Midwest and South of the US to clear ponds choked with weeds. However, the release of fertile fish is illegal and so is the purchase or trade in Ohio and surrounding states. For the very same reason they are used as biological control agents grass carp pose a number of threats. They eat soft-stem vegetation - the kinds of plants that dominate coastal marshes which are prime breeding grounds for game fish and act as filters that clear the water.

Hatcheries are breeding carp, but shock their eggs with drastic changes in water pressure. The shock results in a triploid animal and the third set of chromosomes inhibits the production of viable gametes and causes individuals to be reproductively sterile These sterile fish can then be responsibly used for biological control of invasive aquatic plants, but the release of fertile fish could result in growing populations that could devastate the Great Lakes ecosystems. Although the pressure shock method of creating triploid grass carp is nearly 100 % effective, a small proportion of diploid individuals are produced and those have already been found in in Lake Erie's western basin.

Current methods of determining ploidy of an individual require the use of rather expensive laboratory equipment and cannot be performed under field conditions. Researchers have now developed a fast, inexpensive technique to distinguish diploid and triploid grass carp under field conditions using a compound microscope. The shape of the nuclei in red blood cells of carps looks different depending upon whether the fish has a pair or three or more sets of chromosomes. The proportion of abnormally shaped nuclei grows with the increasing number of chromosomes. 

The colleagues smear a drop of fish blood on a slide, let it dry and fix it with methanol. They then stain the slide to bring out the nucleus, and, after rinsing and drying, view it under a standard microscope. Sterile triploid grass carp have a noticeably larger proportion of red blood cells with abnormal nuclei.

The study also included a blinded test to confirm the diagnostic reliability of the visual assessment of ploidy. By viewing blood-smear slides, 14 of 15 staff and interns of the Natural Resources department of Cleveland Metroparks correctly identified the fish; only a single intern incorrectly identified a single fish's reproductive potential.

This test has the potential to be very helpful. The results are pretty convincing, but I would like to see it field-tested by management agencies.

Tuesday, August 11, 2015

Catastrophic invertebrate extinction

Carelia turricula
The IUCN Red List contains only 733 animal species and 99 plant species listed as extinct since around 1600, a minuscule fraction of total biodiversity, commonly estimated at 5–10 million species. This extinction rate (around 2 species/year) is of the same order of magnitude as the natural background rate based on the fossil record. Such statistics are used by environmental skeptics to downplay the loss of biodiversity.

However, among animals, the focus on birds and mammals and the proportionately negligible assessment of invertebrates masks a real crisis. Although assessment of extinction for all invertebrates is impossible, it may be possible for certain, perhaps representative, groups. Such assessments might permit broad extrapolation and more realistic evaluation of true overall extinction levels.

Mollusks are such a group. Despite the relative lack of focus on invertebrates, almost as many mollusks (311) are listed as extinct by the IUCN (2014) as all chordates combined (338); most (282) are gastropods and half of these (138) Pacific island land snails. Nonetheless, almost twice as many mollusks as are listed as extinct on the IUCN Red List are considered extinct by mollusk specialists, yet the number assessed remains a tiny fraction of the 80,000–100,000 described species and perhaps up to 200,000 real species.

Hawaiʻi has been called the “extinction capital of the world.” But, with the exception of the islands’ birds, there has been no accurate assessment of the true level of this catastrophic loss. Invertebrates constitute the vast majority of the species that make up Hawaiʻi’s formerly spectacularly diverse and unique biota. A team of researchers of the US and France focused on the most diverse group of Hawaiian land snails, the family Amastridae, of which 325 species have been recognized - all known only from Hawaiʻi. They did a rigorous assessment of extinction for this group. 

The colleagues now published their alarming results. Only 15 of these species could still be found alive, and it is estimated that the rate of extinction may have been as high as 14 percent of the fauna per decade. 

In a companion study, members of the team, in collaboration with mathematics and bioinformatics specialists at the Pierre and Marie Curie University in Paris, addressed invertebrate extinction globally. Since the 1980s, many biologists have concluded that the earth is in the midst of a massive biodiversity extinction crisis caused by human activities. Yet only around 800 of the planet’s 1.9 million known species are officially recorded as extinct by the IUCN Red List. Skeptics have therefore asked, “Is there really a crisis?"

We showed, based on extrapolation from a random sample of land snail species from all over the world, and via two independent approaches, that we may already have lost 7 percent (130,000 extinctions) of all the animal species on Earth.

This loss far exceeds official numbers that are primarily based on assessments of birds and mammals and essentially excludes invertebrates, even though invertebrates constitute roughly 99 percent of known biodiversity.

Based on their findings, the researchers show that the biodiversity crisis is real and stressed the need to include assessments of invertebrates in order to obtain a more realistic picture of the current situation, known widely as the sixth mass extinction.

h/t Mario Thomas

Monday, August 10, 2015

Climate change and species distribution

Climate change strongly impacts biodiversity, putting some species at risk of extinction. However, some plant species for example adapt to the new conditions, and go on to thrive and invade areas where they have never grown before.

The black seed grass (Alloteropsis semialata) is the only species known to comprise of individuals that  use both the more common C3 photosynthetic pathway and a pathway called C4, which is a complex combination of leaf anatomical characters and enzymatic reactions that together increase productivity in warm and dry environments. The C4 pathway is present in just three percent of all plant species yet accounts for one quarter of the terrestrial primary production. This impressive productivity is due to C4 grasses, which dominate most open areas of the tropics and subtropics and especially savannahs.

Through genomic analyses a team of international researchers, led by the University of Sheffield were able to understand the ecological changes that happened during the dispersal of Alloteropsis semialata, first in Africa and then in Asia and Australia. The team found that while the non-C4 plants remained confined to a small range of ecological conditions in Central Africa, the evolution of C4 photosynthesis immediately broadened the ecological conditions where the species could grow. C4 plants can disperse broadly across environmental and geographical space, while still surviving in the same habitats occupied by their non-C4 ancestors, showing that this physiological novelty increases the variety of habitats available, which allowed the rapid colonization of three distinct continents.

In a world rapidly affected by climate changes and other anthropogenic alterations of natural systems, understanding how physiological attributes allow some plants to thrive in a variety of conditions might hold the key to the management of more resilient ecosystems. In addition, understanding what allows some plants to be productive in a variety of environments could help direct future crop improvement projects.

Thursday, August 6, 2015

Only 12 more days

Only 12 more days to go before we welcome the world to the 6th International Barcode of Life Conference. The level of excitement, anticipation, anxiety and stress here at the institute is increasing by the day. Everyone is working hard to make this a memorable and enjoyable experience for all our guests. 

The Scientific Organizing Committee has put together a densely packed program with invited plenary presentations, contributed sessions, discussion panels, and social events. The conference will start with a full day of pre-conference workshops on August 17, with BOLD and next-generation sequencing workshops held in the morning. Tours to BIO are also offered throughout the day. The afternoon will be devoted to presentations and discussions for forming the International Society for the Barcode of Life. The day ends with a welcoming reception.

Each day of the main conference (August 18-21) will start with plenary presentations in the mornings, ensuring that a component of the conference experience is shared by all delegates. Afternoons will be comprised of parallel sessions, and a dedicated poster session will be held on the afternoon of August 19. Opportunity for dialogue and refreshment will be provided through shared breakfasts, lunches, and coffee breaks each day.

Here a draft schedule of the parallel sessions (please note that some of the sessions can still be moved around): 

The conference program will be augmented by special plenary presentations and a discussion on the State of Biodiversity on the evening of August 19, to be held at the River Run Centre in downtown Guelph. A Gala Reception will be August 20 at the historic and scenic Cambridge Mill.

We will be tweeting, facebooking, and blogging from the conference and during the time leading up to it. We are also looking into options to stream and record sessions of the conference using Periscope. Stay tuned.

Wednesday, August 5, 2015

Conservation genetics in Latin America

A recently published special issue of the Journal of Heredity focuses on case studies of real-world applications of conservation genetics in Latin America, from nabbing parrot smugglers to exposing fraudulent fish sales. The discipline of conservation genetics has been growing for at least four decades. But only relatively recently have genetic techniques such as DNA Barcoding been used not only to understand conservation issues, but to solve those problems as well. The application of such genetic techniques becomes increasingly important in Latin America, where the vast biodiversity is in decline due to an inexorable economic development. 

Latin America has an unusual level of biodiversity, and is also undergoing unprecedented development, making the region of particular conservation concern. But these factors also contribute to the growth of a scientific community able to provide real help, given the right support.

That support began a decade ago with the establishment of La Red de Genética para la Conservacion (ReGeneC). ReGeneC provides an annual intensive course in conservation genetic techniques and applications for South American students and researchers. ReGeneC's work thus far culminated in a conference in Caracas, Venezuela in May 2014; many of the projects presented at the conference became part of the special issue which includes fifteen papers highlighting the use of genetic techniques to address problems in the conservation of Latin American biodiversity, ranging from trees to toads to tamarins:

Enjoy reading.

Tuesday, August 4, 2015

Equine ringworm and minks

Dermatophytosis is a condition caused by an infection of the skin in a variety of mammals such as humans, pets and domesticated animals. It is usually referred to as "ringworm", but this is a misnomer, as the condition is caused by fungal species of the genus Trichophyton and not by parasitic worms. These fungi feed on keratin present in the outer layer of skin, hair, and nails. The probably most well known dermatophytosis is the athlete's foot caused by Trichophyton rubrum or Trichophyton mentagrophytes.

The condition commonly known as equine ringworm starts out with small skin lesions from which the hair is lost. These spread and usually become scurfy. In many cases there may only be a couple of lesions but if left untreated and especially if spread by grooming, the condition can become extensive. The infection is highly contagious and whole groups of horses can become affected in an outbreak. It is possible but uncommon for people to catch Trichophyton equinum from horses:

Reports of dermatophytosis caused by Trichophyton equinum outside of the regular equine host range are rare and limited to dogs and cats, as well as multiple cases of zoonosis of humans who have been in direct contact with infected horses.

The more surprising is its occurrence on some mink from farms in Canada as reported in July

This report details 2 outbreaks of dermatophytosis in 2 different mink ranches. On the first farm, only kits were affected, while on the second farm, small numbers of adults were infected. Affected mink were otherwise clinically healthy and in good body condition.

Researchers cultured the dermatophyte and used DNA Barcoding (ITS) to identify the species. It was identified as Trichophyton equinum. Not only are dermatophytosis infections relatively uncommon in farmed mink, infections are usually caused by different fungal species.

In dealing with an outbreak of dermatophytosis, environmental disinfection and separation of infected animals from noninfected animals is paramount in order to control and limit the spread of the pathogen.Systemic antifungal treatment is recommended to shorten the course of the infection and reduce dissemination to other animals.

Knowing the exact species that caused the infection will allow for a more specific treatment that is likely more efficient.

I cannot resist but suggest that society should seriously think about the need for fur farms in general. Fur clothing might be one of the oldest form of clothing but does a modern society still need that especially if the main reason to wear it comes from the wish to show off ones wealth? I don't think so.