10 000 !

Thanks so much to all the readers! Today this blog surpassed the 10 000 unique visitors mark :-)

Plant-herbivore networks

Workflow to establish diet identification with barcodes

I was surprised about this number but its true: plants and their associated insect herbivores, represent more than 50% of all known species on earth. This immense biodiversity is in parts the result of coevolutionary processes that have taken place between these two ecological partners

In order to better understand these ecological and evolutionary interactions and how they create and maintain biological diversity we need to determine the associations and networks between insect herbivores and their host plants. In the past there have been a few strategies to identify insect herbivore diets. The most accessible one seems to be direct observations of herbivores in the field but they are problematic in habitats that are difficult to access. Furthermore they are also greatly limited by the ability of the researcher to correctly identify the species involved. Scientists have also use feeding trials in the lab which unfortunately led to overestimates of breadth of diets as insects were often feeding on host plants not normally consumed in the wild. That leaves us with morphological analysis and stable isotope techniques applied to gut content. However, the taxonomic and ecological resolution was often very limited.

The resulting plant-herbivore network

Researchers from the Smithsonian Institution in Washington DC, have now tested a DNA Barcoding based alternative to determine insect-host plant associations for an entire guild of insect herbivores using plant DNA extracted from insect gut contents. Their study is a very convincing contribution to the increasing number of ecological applications of DNA Barcoding. It represents a very nice case study generated for a particular study system (rolled-leaf beetles). I can only agree with the author's conclusions:

Our study demonstrates that host plant identifications at the species-level using DNA barcodes are feasible, cost-effective, and reliable, and that reconstructing plant-herbivore networks with these methods will become the standard for a detailed understanding of these interactions.

Of flies, carcasses and DNA

Blow and flesh flies (families Calliphoridae and Sarcophagidae) feed on carrion, open wounds of living animals and/or faecal matter and generally oviposit on the first two substrates. Weird as it might sound this makes them perhaps ideal candidates for an alternative way of sampling DNA from wild mammals.

A group of researchers from Germany demonstrated that mammal monitoring through carrion flies is possible and may even overcome some of the impediments associated with the use of blood eating insects and leeches. Ttsetse flies and leeches live in restricted habitats and many mosquito and tsetse fly species are host specific. Both problems don not occur with blow and flesh flies. As we all know they are usually not picky when it comes to habitat or host choice.

Cephalophus jentinki

The team captured several flies that emerged from carcasses found in two forests —the Tai National Park in Côte d’Ivoire and the Kirindy Forest in Madagascar—and extracted the DNA in their guts to get a snapshot of the mammals in each area. The random collection of 75 and 40 flies at the two parks allowed them to recover of DNA from 16 and 4 mammal species, respectively. For Kirindy, this corresponds to 13% of the known local mammalian community (31 species). The mammal biodiversity of the Tai National Park is not yet fully characterized but striking outcomes were the sampling of six of the nine species of the local primate community and the detection of Jentink's duiker (Cephalophus jentinki), a very rare and endangered antelope species whose entire population is estimated to be <3500 individuals world wide.

Carrion fly DNA analysis might offer a broad range of potential applications linked with the assessment and monitoring of mammalian biodiversity. Ed Yong calls it census-taking via corpse-eating.

The only critical comment I have is my usual "standards lament". The colleagues used 16S and 12S and I couldn't find any explanation in the paper why they didn't use COI which would have allowed them to tap into a much larger library and allowed us to compare their data to other barcoding studies.

h/t Bob Hanner

Footprints

Without a doubt DNA Barcoding has modernized biodiversity science and opened doors to countless applications. However, it is just another tool in the toolbox of science and other tools are constantly developed.

Credit Wildtrack

One example for such a new tool is a technique that analyzes images of animal footprints to provide reliable species identification. Two researchers from the Duke University just presented a new method that uses a standardized series of digital images along several different trails to extract variables that provide best classification. The so called footprint identification technique (FIT) can identify species based on an algorithm refined through several training sets drawn from captive animals tracked on different substrates. When tested with free-ranging populations of different tiger species, rhinos, polar bear, cougar and cheetah the method provided not only species but also sex and age class with accuracy greater than 90%.

At this point the method requires the positioning of landmark points on the footprints which is the only drawback as this needs some experience and expertise. This is a quite common problem in biometric analysis and morphometrics. However, the authors discuss options for an automated feature extraction that would complement their development and produce a user-friendly tool to monitor species in the wild using footprints.

Barcoding frees a bird

Bubo bubo (Credit Caroline Seidel)

About a year ago a Eurasian Eagle Owl (Bubo bubo) was brought to an animal shelter and breeding station specialised on birds of prey in the Sauerland in Germany. The animal was caught in the city of Duisburg as it seemed unusual tame and sought closeness to humans making it likely that it was brought up by humans as well. The Eurasian Eagle Owl is very rare in Germany as a result of habitat fragmentation and therefore strictly protected. Animals in the shelter are usually either prepared to be released into the wild or at least become part of a breeding program.

The owl in this case showed a very atypical feather coloration and Winfried Limpinsel the station lead suspected that the owl might belong to a sister species from Asia, Bubo bengalensis. In this case the owl wouldn’t have had a chance of being released into the wild as nobody wanted to contribute to the establishment of yet another alien species.

In order to determine the correct species identity of the owl small tissue samples of the quill were send to the Zoological State Collection in Munich. By using DNA Barcoding researchers there identified the owl as Bubo bubo.

This sounds very much like a Happy End for the bird because based on the results authorities and specialists are now looking into moving the animal into a release program. I would find it very nice to see one more of these majestic birds flying over my home country.

New Barcode Bulletin Reader's Digest

Looking for some new papers to discuss in the next group or departmental seminar?
Or are you just wondering what came out last month?
Have a look (just click on the image):

Frogs in peril

Pristimantis museosus (credit Brad Wilson)
one of three out of ten species showing cryptic diversity

There is no doubt that amphibians currently are among the most endangered groups of animals on our planet. 41% of the species throughout the world are threatened. The most insidious and as yet unstoppable agent of amphibian decline is a pathogenic chytrid fungus, Batrachochytrium dendrobatidis.

It infects epidermal cells of its host and often causes death by inhibition of the electrolyte transport. In Central America, this fungus advances in an easterly-moving wave, with the most severe consequences at higher elevation. For example the highland frog faunas of western and central Panama have declined dramatically whereas eastern Panama faunas still seem to be abundant and diverse.

For critically endangered species, captive breeding seems to be a reasonable intervention and represents a short-term attempt to prevent extinction. As a consequence an international consortium of zoos and conservation organizations started an effort to begin captive breeding of many species of frogs from Central Panama. Despite the fact that the number and the rate of new species descriptions per year has been increasing in the past years, the current taxonomic knowledge of amphibians does not represent the true diversity of independent evolutionary lineages. As a result, species’ endangerment may be underestimated and management efforts may unknowingly overlook cryptic species. Frogs that were collected from various locations in an effort to capture a representative sample of genetic diversity of a species may harbor cryptic lineages. 

In a recent study a group of researchers from Columbia, Panama and the US used DNA Barcoding to survey variation in captive populations of 10 species of Neotropical amphibians maintained in a captive breeding program.They found that three of ten species showed substantial cryptic genetic diversity within the breeding program. But as this wasn't enough an additional three species showed cryptic diversity among wild populations, but not in captivity. As careful scientists they did not call these lineages species yet but this study shows that such conservation efforts are vulnerable to incomplete taxonomy. They recommend DNA Barcoding as simple tool to identify cryptic diversity and thereby improving conservation efforts.

More work for Cold Code, the global initiative to barcode amphibians and nonavian reptiles.