Tuesday, September 1, 2015

Genetic diversity in threatened vertebrates

Threatened or endangered populations are identified and ranked by varying methods across states, countries and organizations, but criteria typically are based on demographics.

The International Union for Conservation of Nature (IUCN), for example, identifies species of conservation concern based on the number of mature adults in a population, range size and evidence of population decline. Animal species on IUCN's Red List, the most comprehensive record of threatened species worldwide, are ranked by estimates of how close to extinction they are. However, the criteria currently used to identify at risk species are not correlated with genetic diversity. This suggests that some threatened species could be overlooked because populations with low genetic diversity may not be able to adapt to challenges such as changing environmental conditions, shrinking habitats or new diseases, which could put them at risk of disappearing. 

A new study presents a novel approach for identifying vertebrate populations at risk of extinction by estimating the rate of genetic diversity loss, a measurement that could help researchers and conservationists better identify and rank species that are threatened or endangered.

Genetic diversity is a key component to the long-term survival of a population.The approach we developed identifies populations with limited genetic diversity that isn't going to be enough to allow the population to persist over time. We found that this method performs significantly better than current methods for identifying species in need of conservation efforts.

The colleagues conducted a review of vertebrate genetic data published since 1990 to investigate the relationship between genetic diversity and the at-risk status of animal species. The team used microsatellite datasets from 5,285 studies spanning 17,988 loci to estimate genetic diversity (heterozygosity and allelic richness) across wild populations of birds, fish, reptiles, amphibians and mammals. They found that threatened species had reduced genetic variation, likely due to inbreeding and the random loss of variation that occurs when population sizes are small.

Unless a population with poor genetic diversity has undergone a dramatic decrease in size, it could be overlooked with our current methodology. We should consider genetic diversity in conservation rankings so a species doesn't go extinct simply because it wasn't on our radar.

The team then examined IUCN's criteria for classifying threatened species to determine how effective the criteria were at identifying genetically poor species. If genetic diversity estimates correlated with the Red List criteria, then IUCN would be systematically selecting for populations or species that have declining diversity, the researchers reasoned. However, they found that IUCN's criteria were not closely linked to genetic diversity.

The criteria of many conservation organizations were formulated before the availability of genetic data we have today. But genetic methodology has advanced so rapidly that factoring in genetic diversity is now pretty straightforward. Therefore, we propose that IUCN incorporates an additional criterion that addresses effective population size and genetic diversity for the use in ranking conservation priorities.

Sunday, August 30, 2015

An all taxa inventory

In partnership with the Biodiversity Institute of Ontario and the 6th International Barcode of Life conference, over 100 participants from over 31 institutions and 17 countries searched the rare Charitable Research Reserve -  a 900+ acre land trust located at the confluence of the Grand and Speed Rivers in Cambridge - for all forms of life including birds, bats, spiders, insects, fish, plants, and mushrooms, counting and identifying what was found. Over 1100 species were discovered on the reserve for the first time, including 775 insects, 181 spiders, and even one mammal, a Hoary Bat, never before observed. While more charismatic species like birds and butterflies have been well documented at rare through monitoring and citizen sightings, this BioBlitz shows the magnitude of species existing in front of our eyes and under our feet that we easily miss, e.g. three of the nearly 200 spiders found are new records for the province.

I was one of the participants at the BioBlitz and helped to identify a few fish, some of which belonged to species that were not previously recorded at rare. However, most of my time I spend following colleagues with our video camera and the result is an about 4:00 min long video. Warning! I am not a professional documentary filmmaker. Don't expect BBC or Discovery channel quality.

The BioBlitz spanned nearly 12 hours, covered a variety of different habitats found at rare, and included a BBQ dinner for all participants, but it did not stop there. In the days that followed, over 100 collaborators drafted and published a data release manuscript in the Biodiversity Data Journal that summarizes the findings on the reserve and highlighted the advantages of a rapid blitz approach to species surveys like this one. The paper was published today.

In May of this year the species count for the reserve was at 2 268 species. Now the count is at more than 3 500.

Thursday, August 27, 2015

Protein evolution in Arachnids

Opiliones (Cosmetidae) | by Sidclay Dias
Just at the conference last week it was announced that BOLD, the world's workbench for DNA Barcode data, surpassed the 500 000 species mark. Some 420 000 of those are animal species. With so much information now available for a single gene region (cytochrome c oxidase 1 or COI) we are in a very good position to probe patterns of mitochondrial evolution.

Colleagues here at BIO (Monica Young and Paul Hebert) did just that. In their brand new study they examined levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids. 

Arachnids are the second most diverse group of arthropods with about 100 000 described species but there are colleagues that estimate the real diversity of the group to be at least ten times larger. Certainly a large group to tackle but the with representatives from all 16 orders and 43% of its families (267/625) the dataset studied is equally impressive. 

The colleagues examined divergences at three taxonomic levels—among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10–0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07–0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration.

Indels are an interesting phenomenon especially in animal COI, where they seldom occur.Even more interesting is the relationship between a higher substitution rate and the occurrence of indels and other dramatic changes such as genomic rearrangements. Earlier work has shown that mitochondrial strand-specific nucleotide composition bias in some arachnid groups was among other things caused by an inversion of a fragment containing the COI gene. 

Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is ‘locked down’ in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in ‘locked down’ taxa.

Wednesday, August 26, 2015

Water quality assessment

Caloneis amphisbaena
Diatoms are microscopic algae living in both fresh and salt water.  They are unicellular organisms with silica impregnated cell walls. Living diatoms are among the most abundant forms of plankton and represent an essential part of the food chain in the ocean. Diatoms are responsible for at least 25% of global carbon dioxide fixation. Once dead, their shells accumulate on the seabed and eventually form siliceous sediment deposits.

Given that diatoms are photosynthetic algae, they are restricted to the sunlight zone, i.e. the depth of the water in a lake or ocean that is exposed to sufficient quantities of sunlight to allow for survival. They are highly sensitive to any environmental changes such as light availability, temperature, salinity etc.  In general, diatoms prefer cold, nutrient rich waters. This is what makes them so valuable as indicators for water quality. The specific composition of diatom communities is a very sensitive instrument to measure changes in aquatic environments.

Diatoms have been regularly used as bioindicators to assess water quality of surface waters, especially in developed countries. Many of the widely used diatom indices have been developed as part of studies of European rivers.

Jonas Zimmermann, a German PhD student, developed a reliable DNA Barcoding system for freshwater diatoms which can be used for above mentioned water quality assessments. His protocols and suggestions for extended metadata will likely become part of the methods used to comply with the European Water Framework Directive. He not only provided protocol and tests for optimal marker systems but also discovered four new species in water samples of the nation's capital (Berlin) waterways. His results not only confirmed the utility of the proposed DNA Barcode 18S (V4 region) for protists but he was also able to show that it provided good results for both cultivated samples as well as environmental samples.

For his work he was honored with the Horst-Wiehe Price of the German Botanical Society. This scholarship honors young researchers for exceptional scientific work in the field of botany.

Tuesday, August 25, 2015

Species loss through deforestation

There remains a widespread assumption that concentrating conservation efforts on the protection of isolated reserves is the best way we can safeguard biodiversity. But our work shows that in areas of private land that have already been disturbed -- which dominate much of the tropics -- we need to maintain and protect a wide network of forest areas. Without such a landscape-scale approach we can expect many species to go regionally extinct.

As one of the most comprehensive surveys of the impacts of disturbance on tropical forest biodiversity ever conducted, an international team conducted a detailed analysis of nearly 2,000 species of plants, birds, beetles, ants and bees that were found across more than 300 diverse sites in the Brazilian Amazon. 

The researchers found, where forests had been cleared for cattle ranching and agriculture, plant and animal life was impoverished and remaining species invariably consisted of the same subset of the original flora and fauna, overall irrefutable evidence that biodiversity is declining across the tropics. 

According to their observations, to preserve maximum species diversity, reserves should not be concentrated in one part of a region, but as a widespread network of forest reserves. These should include secondary forests where no primary forests remain. The colleagues emphasize how remaining areas of undisturbed and recovering forest provided the last refuge for many species unable to withstand the impact of human activity.

There remains a widespread assumption that concentrating conservation efforts on the protection of isolated reserves is the best way we can safeguard biodiversity. But our work shows that in areas of private land that have already been disturbed -- which dominate much of the tropics -- we need to maintain and protect a wide network of forest areas. Without such a landscape-scale approach we can expect many species to go regionally extinct.

To preserve maximum species diversity, reserves should not be concentrated in one part of a region, but as a widespread network of forest reserves. These should include secondary forests where no primary forests remain. Over time this would not only help to conserve the local biodiversity but also save money.

These findings are timely as Brazil recently revised its environmental laws regulating forests, allowing a trading system for private reserves and designing plans for environmental restoration. For example, the high variation in biodiversity found in secondary forests indicates the role these ecosystems play in regional conservation. For many areas of the Amazon, conserving existing secondary forests may be much cheaper and even more efficient than planting trees

Monday, August 24, 2015

...and now we're back to meat

Although extensive meat species testing has been carried out in Europe in light of the 2013 horsemeat scandal, there has been limited research carried out on this topic in the United States. To our knowledge, the most recent U.S. meat survey was published in 1995.

Researchers from Chapman University have just published two separate studies on meat mislabeling in commercial products in the US. One study focused on identification of species found in ground meat products, and the other focused on game meat species labeling. Both studies used DNA Barcoding for species identification.

In the first study 48 samples were analyzed and 10 were found to be mislabeled. Of those, nine were found to contain additional meat species and one sample was mislabeled in its entirety. Additionally, horse meat, which is illegal to sell in the United States, was detected in two of the samples. The colleagues think that the presence of multiple species suggests the possibility of cross-contamination at the processing facility. Unintentional mislabeling may occur when several species are ground on the same manufacturing equipment, without proper cleaning in between samples. Another trend observed in the study indicates the possibility of lower-cost species being intentionally mixed in with higher-cost species for economic gain.

The second study, focusing on game meat species labeling, used a total of 54 game meat products collected from online retail sources in the United States. Of these, a total of 22 different types of game meat were represented based on the product label. The results showed 10 products to be potentially mislabeled. Two products labeled as bison and one labeled as yak were identified as domestic cattle. Other mislabeling included a product labeled as black bear that was identified as American beaver, and a product labeled as pheasant that was identified as helmeted guinea fowl.

Game meats represent an important specialty market in the United States with an estimate value of $39 billion. According to the U.S. Food and Drug Administration (FDA), game meats are defined as exotic meats, animals and birds, which are not in the Meat and Poultry Act. Game meats produced in the United States are regulated by the U.S. Department of Agriculture, while game meats imported into the U.S. are regulated by the FDA. The latter is already using DNA Barcoding on a regular basis for seafood and species of their dirty 22 list.

Overall, mislabeling was found to be most common in products purchased from online specialty meat distributors (versus supermarkets), showing a 35% rate of mislabeling.

Friday, August 21, 2015


We are done! The 6th International Barcode of Life Conference is over. A moving and humorous last session with wonderful speakers brought it to a great finish. 

Did you like the drone video? Here is a long version of it:

We'd like to thank everyone for coming to Guelph and for making this conference such a success!