Friday, July 31, 2015

eDNA for turtle conservation

Environmental DNA (eDNA) allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material in their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site. 

Surveys based on eDNA sampling have potential for applied conservation through detection of rare or cryptic species that may be overlooked with traditional survey methods. Species of conservation concern often fall into this category due to low population numbers, and eDNA surveys have facilitated detection of a range of threatened taxa.

According to the IUCN turtles are in serious trouble. They are among the world’s most endangered vertebrates, with about half of their more than 300 species threatened with extinction. They are being collected, traded, and eaten or used for food, as pets,in  traditional medicine. Eggs, juveniles, adults,
body parts, everything exploited indiscriminately, with little regard for sustainability. On top of this, their habitats are being increasingly fragmented, destroyed, and polluted. Here in Canada seven of our eight native freshwater turtle species are at risk. 

Surprisingly, the eDNA approach had not been applied to turtles in aquatic environments. Visual and/or physical detection rates for turtle species vary substantially among sites and species, as well as among survey methods. Rare species can be particularly difficult to detect with traditional methods, especially in turbid waterways. Detection of eDNA could provide a more rapid, cost-effective, and potentially more sensitive survey tool to identify areas where turtle species are present, which can then be prioritized for intensive trapping surveys. 

Colleagues here in Ontario wanted to test whether turtle eDNA can be successfully detected in samples from aquaria and in the wild. They developed DNA primers (using DNA Barcodes) for a suite of nine sympatric freshwater turtles, and used it to compare their results to traditional field survey data from two sites in their target area.

Not only were they able to show that eDNA from turtles can be detected using both conventional PCR and quantitative PCR but also that the cost of detection through traditional survey methods is considerable higher than eDNA methods.

Compared to our simplified cost estimate of $500.00 to detect eDNA from a single turtle species at a site (assuming that detection would be successful), the cost to detect species through traditional field surveys ranged from $100 to $4,100 per detected species, and some species were not detected using either trapping or visual surveys.

This might represent a big step forward for the conservation of many endangered turtle species. Here in Canada it certainly would:

In Canada, federal and provincial conservation legislation provides protection to the habitat of at-risk species in many areas. However, this legislation does not apply until the species’ presence at a site (habitat) is confirmed. Our field data demonstrate that the amount of survey effort required to detect some species may be prohibitive, and that even with hours of intensive visual and trapping surveys, some species may go undetected.

Time to get to the task. Turtles worldwide don't have much time left.

Thursday, July 30, 2015

Piscivore diet

Fish consuming (piscivore) bird species such as the Common Kingfisher (Alcedo atthis) or the Bald Eagle (Haliaeetus leucocephalus) or the Eurasian otter (Lutra lutra) serve as ecosystem indicators and even flagship species for conservation. In Europe, such species the ecosystems they live in are protected under the Habitats Directive and the Bird Directive of the European Union. Piscivore species occurring in high population densities on the other hand are seen as competitors to humans. Good examples are cormorants and herons. The problem is that we still don't have sufficient information on both groups' impact on local fish fauna but on the other hand any management of piscivores aiming at either protecting or regulating their predators requires a much better understanding of their feeding ecology.

DNA-based prey identification of stomach contents and quite a few methods have been developed over the last decade, DNA barcoding being one of them and certainly a very successful one

Whilst sequence-based methods such as next-generation sequencing provide information on the prey range at high taxonomic resolution, they are time-consuming and expensive, especially when dealing with high sample numbers. Diagnostic multiplex PCR provides a valuable alternative to sequence-based approaches when a defined set of prey organisms is to be detected: multiplexing of taxon-specific primers allows the identification of several prey taxa within one reaction, based on differences in amplicon size. Depending on the information needed, the taxonomic level of prey identification can be selected and through balancing primer concentrations, equal sensitivity can be reached across the targeted taxa.

Colleagues from Austria have developed a two-step multiplex PCR system, allowing for the detection of fish DNA in dietary samples of piscivore predators. This system encompasses fish and lamprey species native to Central European freshwaters and enables the identification of 31 species, six genera, two families, two orders and two fish family clusters. The multiplex PCR is based on barcodes and 16S rRNA primers. The authors conducted feeding trials with Eurasian otters at the zoo and collected feces samples. In addition they used field-collected dietary samples from kingfishers (feces) and cormorants (feces and pellets).

The two-step multiplex PCR approach presented here provides an efficient, easy to use and cost-effective tool to examine the diet of piscivores in great detail. Although the system has been developed for Central Europe, it will be applicable to other regions where the targeted fish species occur; however, we strongly recommend evaluating specificity a priori. Furthermore, the application of the multiplex PCR system is not restricted to prey identification, but the assays or single primer pairs will be useful to any approach where fish DNA needs to be identified with high specificity and sensitivity such as environmental monitoring, studies on environmental DNA or species-specific identification of fish eggs, larvae and carcasses.

Wednesday, July 29, 2015

Barcoding intermediate disease hosts

Freshwater snails of the genus Radix are of considerable medical and veterinary importance as vectors of digenean parasites. Radix spp. are known to be intermediate hosts for schistosomatid blood flukes including avian parasites from the genus Trichobilharzia and the cattle parasite Schistosoma turkestanicum, which are agents of human cercarial dermatitis in Eastern Europe and Asia . Radix also transmits the cosmopolitan re-emerging zoonotic disease echinostomiasis caused by echinostomatid flukes in South East Asia, significantly contributing to the global burden of intestinal trematodiasis. However, perhaps the most important role for Radix in Europe and the UK is as intermediate hosts of Fasciola hepatica and Fasciola gigantica, agents of fascioliasis, causing reduced meat and milk production in cows, as well as morbidity in humans with more than 20 million human cases worldwide.

These first lines of the introduction to a new publication by a group of UK researchers might already be enough to spoil breakfast for some of you but I am sure everyone would agree that it is paramount that we are able to accurately identify the snail hosts to help understanding disease epidemiology and to control spread of these diseases. Radix identification is usually done using shell morphology, colouration, and the genital anatomy. However, the utility of these morphological characters is limited e.g. due to the plasticity of shell morphology and colour. The new study shows once more how powerful DNA Barcoding can be in such cases. Not only does it help to reliably identify the UK species tested but it also proved useful for gaining insights into the evolutionary relationships of Radix species populations which might be very helpful to monitor epidemiology of these diseases. 

This is certainly not the first study proposing DNA Barcoding as tool to identify members of the genus Radix but it puts this application in the context  of emerging diseases and food security.

Tuesday, July 28, 2015

Underestimated butterfly diversity in Europe

How common are cryptic species - those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies.

Since 2006, a team of researchers has barcoded all the 228 known species of butterflies of the Iberian peninsula. The result is a report that compiles more than 3500 barcodes for all the species, which were compared to the barcodes of other European populations.

It is this comparison that suggests that up to 28% of the species could be totally new to science as they represent distinct genetic lineages. Many of these represent cryptic species which are morphologically very similar and therefore have been classified as one single species.

European butterflies also include numerous model taxa for biogeography, ecology and speciation and are intensively used as bioindicators and as flagship group for invertebrate conservation efforts. As a consequence, any change in their taxonomy and any improvement of our knowledge will have consequences for both research projects and conservation policies. As noted, superficial taxonomic decisions may jeopardize an intensively studied system such as European butterflies. Given the alarming rates of global biodiversity loss and the limited resources available, the exploration of biodiversity through large-scale molecular approaches such as DNA barcoding combined with automated methods of ESU [Evolutionary Significant Unit] delineation can provide valuable guidelines for future efforts.

The comparisons here focus on three more densely sampled regions in Europe but there are efforts underway to barcode butterflies and moths in other regions of the continent (e.g. Finland, France). If the numbers revealed by this study hold up for future comparisons Lepidopterists in Europe will have a lot to do right in front of their own doors.

Thursday, July 23, 2015

Stop misuse of biodiversity offsets

We conclude that, with care, biodiversity offsets can help reconcile development with conservation - but if they allow governments to renege on their existing commitments by stealth, biodiversity offsets could cause more harm than good.

Biodiversity offsetting relies on the premise that biodiversity lost in one place can be replaced in another, thereby achieving no net loss. In other words if a developer is going to build something that will damage or destroy a habitat of conservation value then they must compensate for that loss elsewhere by creating an ecologically equivalent benefit. Initially, developers undertook the compensatory work themselves, but gradually a credits-based system emerged where a third party with expertise in conservation takes on the work.

Australian scientists now warn governments against using biodiversity offsetting to meet existing conservation commitments, saying that research had shown that interest in offsetting has surged.

As the approach has gained popularity, governments have increasingly been recognising that industry money generated by offsets could help them achieve national conservation goal targets to which they had already committed - such as those under the Convention on Biological Diversity

For an offset to be valid, it has to create biodiversity benefits beyond those that would occur anyway. So offsets can fund protected areas - but using them to achieve a government's pre-existing commitments is an admission that those commitments were not otherwise going to be met. That might be a reasonable admission for developing nations, but is unlikely to be acceptable from wealthy nations. We recommend that future international conservation agreements explicitly require separate accounting of protected areas created as offsets.

Wednesday, July 22, 2015

A hair will do

American Pika (Ochotona princeps)
Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies.

Endangered and elusive species by definition may be both rare and difficult to locate. As a result, conservation geneticists typically have to rely on sources of DNA collected non-invasively, such as from hair, feathers or feces. Up until now, these approaches have been quite successful in obtaining genetic information from a handful of markers across the genome including DNA Barcodes. Next-generation sequencing (NGS) allows researchers to collect massive volumes of genetic data on the scale of entire genomes but often it requires high quality and large quantities of DNA ideally extracted from fresh tissues or blood. Acquiring such materials is trivial for humans; a mere cheek swab will usually do. This is not the case for species that are both rare and elusive. In such cases, scientists and managers must rely on non-invasively collected sources of DNA that typically yield low quality and low quantity of starting material.

A new study by researchers at the University of British Columbia and SNPsaurus LLC demonstrates that the non-invasive sampling that is essential for many conservation-related studies is now compatible with the minimum requirements for NGS technologies. As a result, it will now be possible to further expand the field of conservation genetics in the genomics era.

We were able to collect genome-wide data from natural populations of the elusive and climate-sensitive American pika on a scale unheard of just a few years ago. There are tremendous benefits for expanding our coverage of the genome when studying species of conservation concern, as it vastly improves our inferences of key genetic characteristics of populations and opens up new avenues for inquiry in the form of potentially identifying those parts of the genome that are involved in organisms' ability to adapt to changing environments.

Tuesday, July 21, 2015

Life in a warming ocean

How will different marine species respond to climate change and which species are in greatest jeopardy due to their limited ability to escape warming waters? Two new studies provide insight from different angles.

Galeocerdo cuvier (Tiger shark)
In Eastern Australia, the ocean has been warming at a rate that's 4-times that of the global average. Many marine species have been appearing further south than they ever have before, while others have stayed put. The first study identifies which characteristics seem to be important for species to shift their ranges so quickly. 

As expected, swimming ability is important. Fish are stretching their ranges south faster than other organisms such as starfish and crustaceans. The researchers also found that animals that have large range sizes are also at equilibrium with their environment, and are therefore the most responsive to change and shift the fastest. The tiger shark, short-tail stingray and barren-forming urchin were some of the fish species with the largest range shifts in the region. Filter-feeding barnacles - omnivores that are notoriously invasive - also displayed some of the largest expansions of territory. Meanwhile the spotted handfish, a coastal species in the same region, hasn't extended its distributional range into cooler waters despite shifting temperatures.

We think that this is because species with large ranges are habitat generalists, so their ranges are currently limited more by temperature and not by habitat, allowing them to move freely when temperature changes.

Acanthochromis polyacanthus
Study no 2 examined how fish's genes responded after several generations living at higher temperatures predicted under climate change. Researchers  used a multi-generational rearing experiment to identify the molecular pathways associated with transgenerational thermal acclimation in the common reef fish, Acanthochromis polyacanthus. The project involved rearing fish at different temperatures for more than four years in purpose built facilities at James Cook University, and then testing their metabolic performance.

The research team sequenced and assembled transcriptomes of the different generations of fish and identified 53 key genes that are involved in long-term, multi-generational acclimation to higher temperatures. 

Metabolic genes were among the most upregulated transgenerationally, suggesting shifts in energy production for maintaining performance at elevated temperatures. Furthermore, immune- and stress-responsive genes were upregulated transgenerationally, indicating a new complement of genes allowing the second generation of fish to better cope with elevated temperatures. Other differentially expressed genes were involved with tissue development and transcriptional regulation. Overall, we found a similar suite of differentially expressed genes among developmental and transgenerational treatments. Heat-shock protein genes were surprisingly unresponsive, indicating that short-term heat-stress responses may not be a good indicator of long-term acclimation capacity.

The study is the first to reveal the molecular processes that may help coral reef fishes and other marine species adjust to warmer conditions in the future.

Understanding which genes are involved in transgenerational acclimation, and how their expression is regulated, will improve our understanding of adaptive responses to rapid environmental change and help identify which species are most at risk from climate change and which species are more tolerant.

Monday, July 20, 2015

Productivity and plant species richness

Before we can even begin to hope to reduce the dramatic loss of species the world is currently experiencing, we need to first have a clear understanding of where we should and should not expect biodiversity to be high or low.

Humans depend on high levels of ecosystem biodiversity, but due to climate change and changes in land use, biodiversity loss is now greater than at any time in human history. A leading global initiative is underway to determine whether there are widespread and consistent patterns in plant biodiversity. Sixty-two scientists from 19 countries spanning six continents studied the relationships between plant biomass production and species diversity. 

In a new study they show that a consistent biological rule governing the link between plant biomass and species richness in grassland ecosystems: plant species diversity is generally greatest at intermediate levels of plant biomass. The humped-back model suggests that plant diversity peaks at intermediate productivity. At low productivity only few species can tolerate environmental stress, and at high productivity only a few highly competitive species can dominate.

In this study, we were asking a very simple question: is there a consistent 'rule' governing how grassland plant diversity varies with local productivity? We are trying to determine how many regions of the world operate in the context of biodiversity patterns. Leaning under the hood [of a car] without any clear vision of what parts should be connected will cause all sorts of frustration. It is much easier to make the necessary adjustments once you learn how the system operates.

The results of these findings help unveil how natural systems operate and have global ramifications for the management and conservation of grassland biodiversity. 

As the underlying causes of biodiversity loss are highly contentious, this will be an active area of research for decades. We are hopeful that by understanding the core relationships between land productivity and biodiversity, we can then refine management recommendations for land users with the goal of enhancing both economic and environmental outcomes.

Friday, July 17, 2015

Horsetail identification

Horsetail (Equisetum arvense) is an herbal remedy that dates back to ancient Roman and Greek times. It was used traditionally to stop bleeding, heal ulcers and wounds, and treat tuberculosis and kidney problems. Horsetail contains silicon, which helps strengthen bone. For that reason, some practitioners recommend horsetail as a treatment for osteoporosis. It is also used as a diuretic, and as an ingredient in some cosmetics. However, few studies have actually investigated horsetail's effect in humans. It also contains traces of nicotine and is therefore not recommended for children.

The global herbal products market has grown in recent years, making regulation of these products paramount for public healthcare. For instance, the common horsetail (Equisetum arvense L.) is used in numerous herbal products, but it can be adulterated with closely related species, especially E. palustre L. that can produce toxic alkaloids. As morphology-based identification is often difficult or impossible, the identification of processed material can be aided by molecular techniques.

Researchers from Denmark have therefore explored two molecular identification techniques as methods of testing the purity of these products: a Thin Layer Chromatography approach (TLC-test) included in the European Pharmacopoeia and DNA Barcoding:

We found that each method has advantages and disadvantages, but the TLC-test is the most efficient way of confirming that material in herbal products is indeed E. arvense. On the other hand, the DNA barcoding can be used as a complementary test to determine the identity of adulterant species, particularly E. palustre.

Future work can focus on systematically studying which Equisetum species produce toxic alkaloids, which will assist the quality control of E. arvense herbal products. Further, a chemical method that directly tests for the presence of alkaloids in herbal products can circumvent problems in species identification, directly testing for the quality and appropriateness for human consumption of herbal products. Additionally, the steadily dropping price of next generation sequencing techniques – which massively amplify short DNA fragments – may considerably enhance the success rates of DNA barcoding in degraded or processed material. Finally, given the presence of several putative hybrids between E. arvense and other Equisetum species, further techniques can be applied to investigate the presence of hybrid material in herbal products.

Thursday, July 16, 2015

Fake caviar

Caviar, which is harvested from sturgeons and paddlefishes (Acipenseriformes), is one of the most expensive animal products in world trade. Not surprisingly, poaching is a major threat to the survival of sturgeon species worldwide. According to the International Union for Conservation of Nature (IUCN) assessments in 2009, sturgeons are considered to be the most critically endangered group of animals worldwide. Since 1998, all 27 species of sturgeons and paddlefishes have been listed in the Appendices of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), which should support their protection from illegal trade. Consequently, any international trade of specimens (e.g., fingerlings or farmed fish), parts and products (e.g., caviar, meat, and fertilized eggs) is controlled and includes a mandatory universal caviar labeling system. With this labeling system, any primary sturgeon caviar containers, including tins, jars or boxes, regardless of the size, must bear a non-reusable label with a code providing all important information about the origin of the caviar. Although this caviar labeling system was developed to distinguish legal caviar from illegal caviar, market surveys using genetic tests for species identification have demonstrated that a considerable amount of mislabeled caviar is still in trade

Only ten labeled tins or jars were in agreement with the species code on their label. Four samples were mislabeled, containing caviar from another sturgeon species or more than one species. In at least one case of mislabeling the caviar was "upgraded" from a lower-priced species to a more expensive one. Six samples were counterfeit and should not have been declared as caviar at all. Three of these counterfeits were free from animal DNA and probably made entirely of artificial substances. One sample was identified as lumpsucker (Cyclopterus lumpus) whose eggs are commonly offered as caviar substitute. The other two counterfeits were most likely made of sturgeon meat.

Four other samples were of great concern. These were sold in restaurants or by street vendors as originating from wild Danube sturgeon, which means they were illegally caught. All four samples were identified as the critically endangered beluga sturgeon (Huso huso) whose population in the Danube region is on the brink of extinction. 

Romania and Bulgaria are the only countries of the European Union where viable populations of sturgeons still occur in the wild, e.g. in the Black Sea and the Danube River. Although catch and trade bans were established in both countries, illegal fishing obviously continues. The results of our study demonstrate the weakness of sturgeon protection in Romania and Bulgaria. Therefore, we recommend enhancing conservation and enforcement efforts.

Wednesday, July 15, 2015

Comparing Methods for Prioritising Protected Areas

There are insufficient resources available to manage the world’s existing protected area portfolio effectively, so the most important sites should be prioritised in investment decision-making. Sophisticated conservation planning and assessment tools developed to identify locations for new protected areas can provide an evidence base for such prioritisations, yet decision-makers in many countries lack the institutional support and necessary capacity to use the associated software. As such, simple heuristic approaches such as species richness or number of threatened species are generally adopted to inform prioritisation decisions. However, their performance has never been tested. 

A group of colleagues from Madagascar and the UK now evaluated the performance of some site prioritisation protocols that used to rank the conservation value of 22 established and candidate protected areas of dry forest in Madagascar. The organisms of choice were reptiles for which there is comprehensive inventory data available from a range of sites in the contiguous dry regions of Madagascar. The country’s reptile fauna is very diverse, comprising almost 400 species, most of which are endemic (92%) and forest-dependent. Given the dramatic deforestation in Madagascar, such species may depend on the effective maintenance of protected areas for their long-term survival.

The authors tested if their rankings produced by four different protocols correlated with the results of a widely-used systematic conservation planning software called Zonation. The four indices scored sites on the basis of: 
  • species richness 
  • an index based on the species’ Red List status;
  • irreplaceability (a key metric in systematic conservation planning, where each species is weighted by the inverse of the number of protected areas in which it was recorded); 
  • a novel Conservation Value Index (CVI), which incorporates species-level information on endemism, representation in the protected area system, tolerance of habitat degradation and hunting/collection pressure.
All of the rankings correlated with the software results, but the CVI and Irreplaceability performed better than Species Richness and the Red List Index which lets the authors conclude:

Given that management is limited by insufficient financial resources, it is all the more critical that available funds are targeted towards the most important sites. While sophisticated analytical tools can and should be used to inform such investment decisions, decision-makers often lack the capacity to use them, or choose not to for other reasons. Instead, they frequently rely on non-transparent, subjective processes or simple measures such as species richness or the number of threatened species. It is therefore important to understand how such metrics can perform and in what circumstances they should be used. Our analysis suggests that some heuristic indices can provide a transparent framework to support evidence-based decision-making by practitioners, although their performance is variable and partially dependent on the amount of information required to use them. Our CVI, which incorporates measures of rarity and threat for individual species, appears to provide a useful alternative to more sophisticated systematic conservation planning tools, and emphasises the benefits of integrating species-specific data into conservation assessments.

Tuesday, July 14, 2015

Greetings from Pluto

Image credit: NASA/JHUAPL/SWRI
After a nine year long journey through our solar system, New Horizons made its closest approach to Pluto today, about 12 400 km above the surface, making it the first-ever space mission to explore a world so far from Earth. New Horizon traveled about 4.8 billion km and during the journey Pluto actually lost its status as planet and was downgraded to a dwarf planet. 

According to plan, the spacecraft is currently is data-gathering mode and not in contact with flight controllers. The Scientists are waiting to find out whether New Horizons is going to transmit a series of status updates that indicate the spacecraft survived the flyby and is in good health. This transmission is expected shortly after 9 p.m. EST tonight. First images of this flyby are expected for tomorrow. Judging from the ones send to Earth over the last couple of days they will be spectacular.

New Horizons' flyby of the dwarf planet is providing an up-close introduction to the solar system's Kuiper Belt, an outer region populated by icy objects ranging in size from boulders to dwarf planets. Kuiper Belt objects, such as Pluto, preserve evidence about the early formation of the solar system. Once the Pluto flyby mission is accomplished New Horizon will continue its journey into the Kuiper Belt and the team hopes to arrange for a couple of further flybys at larger objects.

Image credit: NASA/JHUAPL/SWRI

Monday, July 13, 2015

A new species a day

As announced previously, my weekly column "Discoveries of the week" ended with issue 45. However, I did not intend to get rid of it entirely but rather turn it into a daily blog under a different address: One species a day 

There are many reasons for this change. One was mere convenience as it much easier for me to have a daily short write up on one new discovery than a weekly assembly. A separate blog also addresses a less barcode enthusiastic crowd and it does justice to the amount of new discoveries the colleagues world-wide make every day. A new species every day might sound like a lot but it is not. There still will be discoveries I won't be able to cover even if I produce a post 365 times per year. And that number is dwarfed by the number of new species we have not yet encountered let alone described.

I thought it was about time to start an independent blog focusing on the amazing new species we find every day during our work as scientists. We are three species into this new series. Have a look and feel free to share the link with colleagues, friends, family: One species a day

Friday, July 10, 2015

Bumblebees in trouble

For many species, geographical ranges are expanding toward the poles in response to climate change, while remaining stable along range edges nearest the equator. Using long-term observations across Europe and North America over 110 years, we tested for climate change–related range shifts in bumblebee species across the full extents of their latitudinal and thermal limits and movements along elevation gradients.

To investigate bumblebees' responses to climate change, researchers from Canada, Belgium, Germany, UK and US first generated a database of geotagged observations of 67 European and North American bumblebee species from 1901 to 2010.

They compared changes in individual bee species' northward movements in recent decades, against baseline bumblebee activity from 1901 to 1974, when the climate was cooler. To their surprise, bumblebees in recent, warmer decades didn't shift their ranges north. Simultaneously, bumblebee populations disappeared from the southernmost and hottest parts of their ranges, with bumblebees in those locations moving to higher, cooler elevations, where possible. The colleagues also evaluated the roles of factors such as land use and pesticide application, in causing bumblebee range losses - finding no significant correlation.

Bumblebee disappearances from warm, southern areas are just as likely when there is no pesticide use and little agriculture. But we know that increasingly frequent weather extremes, like heat waves, can hit bumblebee species hard, and climate change poses threats that are already being felt.

Global warming has trapped bumblebee species in a kind of climate vise - the result is dramatic losses of bumblebee species from the hottest areas across two continents. For species that evolved under cool conditions, like bumblebees, global warming might be the kind of threat that causes many of them to disappear for good. Unlike so many other species, bumblebees generally haven't expanded into more northern areas. We may need to help these species establish new colonies to the north and at continental scales.

Here is a York university video about this study featuring two of the co-authors, Sheila Colla from Wildlife Preservation Canada and old friend Laurence Packer, world renowned expert on everything Apoidea. 

Thursday, July 9, 2015

Biodiversity loss in fish ecosystems

Fish are a main protein source for over a billion people worldwide and is one of the most traded food commodities. However, many commercial fisheries have become unsustainable due to practices such as overfishing and habitat destruction. The pressure of commercial fisheries created a new category of species depletion: commercial extinction. Fish populations are depleted to the point that it is no longer economically feasible to fish for them. While not extinct, these species are certainly no longer playing their traditional roles in their ecosystems. Because there is little evidence to the contrary, there has been the common impression that marine species and ecosystems are generally in good shape. However, as more is learned, that impression is turning out to be wildly misconceived. Here is another good example for that:

A new study conducted by researchers from Singapore, Ireland and the UK shows that as the fish diversity of complex marine food webs declines, fish production resists the change, thereby masking ultimate rapid loss. The researchers used a unique high performance mathematical model known as the Population-Dynamical Matching Model (PDMM) to represent thousands of coexisting species dynamically interacting as a food web in a complex ecosystem. The model allows the representation of features such as prey-switching, where predators preferentially target prey species in abundant supply in order to improve their chances of survival. At the end of a gradual assembly stands a model food web very similar to the natural process. 

The team sequentially deleted fish species from such complex model marine ecosystems and after each deletion, observed the dynamics of the remaining fish species and measured the change in total fish production.

The study results showed that the prey of the deleted fish species tended to resist the biodiversity loss by increasing their production, which helped to mitigate the decrease in total fish production. However, once the biodiversity losses became too great and only about a third of the species in a food web remained, a collapse ensued whereby production sharply declined with further species loss, as the relatively small percentage of remaining species were unable to provide much compensation.

This resistance to change in wild fish ecosystems may be masking a more serious decline in production potential in situations where biodiversity loss is already reported, posing the danger of providing a false sense of assurance until the biodiversity losses become too great.

Wednesday, July 8, 2015

Discoveries of the week #45

This will be the last issue of the Discoveries of the week in its current form. I have decided to change the format a little and use another blog of mine exclusively for the introduction of newly described species. Starting tomorrow you will find at least one new species a day under a different address. My hope is to interest not only colleagues and collaborators but also non-professionals and the general public in all the diversity of life that is discovered daily. 

So, for the last time in this format and on this blog:

The Iranian species of Paraschistura are reviewed, and diagnoses are presented for all eleven recognized species. Paraschistura bampurensis, P. cristata, P. kessleri, P. nielseni and P. turcmenica are considered valid; P. sargadensis is a synonym of P. kessleri and P. turcomanus is a synonym of P. turcmenica. Six new species are described. Paraschistura abdolii, new species, from the Sirjan basin and the western tributaries of the Hamun-e Jaz Murian basin is distinguished by having a very slender body and scales restricted to the caudal peduncle and to the back in front of the dorsal-fin origin in few individuals. Paraschistura aredvii, new species, from the Zohreh drainage, is distinguished by having scales on the back, no suborbital flap and the pelvic-fin origin posterior to the dorsal-fin origin. Paraschistura hormuzensis, new species, from the Minab drainage, is distinguished by having scales on the back, a pointed snout and a triangular suborbital flap in males. Paraschistura naumanni, new species, from the Kol drainage, the Mond drainage and the Lake Maharlo basin, is distinguished by having scales on the back, no suborbital flap in males and the pelvic-fin origin below the dorsal-fin origin. Paraschistura pasatigris, new species, from the Karun and Karkheh drainages, is distinguished by having scales on the back and a suborbital flap in males pointed downwards. Paraschistura susiani, new species, from the Jarahi drainage, is distinguished by having scales on the back and a roundish suborbital flap in males. The presence of an additional undescribed species is suggested from the Mond River drainage by the molecular data presented. All species, except unstudied P. kessleri are also characterized by fixed diagnostic nucleotide substitutions in the mtDNA COI barcode region. Paraschistura Prokofiev, 2009 is given precedence over Metaschistura Prokofiev, 2009.

Yes, I do have a soft spot for new fish species as regular readers of this blog might have guessed already. After all I am a fish researcher by trade. This new publication comes with six new loach species from different drainage systems in Iran. Iran is home to eleven species of this recently described genus, the new species are included in that number.

A new species of flea of the genus Ctenidiosomus Jordan, 1931 (Siphonaptera: Pygiopsyllidae) is described from Phyllotis osilae J. A. Allen, 1901, from Salta Province, Argentina. This is the first time that Ctenidiosomus has been recorded in Argentina. A key to species of males of Ctenidiosomus is presented.

A new flea species found on birds and small mammals in Argentina. The specific name is derived from the Latin term austrinus (southern) because this new species represents the southern-most record of any known species of the genus.
no DNA Barcode

With 1,400 described species, Megaselia is one of the most species-rich genera in the animal kingdom, and at the same time one of the least studied. An important obstacle to taxonomic progress is the lack of knowledge concerning the phylogenetic structure within the genus. Classification of Megaselia at the level of subgenus is incomplete although Schmitz addressed several groups of species in a series of monographs published from 1956 to 1981. Another problem is the lack of molecular phylogenetic analyses to support morphology-based conclusions. As a contribution towards addressing these problems, we here circumscribe a previously unrecognized monophyletic lineage of Megaselia consisting of species similar to M. lucifrons. We base this taxonomic decision on morphological study of an extensive phorid material from Sweden, complemented by molecular analyses of select exemplars using two markers (COI and 28S). We name the clade the lucifrons species group, and show that it contains three distinct species. Our results also demonstrate that Megaselia subnitida Lundbeck, 1920, previously treated as a synonym of M. lucifrons Schmitz, 1918, is a separate species, and we remove it from synonymy. The third species in the group was previously unknown; we describe it here as M. albalucifrons sp. n.

Scuttle flies are one of the most diverse families of flies. There are currently more than 4,000 described species, and experts think that this may represent as little as 10% or less of the true diversity. The largest genus in this family is Megaselia and it just got another new member from Sweden.

Agaporomorphus julianeae sp. n. is described from the Biological Field Station Panguana, in Huànuco province of central Peru. The new species belongs to the A. knischi-group sensu Miller 2005. Together with A. knischi Zimmermann, 1921 and A. colberti Miller & Wheeler, 2008 this is the third species of the genus with broadly enlarged male antennomeres. The new species can be separated from A. colberti and A. knischi by the smaller please expanded male antennomere VIII, and the form of the median lobe. Important species characters (median lobe, male antennae, metafemur, colour pattern) of the new species and A. knischi are figured, and the habitat, a temporary blackwater forest pond, and its species rich water beetle coenosis are illustrated and described in detail. The Brazilian A. mecolobus Miller, 2001, only known from the type material from Sao Paulo, is here recorded for Minas Gerais. Habitus photos of four additional Agaporomorphus species and Hydrodytes opalinus (Zimmermann, 1921) are provided. Altogether ten species of Agaporomorphus are now known.

A new diving beetle species named after Juliane Diller, deputy director of the Zoologische Staatssammlung in Munich, and head and owner of the Biological Field Station Panguna, in recognition of her longstanding efforts in biological research and nature conservation in Peru.
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Trachionus mandibularoides

The genus Trachionus Haliday, 1833 (Hymenoptera, Braconidae, Alysiinae, Dacnusini) is reported for the first time from China. The genus is represented by four new species from Shaanxi province (NW China), which are described and illustrated. An identification key to the species in China is presented, a key to the genera of the Trachionus group and notes on the relationships with other Palaearctic species are added.

More braconid wasps. The four new species belong to a genus which includes parasitoids of the larvae of the fly genus Phytobia. All names were chosen based on unique morphological features.
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Bolanthus turcicus
A new species Bolanthus turcicus Koç & Hamzaoğlu, sp. nov. was discovered on Hasan Mountain (Turkey, Aksaray province) where it grows on volcanic stony slopes and alpine steppe. its description, images, chorology and ecology, and threat category are provided in this article. It was compared with a closely related species, Bolanthus minuartioides (Jaub. & Spach) Hub.-Mor., B. huber-morathii C.Simon, B. spergulifolius (Jaub. & Spach) Hub.-Mor., B. frankenioides (Boiss) Bark., B. mevlanae Aytaç based on its general morphology and seed micromorphology.

The name of this new species of the carnation family gives it away - it was discovered in Turkey. It is an endemic species known only from the type gathered on the Hasan Mountain.
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Tuesday, July 7, 2015

Range expansion of the Lyme disease vector

Since 1975, Lyme disease has been diagnosed in 49 US states, with about 300,000 cases a year, concentrated in the Northeast and Midwest. Recent years have seen a dramatic increase in diagnoses. In Pennsylvania, for example, diagnoses rose 25 percent between 2013 and 2014. Scientists attribute the spread to the fact that populations of blacklegged ticks (Ixodes scapularis), which carry the bacteria that causes the disease, now flourish in areas once thought to be devoid of ticks. A 2012 study confirmed a tight association between populations of blacklegged ticks and numbers of human cases and also documented increases in tick populations in areas of the Northeast that were previously thought to not harbor ticks.

In a new study, researchers used genetic and phylogeographic analyses to determine the origin and recent migratory history of newly discovered tick populations in the Northeastern United States. The researchers considered two hypotheses: either the "new" tick populations were actually not new but reflected growth in populations that were previously in the area at undetectable levels, or the populations could have arisen from ticks moving in from other areas, likely by hitching a ride on birds or mammals.

To determine the recent population history of blacklegged ticks in the Northeast, they analyzed data collected in four locations in New York's Hudson River Valley between 2004 and 2009. They sequenced portions of the mitochondrial DNA (16S rRNA, COII, Control region) to understand the relationships between tick populations and how they changed over time. Too bad that they did not include COI in their study to allow connection to existing DNA Barcode data. There are hundreds of sequences on BOLD which would perhaps have allowed for a much larger phylogeographic analysis.

In any event, their findings indicate that the ticks moved into new areas from established populations, mainly through short-distance, local moves. The phylogeographic analysis indicates that ticks mainly moved in progressive south-to-north migration events between neighboring locations, with occasional long-distance movements.

We know that migrating birds can transfer ticks over hundreds of miles during their annual movements. But since the majority of movements documented in this study took place over short distances, less than 100 kilometers, it is not clear under what circumstances animals were moving the ticks. The colleagues roughly estimated that the northernmost locations were colonized 14 years ago, the second most northern 31 years ago and the third most northern 40 years ago. These findings are supported by the fact that no ticks were found in the northernmost site when sampling was done in the early 2000s.

The reason for the population expansion remains unclear. It is possible that the ticks are adapting to new local environments, or that changes in land use and climate are making the new environments more suitable for them. While more work remains to be done to understand what is driving the movement and expansion of ticks, knowing more about their migrations could help inform efforts to protect the public from Lyme disease. Any knowledge on patterns of disease spread could have implications for strategies to control ticks in order to reduce disease. 

From a control perspective, if you know they are moving extremely easily, you could control them in your backyard but they might be back in a week. If we want to reduce tick populations over the long term, this means we have to start thinking about more sophisticated approaches.

Monday, July 6, 2015

Save the Bees with High Tech

Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high-throughput identification pipeline.

The UK's National Pollinator Strategy plans a large-scale bee monitoring programme. Traditional monitoring involves pinning individual bees and identifying them under a microscope. But the number of bees needed to track populations reliably over the whole country makes traditional methods unfeasible. New research shows how the process could become quicker, cheaper and more accurate. This would allow conservationists to detect where and when bee species are being lost, and importantly, whether conservation interventions are working.

The group of researchers from the UK and China used metagenomic mining and resequencing of mitochondrial genomes of bulk samples of wild bees. They assembled the mitogenomes of 48 UK bee species and then shotgun-sequenced total DNA extracted from 204 bees that had been collected in 10 pan-trap samples from farms in England and been morphologically identified to 33 species. Each sample data set was mapped against the 48 reference mitogenomes. The process did not require taxonomic experts (with the exception of the morphology-based identification for the proof of concept and still proved to be more accurate. Also, by skipping the PCR step through direct sequencing, the method was able to estimate the biomass contributed by each species, which opens the way to tracking population trajectories.

The big challenge is that there are hundreds of wild bee species per country, almost 300 in the UK alone. Even with the necessary expertise, it would be impossibly time-consuming to count and identify all the bees in each location. Large-scale bee monitoring programmes would really benefit from this type of DNA sequencing. The method can easily be scaled up to track more species, like the 1000 or so total pollinating insects in the UK. We can find out where species diversity or abundance is highest -- for example in the countryside or in city parks- and how species diversity is affected by farming methods -- for example, to see if habitat set-asides support more bees. 

Friday, July 3, 2015

Discoveries of the week #44

A new genus and species of octocoral with a calcium-carbonate skeleton, Nanipora kamurai sp. n., is described from a shallow coral reef in Okinawa, Japan. Contrary to most octocorals, the skeleton is composed of crystalline aragonite as in blue coral Heliopora. The results of molecular phylogenetic analyses of sequences of mtMutS, COI, and ITS1-5.8s-ITS2-28S region suggest Nanipora gen. n. specimens should be included in order Helioporacea. Based on morphological results compared with other Helioporacea including the genus Epiphaxum (family Lithotelestidae), we establish the new genus Nanipora within Lithotelestidae. This is the first time that a close molecular phylogenetic relationship between Heliopora and a related genus within Helioporacea has been revealed.

Octocorals comprise about 3,000 species including the blue coral, soft corals, sea pens, and gorgonians. They have a characteristic internal skeleton and polyps with eight tentacles. The name of this new genus refers to the Japanese ‘nani’ which means ‘what is this?’, as the genus is highly unusual in having an aragonitic skeleton; ‘pora’ means ‘pore’. The name is used for many anthozoan (especially scleractinian) species with porous skeleton. The species name honors the Jazz pianist Hidefumi Kamura,who has continued playing classic style be-bop jazz since Okinawa was ruled by U.S. forces, and who can now be considered as a ‘relict’ classical be-bop jazz musician.

A new species of the order Amphipoda and the family Niphargidae is described. Niphargus cvetkovi sp. n. was found in groundwaters from Bulgaria. The new species can be attributed to the aquilex-tauri species group and undoubtedly to the tauri sub-group. It resembles some species of this group, such as N. tauri Shellenberg, 1933; N. jurinaci S. Karaman, 1950; N. kragujevensis S. Karaman, 1950; N. remus G. Karaman, 1992 and N. osogovensis S. Karaman, 1959. The main morphological characteristics of the new species are discussed and compared with the species of tauri sub-group.

A new cave-dwelling Amphipod species named after the Bulgarian groundwater scientist Lyubomir Cvetkov. 
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A new geophilomorph centipede, Geophilus hadesi sp. n., is described from caves in the Velebit Mountain, central Croatia. Together with Geophilus persephones Foddai & Minelli, 1999, described from Pierre Saint-Martin cave in France, they are the only two remarkably troglomorphic geophilomorphs hitherto known. The new species apparently belongs to a group of Geophilus species inhabiting mainly Western and Southern Europe, with a uniquely modified pretarsus in the second maxillae. G. hadesi sp. n. shows unusual traits, some of which commonly found in troglobitic arthropods, including exceptionally elongated antennae, trunk segments and leg claws. The species is described upon specimens found in two caves at a depth below -250 m. Another two specimens apparently belonging to the same species have been recorded in another deep vertical cave at -980 m and -1100 m. The latter represents the world’s deepest record of Chilopoda as a whole.

The species name is derived from Hades, god of the underworld in the Greek mythology and husband of Persephone, in analogy with the name of the only other known troglobite in the genus.
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A previously unknown species of the North American leafhopper genus Flexamia, F. whitcombi sp. n., is described from pinebarren smokegrass (Muhlenbergia torreyana (Schult.) Hitchc.), a state-listed threatened grass in the New Jersey Pine Barrens. The serrata species group, to which it belongs, is redefined and a key to the species of the group is provided. This is the first reported insect association with M. torreyana.

The new leafhopper species occurs in the most densely populated state in the US where its host , the pinebarren smokegrass (Muhlenbergia torreyana) grows, The species name honors the mentor of the author, the late Dr. Robert Whitcomb.
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Tumidusternus gen. n., along with T. fujianensis sp. n. (Coleoptera, Coccinellidae, Aspidimerini) from China is described and illustrated. A key to the tribe Aspidimerini is given.

The genus name is a combination of the Latin words tumidus and sternum, referring to its tumid (swollen) sternum. The species name refers to the holotype locality, Fujian, China.
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Recent molecular studies indicate that the Pyropia lanceolata species complex on the west coast of North America is more speciose than previously thought. Based on extensive rbcL gene sequencing of representative specimens we recognize seven species in the complex, three of which are newly described: Py. montereyensis sp. nov., Py. columbiensis sp. nov., and Py. protolanceolata sp. nov. The new species are all lanceolate, at least when young, and occur in the upper mid to high intertidal zone primarily in winter and early spring. Pyropia montereyensis and Py. columbiensis are sister taxa that are distributed south and north of Cape Mendocino, respectively, and both occur slightly lower on the shore than Py. lanceolata or Py. pseudolanceolata. Pyropia protolanceolata is known thus far only from Morro Rock and the Monterey Peninsula, California; it occurs basally to the other species in the complex in the molecular phylogeny. A fourth newly described species, Pyropia bajacaliforniensis sp. nov., is more closely related to Py. nereocystis than to species in this complex proper. It is a thin species with undulate margins known only from Moss Landing, Monterey Bay, California, and northern Baja California; it also occurs in the high intertidal in spring. Porphyra mumfordii, a high intertidal winter species that has frequently been confused with species in the Py. lanceolata complex, has now been confirmed to occur from Calvert Island, British Columbia, to Pescadero State Park, California.

Three of the four new marine red algae species were named after their respective type locality, one (P. protolanceolata) after its position in a phylogenetic tree.

Thursday, July 2, 2015

Order of Canada honours father of DNA Barcoding

Established in 1967 by Her Majesty Queen Elizabeth II, the Order of Canada is the cornerstone of the Canadian Honours System, and recognizes outstanding achievement, dedication to the community and service to the nation. The Order recognizes people in all sectors of Canadian society. Their contributions are varied, yet they have all enriched the lives of others and made a difference to this country. Since its creation, more than 6 000 people from all sectors of society have been invested into the Order.

Yesterday the Governor General of Canada, David Johnston announced the new appointments to the order of Canada and among them Paul Hebert for his achievements as an evolutionary biologist, notably as a pioneer of DNA Barcoding. The Order of Canada has three different categories, companion, officer and member, ranked in order. Paul was made an officer which recognizes national service or achievement.

Congratulations to Paul, a well deserved honour.