Thursday, July 31, 2014

Little janitor of the springs

North Florida has the world's highest concentration of large freshwater springs. For decades, crystal-clear water bubbling from the ground has driven tourism in the form of scuba divers, canoeists, boaters and swimmers, but today, many of those springs don't bubble like they used to; green scum in form of algae often obliterates the view.

Although the blame for algae-choked springs is often pinned on excess nitrate, new research indicates that the absence of algae-eating native freshwater snails of the genus Elimia may be a key factor, actually so important that Elimia species could serve as algae control agent and thereby restoring the springs' health. The first author of the new study affectionately calls them "little janitor of the springs".

Elimia species are major players in freshwater systems throughout central and southeastern North America. In quite a few streams in the southeastern United States they can represent more than 90% of the total macroinvertebrate biomass. The region is also the geographic centre of diversity of the genus. In this region 76 species of the 83 described occur, 15 have DNA Barcodes as the result of a ten-year old taxonomic study.

But how did the snails disappear from Florida's freshwater springs in the first place? The present study and others cited therein suggest pesticides and herbicides could be partly to blame for the snails’ decline but the researchers also found a connection between snail population size and the level of dissolved oxygen. The amount of dissolved oxygen could be influenced by (i) droughts or anthropogenic use of younger (shallower) aquifer water leading to relative dominance of older deeper flowpaths and (ii) groundwater organic matter enrichment leading to higher microbial respiration and oxygen depletion.

Given that dissolved oxygen appears to influence the grazers abundance it seems wise to ensure adequate flows by changing human water consumption patterns, and to reduce the amount of organic pollutants (e.g. from septic tanks, wastewater sprayfields). The authors also suggest to reintroduce native gastropods wherever they biomass falls below a certain threshold. The conclude that breeding and restocking native grazers, especially Elimia sp., to their historic ranges and densities may be an effective restorative intervention. 

Wednesday, July 30, 2014

The deep ocean

"... 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." 
William Beebe, 1934.

As fishing and the harvesting of metals, gas and oil have expanded deeper and deeper into the ocean, colleagues are trying to draw attention to the services provided by the deep sea, the world's largest environment. 

In a review of over 200 papers, an international team of researchers points out how vital the deep sea is to support our current way of life. It nurtures fish stocks, serves as a dumping ground for our waste, and is a massive reserve of oil, gas, precious metals and the rare minerals we use in modern electronics, such as cell phones and hybrid-car batteries. Further, hydrothermal vents and other deep-sea environments host life forms, from bacteria to sponges, that are a source of new antibiotics and anti-cancer chemicals. It also has a cultural value, with its strange species and untouched habitats inspiring books and films from "20,000 Leagues Under the Sea" to "Finding Nemo."

Ocean areas deeper than 200 m represent 98.5% of the volume of our planet that is hospitable to animals. They have received less attention than other environments because they are vast, dark and remote, and much of them are inaccessible to humans. But the deep ocean has important global functions. In their paper the researchers e.g. show that deep-sea marine life plays a crucial role in absorbing carbon dioxide from the atmosphere, as well as methane that occasionally leaks from under the seafloor. In doing so, the deep ocean has actually limited much of the effects of climate change.

These type of processes occur over a vast area and at a very slow rate. Manganese nodules, deep-sea sources of nickel, copper, cobalt and rare earth minerals, take centuries or longer to form and are not renewable. Similarly, slow-growing and long-lived species of fish and coral in the deep sea are more susceptible to over-fishing. 

According to the authors it is about time to discuss deep-sea stewardship before exploitation is too much farther underway. The deep sea is already facing impacts from climate change and, as resources are depleted elsewhere, is being increasingly exploited by humans for food, energy and metals like gold and silver. By highlighting the importance of the deep sea and identifying the traits that differentiate this environment from others, the researchers hope to provide the tools for effective and sustainable management of this habitat.

Tuesday, July 29, 2014

Some discoveries of the week

Every week I come across quite a few new descriptions of organisms. Unfortunately, not all of them do get a DNA Barcode right away as they should. There are a multitude of reasons for that one certainly being the lack of funds for the lab work and perhaps also the nonavailability of facilities. It would be great if we could find a group of philanthropists that would be willing to finance just this one element in our efforts to build the all-encompassing reference library. Type specimens associated with the original description are perfect resources for reference barcodes but we still do not make much use of them. 

By the way I think we should be more open to the idea of naming species after donors. For example the purchase of star names has become a fairly lucrative business. I always wondered why taxonomists are rather hesitant when it comes to this idea. Nothing needs to change when it comes to the established thorough process of describing a new species. Only naming will be different and potential 'customers' need to be aware of the fact that there is the small risk that a revision might change names although even synonymized names will be around for a very long time. The proceeds could help to finance the next field trip or a set of DNA Barcodes for all the newly described species. I am sure there are many people out there who would consider to name a species after one of their loved ones and that brings in money to fill the empty coffers of biodiversity science. 

I thought it might be a good idea to list some new discoveries each week and indicate if they have a DNA Barcode yet or not. I will limit myself to 5-6 newcomers. There are far more new descriptions than that but it would be too much to show in this blog. The modus operandi for my choice is a mixture of random choice (whatever lands in my inbox, RSS feed etc.) and educated guess (what I think readers consider interesting). 

Credit: Entomological Society of America
A new species of Labiobaetis Novikova & Kluge, 1987, Labiobaetis soldani sp. nov., is described from the larvae and reared male and female imagoes from Gadana River in the southern Western Ghats in India. Brief ecological notes are appended. The taxonomic status of Labiobaetis is commented on in light of the morphological traits of the larvae and associated imagoes.

The species named in honor of Dr. T. Soldan for his contributions to the understanding of the Ephemeroptera (Mayflies) of the Palaearctic and Oriental regions.
no DNA Barcode 

Credit: Entomological Society of America
The poorly-known genus Conosimus Mulsant et Rey, 1855 (Hemiptera: Fulgoroidea: Issidae) includes six species and is briefly reviewed. Adults and fifth instars of a new species, Conosimus baenai n. sp., are described and compared with other species in the genus. The new species is associated with an endemic shrub, Echinospartum boissieri, in Jaen, Spain, in the south of the Iberian Peninsula, one of the richest botanical areas of the Mediterranean Basin.

The new species has been named after Manuel Baena, a Spanish hemipterologist, for his contributions to the taxonomy of Iberian Hemiptera. The species was found in a medium-high mountain area that is dominated by thorny shrubs (Echinospartum boissieri), of which it seems to be associated. This rare shrub, which is endemic to the Baetic Range in southern Spain, blooms and produces fruit from July to August.
no DNA Barcode

 Credit: João F. R. Tonini
Among Neotropical microhylids, the genus Chiasmocleis is exceptionally diverse. Most species of Chiasmocleis were described in recent years based on external morphology, but recent studies using molecular data did not support the monophyly of the species groups clustered based on feet webbing. Furthermore, a phylogeographic study of C. lacrimae estimated high genetic divergence and low gene flow among populations across small geographic ranges. Increasing the molecular and geographic sampling, and incorporating morphological data, we identified new cryptic species. Herein, we used novel genetic and morphological data to describe a new species of Chiasmocleis.

The newly discovered frog species occurs in the Atlantic Forest of the Espírito Santo State in southeastern Brazil. Despite its modest size, adults reach only about 14 mm, the new species bears a heroic name inspired by the quilombos communities typical of this region. The specific epithet "quilombola" used for the species' name refers to the people who inhabited these communities -- slaves who dared to escape during colonial times and find a refuge in the depths of the Atlantic Forest. Quilombos were used as a refuge for escaped slaves during colonial Portuguese rule in Brazil between 1530 and 1815. Even today in the north of Espírito Santo State quilombola communities still remain and maintain alive their traditions, such as quilombola food and craftwork.
no DNA Barcode (despite extensive molecular work using four genetic markers)

Credit: Daniel Adrian Ciobanu
In a lichen sample collected from a tree in Bârlad town (Vaslui County, Romania), a new tardigrade species belonging to the genus Milnesium (granulatum group) was found. Milnesium berladnicorum sp. n. is most similar (in the type of dorsal sculpture) to Milnesium beasleyi Kaczmarek et al., 2012 but differs from it mainly by having a different claw configuration and some morphometric characters. Additionally, the new species differs from other congeners of the granulatum group by the different type of dorsal sculpture, claw configuration and some morphometric characters.

This new species is named after the Berladnici, an ancient population with a controversial origin (most probably Slavs) who previously lived in the area of the present Bârlad town.
no DNA Barcode

One new species of the genus Ctenophora Meigen, 1803, C. fumosa Men, sp. nov. (southern China: Anhui) is described and illustrated. A key to known species along with a checklist of known species of the genus Ctenophora are provided. The specific epithet is a noun derived from the Latin ‘fumos’ with the feminine termination ‘-a’, referring to the presence of smoky mark on the wing.

This genus is interesting because the name Ctenophora is also used for the phylum of comb jellies. This is not a unique problem but perhaps a more prominent example for what taxonomy calls a homonym. Actually the phylum name is called a 'pseudohomonym' of the crane fly genus which means that both have the same name, but the case has not been ruled by the International Commission on Zoological Nomenclature.
no DNA Barcode

A new species of Solanum is described from Peru. Solanum junctum S. Stern & M. Nee, sp nov. is a member of the Torva clade of the spiny solanums (Leptostemonum clade). Solanum junctum is taken from the Latin “junctus“ for “connect or join, ” referring to the morphological similarities of this species with other sections within the spiny solanums. This has been used as an herbarium name on specimen annotations by M. Nee since at least 1995.

no DNA Barcode (apparently other markers have been sequenced but not published yet)

Thursday, July 24, 2014

DNA Barcoding the oriental latrine fly

 Male and female adult of Chrysomya megacephala
The oriental latrine fly (Chrysomya megacephala), is a blowfly that prefers warmer climates. This fly can be a nuisance to humans and even cause accidental myiasis. Myiasis is a parasitic infestation by maggots growing inside a host while feeding on its tissue. 

The species originates from tropical forests on the South Pacific islands, like Samoa but has spread across vast regions of the world. It is particularly prevalent in the Oriental region and the Australasian region but has been found in Japan and the Palearctic regions as well. Today you can find it also in Africa and the Americas often conquering new territory by means of harbors and airports. Presently, three forms of Chrysomya megacephala are known, namely, the normal form, the synanthropic derived form. and a recently reported feral derived form. The synanthropic derived form is thought to have emerged from Papua New Guinea. Synanthropic means it is ecologically associated with humans and it is this form that spreads so successfully around the globe. It occurs on dead fish, sweets, carcasses, human excrement and fruits. The adult flies are vectors of a few infectious diseases of the digestive tract and reported to carry Morganella sp. (Enterobacteriales: Enterobacteriaceae), which causes summer diarrhoea. It is also associated with many microbial pathogens including polio virus. Besides, this fly has been reported as vector of enteric pathogens in malnourished individuals living under unsanitary conditions. The larvae of C. megacephala are parasitic on semi-dried fish, causing a major problem in the fish industry of Southeast Asia.

Chrysomya megacephala is commonly found in cadavers in many parts of the world, and therefore it is used in forensic investigations to determine post-mortem intervals. Post mortem interval determination is useful in cases of homicide, suicide and accidental or unattended death because of natural causes. The oriental latrine fly is considered one of the most important species of flies to forensic science because it is known to be one of the very first species to show up on a corpse. 

Morphological identification of flies is generally difficult and Chrysomya megacephala is no exception. The common way to identify flies is to examine the adult stage under a compound microscope looking for particular usually minute features. This also requires that any larvae collected needs to be reared until development is complete. Identification of larval flies is extremely difficult especially since critical characteristics are very small and any variation ever so slightly, can lead to misidentification. 

A group of researchers from the University of Madras in India now reports on their efforts to use DNA Barcoding to identify Chrysomya megacephala. They used freshly emerged adults from pupae to obtain identifications by both morphological and molecular studies. This is also the first report of the species in South-East India, so far it was only known from the north and south-west of the country. This comes to no surprise given how successful this species follows humans but in this case the fact that it is widely used as fish bait in India might have contributed substantially to the further spread. The DNA Barcodes can be found both on GenBank and BOLD. A quick look at the BIN page of this species on BOLD also reveals the difficulties of morphological identification as this BIN contains eight different species names, seven of which likely represent misidentifications or taxonomic issues. I leave it to the experts to resolve this but given that there are several DNA Barcode sequences (actually 191 on BOLD alone) available as reference it should be a big step forward for forensics as identification can be provided at every life stage. This means no more wait for the lengthy rearing process which in the case of Chrysomya megacephala can take 40 days. This is certainly good news for applications such as post mortem interval determination or disease vector control. 

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.

Monday, July 7, 2014

DNA Barcoding and the Neutral Theory

COI barcode variation within avian species is uniformly low regardless of census population size. This finding directly contradicts a central prediction of neutral theory and is not readily accounted for by commonly proposed ad hoc modifications. As an alternative model consistent with empirical data including the molecular clock, we propose extreme purifying selection, including at synonymous sites, limits variation within species and continuous adaptive evolution drives the molecular clock.

The neutral theory of molecular evolution that was proposed by Motoo Kimura suggests that most of the genetic variation in populations is the result of mutation and genetic drift and not selection. As a result sequence differences within and among closely related animal species are synonymous, i.e., do not change the amino acid sequence. 

The result of Kimura's theory which was independently formulated by King and Jukes a year later sparked a decade-long debate on to what extent Darwinian selection or neutral processes are driving the molecular evolution of genes and thus the ecological divergence of species. Selectionists argued that a large fraction of those non-synonymous DNA base substitutions in coding genes going to fixation should be driven by positive Darwinian selection. The biological function of these genes should therefore be involved in ecological niche segregation. Under a strict Neutralists view, most fixed amino acid substitutions have no effect on fitness, because purifying selection constantly removes alleles with strongly deleterious effects on fitness and mutations while positive effects were thought to be extremely rare. While the neutral theory was the prevailing model for several decades, e.g. the comparison of whole genome sequences has now produced evidence for a more important  role of natural selection (e.g. here and here). 

What you can find in almost all textbooks today is the statement that under the assumptions of the Neutral theory intraspecific variation equals 2 Nµ, where N is population size and µ is mutation rate per generation. And that is the prediction the authors Mark Stoeckle (famous author of the other DNA Barcoding blog) and David Thaler pretty much busted as they encountered uniformly low intraspecific variation regardless of census population size when they used COI barcode records from two avian families representing the two major divisions of birds, non-passerine and passerine. Why birds - you may ask. Well, the colleagues have good reasons: Birds are uniquely suited this task: they are well represented in barcode libraries, have the best-known species limits of any large animal group, and, most critically, are the only large group with known census population sizes, a key parameter in neutral theory.

I provided their conclusions already at the beginning of this blog post but I wonder if they would think of looking at their results from the perspective of Tomoko Ohta's Nearly Neutral Theory. The most significant difference between the neutral and the nearly neutral theories is that the latter predicts a negative correlation between evolutionary rate and species population size. The nearly neutral theory states that the interplay of drift and weak selection is important and predicts that evolution is more rapid in small populations than in large populations - what ever a small population in this context means. It might not fully explain the uniformity of the low intraspecific mtDNA variation in the paper but it could partially explain the absence of an increase in intraspecific variation with increasing census population size.

I like this kind of paper as it looks closer at the limits to DNA Barcoding and the evolutionary mechanisms that make it work. It would be great if this paper can spark a new discussion about these questions and motivate further research on the 'Secrets of DNA Barcoding'.

Friday, July 4, 2014

Cultivating the unculturable majority

Device to isolate pure bacterial cultures from the environment
It is widely recognized that the overwhelming majority of microorganisms cannot grow in artificial media that is prepared in laboratories. This issue was first realized over a century ago when the direct bacterial counts from environmental samples did not correlate with the number of resulting colony forming units (CFUs), a phenomenon known as “great plate count anomaly”. The problem is not only that very few colonies grow on the plates, but also that only a few species form colonies when compared to direct individual cell analysis of environmental samples. Cultivation-independent approaches, such as rRNA sequencing, have revealed that there remains an immense number of uncultivated species in nature. Thus, the vast complexity of the microbial world is still mostly unexplored and not understood.

We know that there are millions of microbial species that populate the world, but so far only a few have been characterized by more than just a sequence due to this inability to grow in the laboratory. A group of researchers at Northeastern University have now developed a device that allows researchers to cultivate a single species of bacteria that can then be studied and identified.

Over the last years there have been significant efforts made to overcome these limitations in cultivation. Previous research devices e.g. incorporated permeable membranes that allow sequestered bacteria to be exposed to the nutrients and molecules of their native environment. However, competition between species has so far limited the number of species of bacteria that could be isolated. 

The new device permits just a single bacterial cell to enter an inner chamber containing a food source, to which the only access is a microscopic passageway just slightly narrower than a single cell. The passageway is so small that the first cell to enter it gets stuck, blocking entry by any other cell or species. Once inside, this cell proliferates thereby filling up the inner chamber with a pure, single-species sample, since it is protected from any competition with other species.

In the paper, the team demonstrates the device's ability to separate mixtures of cell types in a laboratory setting by separating two different bacterial species whose cells have slightly different sizes (Escherichia coli and Pseudomonas aeruginosa). In a second experiment, they segregated  a combination of similarly sized but differently shaped species that commonly show up together in the marine environment (Roseobacter sp. and Pscyhoserpens sp). Finally, they used the device to separate cells of the same species that had been deferentially tagged to glow either red or green. In their final experiment they used the device to separate cells of the same species that had been differently tagged with either red or green fluorescent markers to validate the hypothesis that the cells grown inside the food chamber are actually daughters cells of the one cell caught in the entryway of the device. 

Who knows - a future form of this device might enable scientists to put more meaning to all those environmental DNA sequences and connect them to more information on individual organisms. A big step forward not only for the bacterial science community but also a shimmer of hope for a lot of fungi and protist researchers.

Thursday, July 3, 2014

New issue of the barcode bulletin

We've just released a new issue of the iBOL newsletter 'Barcode Bulletin' and if you have seen previous issues you might be able to tell from the image on the left that we made a few changes in the layout. A first victim of these changes was the text I wrote for the editorial because it had to be shortened to fit. I thought my blog might be a good venue to present the editorial long version in order to promote the new issue:

Welcome to the 14th issue of the Barcode Bulletin.

For the last thirteen issues the appearance of this newsletter hasn’t changed much. After more than four years we thought it is time for a facelift. You will notice not only a change in layout in favour of a more magazine look and feel but also the introduction of topical sections such as applications, research, education and more. This will allow readers to pick articles that they are most interested in for a first read and browse through the remaining ones. Each issue will also include a feature article we think will appeal to all our readers by highlighting special events or discoveries. For this issue we chose a report on a recent BioBlitz as these intense periods of biological surveying in an attempt to record all the living species within a designated area become more and more popular, and more frequently incorporate DNA barcoding in the program. 

DNA barcoding provides an outstanding basis for science instruction because it bridges disciplines and its workflows are simple enough that everyone can participate in various aspects of the analytical chain from specimen collection to data interpretation. One more reason to also include a section on the growing movement of DIY barcoding, this week with an article on mysterious meat.

A lot of changes that come with this issue but most importantly what hasn't changed is the high quality of contributions by our peers. Let’s not forget, most articles are written by researchers or enthusiasts, and not by professional writers, which makes our newsletter an even more impressive product. I’d like to use the opportunity to thank all of our contributors over the last years. Most of the success of the Barcode Bulletin is owed it to their efforts.

Other stories in this issue introduce you to sweeteners, orchid snacks, provides insight into several community and diversity assessments, and some grade 6 students talk about their barcoding experience. We hope you like the new appearance of our Barcode Bulletin as much as we do.

Wednesday, July 2, 2014

The truth is out there

The clearest sighting of a Yeti according to 'experts'.
I guess for regular visitors to this blog it is no secret that I am more than skeptical when it comes to the existence of creatures such as bigfoot or the yeti. Interestingly, the one post in which I expressed my doubts is the second most accessed one of all ~400 posts I published. Maybe because I simply titled it "Bigfoot doesn't exist". It certainly didn't help in making friends within the cryptozoology community but I strongly believe that there has been enough money and time wasted on the hunt for these mystical creatures. 

The more I am surprised about a new article published in the  Proceedings of the Royal Academy B which reports on a yearlong effort to bring in and analyze samples collected by cryptozoologists. The results are not surprising at all. The researchers tested a total of 30 DNA samples from different locations on the planet all connected to similar but different legends. They used 12S DNA for their test but a COI barcoding approach would have led to identical results.

The Bigfoot samples were matched to black bears, cows, a porcupine, horse, raccoon, sheep, deer, dog, coyote, wolf and one undetermined human. A number of Russian samples correlated with bears, horses, cows and a raccoon. Two of the Yeti samples matched up with that long-gone polar bear, and a third was linked to a goatlike animal called a serow. An orang pendek sample was traced to a Malaysian tapir.

Another nail in the coffin of all these legends but I wonder if it needed a full-blown scientific study to disproof all the claims. Frankly, I was surprised to see this paper published. I am not saying there is any problem with the science - quite the contrary. It is a scientifically sound study that uses state-of-the-art technology. However, all evidence provided for the existence of the Yeti or Bigfoot is either bogus or so absurd (see image above) that it usually deters any researcher. Obviously not in this case but at least it provides proof that none of the submitted and analysed hairs samples returned a sequence that could be interpreted as one belonging to an hitherto unknown primate. 

While it is important to bear in mind that absence of evidence is not evidence of absence and this survey cannot refute the existence of anomalous primates, neither has it found any evidence in support. Rather than persisting in the view that they have been ‘rejected by science’, advocates in the cryptozoology community have more work to do in order to produce convincing evidence for anomalous primates and now have the means to do so. The techniques described here put an end to decades of ambiguity about species identification of anomalous primate samples and set a rigorous standard against which to judge any future claims.

This concluding paragraph might be politically correct and scientifically consequent but to my taste it opens the door to more monster-hunting. The last I want to do is telling people what they should do in their spare time but I strongly believe that such studies are not really on top of our to-do-list when it comes to biodiversity science. Sounds more like one of the X-Files to me.