Friday, February 28, 2014

Sex & Bugs & Rock'n'Roll

Public Engagement (PE) is an umbrella term, which covers a wide variety of activities serving many different agendas. These include justifying the use of ‘taxpayer’ money for research, increasing research impact, identifying research priorities, encouraging discussion about controversial issues, promoting science as a career, broadening the scope of research, and stimulating public behaviour around scientific issues. Effective public outreach contributes to measures of research impact, which has helped to legitimize scientists committing time towards PE and a number of funding bodies now incorporate requirements for ‘stakeholder engagement’ into the criteria for grant proposals. Timely and effective PE can be crucial for the transition of science into policy and dialogue with different sectors of society is essential for identifying and addressing public priorities on contentious topics. For example, PE has played a key role in facilitating discussions of evolution vs. creationism in the USA, and catalysing societal action on environmental issues 

However public engagement is not so easy especially if you want to engage a variety of audiences and not the usual suspects that are interested in your particular field of science. As this is part of my daily bread and butter I know how difficult it can be for the colleagues. We do outreach in schools, we give public seminars, some of us are involved with outreach programs at museums but that is a very small subset of society and it is difficult to develop ways to do outreach with the remainder of the people which not necessarily a captured audience, or that may not have already selected to be somewhere where science was on the agenda. We have to seriously start thinking outside the box and that's why we decide to show up on a Santa Claus parade dressed up as insects.

Some colleagues in the UK had an even better idea. They go to music festivals and set up booths on entomology and microbiology as a way to capture people's curiosity, and bring the science to where the people are. In addition to display materials, they do hands-on activities, and really worked to make the material interesting and creative. They argue that music festivals are perfect places to engage public in science, in part because the people attending music festivals are there with open minds, and are ready to have fun and be 'engaged', at least with music. They are primed for anything out of the ordinary and might just stop by a booth that is displaying honeybee colonies, and taking swabs for microbiology cultures. 

And the absolute best of all - they managed to publish about their work in Trends in Ecology and Evolution. The British Ecological Society actually funded the researchers for three festivals and got them to report at the International Congress of Ecology, held in London last year. The experiment in outreach resulted in the aforementioned publication in Trends in Ecology and Evolution, and an invitation from the society to continue the festival circuit this summer.

I really like this idea, maybe because I like music festivals a lot myself. We have a very famous one here in Guelph as well. Maybe would should show up there this summer with barcodes, bugs, and rock'n'roll.

h/t Valérie Lévesque-Beaudin 

Thursday, February 27, 2014

Predictable extinction risks

Commonly used assessments of threatened species, such as the IUCN Red List, were not developed with the effects of climate change events in mind. However, a new study of 36 amphibian and reptile species endemic to the US has concluded that climate changes may not be fundamentally different from other extinction threats in terms of identifying species in danger of extinction.

A group of american researchers looked at existing information on species of salamanders, turtles, tortoises, snakes and lizards, in the hopes to create a blueprint for judging extinction risk in species in general around the world.

To their surprise they found that most important factors, such as having a small range or low population size, are already widely used in conservation assessments which meant that current systems may be better able to identify species vulnerability to climate change than previously thought.

Through quantitative analysis the team found that across the reptiles and amphibians studied there was a 28% overall chance of extinction by 2100. In contrast, the risk of extinction without climate change was calculated to be less than 1%, suggesting that climate change will cause a dramatic increase in extinction risk for these taxonomic groups over the next century. Unlike most previous studies, which predicted future extinction risks based only on projected contraction of areas with suitable climate for each species, the present study estimated extinction risk as the probability of the population size falling to zero by the year 2100. To do this, the authors used a new methodology that included modeling demographic processes such as reproduction, survival, and dispersal. The approach was not designed to make specific predictions for each individual species; instead, the methods allowed the authors to draw conclusions beyond the limited set of species for which data were available. The result is new understanding of the factors that make some species more at risk due to the changing temperature and rainfall patterns that are expected over the coming century.

The bad news is that climate change will cause many extinctions unless species-specific conservation actions are taken. But the good news is that the methods conservation organizations have been using to identify which species need the most urgent help also work when climate change is the main threat.

The factors identified in this study as predisposing species to high extinction risk due to climate change suggest that conservation actions should focus on species that occupy a small or declining area, have a small population size, or have synchronized population fluctuations. The methodology used in this study offers great potential for adaption to additional taxonomic groups and geographical areas, helping to develop effective measures to conserve biodiversity.

Wednesday, February 26, 2014

Recognition through species names

Are you a taxonomist who is about to describe a couple of new species and you still need some ideas for the names? 

Here is an idea for you - why not honoring the people that worked with you in order to obtain the specimens, or worked with you in the collection, or if your work included some DNA Barcoding, the ones that did all the lab work? 

Apanteles albanjimenezi, named after
the parataxonomist Alban Jiménez
A new study just described the astonishing number of 186 new species of a single genus (Apanteles) of parasitoid wasps attacking caterpillars in the Area de Conservación Guanacaste (ACG), Costa Rica. Most of the new species are named after local parataxonomists, who in many cases collected the caterpillars from which the new species of wasps emerged. More than half a million specimens of wild-caught Lepidoptera caterpillars have been identified and reared for their parasitoids over a period of 34 years from this region in northwestern Costa Rica. This provides the world’s best location-based dataset for studying the taxonomy and host relationships of caterpillar parasitoids, and the cherry on the cake is that many of both hosts and parasites have been assigned a DNA Barcode within the last 10 years. In this new publication the authors reassess the limits of the genus Apanteles sensu stricto, describe 186 new species from 3 200+ parasitized caterpillars of hundreds of ACG Lepidoptera species, and provide keys to all 205 described Apanteles from Mesoamerica – including 19 previously described species in addition to the new species. This represents 20% the world's Apanteles fauna, in less than 0.001 % of the terrestrial area of the Planet.

This is not the first study demonstrating by the shier number of new species described how much we have underestimated the actual diversity of parasitoid wasps. No other area is as well collected and studied as the ACG which means that the number of new species of parasitoid wasps awaiting discovery must be gargantuan.

The study also revealed that 90% of the wasps species only parasitized on one or just a few species of moths or butterflies, suggesting that members of this group of parasitoid wasps (Microgastrinae) are more specialized than previously suspected.

All species are described through an approach that integrates morphological, DNA Barcode and other biological data, computer-generated descriptions, and high-quality illustrations and images for every single species. The combination of techniques allowed the researchers to speed up the process of describing new species, without reducing the quality of the paper. Taxonomic keys are presented in two formats: traditional dichotomous print and links to an electronic interactive version using Lucid 3.5.

Why did the Fungi leave the party?

Although this species is eaten in some places, in other parts of its range it can have a decidedly acid-sour taste. There are reports that it can produce a gradually acquired hypersensitivity that causes kidney failure.

Not recommended although tasty because it is now known to cause a gradually acquired hypersensitivity that can result in massive hemolysis and be life-threatening. 

Good edible, but toxic in the raw state. It is recommended to blanch this mushroom in a very large volume of water for a long time and to throw away the strongly coloured cooking water.

Most of the 15 species of the fungus genus Paxillus are widely regarded as poisonous or even deadly. One of them, Paxillus involutus, is a model species for ecological or physiological studies of ectomycorrhiza, the symbiotic relationship between fungal symbionts and the roots of various plant species. However, assessments whether Paxillus involutus is harmful or not vary depending on different observers' experiences in different countries and such differences in assessments can be the result of undiscovered diversity. After all, there is not even a proper type specimen for Paxillus involutus.

The observation of a large and unusual variation among Paxillus specimens in France led to the suspicion of the presence of a not yet described species and a new publication not only confirms this by using molecular data but also properly describes this new species (Paxillus cuprinus):

Phylogenetic analyses of three nuclear DNA regions (rDNA internal transcribed spacer (ITS), tef1-α, and gpd) confirmed the four European species. Morphology, culture, and ecology features allowed us to delineate species boundaries and to describe the fourth species we named Paxillus cuprinus since it turns coppery with age. As there is no existing original herbarium specimen for Paxillus involutus, one of our collections was chosen as the epitype. The low genetic diversity found in Paxillus cuprinus correlates with stable morphological traits (basidiome colour, ovoid–amygdaliform spores with an apical constriction) and with ecological preferences (association with Betulaceae in open and temperate areas).

For these species the diversity at the genetic level is supported by morphological and ecological variability, often a major obstacle in species delineation. This study establishes species boundaries for the European members of the genus and describes habitat preferences. This knowledge will also help to decrease the amount of accidental mis-identifications that could happen during the next mushroom foray.

Ah yes, in case you didn't know the joke here is the answer to the question in the title: There wasn't mushroom.

Tuesday, February 25, 2014

Genome codes aren't revolutionary

A new naming structure proposed by an American researcher moves beyond the Linnaeus system to one based on the genetic sequence of each individual organism. This creates a more robust, precise, and informative name for any organism, be it a bacterium, fungus, plant, or animal. Coded names could be permanent, as opposed to the shifting of names typical in the current biological classification system. Codes could also be assigned without the current lengthy process that is required by analyzing one organism's physical traits compared to another's. Lastly, the sequence could be assigned to viruses, bacteria, fungi, plants, and animals and would provide a standardized naming system for all life on Earth.

This news bit comes with the headline Revolutionary naming system for all life on earth proposed. I have to admit that such claims make me skeptical and I immediately had a closer look at the paper in PLoSONE. Indeed the more I read through the publication the more I thought the claims are not that new and revolutionary, and frankly I have no idea why the authors submitted a provisional patent for this method (U.S. Patent Application number 61/774,030.).

The proposed naming process begins by sampling and sequencing the genome of an organism. Note that we are talking about bacterial genomes here and in the case of eukaryotes we would be looking at their mitochondrial DNA alone. The sequence is then used to generate a code unique to that individual organism based on its similarity to all previously sequenced organisms. The approach is theoretically based on DNA-DNA hybridization (DDH) which was firstly implemented in the mid sixties as a genome to genome comparison value trying to find an objective numerical measure of what a species could be, and since then it has been recalled to be the gold standard in prokaryotic classification. However, in the age of genomics there was a need to substitute DDH by a database-based method that provides equivalent information. The Average Nucleotide Identity (ANI) among the conserved genes of a pair of genomes was considered as a first reliable attempt. The most modern approach to calculate ANI shifted from using definded sections of the genome and instead splice the query genome in 1020 nucleotide fragments and blast each of them against the subject genome to calculate the average of nucleotide identity. ANI and a percentage of aligned fragments was used by the authors assign a so called genome code that they propose could serve as an alternative to Linnean names.

The authors seem not to give a lot of thought to the size of the task. Millions of species would require a lot of computing power and more sophisticated algorithms. The only reference I could find was this one: ANI will not need to be calculated against all genomes that already have a code. Instead, the group of genomes that is most similar to the new genome could be identified using only a few genes, and then ANI is calculated only against the most similar genomes to precisely identify the most similar genome and the corresponding ANI value. Well, the use of a few genes suggested here as a pre-assignment system sounds very much like DNA Barcoding to me and since we have been showing that DNA Barcodes alone can discriminate species why would we want to sequence full genomes instead? Admittedly the method requires sequencing only of a mitochondrial genome. But for the sole purpose of building a library of all life using the new name/code this seems a bit too much. Although it has become less of a technical issue in the last few years it will always be more costly than utilizing shorter, standard DNA fragments aka DNA Barcodes to do an even better job.

Because animals are much more closely related to each other than bacteria, mitochondrial genomes of all members of the chordata can be aligned with each other using BLAST and thus all chordata mitochondria share the same code at position A. Chordates represent only a very small fraction of the animals and I am very sure that alignments across all animal groups won't be as easy as proposed simply because mt DNA has been rearranged repeatedly. I also have to express my dislike for the equalization of animals and chordates here. All chordates are animals indeed but not all animals are chordates.

Lets face it - there is already a very pragmatic and functional system in place and it is based on one or a few genes (DNA Barcodes). We call the resulting code Barcode Identification Number or simply BIN and it overcomes all challenges also listed by the authors of this publication. It is disappointing that the authors of the present study did not bother to cite any DNA Barcoding study at all thereby ignoring more than 10 years of work on the same problem. The real breakthrough has been achieved already and I also note a difference in style. Ratnasingham and Hebert published their BIN paper last summer with much less ballyhoo and after quite a few years of careful evaluation. 

All this paper represents is the advancement of the ANI method proposing a more formal system to register species (and I would like to add 'prokaryotic' species). It is a great achievement consequently building on previous work but there is no need to oversell this especially not if an entire line of parallel research is ignored at the same time.

Monday, February 24, 2014

The cat flea

The cat flea, Ctenocephalides felis, is the most common flea species. Its primary host is the domestic cat, but the it is also the primary flea infesting dogs. Humans can be bitten but this flea species was never able to build a stable long-term population that subsequently infested other people. Cat fleas can transmit other parasites and infections but pet owners are spending millions of dollars annually on flea control products because fleas cause up to 50% of all dermatological cases of cats and dogs .

Within Ctenocephalides felis many scientists have distinguished four subspecies based on morphology, however a recent revision suggested that two of those likely represent species. Differentiation of the subspecies based on minute morphological differences (e.g. chetotaxy, phallosome morphology and cephalic curvature) coupled with the encroachment of Ctenocephalides felis felis into other subspecies-specific geographical regions has led to assumptions of interbreeding between subspecies, making differentiation even more complex if not impossible. 

In a new study a group of Australian researchers investigated the genetic identity of Ctenocephalides felis and determined the diversity of cat fleas from Australia, Fiji, Thailand and the Seychelles using DNA Barcoding and another mtDNA marker (COII). They now recognized two putative species within Ctenocephalides felis (Ctenocephalides felis and Ctenocephalides orientis). As I have stated before I am not a strong believer in subspecies and I am somewhat puzzled that four subspecies have been maintained for a very long time despite very weak evidence. However, it does seem that the consequent inclusion of molecular data will help to sort out this rather old problem. Interestingly one of the main conclusions of this study is that it is intriguing to realize that we know essentially nothing about the population structure of Ctenocephalides feli elsewhere (but Australia) in spite of its global importance. 

Wednesday, February 19, 2014

Pepper as hot as chilli

Black pepper (Piper nigrum) is by monetary value, the most widely traded spice in the world, accounting for 20 percent of all spice imports. The global pepper production peaked in 2003 with over 355 000 tons , but has fallen to 271 000 tons in 2008 and still declines due to a series of issues including poor crop management, disease and weather. The global trade in black pepper powder alone is estimated to be 32 400 tons worth about 99.5 million U.S. dollars, which represents about 12% of the total global pepper export revenue.

The rather high cost coupled with the decreasing volume of this commodity is an invitation to adulteration. Especially spice powders are highly subjected to admixing or substitution with inferior substances. Compared to whole spices, spice powders and paste are more vulnerable to adulteration because foreign matters go into it largely undetected.

With increasing globalization, and liberalization of markets many countries are importing black pepper and re-exporting it as whole commodity or as value-added products. It has been discovered that in some cases left over pepper used for the extraction of piperine (alkaloid responsible for the pungency of pepper) was sold as black pepper powder, fortified with other pungent substances. Pepper was also reported to be adulterated with papaya seeds (Carica papaya) and wild Piper species (Piper attenuatumPiper galeatum). On the other hand researchers in India found out that ginger powder was also adulterated with chilli (because of the pungency). This led to the question if chilli (Capsicum sp.) is perhaps more widely used to substitute black pepper especially in powdered products.

I guess it comes to no surprise that indeed results of a study by Indian researchers showed chilli adulteration in two out of nine market samples. The markers psbA-trnH, rbcL, rpoC1 were used in their study - one of them, rbcL, is actually an official DNA barcode region, the others were once discussed and tested for their inclusion in the standard. All three markers were capable to detect the adulteration and what's even more striking is the fact that the colleagues were able to detect the presence of chilli in as low as 0.5% of the total amount of spice powder.

When it comes to the use of black pepper in the kitchen I prefer the freshly grounded and thereby more aromatic one. Seems it was a good decision not to buy any powder.

Friday, February 14, 2014

Darwin's beetle

Darwinilus sedarisi
A few days ago on February 12th we were celebrating Darwin's 215th birthday. The international Darwin Day is a celebration to commemorate the anniversary of the birth of the great mind. Usually the day is used to highlight Darwin's contribution to science and to promote science in general. One scientist used to occasion scientists to name a long lost new beetle genus after him to commemorate the legacy of the father of evolution. Here is the story:

In 1832 Charles Darwin disembarked from the HMS Beagle in Bahia Blanca, Argentina where he traveled by land to Buenos Aires. In Bahia Blanca, Darwin collected several fossils of large mammals along with many other living organisms, including several insects. Among those was a beetle specimen which was considered lost for many years until it was rediscovered recently in the Natural History Museum, London.

The beetle was discovered and described by Dr. Stylianos Chatzimanolis, an entomologist at the University of Tennessee at Chattanooga, USA as a new genus and species of rove beetles, the largest family of beetles with more than 58,000 described species. The scientific name for the new species is Darwinilus sedarisi. The genus name (Darwinilus) was given in honor of Charles Darwin, while the epithet (sedarisi) was given in honor of Mr David Sedaris, an American Grammy Award-nominated humorist, comedian, author, and radio contributor.

Only two specimens are known for this new species, both collected before 1935. Despite extensive work  in many major European and North American museums no other specimens have been found. Most of the habitat where the species is found has been transformed into agricultural fields so there is a danger that it might be forever lost due to extinction. But who knows, rove beetles are taxonomically not fully understood. About 400 new species are being described each year, and some estimates suggest 3/4 of tropical species are as yet undescribed.

May I humbly ask for a small piece of the leg? This species really deserves a DNA barcode which in turn might be helpful one day in finding a few more living members of the species.

Thursday, February 13, 2014

Fossilized goat droppings

The Balearic Islands represent an archipelago of Spain in the western Mediterranean Sea, near the eastern coast of the Iberian Peninsula. The four largest islands are Mallorca, Menorca, Ibiza and Formentera. All of them are among the most famous vacation destinations in Europe.

Humans colonized the Balearic Islands about 4000-5000 years ago. Their arrival had a profound impact on the fauna of the major islands Mallorca and Menorca. Diverse datings indicate that three native and endemic terrestrial mammals of Majorca disappeared shortly after the arrival of humans. The Majorcan giant dormouse (Hypnomys morphaeus) with a body length of up to 30 cm and the giant shrew (Nesiotites hidalgo) seem to represent cases of insular gigantism which is a phenomenon in which the size of animals isolated on an island increases dramatically in comparison to their mainland relatives. A compelling explanation for this phenomenon is that it represents an evolutionary trend that results from the removal of constraints on the size of small animals related to predation and/or competition. 

The third mammal species  that disappeared about 4000 years ago was the Balearic Islands mountain goat (Myotragus balearicus), also known as the Balearic Islands cave goat, a species of the subfamily Caprinae which lived on the islands of Mallorca and Menorca. Several hypotheses have been proposed to explain the extinction of Myotragus balearicus but apparently none of them was fully accepted simply because of a lack of data. A new study sheds some more light on the fate of the goat that was actually more related to sheep than to goats:

For the present study ancient DNA analysis (Sanger sequencing, Roche-454, Ion Torrent), and pollen and macrofossil analyses were performed on preserved coprolites from Myotragus balearicus, providing information on its diet and paleo-environment.

The results of the study (and yes they used plant DNA Barcoding markers on the fossilized poop) are quite intriguing and it seems that more than one factor was likely involved in the extinction of the species. Hypotheses relating the extinction of Myotragus balearicus directly to the arrival of humans on the islands might need a bit of adjustment.

The information retrieved shows that Myotragus balearicus was heavily dependent on the Balearic box species Buxus balearica during at least part of the year, and that it was most probably a browser. Hindcast ecological niche modelling of B. balearica shows that local distribution of this plant species was affected by climate changes. This suggests that the extinction of Myotragus balearicus can be related to the decline and regional extinction of a plant species that formed a major component of its diet. The vegetation change is thought to be caused by increased aridity occurring throughout the Mediterranean. 

Wednesday, February 12, 2014

Environmental hacking

No doubt, new technologies are changing the way we collect biodiversity data. Data that once required taking expensive, bulky and fragile equipment on field trips can now be collected on cheap, compact and robust devices. Low power and cheap computational platforms such as Arduino and Raspberry Pi are increasingly used in biodiversity science for data collection often as a consequence of dwindling resources available to individual researchers. 

We also increasingly rely on citizen scientists to collect data for our research, in particular the network of biological enthusiasts who provide much of our knowledge on the changing distribution of species. Many of these people are interested in using technology to maximize the value of the data they collect, but don't have the financial or technological resources to make full use of the opportunities technology provides. Low cost and easy-to-use micro-controller devices such as the Arduino have changed this in the past years and the result is a very lively Open Hardware movement very similar to Open Access or Open Source efforts. 

A nice example for such an open hardware project that can be used by biodiversity researchers, electronics hobbyists and electronics engineers alike has been published in the Biodiversity Data Journal:

This paper describes the construction of an open source environmental data logger based on the Arduino platform and its integration with the web content management system Drupal which is used as the basis for Scratchpads among other biodiversity tools.

The data logger is able to record the temperature and humidity at a regular time interval and submits data collected automatically and in real time to a Drupal website using a build-in Ethernet connection. I went through the parts list and some websites in order to come up with a rough cost estimate: $100-$130 for one unit which is indeed very easy to build based on the instructions provided in the paper. The price it at least half of some comparable standard data loggers in the lower price range. I am sure that one could get all necessary parts even cheaper with some more extensive research which makes this alternative even more attractive. As an educator I would also like to point out the pedagogical value of building such data loggers instead of just buying a finished product. Understanding the technology we are using to collect data is crucial and students might enjoy this way of learning about it much more than any dry physics lecture (unfortunately not every physics teacher is as good as MITs Walter Lewin). 

Tuesday, February 11, 2014

Butterflies and climate

Global change seriously threatens biodiversity at all ecological levels ranging from single species, through communities and species assemblages to whole ecosystems including the provision of ecosystem services for human well-being. Detailed information on species' ecological niche characteristics is indispensable for a better understanding of the relationship between the occurrence and performance of wild species and their environment and, moreover, for an improved assessment of the impacts of global change.

When it comes to butterflies in Europe there is a great body of knowledge on species characteristics such as habitat requirements already available in the ecological literature, but information about their climatic requirements is still lacking.  Scientists from the Helmholtz Centre for Environmental Research -- UFZ have closed this gap and present CLIMBER: Climatic niche characteristics of the butterflies in Europe -a dataset on the climatic niche characteristics of 397 European butterflies representing 91% of the European species.

The information provided in this dataset is of great relevance for basic and applied ecology and provides data ready to use for a broad range of applications such as assessments of past niche evolution or analyses of trait interdependencies to the very applied aspects of measuring, monitoring and projecting historical, ongoing and potential future responses to climate change using butterflies as an indicator. 

Good knowledge of the ecological characteristics relevant for the reaction of species and communities to particular drivers of global change is badly needed and can then be utilized for more informed conservation planning and action.

By providing public access to this dataset, we hope to contribute to improvements of the scientific understanding of how climate change affects species and communities and to improve monitoring and conservation actions for climate change mitigation.

World Conference Fish Barcoding

Mark your calendars!

Friday, February 7, 2014

An old new whale species

Mesoplodon hotaula, Seychelles, 2009
Beaked whales are a widespread but little-known family of toothed whales that are distantly related to sperm whales. They are are found in deep ocean waters beyond the edge of the continental shelf throughout the world's oceans and rarely seen at sea due to their elusive habits, long dive capacity and apparent low abundance for some species. A lot of what we know about the diversity of beaked whales is actually the result of strandings on the world's shores.

On 26 January 1963, a female beaked whale washed ashore at Ratmalana, Sri Lanka. The stranding was reported by the director of the National Museums of Ceylon, P. E. P. Deraniyagala, who described the whale as a new species, Mesoplodon hotaula, deriving the species name from the local Sinhala words for “pointed beak.” Deraniyagala provided no diagnosis by which Mesoplodon hotaula could be differentiated from the other Mesoplodon beaked whales known at that time, except to note that the position of the teeth differed from that of Mesoplodon bidens and Mesoplodon hectori. Two years after it was described, Mesoplodon hotaula, still known only from the holotype, was synonymized with the ginkgo-toothed beaked whale, Mesoplodon ginkgodens. 

Now it turns out that Deraniyagala was right regarding the uniqueness of the whale he described. While the specimen is closely related to the ginkgo-toothed beaked whale, it is actually a representative of a distinct species. An international group of researchers provided genetic and morphological evidence for the distinctiveness of Mesoplodon hotaula, now known from at least seven specimens. The new specimens are held by various institutions and groups, including the US Smithsonian National Museum in Washington DC, the Island Conservation Society in the Seychelles, and the University of Auckland, New Zealand. 

The researchers were able to get good quality DNA from tissue samples from only one specimen. For the remaining ones, they drilled into the bones of the whales in order to analyse short fragments of 'ancient DNA' relying on techniques commonly used with old sub-fossil material from extinct species. The colleagues were able to show that both lineages can be differentiated by maternally (DNA Barcodes), biparentally (autosomal nuclear introns), and paternally (Y-chromosome intron, DBY7) inherited DNA sequences, as well as by morphological features (Cranial and mandibular measurements). The analysis also included all other known beaked whale species to confirm the distinctiveness of Mesoplodon hotaula, including six specimens of the closely related, gingko-toothed beaked whale. The latter is only known from about 30 strandings and has never been seen alive at sea with any certainty.

Wow - it took us 50 years to collect enough evidence to resurrect a species. It is so little we know about life in the ocean despite all the hard work put in so far. That reminds me of a quote from the book "Half Mile down" by William Beebe (1934):

"... the only other place comparable to these marvelous nether regions, must surely be naked space itself, out far beyond atmosphere, between the stars, where sunlight has no grip upon the dust and rubbish of planetary air, where the blackness of space, the shining planets, comets, suns, and stars must really be closely akin to the world of life as it appears to the eyes of an awed human being, in the open ocean, one half mile down." 

Thursday, February 6, 2014

Why the mammoth disappeared

So far the common image of much of the northern hemisphere during the latest Ice Age has been of a landscape dominated by grass steppe. However, it seems that this conception doesn't hold any longer. The landscape was far more diverse and stable than today, and large well-known mammels animals like woolly rhino and mammoth fed on grasses and particularly on protein-rich forbs. Forbs are plants that have leaves and stems but no persistent woody stem above ground, and that are not grasses. At the Last Glacial Maximum 25,000 -- 15,000 years ago, at a time when the climate was at its coldest and driest, a major loss of plant diversity took place. As a result the animals barely survived. After the Ice Age ended about 10,000 years ago it became warmer again. After the large reduction of plant diversity during the Last Glacial Maximum another kind of vegetation now appeared. One of the key food sources of the large mammals- the protein-rich forbs -- did not fully recover to their former abundance. This likely proved fatal for species like woolly rhino, mammoth, and horse in Asia and North America. Even though it became warmer again after the end of the Ice Age the old landscapes did not return.

This scenario is based on findings of a new study just published in Nature. 30 teams from 12 countries worked on this study and they present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr before present.

The researchers were using mostly permafrost samples that contain large amounts of frozen DNA. They sequenced the short P6 loop sequence of the trnL plastid  region and a part of the ITS1 spacer region through metabarcoding, generating a total of over 14 million trnL plant DNA sequence reads and 1,6 million ITS reads. Those sequences were identified by comparison with an Arctic trnL taxonomic reference library, extended with ITS sequences for three families, a new north boreal trnL taxonomic reference library constructed by sequencing some 1300 modern plant samples representing 835 species; and with GenBank

Impressive work and the results are quite fascinating.

Wednesday, February 5, 2014

Microlepidoptera in Kenya

Scott Miller (senior author of the study)
About ten years ago researchers ended an insect-rearing program from native fruit collected at sites throughout Kenya. The initial focus of the 5-year survey lay on fruit flies (Tephritidae) and their parasitoids but as it turned out 19% of the catch were actually lepidoptera. Today I got my hand on the third in a series of papers focused on the lepidoptera of this large collection and it uses DNA Barcoding to sort through the microlepidoptera. The authors provide a data release paper that aims to make DNA Barcode data available to document ongoing research, to contribute to the efforts of building a global library of DNA Barcodes, and to encourage enhancement in identifications, following the Fort Lauderdale principles for genetic data. 

What are those principles?

In response to requests from the large-genome sequencing scientific community,  in January 2003 an international meeting was organised to discuss pre-publication data release. Held in Fort Lauderdale, Florida, the meeting primarily brought together representatives of the producers of large-genome sequence data, the users of such data, funding agencies and scientific journals. The meeting concluded that pre-publication release of sequence data  was beneficial to the scientific research community in general and the following suggestions were made:

  • The meeting attendees enthusiastically reaffirmed the 1996 Bermuda Principles, which expressly called for rapid release to the public international DNA sequence databases (GenBank, EMBL, and DDBJ) of sequence assemblies of 2kb or greater by large-scale sequencing efforts and recommended that that agreement be extended to apply to all sequence data, including both the raw traces submitted to the Trace Repositories at NCBI and Ensembl and whole genome shotgun assemblies.

  • The attendees recommended that the principle of rapid pre-publication release should apply to other types of data from other large-scale production centers specifically established as ‘community resource projects’

  • The attendees recognized that pre-publication data release might conflict with a fundamental scientific incentive – publishing the first analysis of one's own data. The attendees noted that it would not be possible to absolutely guarantee this incentive without applying restrictions that would undermine the rationale for rapid, unrestricted release of data from community resources. Nonetheless, it is essential that excellent scientists continue to be attracted to these projects. To encourage this, the scientific community should understand that pre-publication data release needs active community-wide support if it is to continue to receive widespread support from the producers. The contributions and interests of the large-scale data producers should be recognized and respected by the users of the data, and the ability of the production centres to analyse and publish their own data should be supported by their funding agencies.

Many of the records made public in the paper on microlepidoptera represent undescribed species, and the authors have purposefully refrained from assigning new names until the relevant taxa can be studied in sufficient detail. Under the Fort Lauderdale principles, they ask others to refrain from assigning new species names to these records outside of the context of proper systematic study. The authors have made their data publicly available knowing that it can take many years until all the specimens are properly named or described. I think this is a great example on how we should change our academic workflow. By making these data available, while identifications are in progress, DNA cluster-based species (or MOTUs, BINs or whatever you want to call them) can be used as species hypotheses as long as we need to wait for the confirmation of taxonomic experts or follow-up studies. 

Tuesday, February 4, 2014

Coffee for birds

My personal allotment
Like it or not - one of the main drivers of research is not funding. It is coffee! Coffee is what kept many of us awake at night as students while we were writing an assignment or on our thesis. Coffee is the most favorite beverage in labs all over the world and many have established almost religious rituals to celebrate their morning coffee. No conference, workshop or meeting without coffee breaks and many colleagues are not sociable before they had their first cup of the magic brown liquid.

I am also a coffee drinker and my work in biodiversity science makes me more alert to potential problems that are connected to what I consume. Due to changes in coffee production and marketing over the last few decades traditional ways of growing both coffee and cacao have changed considerably. Traditional coffee plantations can be thought of as modified forest habitats. Coffee bushes are cultivated under a forest overstory using indigenous agroforestry techniques, originally developed for growing cacao. This involves planting a mixture of nitrogen-fixing trees with other useful species to provide shade. Up to 40 species of trees can be found in some traditionally managed plantations, and many of these are managed for household or commercial commodities such as wood or fruit. 

However, in the past 40 years, coffee has begun to be grown with no shade canopy at all. While this manner of cultivation produces substantially increased yields, these cannot be sustained for many years without intensive management (which includes the use of chemical fertilizers and a range of insecticides, herbicides and fungicides). The crops are also subject to premature death in environments possessing a marked dry season, and they need to be renovated (plants replaced) much more frequently than the shade varieties. 

Aside from the agronomic risks, sun coffee production has resulted in major habitat change for migratory birds. As a result the diversity of migratory birds plummets when coffee was converted from shade to sun. As for the overall avifauna, studies in Colombia and Mexico found 94-97% fewer bird species in sun grown coffee than in shade grown coffee. This comes as no surprise since over two-thirds of the birds are found in the canopy of shade plantations and less than 10% are found foraging in coffee plants. In eastern Chiapas, Mexico, researchers from the Smithsonian Migratory Bird Center (SMBC) found that traditionally-managed coffee and cacao plantations support over 150 species of birds, exceeded only in undisturbed tropical forest.

Already back in 1996, the movement to support shade grown coffee was sparked by the SMBC, which gathered environmentalists, farmers and coffee companies to address the problem and promote awareness of shade coffee. Today, sales of organically grown, shade coffee represent about 1%, or $30 million, of the U.S. market for coffee beans. The SMBC has also developed the only 100%-organic shade-grown coffee certification

Last weekend we went to the Guelph Organic Conference and my wife discovered a Canadian coffee distributor specialized on certified shade-grown and fair traded coffee. Birds & Beans sells a variety of blends and they taste quite nicely. The latter is quite important because many coffee aficionados claim that most fair trade, organic grown coffee are not as superior in taste. Well, I strongly suggest to give those shade-grown alternatives a chance because they might taste even better. As a matter of fact coffee beans mature more slowly in the shade allowing the accumulation of more natural sugars which enhances the flavor of the coffee. 

I am sold to the Birds & Beans alternative and will enjoy my morning cup of coffee at the office knowing that the bit of extra money I spent is used for extension services and affordable credit for coffee farmers to survive and to grow coffee in a more bird-friendly and sustainable manner.

Monday, February 3, 2014

Animals in traditional medicine

The use of threatened animals as a source of traditional medicines is accelerating the extinction of such species and imposes great challenges to animal conservation. In this study, we propose a feasible strategy for the conservation of threatened medicinal animals that combines trade monitoring and the search for substitutes. First, DNA barcoding provides a powerful technique for monitoring the trade of animal species, which helps in restricting the excessive use and illegal trade of such species. Second, pharmacological tests have been adopted to evaluate the biological equivalence of threatened and domestic animals; based on such testing, potential substitutes are recommended. Based on a review of threatened animal species and their substitutes, we find that the search for substitutes deserves special attention; however, this work is far from complete. These results may be of great value for the conservation of threatened animals and maintaining the heritage of traditional medicine.

This is the abstract of a new publication in Scientific Reports that introduces a study done by  a group of Chinese researchers.

Animal products play an important role in traditional medicine within countries such as China, Japan, or Brazil. There is no doubt that quite a few animal species are becoming threatened or endangered due to their excessive use as complementary medicine. Next to no measures have been proposed for the sustainable development of traditional medicine. As a consequence many conservational efforts encountered great resistance as they supposedly disregarded the traditional use of wildlife in medicine. The authors claim that a feasible solution would be to substitute the organs of closely related domestic animals and their study not only establishes DNA Barcoding as primary identification tool in the trade but also examines the medicinal values of potential substitutes. They conducted pharmacological tests on animal-derived drugs obtained from both threatened and domestic animals, and compared resulting bioactivities both in vitro and in vivo. 

Those are great intentions and it would be commendable if this would become a line of applied research that is pursued more often. However, there are also some sobering facts: ...studies of the substitution of threatened animal species have just begun, and many critically endangered species, such as Père David's deer, saiga antelope and hawksbill turtle, cannot be substituted and have no alternative uses. ...The use of substitutes not only relates to the bioactivities of these drugs, it also involves traditional and cultural concerns. The functions of organs threatened animals are often exaggerated based on value orientations, religious beliefs, superstitions and totem culture, and the blind faith of some high-end consumers, with complete disregard for the exploitation of wild animal resources.