DNA Barcoding Online Course

One of the projects that currently keep me busy is the development of an online course that introduces attendees to the principles of DNA Barcoding. We are working closely with our experts for distance education here at the UofG and this week is the start of the advertisement campaign for the first offering. This course is an exclusively web-based course which is offered over an eight week period starting on July 8th. On average, six to eight hours of study time are required each week to study the course material which will consist of reading, audio and video material. Participants will have weekly assignments/quizzes and have plenty of opportunities to participate at discussions that are happening in designated chatrooms. The number of participants is limited to ensure adequate mentoring by the instructor.

I am a big fan of distance learning as it provides access to learning when the source of information and the learners are separated by time and distance, or even both. Especially its asynchronous nature makes it very attractive to many as learning is self-paced and allows participants to engage in the exchange of ideas or information without the dependency of other participants involvement at the same time or the need to show up at a particular time for a lecture or seminar. It requires some learning skills and self discipline though.

Eventually this will hopefully develop into a full university course that includes a suite of modules and a hands-on unit. However, first things first. We will start with the Introduction to DNA Barcoding Course in July. I am currently working on the course content and I will also be the instructor.

If you are interested please have a look at www.dnabarcodingcourses.com. The site details course content, tuition fees, requirements, etc.

Coming this week!

The DNA Barcoding blog is the proud host of the 59th Carnival of Evolution.

In case you don't know what the Carnival is all about:

Do you care about the science behind evolution? Do you marvel at the tiny molecular machines spewing out coded messages to the microscopic inhabitants of your own bodied world? Do you grow irate at the ignorance pushers and the disintegration of evolution education in the modern world? Do you like to stay abreast of current topics and scientific findings in the study of the organismal existences surrounding us or those long gone?

If so, this is the blog carnival for you. (Don't know what a "blog carnival" is? Read this.)

In the past hosts have been creative and came up with some unique, funny, clever, and artistic ways to present them. Have a look at some of the past editions: dictionary, dear diary, museum visit, submissions statistics, virtual voyage of the Beagle, phylogenetics on URLs, brain evolution theme, personal art, menu, featuring a blogger, letter from Darwin, quotes, verbosity, Hitchhiker's Guide to CoE, history of human thought, conference proceedings, animations, phylogenetic trees, travel pictures

I am working on my hopefully creative contribution. Stay tuned.

60 schools later

Today was the last day of school visits with the BIOBus for our School Malaise Trap program. 

Now we have 83 traps in 60 schools and a few adjacent National Parks and Conservation Areas. They are up and running since Monday and will hopefully fill up quickly. One more week and all those samples will come back. Then the big sorting, imaging, sub-sampling and sequencing will begin. All schools need their results back by early June.

Meet our Team! These folks have been on the school visits and will be working hard to barcode perhaps some 20 000 samples collected over two weeks.

B for Brazil

The second stop on my virtual journey through the DNA Barcode cosmos is Brazil. 

If you are interested in Brazil's DNA Barcoding efforts the best way to start is having a look at the BrBOL website from which I stole this pretty cool banner image. 

Home to 60% of the Amazon Rainforest, which accounts for approximately one-tenth of all species in the world, Brazil is considered to have the greatest biodiversity of any country on the planet. It is also the country with the most known species of plants (55,000), freshwater fish (3000) and mammals (700). With 170,000 to 200,000 species Brazil is home to around 9.5% of all the species worldwide but researchers have estimated the country's total biota at 1.8 million species. A quick search on BOLD told me that about 5,000 of those species have been assigned a DNA Barcode.

A Brazilian consortium with almost one hundred member institutions aims to increase this number considerably. The Brazilian Barcode of Life (BrBOL) project consists of 11 projects aimed at different taxonomic groups and scientific fields.

As I am still very much into ichthyology I had a closer look the current status for the fishes of Brazil for which there is also a BrBOL project that plans to generate DNA Barcodes for 2,100 species. A search for "Brazil" and "Actinopterygii" in BOLD's public record section showed 4192 public records forming 646 BINs which likely represent species. I believe it is fair to say that 600 species of the Brazilian bony fish have been barcoded and are publicly accessible. More than 28% of the planned work has been done already and for those that are interested in more detail there is an interesting paper that was recently published in BMC Genetics.

More than one-fifth of the Amazon Rainforest in Brazil has been completely destroyed, and more than 70 mammals are endangered. The threat of extinction comes from several sources, mostly deforestation and poaching. Currently, 15.8 million acres of tropical ecosystem have been completely eliminated to farm sugarcane for ethanol production. There are plans to plant an additional 4.5 million acres during the next four years. 70-85% of Brazil's transportation energy is derived from ethanol, or various mixtures of ethanol and petroleum-based fuels. Only about 15-20% comes from imported petroleum. This massive national biofuel program has been devastating to tropical wildlife diversity, and to the global climate.

A national program such as BrBOL represents a modern approach to speed up cataloging a country's biodiversity.  The more we know about what lives around us the more we appreciate and care about it. And only that will motivate us to be creative when it comes to protect it.

Engaging kids in science

Five reasons why I really enjoy these school outreach activitites:

Diatoms

Diatoms are amazing often beautiful microscopical algae whose typical feature is a siliceous coverage, called frustule, extremely diverse in shape. Diatoms live in almost all types of superficial waters. Depending on their habitats, diatoms are either planktonic, benthic, or both planktonic and benthic.

 

The ecological requirements of many diatom species are known and therefore many diatom-based indexes of water quality have been developed and are used to monitor water quality. However, producing taxonomical inventories for diatom communities is time-consuming, costly, and requires a high level of taxonomic expertise. On the other hand a comprehensive assessment of the taxonomic composition of an environmental community is often essential for studying an ecosystem in order to evaluate the impact of environmental stressors or to establish a baseline that evaluates ecosystem functions.

A group of French researchers has now published the results of a test to evaluate the suitability of Next Generation Sequencing for the taxonomic characterization of freshwater diatom communities. They used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and COI) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. 454 pyrosequencing was used to produce libraries for each of the three samples and for each marker. Three DNA reference libraries obtained by conventional Sanger sequencing  were used for read assignment and evaluation of accuracy.

Of all the markers tested RbcL showed the highest resolving power in conjunction with a large DNA reference library. The authors conclude: Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.

Diatoms are one of the largest and ecologically most significant groups of organisms on Earth. Because of their abundance they probably account for as much as 20% of global photosynthetic fixation of carbon, which is more than all the world's tropical rainforests. Understanding their community structures is probably a more important task than most of us would think. Maybe it helps to think of it this way:

Another way to appreciate diatoms is to realize that they give us every fifth breath, by the oxygen they liberate during photosynthesis (David Mann, Tree of Life website).

For iBOL fans

Found this in Cambridge, Ontario while on one of our school visit tours.

(photo by Brianne St. Jacques)

A for Austria

A few weeks ago I posted that the DNA Barcoding community reached another milestone and assembled 2 Million barcodes in the past 10 years. This is a remarkable accomplishment but I thought it would be nice to highlight a couple of projects that helped building this immense library that is still so far from being complete.

My contribution to the 'celebrations' of 10 years DNA Barcoding is to present people and their work from around the globe. Once a week I will pick a project and provide a few information bits and links for everyone interested in how much the field has grown already.

Let's start with 'A' for Austria and Peter Huemer, a researcher at the Tiroler Landesmuseum Ferdinandeum. Very recently he published an updated checklist of all lepidoptera species of Austria (in German) which comprises of 4071 species. A quick search on BOLD told me that some 2000 of those have been barcoded in the last 3 years and the project is far from finished. This effort is part of a larger project that aims to barcode the lepidoptera of the alps a fauna that is encompassing about 6000 species.

In contrast to national barcoding initiatives the study area covers a major European biogeographic region shared by 8 countries. Despite the fact that the Alps are among the best studied mountain areas in the world researchers such as Peter were astonished by an unexpected amount of cryptic species revealed by those early studies.

In the next three years the Austrian researcher and his counterparts from the autonomous province Bozen – South Tyrol, Italy will collect and barcode 2000 more species from both sides of a major ridge of the Alps. This ridge divides North and South Tyrol and the researchers on both sides hope that the results of their study will provide insights into speciation processes driven by the glacial history of the region.

Delayed extinction

Earth went through several larger extinction events. They were perhaps caused by meteorite impacts, increased volcanic activity or other major shifts of environmental conditions. In light of the current rate of species loss many experts are referring to the sixth major extinction event in Earth's history. But this time the main causes are related human activities and the main ones are pollution, habitat loss and fragmentation, and the spread of invasive species.

In order to better understand present species extinction a group of researchers related numbers of threatened species appearing on national red lists to historical and contemporary levels of socioeconomic pressures across 22 European countries. 

Their findings are concerning. Proportions of species facing medium-to-high extinction risks are more closely matched to indicators of socioeconomic pressures (i.e., human population density, per capita gross domestic product, and a measure of land use intensity) from the early or mid-, rather than the late, 20th century.

The researchers conclude that irrespective of recent conservation actions, large-scale risks to biodiversity lag considerably behind contemporary levels of socioeconomic pressures. The negative impact of human activities on current biodiversity will not become fully realized until several decades into the future. Mitigating extinction risks might be an even greater challenge if temporal delays mean many threatened species might already be destined toward extinction.

 

The current Red List status of plants, dragonflies and grasshoppers is best explained by historical data of the years around 1900. Species are disappearing although causes such as increased use of fertilizer and drainage already reached a peak decades ago. The situation of mammals and reptiles also highly correlates with the first half of the 20th century. Only the decline of fish species could be related to more recent data which could be explained by the immediate and strong impact of pollution and building activities.

Minimizing the magnitude of the sixth extinction crisis might be an even greater challenge when temporal delays are taken into account.

The Rosette Agent

Sphaerothecum destruens or the rosette agent is a unicellular eucaryotic parasite of fish which has caused disease and moralities up to 80% in north American Chinook salmon (Oncorhynchus tshawytscha) and chronic mortalities in cultured salmon (Salmo salar).  It was first discovered in the United States in association with invasive species including topmouth gudgeon (Pseudorasbora parva) but was  also found to be the causative agent of a disease in the UK affecting other salmonid species such as brown trout. It is thought to pose more of a risk in Europe than in the USA as native species there are more susceptible to the parasite. The disease causes high rates of morbidity and mortality in a number of different salmonid species and can also infect other freshwater fish such as bream, carp and roach.

Researchers at Bournemouth University in the UK are very concerned and this was triggered by a study they conducted and published already last year. They were able to link the rapid population decline of sunbleak (Leucaspius delineatus), a cyprinid fish native to Europe to the spread of the invasive topmouth gudgeon (Pseudorasbora parva). In addition they were able to isolate and culture Sphaerothaecum destruens from sunbleak. 

The UK Environment Agency is already attempting to eradicate topmouth gudgeon from UK waterways. They have already removed hundreds of thousands of the fish from English rivers. Despite this, very little is known about how many UK lakes, rivers and fisheries the topmouth gudgeon let alone the parasite are present in. Another question is how wide-spread both invasive species and parasite are in continental Europe.

There are more than four million anglers in the UK alone and the sport generates an estimated £3.5 billion for the country's economy. The use of environmental DNA (eDNA) methods comes to mind. The colleagues from Bournemouth University are certainly looking into the option of detecting the parasite directly in the water instead of going through the lengths of extracting it from an infected fish and culturing it. A smartly designed eDNA probe could help with screening many river systems in the UK and Europe in a far more timely fashion than any traditional approach.

It Is Not Extinct, It Never Existed

Turtles are at a much higher risk of extinction than many other vertebrates. About half of all 328 of their species are considered threatened. One of them -- or at least it was thought so -- is the Seychelles mud turtle Pelusios seychellensis. Just three specimens were collected at the end of the 19th century; they are still kept at the Natural History Museum in Vienna and the Zoological Museum in Hamburg.

Despite an intensive search for this species, which was declared extinct by the International Union for Conservation of Nature (IUCN), no further individuals were found. Consequently, it was assumed that the species had been eradicated.

former Pelusios seychellensis

Researchers of the Museum of Zoology at the Senckenberg Natural History Collections in Dresden now examined several mitochondrial loci of the original specimen from the museum in Vienna and discovered that these turtles in fact never represented a distinct species.

The genetic analyses showed that the Pelusios seychellensis individuals are actually members of another species, Pelusios castaneus. This species is widespread in West Africa and for a long time researchers thought that Pelusios seychellensis had to be a different species although the Seychelles turtles looked deceptively similar to the West African ones. 

The species Pelusios seychellensis has therefore never existed.

The Mongolian Death Worm

It is shaped like a sausage about two feet long, has no head nor leg and it is so poisonous that merely to touch it means instant death. It lives in the most desolate parts of the Gobi Desert…

The 'Mongolian Death Worm', called olgoi-khorkhoi by the locals is a legendary animal that has preoccupied the imagination of both the inhabitants and travelers in the region. It is said to live the southern Gobi Desert where it terrorizes travelers with its deadly abilities to project acid that, upon contact, turns anything yellow and corroded. It is described as a bright red worm with a wide body that grows up to 1.5m length.

However, until recently there was only one record for a native Mongolian earthworm (Eisenia magnifica) and some authors believed that in those regions with extreme low amounts of rainfall (less than 400mm annually) no species let alone an endemic can exist. But now with the help of DNA Barcoding two new sub-species of earthworms, Eisenia nordenskioldi mongol and Eisenia nordenskioldi onon, are reported from the same region. Although neither of them possesses the fatal characteristics of olgoi-khorkhoi, the sibling species exhibit the ability to partly regrow body parts when cut in two. Relatives of the new sub-species are found in habitats as diverse as high mountains, deserts and hot-springs. They demonstrate extreme temperature tolerances and survival ranges thriving in environments with temperatures ranging from as little as -30°C up to +40°C. 

Eisenia nordenskioldi mongol was named after the region of its discovery. The name Eisenia nordenskioldi onon was inspired by the Onon River in Outer Mongolia, where Genghis Khan was born and grew up. The region is also supposed to be his final resting place.

Whether olgoi-khorkhoi really exists, and whether the two new sub-species of the Siberian Eisenia nordenskioldi species-complex are in any way related to it, is yet to be confirmed. In the meantime it can continue to inspire peoples minds.

Ray albinos

Albinism is characterized by an absence of pigmentation in the skin, hair and eyes. It is a congenital disorder and is caused by a disruption of the enzymic pathway responsible for producing melanin. Albinism has been widely reported for many invertebrates and vertebrates and is very commonly documented in bony fishes.

There are, however, only a few records for sharks and rays, and most of them were partial albinism, where skin pigmentation is lacking or reduced but retinal colouration is normal.  Overall, albinism in sharks is rare and no case of full albinism has ever been described for a skate species.

Taken from Ball et al. 2013

Now a paper published in the Journal of Fish Biology reports three cases of albinism in recent years (2008, 2011), which compares to only four documented accounts of partial albinism in rays since 1893. The three albino skates were captured from the North Sea and the English Channel. A high level of morphological conservatism among skates and rays usually makes them challenging to identify even when the regular coloration is present. By using DNA Barcoding and morphometric analyses, the researchers were able to identify the albino individuals as a spotted ray Raja montagui, a blonde ray Raja brachyura and a thornback ray Raja clavata.

It remains unclear whether this find represents a genuine increase in albinism with some biological significance. Widely reported declines in U.K. skate populations have given rise to concern over their conservation status and an increased focus on their fisheries management. The albino findings may be purely coincident with a general increase in fishing intensity and reporting requirements. Rajids were not subject to mandatory species specific landing according to European law until 2008, hence, before this time, any unusual morphology may have been overlooked.

"We caution researchers..."

Even in the rather young discipline of DNA Barcoding history seems to repeat itself. About six years ago researchers had a closer look at some leech species of the genus Helobdella that had been workhorses of annelid developmental biology for decades. Helobdella robusta is a widely used model organism and its genome was sequenced recently. However, the study revealed that, collectively, the Helobdella development community had been working on five distinct species. As a consequence the authors stated:

We caution researchers similarly working on multiple wild-collected isolates to preserve voucher specimens and to obtain from these a molecular "barcode," such as a COI gene sequence, to reveal genetic variation in animals used for research.

A bit over a week ago an international group of researchers published a study with a similar approach. The species they were interested in was Stylophora pistillata a widely used coral species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). They showed that this species in fact comprises four deeply divergent clades corresponding to different geographical regions. Furthermore on the basis of the fossil record of Stylophora, they estimated that these four clades diverged from one another 52-30 Million years ago and propose to recognize them as four distinct species.

These findings have broad implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.

Another good reason to have a closer look at genetic variation in species used as model organisms in research.

Turbo taxonomy

The taxonomic impediment has been recognized as a major obstacle to biodiversity research for the past two decades and the foreseeable future. A world-wide shortage of important taxonomic information, gaps in our current taxonomic knowledge despite over 200 years of intensive work, and the shortage of trained taxonomists and curators are the key characteristics of the problem. Numerous remedies were  proposed over the last years but no significant progress in terms of formal species descriptions, nor a minimum standard for descriptions have been achieved so far.


Not long ago the term "turbo-taxonomy" was coined for an approach combining DNA Barcodes, concise morphological descriptions by an expert taxonomist, and high-resolution digital imaging to streamline the formal description of larger numbers of new species. This strategy could perhaps represent a big step forward when it comes to close the gaps of our taxonomic knowledge faster than at the current speed.

Building on this a group of German and Indonesian researchers now propose a procedure which, together with open access web-publication and automated content transfer from journal into a wiki, may create the a very efficient and sustainable way to conduct taxonomy in the future. Descriptions initially highly concise could be gradually updated or modified in the fully versioned wiki-framework.

This means that the visibility of additional data is not compromised, while the original species description -the first version- remains preserved in the wiki, and of course in the journal version. A DNA sequence database with an identification engine aka BOLD could replace the classic identification key, but also helps to avoid synonyms. All the work researchers have been doing with BOLD has demonstrated already that it has the potential to detect grossly incorrect taxonomic placements.

The group goes on and demonstrates what they had in mind by presenting a species-description pipeline in which they named 101 new species of the hyperdiverse genus Trigonopterus (weevils from New Guinea).  In another paper they describe the advantages of their approach for community ecology studies.

Three papers that represent a large body of work but also a nice compendium on fast track integrative taxonomy. I let the authors have the last word as they clearly name the advantages an adoption by the community at large would have:

Fast track taxonomy will not only increase speed, but also sustainability of global species inventories. It will be of great practical value to all the other disciplines that depend on a usable taxonomy and will change our perception of global biodiversity. While this approach is certainly not suitable for all taxa alike, it is the tool that will help to tackle many hyperdiverse groups and pave the road for more sustainable comparative studies, e.g. in community ecology, phylogeography and large scale biogeographic studies.

Zoo Action Project

Meet the Biotech club from Donald A. Wilson Secondary School in Whitby and learn about their DNA Barcoding Action Project, created to help teach other students & visitors to the Toronto Zoo about the many uses of DNA Barcoding! These videos were developed as part of the DNA Barcoding at the Zoo Action Project by Let's Talk Science.

Let’s Talk Science is a Canadian organization that delivers science learning programs and services that aim to turn children and youth on to science and keep them engaged in learning.

Their approach to science education engages children from the early years through high school with fun, exciting hands-on/minds-on activities that improve their understanding of physical and life science, mathematics and technology. 

Maria Sibylla Merian

Maria Sibylla Merian

That a fat, brown caterpillar could turn into a wonderful butterfly was hard to believe. Contemporaries of  Maria Sibylla Merian a Swiss naturalist and scientific illustrator, were highly suspicious of the findings of entomologists at the time. Moreover, although certain scholars were aware of the process of metamorphosis from the caterpillar to the butterfly, the majority of people did not understand the process mostly because the official language of science was still Latin. 1679 Merian published, Der Raupen wunderbare Verwandlung und sonderbare Blumennahrung (The Caterpillars' Marvelous Transformation and Strange Floral Food), which became very popular as a result of being published in the vernacular. However, it is notable that her work was largely ignored by scientists of the time.

Nevertheless, being a trailblazer, Merian and her daughter Dorothea traveled together (without a male companion) to Suriname to study, document and draw insects. Such an expedition was completely unheard of at the time, and the women reportedly survived a number of dangerous encounters.Over two years she discovered a whole range of previously unknown animals and plants in the interior of Suriname. Merian spent a considerable amount of time studying and classifying her findings and described them in great detail. Her classification of butterflies and moths is still relevant today.

Maria Sibylla Merian created an incredible merger of science and art with her tireless study and stunningly beautiful copperplate engravings. Metamorphosis Insectorum Surinamensium is her most influential work and by many considered a forerunner of modern scientific illustration.

Today (her birthday, 2. April 1647) Google honored her with a Google Doodle.