Wednesday, June 29, 2016

The demise of a stonefly

Much remains unknown about the genetic status and population connectivity of high-elevation and high-latitude freshwater invertebrates, which often persist near snow and ice masses that are disappearing due to climate change.

The four members of the stonefly genus Lednia are only known from high-elevation regions of western North America, e.g. Lednia tumana  is endemic to the Waterton-Glacier International Peace Park region of Montana, Alberta, and British Columbia. These species are adapted colder water temperatures as they occur in meltwater streams below glaciers, permanent snowfields, and alpine springs. Global climate change is expected to have dramatic effects on the structure and function of freshwater and the rise of ambient temperature has been correlated with increases in stream temperatures. Here we might have a good example of what might happen to a species that is adapted to colder temperatures. The region in where Lednia tumana is found used to be home to about 150 glaciers (around 1850), 125 of those have disappeared, and if we can believe the latest predictions based on current warming trends it will take less than 15 years for the remaining 25 to vanish as well. This will reduce the amount of suitable habitat for this stonefly by over 80% .

A group of US researchers now explored population genetic structure of this species over the last decade by using DNA barcodes and cytb sequence data. They collected nymphs and adults in 2010 and supplemented with those with older samples collected in 1997, 1998, and 2005. The results were quite sobering: The dominant haplotype was common in both time periods, while the second-most-common haplotype was found only in historic samples, having been lost in the interim. The 2010 populations also showed reduced gene and nucleotide diversity and increased genetic isolation. Our results imply small effective sizes, increased fragmentation, limited gene flow, and loss of genetic variation among contemporary L. tumana populations, which can lead to reduced adaptive capacity and increased extinction risk. This study reinforces concerns that ongoing glacier loss threatens the persistence of L. tumana, and provides baseline data and analysis of how future environmental change could impact populations of similar organisms.

Today all the newspapers and outlets are talking about Adélie penguins and the fact that habitat loss caused from warmer water and loss of sea ice could bring a 60% population decline of this penguin species by 2099. A new study shows that warming in Antarctica, once beneficial to the penguins, has reached a tipping point and is causing the sharp decline. However, as per usual nobody is talking about something as uninteresting as a stonefly and the fact that it is perhaps already too late to reverse the developments that will eventually lead to its extinction. 

Tuesday, June 28, 2016

Courses at Transmitting Science

Sharing knowledge between scientists is our objective. New methodologies need to be learned, and new ideas must be shared and debated in order to advance scientific knowledge.
Our courses cover a wide range of research methods and are aimed at postgraduate students, postdoctoral researchers and established academics from all over the world.

Transmitting Science started in 2012 to manage and offer courses and workshops on different topics related to Life Sciences. The organisation is based in Barcelona, Spain most of the course are held in the region although they also offered some in collaboration with colleagues in Argentina and Canada.

I find their portfolio striking and many courses offer up-to-date training in highly relevant analytical methodologies. Certainly worth a look for a lot of us.

Monday, June 27, 2016

5 Million barcodes

Did anybody notice? Perhaps not, as it happened with no celebratory noise or big announcements. A few days ago BOLD surpassed the 5 Million Barcode mark. The species count is very close to 550,000.

In the days of High-Throughput Sequencing it is not a big thing to upload Millions of sequences to one of the short read archives on the large genomic databases but hosting 5 Million DNA barcode records is a very different thing. These records come with a wealth of metadata, invaluable information that connects a short sequence to a specific specimen, a barcode voucher. 

By now everybody who uses DNA barcoding in one way or another should know that BOLD is the go-to site for DNA-based identification and barcode data management and analysis. Over the last 12 years it served as the central informatics platform for DNA barcoding and played a crucial role in assimilating and organizing data gathered by the international barcode research community. It is a very powerful workbench and analytics tool even more powerful now with more than 5 Million records under the hood. 

Behind every record stands a precious specimen, collected, databased, imaged and sequenced by researchers working on the vision of a bio-literate world. So, it is not only time to congratulate the BOLD team to this important milestone but also the large international barcoding community that has been tirelessly building this invaluable source of biodiversity knowledge. 

Thursday, June 23, 2016

What's inside a rumen?

Roe deer fawn (Capreolus capreolus)
Many central questions in ecology focus on the use and selection of food by individuals, populations or species. Particularly, in large herbivores the applications of such knowledge of the diet is wide ranging. For example, management related questions and the consequences for commercially valuable crops and trees are dependent on knowledge about diets. Most studies of wild ungulate diets use traditional techniques such as macroscopic ruminal, or histological fecal analysis. However these techniques are hampered with inherent methodological problems that involve inaccurate determination of fragmented plant material or simply missing the very small fragments.

This likely introduces bias related to digestibility. Some food items are digested faster than other components and often the latter remain the only identifiable bits for macroscopical ruminal analysis. Quantitative comparisons of diet components based on such analyses will only be of limited used for interpretations of relative importance of food items. In a new studies colleagues compared "metabarcoding" to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates. I set the term metabarcoding in quotation marks simply because the authors did not use a standard plant barcode marker but rather the trnL (UAA) intron. The locus has been used successfully in the past but it is not a DNA barcode.

The authors used Ion Torrent PGM system to analyze diet composition based on rumen content from two large herbivores living in sympatry, roe deer (Capreolus capreolus) and fallow deer (Dama dama), and compared it to a classical macroscopic method to determine food items.

Overall we found a greater number of identified taxa when using DNA. This may reflect the fact that food material stays in the rumen for only a few hours before it is ruminated and later passed along to the stomach. Thus, after rumination some plant species might become unidentifiable macroscopically, while they still are detectable using DNA. Thus, using DNA methods may also increase the window of time for detection of some food items. 

Overall, the high-throughput sequencing data did prove to be more sensitive and taxonomically more reliable. More taxa could be identified and it showed a positive correlation with the amount of biomass identified traditionally, suggesting that the number of DNA sequences obtained may be used as an indicator for how much biomass was consumed.

Wednesday, June 22, 2016

Plant virus detection

Plant viruses in the genus Begomovirus, family Geminiviridae often cause substantial crop losses. These viruses have been emerging in many locations throughout the tropics and subtropics. Like many plant viruses, they are often not recognized by plant diagnostic clinics due in large part to the lack of rapid and cost effective assays. 

When a plant gets infected with a pathogen, it often shows very general symptoms. An accurate diagnosis is essential to knowing which disease one is looking at. However, a number of different pathogens can cause the same symptoms and there are about 1,600 plant viruses out there. BEcause viruses can't be cultured, plant pathology labs use PCR and RT-PCR based tests to detect a part of the virus. Although used regularly in research these tests can be time-consuming and expensive. As a consequence diagnostic laboratories don't test for viruses, and the diseases go unmanaged or managed incorrectly, which is expensive for the grower. 

In a newly published study UF/IFAS scientists examined several ways to detect DNA of begomoviruses. These viruses have emerged over the last 30 years to become plant pathogens that threaten crop production in tropical and sub-tropical regions globally. The researchers found that recombinase polymerase amplification identified the cause of a disease faster and cheaper than commonly used assays.  RPA relies on the extension of primers induced by recombination proteins. These and DNA binding proteins bind the primers and scan for their target. The primers recombine with the target, and a mesophilic polymerase (Bacillus subtilis DNA polymerase I) extend the 3’ end of the invading primer using the opposite strand as a template. As opposed to PCR these reactions can be done at low temperatures (25 °C to 42 °C), with amplification in as short as 15 min which means that there won't be a need for thermocyclers.

The colleagues conclude: RPA could prove useful for the cost effective detection of plant viruses by plant diagnostic clinics. It can be performed in one hour or less with a reagent cost similar to that of PCR but with a lower labor cost, and with an acceptable level of sensitivity and specificity.

Perhaps something to look into not only for plant virus detection.

Tuesday, June 21, 2016

Phlebotomine sand fly identification using HTS

Lutzomyia longipalpis
Phlebotomine sand flies are hematophagous dipterans of primary medical importance. They
represent the only proven vectors of leishmaniasis worldwide and are involved in the transmission of various other pathogens. Studying the ecology of sand flies is crucial to understand the epidemiology of leishmaniasis and further control this disease. A major limitation in this regard is that traditional morphological-based methods for sand fly species identifications are time-consuming and require taxonomic expertise. DNA metabarcoding holds great promise in overcoming this issue by allowing the identification of multiple species from a single bulk sample. 

According to the WHO about 12 million people worldwide are currently infected with Leishmania. Each year about 20000 - 50000 people die from the disease and 2 million new cases are reported annually. About 200 million people live in areas where the disease is common. The disease is transmitted by the bite of infected female phlebotomine sandflies which can transmit the protozoan.

The sandfly genus Lutzomyia genus currently includes 477 described species, among which 56 are proven or suspected vectors of Leishmania. A new study of colleagues from France and French Guiana now assessed the reliability of mitochondrial 16S rRNA sequences using paired-end sequencing on a MiSeq platform. They call their approach metabarcoding but I beg to differ as 16S is not a barcode marker for animals. Not sure what to call it and I also disagree with their assessment that  the standard COI barcode is however not well suited for metabarcoding applications. There are a number of good studies that show that this claim is rather premature. The authors actually suggest the construction of a further reference library for 16S rRNA. 

Nevertheless, the study as such is very good. It is based on a newly constructed reference database for 40 species found in French Guiana. The colleagues successfully experimented with sand flies mixtures of known content and with field samples caught in a 1 ha forest plot in French Guiana. Given the serious basis for the study every progress in species identification should first and foremost be considered a very positive development and disagreement on markers is rather a question of efficiency and community standards but one that should be discussed further.

Thursday, June 16, 2016

BID funding for sub-Saharan Africa announced

In 2015 the European Union announced funding for the multi-year, €3.9 million program Biodiversity Information for Development (BID), led by GBIF. Its aim is to increase the amount of biodiversity information available from the so-called APC (African, Caribbean and Pacific region) nations. The first call for proposals from sub-Saharan Africa, brought in 143 initial concept notes for projects coordinated from 34 African countries. The GBIF Secretariat selected 23 projects with a total funding of €1 million and announced them earlier this week.

The selected projects range across not only diverse geographies but also many thematic areas. The proposed collaborations will seek to build institutional capacity, to mobilize data on Red Listed species and targeted groups of species, and to digitize and share data from museum collections, parks and protected areas. Others harvest species data from activities focused on human health, food security and the reduction of emissions from deforestation and forest degradation.

Here they are: