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.