Monday, July 21, 2014

A cousin of the dodo

The closely related and extinct Dodo (Raphus cucullatus) and Rodrigues Solitaire (Pezophaps solitaria), both in the subfamily Raphinae, are members of a clade of morphologically very diverse pigeons. Genetic analyses have revealed that the Nicobar Pigeon (Caloenas nicobarica) is the closest living relative of these birds, thereby highlighting their ancestors’ remarkable migration and morphological evolution. The Spotted Green Pigeon (Caloenas maculata) was described in 1783 and showed some similarities to the Nicobar Pigeon. Soon however the taxon fell into obscurity, as it was regarded as simply an abnormal form of the Nicobar Pigeon. The relationship between both taxa has occasionally been questioned, leading some ornithologists to suggest that the two may in fact be different taxa. 

The spotted green pigeon is a historically elusive species. The only known example can be found at the World Museum in Liverpool, and another known specimen is lost. There are no records of the bird in the wild, no one knows where it was found and as described in the paragraph above researchers weren't even really sure if it was its own species - they thought it was just an unusual form of the Nicobar pigeon from around Indonesia.

Researchers from Australia and the UK now used ancient DNA methodologies to investigate the phylogeny and authenticity of the Spotted Green Pigeon. They took DNA from two feathers of the last specimen of the spotted green pigeon. Because of its age, the DNA was highly fragmented, so they focused in on what they called three DNA 'mini barcodes'.  Well, as it turns out those were not DNA Barcodes as they've used some small (~64 bp) 12S fragments. I've often talked about the importance of standards and although this study is really well done and delivers very interesting finds, the generated sequences fail to contribute to any DNA Barcode reference library. If anyone every wanted to compare the results to the some 5 100 species barcodes on BOLD (compared to about 2 200 species with a 12S sequence) they would not be able to do that. Again, a great story but it would be even better if the authors would have abstained from the use of the word 'barcode' as it is clearly misleading in this case.

But let's go back to their findings. They showed that the spotted green pigeon is indeed a separate species, showing a unique mtDNA sequence compared to other pigeons. The pigeon is genetically most closely related to the Nicobar pigeon and the dodo and Rodrigues solitaire. 

Early reports suggested that the spotted green pigeon has a semi-terrestrial island lifestyle and the ability to fly. The closely related Nicobar pigeon shows similar habits and has a preference for travelling between small islands. The researchers conclude that this lifestyle, together with the relationship of both pigeons to the dodo and Rodrigues solitaire supports an evolutionary theory that the ancestors of these birds were 'island hoppers', moving between islands around India and Southeast Asia. The birds that settled on particular islands then evolved into the individual species. The dodo's ancestor managed to hop as far as the island of Mauritius near Madagascar where it then lost the ability to fly.

This study puts an end to any discussions about the species status of the spotted green pigeon. Too bad that the species was never observed again and was consequently added to the list of extinct bird species in 2008. The reasons for its extinction remain unknown.

Friday, July 18, 2014

Drones in Biodiversity Research

Ecologists require spatially explicit data to relate structure to function. To date, most of such data came from remote-sensing instruments mounted on spacecraft (satellites) or manned aircraft. However, the spatial and temporal resolutions of those data are quite often not suitable for smaller local-scale investigations.

Relatively cheap and portable, unmanned aerial vehicles (UAVs) better known as drones fill a gap between satellite and manned aircraft imagery and on-the-ground observations. They are lightweight, low-cost aircraft platforms operated from the ground that can carry imaging or non-imaging payloads. Flying low and slow, drones can deliver fine spatial resolution data at temporal resolutions defined by the user. New models can operate completely independent using GPS data for autonomous flight. Other models can be remotely controlled even with live video transmission to a smartphone.

Not surprisingly a lot of field biologists (not limited to ecologists) are flocking to drones. UAVs are also becoming an essential tool for managing wildlife and fighting poachers:

This was reason enough for us to get one of the more affordable models (dji Phantom 2), equip it with a GoPro Hero and test it for a variety of uses. The potential uses are almost unlimited but we were first focusing on its use to provide quality footage for our educational video resources.

So far we had a few test flights and the footage hasn't been edited properly but it is impressive what one can do with these little toys. Here are two examples of raw video material just slightly edited. The first video shows the Biodiversity Institute of Ontario (BIO) from a different perspective.

Video number two is an early version of a short video about one of the researchers here at the university - Dr. Alex Smith and his work with the GigaPan system. Note the use of the GoPro time lapse function

Both videos end rather abruptly which is the result of the unfinished editing process and not a technical problem although we had a few minor crashes. Overall, the UAV we are using is easy to handle, very versatile. It works quit nicely with the equally versatile GoPro camera. The system is also capable of pre-programmed autonomous flight (using an iOS app) but I haven't tested that yet. The remote control of the system is not as intuitive as it could be and even for someone with experience in RC model operation it requires some relearning. The Phantom drone is small and lightweight but there also lies a problem as it is very sensitive to stronger wind and occasional gusts which is a bit challenging for the pilot. The drone batteries allow for a flight time of about 20 min, the range of the remote is 1 km. Together with a good GoPro camera you are looking at an expense of  about $1500.

We will test the UAV further and will soon move on to more scientific use. As the GoPro is capable of very high resolutions we will test how well the system works to map and document habitat in which we place our traps. I'll keep you posted.

Wednesday, July 16, 2014

Snake Fungal Disease

Credit: Julie McMahon
Snake Fungal Disease (SFD) is an emerging disease in certain populations of wild snakes in the eastern and midwestern United States. Laboratory analyses have demonstrated that the fungus Ophidiomyces ophiodiicola is consistently associated with SFD. Ophidiomyces consumes keratin, a key ingredient in snake scales. It can cause scabs, nodules, abnormal molting, ulcers and other disfiguring changes to snake skin. Mortality is 100 percent in Illinois massasauga rattlesnakes (Sistrurus catenatus) found with outward signs of infection. There are only 100 to 150 massasaugas left in Illinois, and about 15 percent of those are infected with the disease.

Researchers first took notice of Ophidiomyces in snakes in the mid-2000s. Today the fungus threatens the not only the last remaining eastern massasauga rattlesnake (Sistrurus catenatus) population in Illinois but has also been found to infect timber rattlesnakes (Crotalus horridus), mud snakes (Farancia abacura), rat snakes (various Pantherophis species), garter snakes (Thamnophis sirtalis), milk snakes (Lampropeltis triangulum), racers (Coluber constrictor), and many water snakes in several US states.

Some mycologists liken this emerging fungal disease in snakes to white-nose syndrome, another fungal disease that has killed millions of North American bats. Researchers from the University of Illinois recently published an analysis of Pseudogymnoascus destructans, the fungus implicated in white-nosed syndrome, and are now repeating their analysis on Ophidiomyces. It looks like the fungus killing snakes is very similar in its basic biology to the fungus that has killed over 6 million bats. It occurs in the soil, seems to grow on a wide variety of substances, and possesses many of the same enzymes that make the bat fungus so deadly.

A team of mycologists and herpetologists at the University of Illinois have now developed a faster and more accurate way to test for infection with Ophidiomyces ophiodiicola using quantitative polymerase chain reaction (qPCR), not only to amplify fungal DNA to identify the species present but also to measure the extent of infection. As qPCR is more than 1,000 times more sensitive than conventional methods  testing does not have to rely on tissue or blood samples anymore. A simple skin swab will do and with a properly refined protocol researchers can tell which fungal species and how many fungal spores are in a swab. Infections can be detected much earlier, intervention can start earlier and overall success of treatment or therapy could increase.

Unfortunately, preliminary studies show that the common disinfectants used are not effective and everyone handling infected snakes needs to rethink procedures to avoid the inadvertent spread of the disease.

This new qPCR test represents a big step forward in the efforts  to characterize both biological and health factors that lead to infection. It also will help the team develop new therapies to treat infections in snakes.

Here a nice video describing the entire project:

Tuesday, July 15, 2014

Welsh liquid gold

One question I hear rather frequently from people interested in our work is: Once you finished cataloging all life what are you going to do with all that information? For someone who works with DNA Barcoding for almost 10 years it is rather easy to respond with a number of examples especially those we had in mind all along when we build our reference libraries. However, it is much better to refer to examples where DNA Barcoding libraries have already been put to good use:

Wales is the first nation in the world to have barcoded all of its native flowering plants and conifers, enabling the identification of any plant species in Wales from the tiniest fragment of leaf, seed or pollen grain. In total 98% of the Welsh native flora (1143 species) has DNA barcodes for rbcL and 90% for rbcL and matK. The creation of this reference library was already reported in PLoS ONE about two years ago

In a joint project between the National Botanic Garden of Wales and the School of Pharmacy and Pharmaceutical Sciences at Cardiff University  researchers started to work with honey. They collected honey from across the UK to see if it contains antibiotic elements. If any is found, DNA Barcoding was used to determine what plants bees visited to make it. The antibiotic elements of honey are known for many years, and honey was used in wound dressings as long ago as the Middle Ages:

The antibacterial effects of Honey have been observed for over a century and it has been widely used as a therapeutic addition to wound dressings. The activity of honey is due to a range of factors which include the hyper-osmotic properties of the sugar, the production of hydrogen peroxide by natural enzymatic reactions, metabolic byproducts such as Methylglyoxal (MGO), bee derived peptides and phyto-chemicals donated by the plants. The contribution of these phyto-chemicals to the overall antimicrobial activity of a particular honey will depend on the properties of the plants visited by the bees. For example Manuka honey from New Zealand is produced by allowing bees to forage on the Manuka bush (Leptospermum scoparium) a plant which produces a compound called Leptospermone which has potent antibacterial activity.

The search will also be part of the science and technology exhibitions at this year's National Eisteddfod in Llanelli. The Eisteddfod is one of the world’s largest cultural festivals, held during the first week of August every year attracting about 150 000 visitors. Welsh Beekeepers are know being asked to send in samples of their honey to see if it contains antibiotic elements. They traditionally present their honey products on the festival and now they can either take a 200 g honey sample to the Eisteddfod or send it beforehand. The hope is to find antibacterial phyto-chemicals, to identify the plant source, and to subsequently create a special honey by allowing the bees to forage on plants that provide high antibacterial properties. 

Monday, July 14, 2014

Biodiversity of the Congo Basin

The forest ecosystems of the Congo Basin constitute the second largest area of contiguous tropical forest in the world and represent approximately twenty percent of the world’s remaining closed canopy tropical forest. They are home to conservation worthy animal species such as bonobos, mountain gorillas and okapis. These forests do not only play a significant role for global biodiversity conservation, they also provide essential regional and global ecological services as carbon sink and as a freshwater catchment basin. Millions of people depend on these natural resources for their survival in a unique ecosystem that is endangered by deforestation, poaching, over-fishing and mining activities.

This conference brought together African and international scientific communities and other stakeholders to exchange information, compare and jointly analyze data to facilitate efforts to conserve the biodiversity and the natural resources of the Congo basin. 

The main outcome of this conference will be a strengthened network of interested parties, also from the Amazon Basin, that provides improved access to up-to-date information on their biological and ecological resources to the governments of the DR Congo and other countries of the Congo Basin. This enhanced flow of information can be helpful to these countries to develop the national strategies on their renewable natural resources and to facilitate well-founded decision making in this regard.

Over 220 participants from 23 countries attended the conference in early June. Their contributions were made available via the conference website which also contains a joint statement of all participants. It contains recommendations for a future research agenda for the biodiversity in the Congo basin and the conditions required to support their implementation.

Thursday, July 10, 2014

You might have been eating undiscovered species

Pack of dried porcini containing three species
new to science (Photo: B. Dentinger)
As much as Earth's unexplored wilderness shrinks every day, we are actually discovering more species than ever before. By doing more systematic and thorough surveys, by heading deeper into unknown territory and by using advanced tools like DNA barcoding, we are uncovering new species at a record rate. Last year scientists found some 18 000 new species and that does not include new species of microbial life.

A group rife with such new discoveries is the kingdom of Fungi which might be one of most diverse groups of eukaryotes with estimates ranging from 500,000 to nearly 10 million species, yet they remain vastly underdocumented. 

Over the last 40 years the way that we have defined fungi has changed several times. In the early 20th. Century, until around the 1950's, botanists used the term fungi to include all members of the "plant kingdom" that did not have stems, roots, leaves and chlorophyll. In 1952, Constantine Alexopoulos defined fungi, as being "nucleated, achlorophyllous organisms which typically reproduce sexually and asexually, and whose usually filamentous branched somatic structures are surrounded by cell walls". In 1962, when the second edition of Alexopoulos' Introductory Mycology was published he specified that the cell walls of fungi contained cellulose or chitin or both. The definition hasn't changed much despite the inclusion of modern technology.. Currently, most mycologists define fungi as those organisms that are nucleated, achlorophyllous, typically reproduce sexually and asexually by spores, and whose somatic structure is composed of filamentous branched or yeast, which are surrounded by cells walls composed of chitin.

The present rate of description with an average of about 1200 new fungi species annually, is certainly inadequate for the task of describing all species and new discoveries are often the result of unexpected encounters. In a new study by researchers from England's Kew Royal Botanic Gardens, colleagues found three previously unknown species of mushroom in a commercial packet of dried Chinese porcini purchased from a shop in London.

Porcini mushrooms (Boletus section Boletus) are one of the most traded wild edible mushrooms, but although relatively well known, recent research at Kew had already shown that they are more diverse than previously thought. China is a major exporter of porcini, mainly to Europe, but reliable identification of wild collected porcini can be difficult, especially from less well-known regions.

Although it had been shown previously that unknown species were entering the porcini trade, even the Kew mycologists were surprised when they used DNA barcoding to identify 15 mushroom pieces from the commercial packet and found that all belonged to three distinct species, none of which were known to science:

Surprisingly, all three have never been formally described by science and required new scientific names. This demonstrates the ubiquity of unknown fungal diversity even in widely traded commercial food products from one of the most charismatic and least overlooked groups of mushrooms. Our rapid analysis and description makes it possible to reliably identify these species in the food chain, leading to an improved ability to regulate their harvest and trade, and to monitor potential adverse health effects from their consumption.

Tuesday, July 8, 2014

School of Ants

Scientists from North Carolina State University and the University of Florida have combined cookies, citizen science and robust research methods to track the diversity of ant species across the United States, and are now collaborating with international partners to get a global perspective on how ants are moving and surviving in the modern world.

The so called School of Ants (SoA) project was developed at North Carolina State University to help researchers get a handle on the diversity of ant species across the United States, with a particular focus on Chicago, Raleigh and New York City. In short, to discover which ant species are living where. However, it also serves as a good model for how citizen science can be used to collect more data, more quickly, from more places than a research team could do otherwise. The researchers were working with teachers to incorporate the project into K-12 instruction modules that incorporate key elements of common core education standards. They also collaborated with a science writer to produce a free series of iBooks featuring natural history stories about the most common ants that were collected.

The project approach is very similar to our School Malaise Trap Program. The colleagues developed a simple protocol involving Pecan cookies and sealable plastic bags, detailing precisely how the students should collect and label ant samples before shipping them to the researchers. This process was designed to engage the public in the aspect of the research that was easiest for non-scientists to enjoy and participate in, while also limiting the chances that the public could make mistakes that would skew the findings.

Once the samples arrive at either university, they are sorted, identified by experts and entered into a database. That information is then made publicly available in a user-friendly format on the project's site, allowing study participants to track the survey. More than 1,000 participants, with samples from all 50 states, have taken part in the project since its 2011 launch - and there have already been some surprising findings.

For example, the researchers learned that the venomous invasive species, the Asian needle ant (Pachycondyla chinensis), had spread thousands of miles farther than anyone expected. It was known that the species had established itself in the Southeast, but study participants sent in Asian needle ant samples from as far afield as Wisconsin and Washington state.

Still not convinced? Here some more findings as reported in their paper:
To address concerns about the validity of citizen scientist-derived data, we conducted a ground truthing trial that confirmed that trained and untrained volunteers were equally effective at collecting ants. Data from SoA samples indicate that ant diversity varies across wide geographic scales and that there can be high levels of native ant diversity where people live. SoA volunteers collected 7 exotic and 107 native ant species. Although exotic ants were common, ants native to North America occurred in ~70% of all sites. Many of the ants common in backyards were species that tend to be very poorly studied.

This is another great example on how we as researchers can engage the public in our work. I often heard colleagues complaining that nobody except their peers really understands and appreciates what they are working on. The School of Ants program is a good example for a way out of this dilemma as it represents a citizen science project that both increased the public's scientific literacy and addressed criticisms that public involvement made citizen science data unreliable. The only thing we need to change our mindset: Citizen science is not a burden, it is an enrichment.