Tuesday, August 23, 2016

Regulatory and Forensic Applications of DNA Barcoding course

As promised earlier yet another announcement for a new online course. The third course developed by us and the Open Education group on the University of Guelph campus revolves around the use of DNA barcoding in regulatory and forensic science:

Regulatory science can benefit from barcoding technology to give precise identification to the species level of traded commodities, as well as preserving identity chains where close substitutes or counterfeits disrupt economics and trust between partners. Barcoding is relevant in these respects to trade associated with forestry, capture and culture fisheries, terrestrial agriculture including commodity crops, fruits and food animals.

In addition to the authentication and traceability functions, barcoding can also serve an important role in the identification and surveillance of pests. It may even be possible to use barcoding technology for identity preservation systems traded commodities such as crops where adventitious presence of un-approved varieties threatens trade and brings the risk of economic loss.

This 6-week program will provide an overview of the state of current technology and the various platforms used. It consists of a series of online lectures and research exercises introducing different aspects of regulatory and forensic DNA barcoding research. There will be a strong emphasis on case studies and support for protocol/standard operating procedure adaptation and development. 

We are also collaborating with researchers of the Canadian Food Inspection Agency (CFIA) in order to design a course that is as close to the needs of the regulatory and forensic communities as possible.

Registration for the first offering (October 31 to December 9, 2016) is already open

Thursday, August 18, 2016

How old is the Isthmus of Panama?

The formation of the Isthmus of Panama stands as one of the greatest natural events of the Cenozoic, driving profound biotic transformations on land and in the oceans. Some recent studies suggest that the Isthmus formed many millions of years earlier than the widely recognized age of approximately 3 million years ago (Ma), a result that if true would revolutionize our understanding of environmental, ecological, and evolutionary change across the Americas.

Long ago, one great ocean flowed between North and South America. When the Isthmus of Panama joined the continents, it also separated the Atlantic from the Pacific Ocean. If this took place much earlier than the accepted date of 3 million years ago as recently asserted by some, the implications for both land and sea life would be revolutionary. Estimates of rates of evolutionary change, models of global oceans, the origin of modern-day animals and plants of the Americas and why Caribbean reefs became established all depend upon knowing how and when the isthmus formed.

An international team of researchers from 23 institutions now reevaluated all of the available lines of evidence, such as geologic, oceanographic, genetic and ecological data to come up with a firm estimate of when the Isthmus formed. Their work provided three key pieces of evidence that define when the land bridge was finally in place:

  • Analysis of the family trees of shallow-water marine animals such as fish and sand dollars from the Pacific and Caribbean (Atlantic) sides of the isthmus show genetic mixing until after 3.2 million years ago.
  • Surface waters from the Pacific and Caribbean mixed until about 2.8 million years ago, as seen in deep-ocean sediments.
  • Massive migrations of land animals between North and South America began sometime before 2.7 million years ago.
These independent lines of evidence converge upon a cohesive narrative of gradually emerging land and constricting seaways, with formation of the Isthmus of Panama sensu stricto around 2.8 Ma. The evidence used to support an older isthmus is inconclusive, and we caution against the uncritical acceptance of an isthmus before the Pliocene.

Tuesday, August 16, 2016

Endangered species? Get in line.

The U.S. Endangered Species Act of 1973 (ESA) was signed on December 28, 1973, and provides for the conservation of species that are endangered or threatened throughout all or a significant portion of their range, and the conservation of the ecosystems on which they depend. Approximately 2,270 species are listed as endangered or threatened under the ESA but species must first be listed as threatened or endangered before receiving protection under the Act. In an attempt to accelerate the latter process, Congress passed an amendment in 1982 declaring a two-year timeline for the process, which starts with submission of a petition and ends with a final rule in the Federal Register.

But how close is this timeline to the reality? A group of U.S. researchers now evaluated factors affecting the number of species listed annually under the Endangered Species Act between 1983 and 2014. They used an information theoretic approach to assess whether listing budget, policy phase, or both factors were associated with the number of species listed and they calculated processing times for those.

While the law lays out a process time of two years for a species to be listed, what we found is that, in practice, it takes, on average, 12.1 years. Some species moved through the process in 6 months but some species, including many flowering plants, took 38 years to be listed - almost the entire history of the ESA.

It comes to no surprise that annual listing rates were positively affected by budget increase. However, the listing process for any species spans multiple years. Therefore, the colleagues also evaluated how taxonomy, the initiating organization, and lawsuits affected the duration of the listing process. They found that vertebrates had a significantly shorter wait time than did invertebrates and flowering plants. For example, the island night lizard (Xantusia riversiana) was listed in 1.19 years, whereas the prairie fringed orchid (Platanthera leucophaea) took 14.7 years to be listed. The lizard has since recovered and been removed from endangered status; the orchid is still considered threatened.

While the [US Fish and Wildlife] Service can account for species groups in its prioritization system, it’s not supposed to be mammals versus insects versus ferns but, rather, how unique is this species within all of the ecological system. However, our findings suggest some bias that skews the process toward vertebrates...Our results show that the process time from petition to listing would need to increase in speed 6-fold to meet statutory limits under the ESA. An increase in number of species listed annually, which currently stands at roughly 50 species per year, would be needed to provide protection to the hundreds of species not currently recognized as candidates, but that are in fact imperiled.


Thursday, August 11, 2016

DNA barcoding of consumer-relevant mushrooms

The dietary supplement industry has grown from $4 billion in 1994 to an estimated value of $35 billion in 2015 in the United States, and many “mushroom” containing dietary supplements are formulated with one to several fungal species. The world production of mushrooms for this industry has been estimated to be around $18 billion, and their trade has been compared to the value of coffee sales worldwide. In 2002, the global market value of mushrooms in dietary supplement was approximated to range from $5-6 billion.

However, the industry is facing the challenge of ensuring reliable species identifications for process material. A multitude of modifications along a multilevel supply chain makes it particilar difficult for samples containing fungal mycelia. Processes such as milling, drying, and extraction usually destroy important morphological characters and as a consequence species identification based on such methods is out of the question.

A group of US researchers has now successfully demonstrated the utility of the DNA barcode standard marker ITS to provide reliable species IDs for all sorts of fungi found in the food and dietary supplement products. Their results confirm - not unexpected - that barcoding works quite well and, if properly executed, could enrich the tool set available to regulators and researchers.

Barcoding methods highlighted here could ensure the industry of product reliability, thereby ensuring both consumer safety and product integrity. Even when morphology can be discerned, for example in culinary mushrooms, we have revealed that a sample labeled as B. edulis and sold in a U.S. grocery store was actually a new species that was recently reported from grocery stores in the UK. We have also demonstrated that some fungal containing products sold commercially as dietary supplement are not entirely accurate in terms of the scientific names that were displayed on the product label.

Wednesday, August 10, 2016

eDNA to detect largetooth sawfish

Sawfishes (Family Pristidae) are the most threatened family of elasmobranch (sharks and rays), with all 5 species listed on the IUCN Red List of Threatened Species as either Critically Endangered or Endangered. Limited observational data and expert opinion suggest that sawfish species are now extinct in at least 20 countries within their former distribution, and are possibly extinct in many more.

A lack of understanding the remaining extant range of sawfish due to their rarity and scattered occurence in remote regions has hampered our ability to implement recovery strategies. Researchers from James Cook University and Charles Darwin University have tested the utility of DNA barcodes obtained from environmental DNA (eDNA) to find the freshwater largetooth sawfish (Pristis microdon) in remote northern Australia.

Before trying the technique in the wild some initial tests were done on water samples from different aquaria and the colleagues were able to correctly tell which contained largetooth sawfish. Traditional methods to search for sawfish, such as fishing surveys, can be expensive and time-consuming. To test the approach in the wild, the research team sampled known largetooth sawfish habitats in the Daly River, Northern Territory. They partnered with indigenous owners and rangers. 

The method was mostly accurate in waterholes but not as good in flowing rivers likely the result of the high water flow and the associated turnover rates . This is not a big problem, this is very much a trial phase and it will be solved quite easily given some more timeWithin five to ten years it's hoped that all eDNA analysis will be able to be completed in the field, with no need to take samples back to the lab.


Tuesday, August 9, 2016

What snow leopards really eat

Declining prey populations are widely recognized as a primary threat to snow leopard (Panthera uncia) populations throughout their range. Effective snow leopard conservation will depend upon reliable knowledge of food habits. Unfortunately, past food-habit studies may be biased by inclusion of nontarget species in fecal analysis, potentially misinforming managers about snow leopard prey requirements.

It was estimated that there are only 4,500–7,500 snow leopards left in the wild and consequently the species is listed in CITES Appendix I. Knowledge of their dietary habits is a life-history parameter needed for effective conservation but it seems that as a result of the inclusion of non-target species samples in past studies, our understanding of the snow leopard has been biased to say the least. The issue with collecting and identifying scat in the field is that researchers mostly rely on morphological characteristics such as shape, size or associated signs of snow leopards, and since scat from different species can look similar, this can lead to misrepresented population estimates and errors in reporting what the snow leopards are actually eating.

It has been thought that they consume great numbers of small mammals such as marmots, hares and pika, as well as wild ungulates, such as ibex. Older estimates of the amount of small mammals snow leopards consume may have been overstated, and the importance of large ungulate populations to the snow leopard's diets may have been understated, as a new study suggests. Stable snow leopard populations are possibly more reliant upon large ungulate prey than previously understood.

This can affect conservation plans because if snow leopards are eating more large ungulates, we need to make sure we're maintaining those large ungulate populations. Otherwise, a population of snow leopards might not survive because there's not enough prey, or they may start eating more domestic livestock, which can cause problems with local human populations. That could result in people going out and killing snow leopards in retribution.

The colleagues analyzed 199 suspected snow leopard scat samples collected from two study sites in Tajikistan and from two study sites in Kyrgyzstan utilizing mitochondrial genetic markers. Overall, only about a third of collected scats thought to be from snow leopards were confirmed as snow leopard, many turned out to be from red fox . The snow leopard samples were most often confused with red fox (Vulpes vulpes) scat, which comprised almost 40% of collected samples.


We don't want to overstate our results because this was just one study, but we did notice that if we were using the blind approach, we definitely had a lot more small mammal occurrence in those scats. When we used genetics to pre-screen the scat and find out which ones were actually snow leopard, there were many fewer small mammals in those scats. It's a little bit of conjecture, but our thought is that a lot of food habit studies that have not been able to verify that their scat is actually from the species that they're studying probably do have this bias soaking in from other species.

Monday, August 8, 2016

The microbiome of wine

Source: cupegraf
Culture-independent methods of microbial identification have been developed, which allow for DNA extraction directly from environmental samples without subjecting microbes to growth on nutrient media. These methods often involve next generation DNA sequencing (NGS) for identifying microbes and qPCR for quantifying them. Despite the benefits of extracting all DNA from the sample, results may be compromised by amplifying DNA from dead cells. 

In a recent study, researchers of the University of British Columbia developed a technique that combines a process to identify the full spectrum of DNA in yeast and bacteria samples with a technique that distinguishes between live and dead micro-organisms. Key in the development of their method was the use of a light-sensitive dye, propidium monoazide, which deactivates DNA in non-viable cells and thereby prevents it from being detected. The colleagues tried to identifying the yeast and bacterial diversity of wines.

Since only live micro-organisms are relevant in the various stages of fermentation as they relate to the senses, this study provides some of the important tools that will be necessary to determine why different types of wine taste and smell as they do. While more research needs to be conducted, these findings could also lead to the identification and elimination of micro-organisms that are responsible for spoilage.

The new technique allows for a much faster and more accurate assessment. What previously could have taken multiple experiments and months of trial and error, can now be done in a single experiment. 


The next stages of research will focus this technique on different types of wine making methods to see how they change micro-organisms that affect the final wine product.