New tools and threatened species

New technologies help. Genetic barcoding offers the potential to identify animal species quickly for US$1 per sample from a small, but unique, DNA sequence. Barcoding for plants is slightly more difficult. For the great majority of unknown species in animal taxa with few taxonomic specialists, this will surely become the predominant method of discovering new species. It raises the controversial idea that many species may become known by a number derived from barcoding and not—or not only—from conventional descriptions. The potential to find new species and untangle clusters of cryptic species is also being realized. Less appreciated is that cost-effective barcoding by batches of species is now possible. Powerful new statistical methods estimate how many species may be present in an area and how these overlap with other samples from increasing sampling efforts. Combined with batch barcoding, there is the promise of rigorous estimates of what fractions of undescribed species are present in poorly sampled areas—the most direct way of estimating how many species there are.

This paragraph is from a new paper just published in Science in which an international teams claims that new tools to collect and share information could help stem the loss of the world's threatened species. The study reviewed recent studies in conservation science, looking at rates of species extinction, distribution and protection to determine where there were crucial gaps in knowledge, where threats to species are expanding and how best to tailor protection efforts to be successful.

By combining studies of the fossil record and of molecular analyses, they found the current rate of extinction - driven primarily by human activity - was roughly 1,000 times higher than the natural, background extinction rate - an alarming number that is likely to grow. 

The authors also state that online databases, smart phone apps, crowd sourcing and new hardware are making it easier to collect data on species. If those could be combined with data on land-use change and the species observations of millions of amateur citizen scientists, they are increasingly allowing closer monitoring of the planet's biodiversity and threats to it.  I couldn't agree more with them on that. Actually we need to support the expansion of all these technologies, and resources that allows us to develop even more powerful technologies for the future. 

Projects that allow the general public to collaborate with scientists are becoming important sources of knowledge. Personally, I find this to be one of the most exciting developments in recent years and I am quite happy that I have the chance to help developing these interactions. 

There are still enormous gaps in knowledge about how many species there are, where they live and their risks of extinction. Only about 13% of the world's land area and roughly two percent of its ocean area are currently under any sort of legal protection which often doesn't mean anything is really protected. And for aquatic species, whose threats often come from activities taking place on land far from where they live, land use management may prove just as important as protecting their habitat.

A very interesting meta-data study which I highly recommend for a read through on the weekend. Even more so since DNA Barcoding found it's way into it.

Birdsnap

Researchers at Columbia Engineering and the University of Maryland have taken bird-watching to a new level. Using computer vision and machine learning techniques, they have developed Birdsnap, a new iPhone app that is an electronic field guide featuring 500 of the most common North American bird species. The free app, which enables users to identify bird species through uploaded photos, accompanies a visually beautiful, comprehensive website that includes some 50,000 images. Birdsnap, which also features birdcalls for each species, offers users several ways to organize species -- alphabetically, by their phylogenetic relationship, and by the frequency with which they are sighted at a particular place and season. 

The researchers realized that many of the techniques that were developed for face recognition could also be applied to automatic species identification. State-of-the-art face recognition algorithms rely on methods that find correspondences between comparable parts of different faces, so that, for example, a nose is compared to a nose, and an eye to an eye. Birdsnap works the same way, detecting the parts of a bird so that it can examine the visual similarity of its comparable parts (each species is labeled through the location of 17 parts). It automatically discovers visually similar species and makes visual suggestions for how they can be distinguished. The app can also identify which parts of the bird the algorithm used to identify each species. It then automatically annotates images of the bird to show these distinctive parts often called 'field marks'. That way a user can learn what to look for.

The team also took advantage of the fact that modern cameras, especially those on phones, embed the date and location in their images and used that information to improve classification accuracy. Not only did they come up with a fully automatic method to teach users how to identify visually similar species, but they also designed a system that can pinpoint which birds are arriving, departing, or migrating.

The first in a series of electronic field guides was Leafsnap an app to identify tree species from photographs of their leaves. It was developed two years ago by the same group of researchers and institutions.

The group hopes next to work with Columbia Engineering colleagues on adding the ability to recognize bird songs, bringing audio and visual recognition together. They also wants to create "smart" binoculars that use this technology to identify and tag species within the field of view.

Fish eggs and larva

The declining state of fisheries in many parts of the world, combined with the call for more fisheries-independent monitoring, highlights the need for novel ways of identifying and assessing the dynamics of fish populations. Fish life cycles often involve development stages with different habitat needs, which are reconciled by adult movement to spawning grounds, followed by egg and larval dispersal, and then migration to habitats used by pre-adult and adult stages.

Studies on fish eggs and larva are usually limited by the ability to properly identify species. However, this information can be important especially when it comes to the design of marine protected areas. The presence of eggs at particular locations can reveal spawning areas. Egg and larval distribution can also provide us with information on dispersal mechanisms and how (and how deep) habitats are connected.

DNA-based identification systems such as DNA Barcoding can provide a lot more detailed information, in many cases they are probably the only method that will give a reliable answer. For example earlier stock estimates based on egg surveys for Irish Sea cod assumed that the majority of 'cod-like' eggs were actually from cod. When this was tested with a DNA-based method years later it turned out that only 37% of those eggs originated from cod.

There is no doubt that DNA Barcoding can help a great deal with such surveys. About 15 000 fish species have been barcoded so far (Number taken from BOLD's taxonomy browser) which provides a good basis for any egg or larval identification attempt. In a new study a group of researchers from the University of South Florida used DNA Barcoding to compare the community compositions of planktonic fish eggs and larvae within a coastal embayment, testing the hypothesis that the composition of the planktonic larval fish community proportionately reflects the composition of the planktonic fish egg community (excluding species with non-planktonic eggs).

The study revealed an unexpected high degree of spatial heterogeneity in fish egg compositions within the sampled area. Species that dominated the egg community (Eugerres plumieri, Cynoscion nebulosus, Centropomus undecimalis, and Prionotus spp.) were not particularly abundant amongst the 276 larvae identified, and the most abundant larval species (Achirus lineatus and Cynoscion arenarius) only comprised a minor proportion of the identified eggs.

The authors conclude that the clear disparities observed between the species compositions of the egg and larvae highlight the need for directly identifying eggs when studying habitat connectivity or performing stock assessment with egg production model-based methods.

Thismeans that there is actually no reasonable alternative to DNA Barcoding as it is the only method around that provides the necessary level of accuracy and reliability. 

eDNA particle size

Aquatic eDNA monitoring is emerging as a powerful way to detect harmful species like invasive Asian carp (a variety of carps including Silver Carp and Bighead Carp) and Burmese pythons or beneficial species like Chinook salmon and Idaho giant salamander. Because this approach is rather new, little is known about these small DNA fragments and how to best capture them from water.Origin, state, and fate of those DNA containing particles collectively determine how well eDNA can serve as a proxy for directly observing organisms and how it should be captured, purified, and assayed.

Actually the size of aquatic particles provides clues about all of the three parameters mentioned above (origin, state, fate). 

A new study from the University of Notre Dame compared performance across different types of eDNA capture methods such as centrifugation and filtration by measuring the particle size distribution. One outcome is a simple equation for calculating combinations of filter pore size and water volume to capture equivalent amounts of eDNA. Using common carp, one of the 30 worst invasive species worldwide in terms of impact, the researchers found eDNA in particles ranging from smaller than a mitochondrion to larger than a grain of table salt. They used a highly specific quantitative PCR test to measure carp eDNA, but they also quantified total eDNA—the DNA from any species—and found it was most concentrated in particles smaller than 1 micrometer. Because abundant total eDNA can interfere with the detection of eDNA from a rare species, this result further recommends the use of filter pore sizes greater than 1 micrometer.

Our results suggest that aqueous macrobial eDNA predominantly exists inside mitochondria or cells, and that settling may therefore play an important role in its fate. For optimal eDNA capture, we recommend 0.2 µm filtration or a combination of larger pore size and water volume that exceeds the 0.2 µm isocline. In situ filtration of large volumes could maximize detection probability when surveying large habitats for rare organisms.

Our description of  particle size for aqueous macrobial eDNA provides immediate guidance for practitioners and a tested method for researchers. For example, because large particles sink faster than small particles eDNA-based surveys aimed at determining very recent and local organism presence may need to target larger eDNA-containing particles. 

To my knowledge this is the first detailed investigation of just how small (or big) eDNA particles really are, results that provide important guidance for all eDNA-based monitoring programs.

Top 10 New Species 2013

An appealing carnivorous mammal, a 12-meter-tall tree that has been hiding in plain sight and a sea anemone that lives under an Antarctic glacier are among the species identified by a global committee of taxonomists as the top 10 species discovered last year. Each year, the SUNY-ESF International Institute for Species Exploration (IISE) international committee of taxon experts evaluates the hundreds of new species that have been nominated by the public, IISE staff, scientists, scientific journal editors and by the committee members themselves. 

And here we go - the top 10 with short descriptions by the IISE:

Olinguito

Bassaricyon neblina

Country: Ecuador

The appealing olinguito, resembling a cross between a slinky cat and a wide-eyed teddy bear, lives secretively in cloud forests of the Andes mountains in Colombia and Ecuador. It is an arboreal carnivore that belongs to the family Procyonidae, which includes the familiar raccoon. The olinguito is smaller, though, typically topping out at about two kilograms (approximately 4.5 pounds). It is the first new carnivorous mammal described in the Western Hemisphere in 35 years. Its apparent dependence on cloud forest habitat means deforestation is a threat.

Kaweesak's Dragon Tree

Dracaena kaweesakii

Country: Thailand

Sounding like something out of Game of Thrones and standing 12 meters (nearly 40 feet) tall, it's hard to believe the dragon tree went unnoticed this long. Beautiful, soft, sword-shaped leaves with white edges and cream-colored flowers with bright orange filaments are the hallmarks of this impressive plant. The dragon tree is found in the limestone mountains of the Loei and Lop Buri Provinces in Thailand and may also be found in nearby Burma. Valued as a horticultural plant, its small number (perhaps 2,500), and the fact that it grows on limestone that is extracted for the manufacture of concrete, has earned this species a preliminary conservation status of endangered.

ANDRILL Anemone

Edwardsiella andrillae

Country: Ross Ice Shelf, Antarctica

A species of sea anemone, living under a glacier on the Ross Ice Shelf in Antarctica, raises questions by its very existence. It is not clear how the species withstands the harsh conditions in its habitat. It is the first species of sea anemone reported to live in ice. It was discovered when the Antarctic Geological Drilling Program (ANDRILL) sent a remotely operated submersible vehicle into holes that had been drilled into the ice. This revealed the presence of small creatures, less than 2.5 centimeters long (one inch) with most of their pale yellow bodies burrowed into the ice shelf and their roughly two dozen tentacles dangling into the frigid water below.

Skeleton Shrimp

Liropus minusculus

Country: USA

This tiny shrimp, the smallest in the genus, was identified from among specimens originally collected from a cave on that island of romance, sunny Santa Catalina, off the coast of Southern California. Part of a marine family known as skeleton shrimp, only distantly related to the ones some humans love to dip in cocktail sauce, this crustacean is the first of its genus to be reported in the northeastern Pacific. The new species has an eerie, translucent appearance that makes it resemble a bony structure. The male's body measures just 3.3 millimeters (about an eighth of an inch); the female is even smaller at 2.1 (less than a tenth of an inch).

Orange Penicillium

Penicillium vanoranjei

Country: Tunisia

Distinguished by the bright orange color it displays when produced in colonies, this fungus was named as a tribute to the Dutch royal family, specifically His Royal Highness the Prince of Orange. It was reported in a journal published by the National Herbarium of the Netherlands. The newcomer was isolated from soil in Tunisia. This species also produces a sheet-like extra-cellular matrix that may function as protection from drought.

DNA Barcode available

Leaf-tailed Gecko

Saltuarius eximius

Country: Australia

It's not easy to spot this gecko, which has an extremely wide tail that is employed as part of its camouflage. With longer limbs, a more slender body and larger eyes than other Saltuarius species, this one has a mottled coloration that allows it to blend in with its surroundings. Native to rainforests and rocky habitats, this gecko is a bit of a night owl. It is found on the vertical surfaces of rocks and trees as it waits for prey. Surveys of similar habitat near the area where this species was found did not reveal additional populations, so this may be a rare species. The gecko was discovered on rocky terrain in isolated rain forests of the Melville Range of northeastern Australia.

Amoeboid Protist

Spiculosiphon oceana

Country: Spain

This one-celled organism is four to five centimeters high (1.5 to two inches), making it a giant in the world of single-celled creatures. This foram (part of a distinct group among the many amoeboids) from the Mediterranean Sea gathers pieces of silica spicules, which are actually sponge fragments, from its surroundings and uses them like so many Lego blocks to construct a shell. It ends up looking much like a carnivorous sponge as well as feeding like one, extending pseudopods (a protist's version of arms) outside the shell to feed on invertebrates that have become trapped in the spiny structures. This species was discovered in underwater caves 30 miles off the southeast coast of Spain. Interestingly, they are the same caves where carnivorous sponges were first discovered.

Clean Room Microbes

Tersicoccus phoenicis

Country: Kennedy Space Center, Fla., USA

There are some things we don't want to send into space and the newly discovered clean room microbes are among them. Found in rooms where spacecraft are assembled, this microbial species could potentially contaminate other planets that the spacecraft visit. Tersicoccus phoenicis was independently collected from the floors of two separate clean rooms around 2,500 miles apart, one in Florida and one in French Guiana. While frequent sterilization reduces the microbes found in clean rooms, some resistant species persist that can tolerate extreme dryness; wide ranges of pH, temperature and salt concentration; and exposure to UV light or hydrogen peroxide. This work was performed in collaboration with Jet Propulsion Laboratory, California Institute of Technology (USA), University of Regensburg (Germany), Leibniz-Institute DSMZ (Germany) and California State University Los Angeles (USA).

Tinkerbell Fairyfly

Tinkerbella nana

Country: Costa Rica

The tiny size and delicately fringed wings of the parasitoid wasp family Mymaridae led to their common name: fairyflies. Tinkerbella nana, named for Peter Pan's fairy sidekick, measures just 250 micrometers (0.00984 inches) and is among the smallest insects. It is the latest addition to the 1,400 or so known species of the family. The new species was collected by sweeping vegetation in secondary growth forest at LaSelva Biological Station in Costa Rica. Although its host is not yet known, like other fairyflies it presumably has a life span of not more than a few days and attacks the eggs of other insects.

Domed Land Snail 

Zospeum tholussum

Country: Croatia

Living in complete darkness some 900-plus meters (nearly 3,000 feet) below the surface in the Lukina Jama-Trojama caves of western Croatia is Zospeum tholussum. This land snail lacks eyes as they're not necessary in the total darkness of the caves, and it has no shell pigmentation giving it a ghost-like appearance. Only one living specimen was collected in a large cavern among rocks and sand with a small stream of running water nearby, however many shells were also found in the area. Even by snail standards, Zospeum tholussum moves slowly, creeping only a few millimeters or centimeters a week. Researchers suspect these small snails, measuring only 2 millimeters in length (0.08 inch), travel in water currents or hitchhike on other cave animals, such as bats or crickets, to travel longer distances.

DNA Barcode available 

Two out of ten have DNA Barcodes. That is sub optimal. We can do better for sure.

Malus ecclesia

Joe Davis is a research affiliate in the Department of Biology at MIT and in the George Church Laboratory at Harvard Medical School. His research and art includes work in the fields of molecular biology, bioinformatics, "space art", and sculpture, using media including but not limited to centrifuges, radios, prosthetics, magnetic fields, and genetic material. (Wikipedia)

Davis' works include a project in which he encoded a 60-character fragment of a Greek text by Heraclitus into the white-eye gene of a fruit fly and now the bio artist wants to create his own version of the tree of knowledge - using Wikipedia. He has devised a mathematical formula to add layers of data to DNA.

He now plans to add a decoded version of the online encyclopedia into the DNA of a 4,000-year-old strain of apple, which he claims is the closest he could get to fruit from the biblical tale and he dubbed the project Malus ecclesia (Malus, the genus name for all apples, means both “bad, evil” and “apple tree” in Latin. Ecclesia translates to “church”—an homage to George Church.).

Due to the size of Wikipedia, Davis and his team chose to decode only the top 50,000 pages of the online encyclopedia, which make up 50 per cent of the most visited pages across the site. The amount of data equates to around 350MB. Once coded, the letters can be assembled into biologically viable, functional strands of DNA. To get the DNA into the apple, Davis will use a type of bacteria uniquely evolved to insert its genome through plant cell walls. The bacteria will be tricked into putting the DNA-encoded Wikipedia into apple saplings, which are then grafted onto apple stock and allowed to grow into adult trees. Because the changes to the fruit are biologically inert, the final apples will look like normal apples hanging from normal apple trees.

Well, that's a form of art I had never thought of and I have no doubt that it is technically possible to create such an apple. After all transfection methods are around for quite some time already. I just fail to see its significance but hey, its art, what can I say? 

The engineered apple, when complete, will be twice forbidden. It is not only the forbidden fruit in the biblical sense but also in the secular world because the Animal and Plant Health Inspection Service of the U.S. Department of Agriculture has strict rules against the unregulated eating of genetically altered plants. I am sure the opponents of GMO won't approve of this work of art.

Google Doodle for Mary Anning

You probably have to be either a palaeontologist or somebody like me who has a hobby interest in fossils to know about Mary Anning. However, her life's story can't be told often enough to teach us a lesson about women's contribution to science which never received proper credit throughout their lifetime, and the struggles those women had to go through simply because they were female. Unfortunately, the world's academia hasn't fully resolved this issue despite all efforts on gender equity (just two examples here and here).

Today Google is celebrating Mary Anning's 215th birthday with a special doodle, which shows Anning uncovering a dinosaur's fossilised remains. But who was Mary Anning? I took the following text from today's Daily Telegraph as this article provides a concise answer to the question:

Mary Anning, born on 21 May 1799, was a British fossil collector, dealer, and palaeontologist who became known around the world for the discoveries she made while exploring the marine fossil beds at Lyme Regis in Dorset.

Anning searched for fossils in the area's Blue Lias cliffs – particularly during the winter months when landslides exposed new fossils that had to be collected quickly before they were lost to the sea. It was dangerous work, and she nearly lost her life in 1833 during a landslide.

Her discoveries included the first ichthyosaur skeleton correctly identified, which she and her brother Joseph found when she was just twelve years old, the first two plesiosaur skeletons ever found, the first pterosaur skeleton located outside Germany, and important fish fossils.

Anning's work contributed to fundamental changes in scientific thinking about prehistoric life and the history of the Earth, at a time when there was little to challenge the biblical interpretation of the story of creation.

However, although Anning was well known in geological circles in Britain, Europe, and America, her gender and social class prevented her from fully participating in the scientific community of 19th-century Britain, which was dominated by wealthy Anglican men.

She struggled financially for much of her life. Her family was poor, and as religious dissenters, were subject to legal discrimination. As a woman, she was not eligible to join the Geological Society of London, and she did not always receive full credit for her scientific contributions.

The only scientific writing of hers published in her lifetime appeared in the Magazine of Natural History in 1839 – an extract from a letter that Anning had written to the magazine's editor questioning one of its claims. It was only in 2010, 163 years after her death in 1847, that the Royal Society included Anning in a list of the ten British women who have most influenced the history of science.

If you want to learn more about Mary Anning and her life, there are two historical novels that are recommended by the Telegraph writer, Sophie Curtis: Remarkable Creatures by Tracy Chevalier, and Curiosity by Joan Thomas.

$2.5 Million for barcoding in Australia

The Australian Government program BioPlatforms Australia is tasked with building research capabilities and expertise in the fields of genomics, proteomics, metabolomics and bioinformatics. This national program supports research infrastructure in Australia since 2007.

Today the University of Adelaide announced an investment of $2.5 Million by BioPlatforms Australia to advance DNA Barcoding in Australia. The project is led by the Andrew Lowe in partnership with a number of Australian Institutions*.

The project will focus on five key areas with immediate strategic value:

- verifying timber origins to combat illegal timber trading;

- authenticating labelling and geographical origin of fish in the retail marketplace;

- mapping plant biodiversity in the Pilbara to help with mine site environmental impact assessment 

  and restoration management;

- biodiversity discovery and impact assessment of invertebrates that inhabit underground aquifers 

  utilised by mining and farming; and

- generating barcodes for Australia’s orchids to enhance conservation.

Congratulations to the colleagues in Australia - this is a nice boost for DNA Barcoding down under.

* - Kings Park Botanic Garden, CSIRO, Australian Tropical Herbarium, the South Australian Museum, ARC Centre of Excellence in Plant Energy Biology and WA Department of Parks and Wildlife

Cryptic bird species in Japan.

The Japanese archipelago comprises the islands that form the country of Japan. It consists of 6,852 islands with at least 100 m circumference, 430 of those are inhabited. The four main islands, from north to south, are Hokkaido, Honshu, Shikoku, and Kyushu. Honshu is the largest and referred to as the Japanese mainland.

The archipelago has been recognized as a biodiversity hot spot and a new zoogeographic region based on the phylogenetic relationships of its birds and other vertebrates. 

The high degree of biodiversity in Japan is the result of a wide variety of climates and ecosystems, ranging from the humid subtropics in the Ryukyu and Ogasawara islands to the boreal zones in northern Japan, the alpine zone at over 3000 m above sea level, and all its islands and straits between them that have separated species extended periods of time.

The bird fauna of Japan consists of 633 described bird species, including birds that also occur on the eastern Eurasian continent. The Japanese Archipelago is home to 11 endemic resident bird species and six migratory species breeding only in that area. A total of about 250 species are known to breed in Japan. It has been repeatedly disputed whether some populations isolated on the many islands should be recognized as subspecies or as distinct species as many of those birds form morphologically well-defined groups. For a very limited number of species researchers had conducted molecular analyses and found that those groups are rather distinct lineages and a new study using DNA Barcoding adds more species to this list.

The researchers build a DNA Barcode library comprising 93.2% of the bird species breeding in Japan. They found 24 cryptic species candidates in their study. Patterns of these deep intraspecific sequence divergences were consistent with some of the biogeographical boundaries across the Japanese Archipelago such as the Tsugaru Strait, or the Ryukyu Islands. About 10% of the species the team looked at seem to contain some cryptic representatives and they have some explanations for this:

The fluctuating sea levels during the Quaternary would have led to repeated periods of connection, isolation and submergence of the islands of the Japanese Archipelago, which could have isolated bird populations for lengthy periods. Such populations would have retained geographical and temporal isolation without admixture of other populations and extinction for glacial and interglacial periods.These isolated populations may lead to the deep intraspecific genetic divergence observed in 11 Japanese bird species. The distinct intraspecific divergence observed between 23 trans-Palearctic species may reflect the history of isolation and gene flow of these bird populations with respect to the changes in the land-bridges over the straits between the Japanese Archipelago and the Eurasian continent.

This is an extraordinary amount of potentially new species of birds. Finding so many new species in a vertebrate group other than fishes is quite rare. Usually we hear about one or two but not two dozens. 

6th International Barcode of Life Conference

NEWSFLASH

- The 6th International Barcode of Life Conference will be held in Guelph, Ontario August 18-22, 2015.-

Mark your calendars! More details coming soon. are now available. Here is a more current blog post.

Global species shake-up

Habitat destruction, pollution, and overharvesting, as well as climate change and invasive species, have led to conspicuous reductions in biological diversity. Globally, increasing numbers of species are under threat, populations of vulnerable taxa are declining, and ecosystem function is changing as a result. Although these large-scale patterns emerge from processes that are based on local community structure, as yet there is no comprehensive analysis of how temporal change in ecological assemblages contributes to this global picture.

An international team of researchers re-examined 100 world-wide monitoring studies and were surprised to discover that, over decades, the number of species in many places has not changed much -- or has increased. But the researchers did discover something changing rapidly: which species were living in the places being studied. Almost 80 percent of the communities the team examined showed substantial changes in species composition, averaging about 10 percent change per decade -- significantly higher than the rate of change predicted by any models. This shows that a rapid global turnover of species is happening, resulting in novel biological communities. One potential driver for this is the intensification of trade and transport, combined with the rapid increase in invasions of exotic taxa.

For this study the colleagues gathered all data sets representing more than 6.1 million species occurrence records from 100 individual time series. The study incorporated data for some 36 000 species including mammals, birds, fish, invertebrates, and plants. The geographical distribution is global, and includes main ecosystems such as marine, freshwater, and terrestrial biomes. The time interval ranges from 1874 to the present, although most data series were obtained for the past four decades.

I am fairly certain that most of the studies included in this meta-analysis were not studies that used DNA-based identification systems (not even the more recent ones) although I would strongly recommend doing that at some point in the future. The last decade has shown how many species there might be out there which we haven't discovered let alone described yet. Any such study should take into account that there is a considerable number of species that goes undetected either because it wasn't considered as different (e.g. cryptic lineages) or too small and therefore not interesting enough to be part of a study. It would be very interesting to start such time series utilizing e.g. metabarcoding and see if the patterns observed the present study remain.

A word of caution - the results of this study are by no means an 'all-clear' signal as biodiversity change may be as large a concern as biodiversity loss. The authors thankfully make this very clear:

Our core result—that assemblages are undergoing biodiversity change but not systematic biodiversity loss—does not negate previous findings that many taxa are at risk, or that key habitats and ecosystems are under grave threat. Neither is it inconsistent with an unfolding mass extinction, which occurs at a global scale and over a much longer temporal scale. The changing composition of communities that we document may be driven by many factors, including ongoing climate change and the expanding distributions of invasive and anthrophilic species. The absence of systematic change in temporal α diversity we report here is not a cause for complacency, but rather highlights the need to address changes in assemblage composition, which have been widespread over at least the past 40 years.

Endocrine disruption through oxygen depeletion

Endocrine disruptors are substances, man-made or natural, which can interfere with the hormone systems of humans and wildlife, with potentially adverse effects, for example, on fertility and neural development. They interfere with the hormonal (endocrine) system, e.g. by mimicking the action of a naturally-produced hormone, such as estrogen or testosterone, and thereby setting off similar chemical reactions in the body. They are also known to block hormone receptors in cells, thereby preventing the action of normal hormones, and they can affect the synthesis, transport, metabolism and excretion of hormones, thus altering the concentrations of natural hormones in the body.

Numerous recent studies identify mechanisms and effects of endocrine disruption in invertebrates. Vertebrate steroid hormones (testosterone, estradiol, and progesterone) that are synthesized from cholesterol are found in molluscs, and evidence shows that such sex steroids can serve as ideal biomarkers of endocrine disruption. While the specific function of steroid hormones in molluscs’ endocrine system is still speculative, reports emphasize steroids’ influence on gender differentiation, gametogenesis, gonadal maturation, fertilization and embryonic development, and reproduction. Specifically, testosterone and estradiol concentrations in the gonads vary during different stages in the reproduction process, largely affecting gender determination and gamete growth.

In the 1980s and 1990s the use of tributyltin (TBT) was hotly debated in science and politics. Because TBT was the most effective anti-fouling agent known, it was frequently used in anti-fouling paint. However, TBT disrupts the endocrine system in a variety of animals most prominently in mollusks. The disruption leads to masculinization in females, because the androgen levels are higher than normal. Since less fertile females are available for mating, the population begins to decline and seriously impacts the balance of the ecosystem. After endless discussions and negotiations TBT was worldwide banned in 2008.

But not only specific chemicals can interfere with the hormonal system. There also seems to be a correlation between low dissolved oxygen which you can find e.g. in urbanized watersheds and endocrine disruption. 

A group of researchers from New York did a  five-year bio-monitoring study of the Bronx River Estuary and they found altered hormonal levels, resulting from endocrine disruption, in Geukensia demissa (Atlantic ribbed mussel):

Testosterone, estradiol, and progesterone levels were collected from male and female mussels in the oxygen depleted Bronx River and well-oxygenated Greenwich Cove. Bronx River mussels exhibited higher testosterone levels and lower estradiol levels than Greenwich Cove mussels. The resulting abnormal hormonal ratio seems to indicate that environmental conditions in the Bronx River facilitate an allosteric inhibition of the cytochrome P450 aromatase enzyme, which aids conversion of testosterone to estradiol. Low progesterone levels suggest Bronx River mussels are experiencing a delay in sexual maturation, and morphometric data show a stalling of shell and tissue growth.

In order to confirm that the mussels collected from both sampling sites are the same species, the researchers used DNA Barcoding. Minimal sequence variation confirmed the mussels were from the same species which suggests that there is intraspecific divergence in various endocrine processes, resulting from environmentally induced stress. 

GeneStream

Biodiversity on Earth is in rapid decline, and flowing waters are particularly affected by this. There is a long list of reasons for this starting with the impact of increased nutrient supply in the form of phosphates and nitrates from fertilizers that are washed into the water. Fine sediment such as sand  from cultivated land also often moves from open soil into the rivers. When water is used for agricultural irrigation or flowing waters straightened because of land use flow velocity is reduced which can have large impact on water organisms.

In Germany for example more than 1,000 different species typically inhabit a healthy stream and despite ongoing European-wide conservation efforts, intact water bodies have become extremely rare in my home country. 

Researchers from the Ruhr-Universität Bochum are investigating which environmental conditions are particularly harmful to water organisms and how to protect biodiversity in rivers and how to optimize stream restoration. Their project is called GeneStream and I believe it runs since 2013. Instead of explaining in many works what they are actually doing I let them speak as they did a nice video on the project:

The Breitenbach in Hesse is perhaps the most intensively studied stream in the world especially when it comes to its ecology and biodiversity. For more than 50 years it was the field research area for the Max Planck Institute for Limnology in Schlitz. Unfortunately, in 2006, as a result of a restructuring of Max Planck institutes, the station in Schlitz was closed but the data collected over all those decades are still used. I have been at the Breitenbach myself a few times as an undergrad and it is great to learn that this irreplaceable study site is in use again. 

Two months into the experiment, the researchers analysed which organisms had settled down under different environmental conditions in the containers including some controls which were not subject to any particular environmental stress. They used DNA Barcoding to assist with the species determination. The colleagues found that all three stress factors had a negative impact on most of the species. That means that due to an increase in sediment or nutrient volume in combination with lower flow velocity the number of individuals in the test containers was significantly lower than in the control containers. An increase in sand volume had the strongest effect on the organisms. This is actually a fairly normal phenomenon but only if it happens sporadically. High sediment accumulation over years on the other hand is causing difficulties for a variety of freshwater organisms.

The GeneStream team is currently setting up a series of tests at the Felderbach stream in North Rhine-Westphalia. In this experiment, the researchers will not only identify the species present but also use population genomics to determine their genetic variation. Genetic diversity is the basis for adaptability and evolutionary 'success' of an organism. Any reasonable conservation measure should allow for gene flow between populations to counteract the detrimental effects of habitat fragmentation. You can follow the progress of the project on their website and their Youtube channel (with some funny time lapse videos). 

Indian dancing frogs

Dancing frog (credit S.D. Biju Via AP)

After writing about the decline of the amphibians world-wide I am really glad that I actually found something more positive to post about:

Researchers from the University of Delhi have discovered 14 new species of dancing frogs in the Western Ghats, a mountain range along the west coast of India. This region is supposedly one of the ten "hottest" biodiversity hot-spots in the world which makes it a very likely region to find new species. So far about 180 amphibian species were already known. The new  discoveries are a result of field studies conducted across the mountains of Western Ghats, over the past 12 years.

Only 11 species were recognized in the dancing frog family Micrixalidae previously. The family contains only one genus Micrixalus which is endemic to India. These frogs have been named dancing frogs as the males of exhibit a behaviour that is called foot-flagging, where they lift up their feet and display the colourful soles of to potential mates:

In the BBC's 'Life in Cold Blood' (episode 2) there is another example of such a behaviour shown (about 25 min in). Some of the newly discovered species are known to do similar things. The tiny frogs, about the size of a walnut, extend and whip their legs out to the side.

The new species were identified using DNA Barcoding and morphology and the authors are quick to point out that their study also showed that many of the original habitats of these frogs are highly degraded and threatened by human intervention, highlighting the need for urgent conservation action. 

In a scenario where new information is available, conservation assessment of individual species and threats in their habitats need to revisited. Micrixalidae, previously a family of 11 species with taxonomic confusions, ambiguous distinguishing characters and patchy distribution records, and which is now known to be a two-fold more diverse lineage with restricted distribution range of species, is in an urgent need of conservation reassessment. Immediate attention in this regard can go a long way in conserving extant members of this ancient and endemic group of frogs.

So after all I am not ending on a fully upbeat note but there might be hope. The Indian environment ministry earlier this year declared around 50 000 sq.km of the Western Ghats as ecologically sensitive. An earlier report had recommended that approximately 37% of the Western Ghats be kept free from activities that have “maximum interventionist and destructive impact on the environment” and be labelled an ecologically sensitive area.

The impact of fish farming

Salmon farming is one of the most widespread activities in marine aquaculture. Salmonids fishes, along with carp, are the two most important fish groups in aquaculture. The aquaculture of salmonids is likely worth more than US$11 billion.  However, the farming has considerable impact on the environment through factors such as nutrient enrichment due to the accumulation of waste food and faecal matter, as well as the ecotoxic effects of discharged medicines and antifouling compounds.

The impact of such farms on the coastal environment is traditionally assessed by monitoring some of the smaller species found in marine sediment samples collected at specific distances from farming sites. Visual identification of these animals under a microscope is time consuming and very expensive. It also requires highly-trained taxonomists, which renders this method unsuitable for any large-scale use.

Foraminifera

A team led by Jan Pawlowski of the Faculty of Science of the University of Geneva in Switzerland, analysed this type of sediment using DNA Barcoding. Their target organisms are foraminifera because they provide well-established biomarkers of pollutions in the marine environment. Moreover, they possess the attributes of a reliable bioindicator, namely ubiquity, short life and reproductive cycles, and sensitivity to local abiotic conditions, making them highly responsive to environmental perturbations such as organic matter enrichment and physical disturbance. Previous studies showed that foraminiferal communities rapidly change under organic pollution exposures associated with fish farming . They also represent good indicators of the impact of offshore drilling activities  and heavy metal pollution, as well as are sensitive to anoxia . However, all these studies have been restricted to the morphological identification and counting of hard-shelled foraminiferal species in dried sediment samples.

The researchers analysed both eDNA and RNA sequences from samples collected at various distances from two sets of salmon cages in the heart of the Scottish fjords. The goal was to estimate the foraminiferal diversity based on ribosomal sequences generated by the next generation sequencing technology which is perhaps better known as metabarcoding. 

Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for species richness decrease in impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.

This study is further proof that metabarcoding can be used for a wide range of micro- and meiofaunal taxa, some of which may turn to be much better ecological indicators than the macrofaunal species we are currently using for most assessments.

An armadillo and the FIFA

Three-banded armadillo (Tolypeutes tricinctus)

Although I am now living in Canada for over 8 years I am clinging on to some of my European habits and preferences. One is that when it comes to sports I clearly favor football and I mean the real football which in some regions of the planet is called soccer. Somehow, I am not really warming up to the game in which you use wooden or carbon fiber sticks to shoot a small disc made of solid, vulcanized rubber into a very small goal. 

Like it or not I am not alone:

Football is the most popular sport in the world, with an estimated 270 million people actively involved in the game. With 209 national associations, the football's principal governing body—the FIFA—has more members than the United Nations, and the estimated audience of the final match of the FIFA World Cup in South Africa in 2010 surpassed one billion people.

For the 2014 World Championships in Brazil, the FIFA has adopted the endemic Brazilian Three-banded armadillo (Tolypeutes tricinctus), an endangered species, as its mascot. They named it Fuleco™ by combining the Portuguese words for football ("futbol") and ecology ("ecologia"). The armadillo, when threatened, will protect itself by rolling up into a ball. The mascot plays an essential part in driving the environmental awareness of the World Cup.

Two species of Tolypeutes occur in Brazil, the endangered and endemic Tolypeutes tricinctus and the lesser-known Tolypeutes matacus. Although decreasing in population, there is no conservation plan for both species. The animals, and some 20 million people live in an area known as Caatinga, a tropical dry forest that once covered 845,000 square km in northeastern Brazil. This area has been reduced in by 53% . Despite being known as a biodiversity-rich region, the Caatinga is among the least known and least protected of all Brazilian ecosystems.

In an article published in the upcoming issue of Biotropica, researchers challenge the role that the FIFA and the Brazilian government play in protecting the environment. They are asking both to protect 1,000 hectares of the critically endangered Caatinga ecosystem for each goal scored in the World Cup. A scientific publication to raise awareness is certainly unusual but why not? Organizers of big events are nowadays quick to point out that they plan environmentally friendly and in a sustainable fashion. Unfortunately, these plans are only partially realized and so it seems the case again:

FIFA's environmental aim for the 2014 FIFA World Cup is described in the ‘Football for the Planet’ program: (1) monitoring of and compensation for greenhouse gases emissions resulting from the main activities related to the event; (2) certified ‘green stadiums’; and (3) waste management and recycling. After the initial frenzy surrounding, Fuleco™'s selection as mascot, the rich Brazilian biodiversity, this species was chosen to represent seems to have been completely forgotten by the FIFA's official environmental program. Indeed, not a single action for protecting this endangered species or its habitat has been proposed by the organizers of the 2014 FIFA World Cup. 

So, this challenge has my full support both as biodiversity researcher and as football fan.

Is DNA Barcoding cheaper?

Taxonomic identification accounts for a substantial portion of cost associated with bioassessment programs across the United States. New analytical approaches, such as DNA barcoding have been promoted as a way to reduce monitoring costs and improve efficiency, yet this assumption has not been thoroughly evaluated. We address this question by comparing costs for traditional morphology-based bioassessment, the standard Sanger sequencing-based DNA barcoding approach, and emerging next-generation (NGS) molecular methods.

So far the authors of a new paper published in PLoSONE. The question asked is a very important one as DNA Barcoding was indeed promoted to be a cheaper alternative to traditional taxonomy. However, this was just one of many promises and my feeling is that any such cost analysis can only provide limited insights. any such analysis is biased towards the availability of services and their costs. The latter can vary immensely between countries or even regions within a nation but the least this publication should give us is a general idea on the tendency.

The results are quite sobering as current costs for DNA Barcoding using the standard Sanger sequencing approach are between 1.7 and 3.4 times the cost of traditional taxonomic identification and could increase even more (10x) if significant failure-tracking and re-sequencing is required. The per sample cost are at $5 which has been reported all along by proponents and opponents of DNA Barcoding (plant samples cost about $7.50 per sample). The costs include the the lab work (extraction, PCR, purification, and sequencing) but also the need to pick, sort and subsample individual specimens prior to barcoding. 

It looks much better when next-generation methods are considered. The cost for a next-generation sequencing run can be less than $1 per specimen, which is shown to be cheaper than or similar to morphology-based identifications.

My only criticism with respect to this publication is the fact that I can't see how the costs for morphology-based identifications have been calculated. The authors state that they have surveyed labs that do this service but there is not such a clear-cut calculation available as for both sequencing methods. Frankly, I think the costs provided are at the lower end. I don't think that e.g. $3 per fish identification is enough for some cases. Another issue is the resolution of identification. Especially for invertebrates identification to the species level is often not possible but still costs the same. I doubt that the estimates given guarantee full resolution. DNA Barcoding at least delivers a sequence characteristic for a species. So, maybe we are on par even when considering Sanger methods.

DNA Barcoding certainly has other advantages and the authors state some and any business person would probably assign costs and benefits to them as well:

Although current barcoding approaches are more expensive, they do provide additional benefits of being able to obtain answers in substantially less time. For example, in the time it takes to complete traditional taxonomic analysis, 3–4 times as much barcoding could be done. The reduced time to obtain answers could also allow for easier adaptive management of monitoring and could facilitate use of biological indicators in situations where a more immediate answer is necessary, such as environmental damage assessment following spills. Furthermore, as shown by others, the increased taxonomic resolution provided by DNA barcoding can improve the sensitivity and performance of commonly used bioassessment metrics

But read for yourself. The paper is open access.

Malaisetraps at Schools

Did I mention that the School Malaise Trap Program is running again. 55 schools in Ontario have a trap and are already collecting insects. Next Tuesday the traps will be put down again and all sample bottles shipped to us for DNA Barcoding. This time we asked the schools to send us some photos of their traps. Here we go:

A reference site at Lake Laurentian, Sudbury

Three larger specimens from Alliance St-Joseph school in  Chelmsford

Checking for bugs at Notre Dame Catholic School in Orillia

Trapped - St. Elizabeth CHS - Thornhill

Future entomologists from St. Pius X in London, Ontario

DNA Barcoding and Avian Flu

Influenza viruses that infect birds are called avian influenza viruses (AIV). Only influenza A viruses infect birds, and all known subtypes of influenza A viruses can infect birds. However, there are substantial genetic differences between the subtypes that typically infect both people and birds. Two subtypes called H5 and H7 each can be separated into low pathogenic and high pathogenic forms on the basis of genetic features of the virus and the severity of the illness they cause in poultry.

The subtype H7 is repeatedly found in wild birds across the world but usually not in a pathogenic form. However, once introduced into domestic birds such as poultry it may become highly pathogenic and cause outbreaks of avian influenza. We know that since 2002, H7 viruses have infected more than 100 humans who as a consequence usually showed mild clinical signs of conjunctivitis, with the exception of one fatal case in the Netherlands.

In South Korea, active surveillance has been applied to wild birds and domestic birds since a first outbreak in 2003–2004. Swab samples are obtained from poultry farms on a regular basis and authorities also scree wild bird habitats by collecting fecal samples. These habitats are located mainly along the western and southern plain regions of South Korea where migratory birds mostly aggregate in overwintering locations for species that migrate from northern Asia, including Russia and Mongolia in the fall. 

Until about 2007 the avian influence subtypes identified in the fecal samples could not be associated with bird species. Only the development of DNA Barcoding and the efforts of the bird barcoding initiative enabled researchers to identify host species, using mitochondrial DNA recovered from fecal samples. The potential of this approach is shown in a new paper that was published in PLoSONE a few days ago. 

The results provide insights into the origin of virus strains. All Korean H7 viruses belong to an Eurasian lineage and they showed substantial genetic variation, in particular in the wild birds. The team could also show that the H7 viruses from poultry were closely related to those of wild birds.

Our results suggest that domestic Korean viruses were transferred directly from wild birds through at least two independent introductions. Our data did not indicate that wild birds carried poultry viruses between Korea and China, but rather, that wild-type H7 viruses were introduced several times into different poultry populations in eastern Asia.

The idea to use DNA Barcoding to help with vector identification is not a new one but so far there haven't been many examples that clearly showed the advantage of this additional layer of information for disease prevention and management. Here is another one.