Genetic diversity of coral reefs

Coral reefs are widely known for their stunning array of color, shape and forms of life, making them a model for extreme biodiversity. Hidden within the multitude of reef inhabitants, but no less important, is their genetic diversity which is linked to adaptive capacity, extinction risk of species, and the overall functioning of ecosystems, so conservation strategies often call for preserving areas of high genetic diversity.

However, there is little direct data to guide debates such as whether many small versus one large reserve would be better to protect genetic resources. Researchers from the University of Hawai'i at Mānoa (UHM) School of Ocean and Earth Science and Technology, the University of California, Santa Barbara (UCSB), University of St. Andrews, and University of Melbourne discovered that large areas of intact coral reef with extensive live coral cover, not disturbed by humans or climate change, harbor the greatest amount of genetic diversity.

The colleagues assessed genetic diversity from over 17,000 samples taken from 47 common reef-associated species across the Hawaiian Archipelago and found that genetic diversity varies across the inhabited Main Hawaiian Islands, extending the argument for targeted protection of reefs throughout the Main Hawaiian Islands. Notably, Hawai'i Island has the greatest amount of coral reef area, harbors the greatest proportion of genetic diversity, and serves a unique, and particularly influential role due to its large size at the margin of the chain. Nihoa and Ni'ihau, which sit at the transition between Papahānaumokuākea Marine National Monument and the Main Hawaiian Islands, also stand out and warrant future research and protection due to intriguing combinations of high genetic divergence and unusual fish composition.

Genetic diversity is widely accepted as critical for adaptation to a changing climate. Although coral bleaching in Hawaii has been relatively rare over the past few decades by comparison to many other places in the Pacific, this stressor still exerts a large impact on the reef communities studied. Research shows that areas which experienced the most frequent coral bleaching conditions also showed depressed levels of genetic diversity, not just for corals but for the entire community of fishes and other invertebrates associated with those habitats.

This negative impact of thermal stress on genetic diversity suggests that climate change will compromise the adaptive capacity and genetic integrity of not just corals but the entire coral reef community.

Identifying features of the landscape that are associated with biodiversity hotspots is one of the key strategies for conservation. The researchers involved in the study plan to follow up on evidence in their dataset that the same large-scale ecological rules that predict species diversity also predict genetic diversity. If that is true it would allow rapid assessment of species diversity using DNA analysis and thereby new metrics of resilience and adaptive capacity.

It is all about the building materials

Leafcutting bees like to make their nests in cavities or in soft rotting wood provided through hollow plant stems or decaying logs. Once a suitable spot has been found, they will build cells using pieces of leaf as lining, by overlapping segments of leaf to make a cylindrical cavity that looks a little like a cigar. Each cell is sealed up with a little segment of leaf. The bees cut leaves from various trees, shrubs, and wildflowers. In parts of Europe, some species line their egg cells with petals instead of leaves. 

The availability of suitable nesting material may limit the geographical ranges and abundances of particular leafcutter bee species. The problem is that their preferences have rarely investigated. For good reasons as the identification of preferred plant species via morphological characters of the leaf fragments is very challenging and direct observation of bees cutting leaves is more than tedious.

Reason enough for a Canadian researcher to barcode the leaf fragments used for cell construction by three different species of the genus Megachile. Two of those species were introduced (Megachile rotundata and Megachile  centuncularis), the third was a native species (Megachile pugnata).  

Interestingly, there was considerable overlap between the preferred species for both introduced bees while the native species showed the least diverse suite of plant species it uses. In addition, the study shows that antimicrobial properties were present in all but six plants collected; all these were exotic plants and none were collected by the native bee, M. pugnata. 

Citizen scientists key to future ecology field research?

Today, research universities scrutinize prospective environmental science faculty candidates, weighing in particular their potential to produce impactful publications and secure large external grants. When can any of us recall a job posting for an academic, tenure-track faculty position that mentioned a transdisciplinary background in natural history as a selection criterion? That omission may exclude those self-identified naturalists and in doing so may be affecting our field in ways we have yet to fully understand. If natural history has lost relevance and has been relegated to the dusty shelves of museums and the weekend pursuits of amateur enthusiasts, then this academic hiring trajectory is justified. However, if it is relevant and arguably constitutes the building blocks for fostering the development of the next Robert MacArthur, E. O. Wilson, or Ruth Patrick, then we should reconsider the path we are on.

A new survey of early-career scientists and environmental-science professionals found that only 11 percent felt their academic training alone provided the needed exposure to natural history, which can be defined as the observation of organisms in their natural environment. The survey coincides with a shift in ecology away from teaching and research rooted in natural history and toward modeling, laboratory and theoretical research, which tend to attract more grant funding and publications in higher-impact academic journals. This shift is occurring despite the cross-disciplinary connections natural history research creates among species, habitats and ecosystems.

For the survey project, researchers questioned 185 professionals, assessing the attitudes and perceptions related to natural history by early-career scientists and environmental-science professionals across 31 universities in California.

Among the findings:

• Of the scientists surveyed, 93 percent agreed that natural history is relevant to science.
• About 70 percent believed it is essential to conduct field-based research.
• Only 54 percent felt inadequately trained to teach a natural-history course.
• More than 80 percent said they would benefit from additional training in natural history.
• Nearly 82 percent of respondents indicated that writing grants, research reports and manuscripts for publication was a daily to monthly component of their job.
• Just more than half indicated that conducting field research was a regular aspect of their employment.
• Only 24 percent had been given the opportunity to participate in a citizen science-type field campaign, which is defined as the collection and analysis of data relating to the natural world by members of the general public, typically in collaboration with professional scientists.

Building on previous experience with citizen science research, the researchers argue that citizen science may be the key to keeping natural history relevant in the 21st century and keeping pace with the direction of modern ecology.

Modern natural historians are in a unique position to act as a bridge between science and nonscientists and should capitalize on the inclusion of the public in ways that will empower them to make societal changes to combat looming environmental and conservation issues.

Biodiversity threat data gaps

Reducing rates of biodiversity loss and achieving environmental goals requires understanding what is threatening biodiversity, where risks occur, how fast threats are changing in type and intensity, and what are the most appropriate actions to avert them. A UN report proposed specific policy recommendations for mobilizing the “big data” revolution for sustainable development and environmental protection. The combination of crowd-sourced data, large-scale ground-based monitoring schemes, and satellite earth-observation missions is seemingly capable of unprecedented insight into global threats to biodiversity and how human interventions are altering those threats.

But, do we have the reliable and accessible data we need to understand the threats to biodiversity, where they occur and how quickly change is happening? It seems not. A new study shows those data are largely missing. We are lacking key information on important threats to biodiversity such as invasive species, logging, bush meat harvesting, and illegal wildlife trade. 

Over the past two years a consortium of 18 organizations compiled available global data on biodiversity threats. They reviewed 290 data sets ranging from remote sensing via satellites to citizen-science initiatives and marked them on five attributes required for conservation assessments. Datasets should be freely available, up to date, repeated, at appropriate spatial resolution, and validated for accuracy. 

Only 5% of the datasets satisfied all attributes. In some cases, the data needed for effective conservation policy already exists but are not accessible due to associated costs, commercial considerations or intellectual property arrangements. What's needed in such cases are agreements between conservation organizations and private companies, such as the one between IHS Energy and UNEP-WCMC that allow non-commercial use. The authors of the study consider governments as another  valuable future source of information. Some recent Open Government Initiatives e.g. in the UK and US have made more than 200,000 datasets freely available, including several that are relevant to environmental conservation. This should be adopted in other nations as well.

The colleagues also stress that filling these data gaps need not start from scratch. Several existing datasets, such as those dealing with invasive species on islands around the world, can be scaled up if appropriately resourced.

We were surprised that so few datasets met all of the five attributes we believe are required for 'gold standard' of data. We live in the age of Big Data, but are effectively flying blind when it comes to understanding what is threatening biodiversity around the world.

DFO PostDoc Position

Developing metabarcoding tools for environmental DNA-based biomonitoring in aquatic ecosystems

Fisheries and Oceans Canada: Pacific Biological Station, Nanaimo, British Columbia

A post-doctoral fellow with an interest in applied ecological and evolutionary genomics and aquatic ecosystems is being sought to lead the development of metabarcoding-based biomonitoring approaches to meet federal regulatory needs.

Multiple projects are underway. The successful candidate will play a lead role in a multi-disciplinary project on validating the use of environmental DNA (eDNA)-based metabarcoding (targeting meoifauna) for benthic impact assessments of salmon farms in coastal British Columbia. Salmon aquaculture causes organic enrichment of surrounding sediments which affects biodiversity and biomass of benthic fauna concomitant with sediment chemical changes. Existing environmental impact assessments rely on manual morpho-taxonomy or abiotic proxies of organic loading with uncertain accuracy. The project aims to develop an efficient and reliable lower-cost alternative based on cataloging the diversity and abundance of benthic communities through metabarcoding of environmental DNA (eDNA).

The successful candidate will also play a key collaborative role within two other projects aimed at developing metabarcoding based eDNA biosurveillance of aquatic invasive species (AIS). Aquatic invasive species (AIS) pose a major threat to freshwater aquatic ecosystems and fisheries in BC; detecting new invasions early and accurately assessing existing AIS distributions are important to maximize the chance for effective management intervention.

The successful candidate will have a PhD in ecological and/or evolutionary genomics or another relevant area and will demonstrate well-developed bioinformatics and computational skills (including programming, e.g. Perl, R, Unix, Python) as applied to the analysis of next-generation sequencing data. Experience in the preparation of samples for NGS (Illumina) and knowledge of barcoding, metabarcoding, and/or environmental DNA sampling in aquatic systems would be an asset but not a requirement. Candidates should demonstrate a strong track record of publication and be willing to work as part of a collaborative team.

A 2 year Postdoctoral Fellowship position starting by January 2017 is available with stipend funding at NSERC Visiting Fellowship rates. Applications from international candidates will be accepted. For more information and to review eligibility criteria.

To be considered for this position, please send your CV and brief email text explaining your suitability to 

Cathryn Abbott, Ph.D.

Research Scientist, Pacific Biological Station

DNA Day

Every year in April countries around the world celebrate DNA Days. These national DNA Day are very often used to educate the public about current DNA science. Students, teachers and the public can learn more about genetics and genomics. The day commemorates both the completion of the Human Genome Project in April 2003, and the discovery of DNA's double helix in 1953.

Canada’s DNA Day brings together students and the science community.  Established by Let’s Talk Science and Genome Alberta, it includes live virtual Q&A sessions with Canadian experts. This year the events cover personalized medicine and DNA barcoding. The barcoding part will be broadcasted from of our institute on April 21st and yours truly and two colleagues will give short talks and serve as experts in the Q&A sessions.

Sounds like fun and I am really looking forward to it.

Another round of the intro course

By the way, we are running another round of the DNA barcoding intro course. It will start in a week from now: April 18 to June 10, 2016

Meanwhile I am busy developing two new modules, one on metabarcoding and another on of DNA barcoding in regulatory contexts and forensics

Distribution and diversity of a potato cyst nematode

Image from http://nematode.unl.edu

Potato cyst nematodes (PCN) are small (1 mm) roundworms belonging to the genus Globodera, which comprises 12 species. These worms live on the roots of plants of the Solanaceae family with prominent members such as potatoes and tomatoes. The nematodes cause growth retardation and, at very high population densities, damage to the roots and early senescence of the plants. PCN are thought to be originated in the Andes but are now widespread both in Europe and North America .

These nematodes can cause significant economic damage. Estimated costs due to yield loss and control measures are thought be at the range of billions of US dollars. PCN species are present on both EPPO and USDA quarantine organism lists.

Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species.

In a new study researchers identified a section of cytb (<450bp) descriptive of three main mitotypes of one species (Globodera pallida) present in the UK and used a high throughput sequencing approach to the simultaneous analysis of all SASA samples (>800). By using this approach, the colleagues were able to describe the distribution of Globodera pallida mitotypes across Scotland with field-scale resolution. In addition they could quantify the relative abundance of each mitotype across an order of magnitude.

This study provides a method for accurate, quantitative and high-throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.

The future of biodiversity collections

The time for business as usual has passed. Threats to biodiversity are increasing. There is a real concern that the scientific community does not have the resources necessary to answer important questions.

This concern has been reinforced recently as e.g. in the US state and federal agencies have reduced or withdrawn support for biodiversity collections. The biodiversity community has responded to these developments in the usual ways, reactive, but not proactive.

Biological diversity collections leaders, scientists, communications professionals, and scientific organization leaders met last Fall at The Field Museum of Natural History in Chicago for a workshop organized by the Biodiversity Collections Network. They identified poor communication within the biodiversity collections community and between the community and decision-makers as a contributing factor. 

Seven recommendations emerged from this workshop and are outlined in a report. The general recommendations are:

1) The community must articulate a compelling and inclusive long-term vision for natural history collections.

2) The community should work with an existing community-serving organization with links to administrators, policymakers, and communicators to foster greater coordination of targeted messages.

3) The community must engage new stakeholders to increase the sustainability (i.e., new funding, proper institutional support, adequate workforce) of digitization efforts.

4) The community must do a better job of communicating outcomes and benefits of digitization efforts to policymakers, administrators, other scientists, and the public.

5) The community must develop metrics for assessing the impact of current and new communication tools and practices.

6) The community must develop and embrace innovative communication methods and tool kits.

7) The community must support and engage in communications training programs that help all biodiversity collections stakeholders, particularly scientists, become more effective spokespeople for natural history collections.

These developments show how important it is that we do a better job of communicating about both the increased demand for spatial and temporal data on biodiversity and the vitally important research that biodiversity collections enable. The report includes a number of significant recommendations for the Natural Science Collections Alliance and we are eager to begin addressing these in collaboration with our membership and partners.

Hope for cold water species

The great irony is that the cold headwater streams that were believed to be most vulnerable to climate change appear to be the least vulnerable. Equally ironic is that we arrived at that insight simply by amassing, organizing and carefully analyzing large existing databases, rather than collecting new data that would have been far more expensive.

A research team led by the U.S. Forest Service drew information from huge stream-temperature and biological databases contributed by over 100 agencies and a USGS-run regional climate model to describe warming trends throughout 222,000 km of streams in the northwestern United States.

The colleagues found that over the last 40 years, stream temperatures warmed at the average rate of 0.10°C per decade. This translates to thermal habitats shifting upstream at a rate of  300-500 meters per decade in headwater mountain streams where many sensitive cold-water species currently live. The authors are quick to point out that climate change is still detrimentally affecting the habitats of those species, but at a much slower rate than earlier studies forecast. This indicates that many populations of cold-water species will continue to persist this century and mountain landscapes will play an increasingly important role in that preservation by becoming climate refugia. This also means that resource managers will have more time than previously thought to complete extensive biological surveys of ecological communities in mountain streams so that conservation planning strategies can adequately address all species.

One of the great complexities of restoring trout and salmon under a rapidly changing climate is understanding how this change plays out across the landscape. Dr. Isaak and his colleagues show that many mountain streams may be more resistant to temperature change than our models suggest and that is very good news. This provides us more time to effect the changes we need for long-term persistence of these populations.

A DNA diode

It looks as if this week will become my "what-else-is-happening-in-DNA-research" week. Yesterday the alternate use of stop codons in some bacteria and today the fascinating research by colleagues from the US and Israel - a nanoscale diode made out of DNA.

Continuous demand for more computing power is pushing the limitations of present day methods. This need is driving researchers to look for molecules with promising properties and find ways to establish reliable contacts between molecular components and bulk materials in an electrode, in order to mimic conventional electronic elements at the molecular scale.

An example for such an element is the nanoscale diode (or molecular rectifier). A diode operates like a valve to facilitate electronic current flow in one direction. Researchers envision that a collection of these nanoscale diodes, that are essentially molecules, has properties that resemble traditional electronic components such as a wire, transistor or rectifier. The emerging field of single molecule electronics hopes to find ways to overcome Moore's Law - the observation that over the history of computing hardware the number of transistors in a dense integrated circuit has doubled approximately every two years - beyond the limits of conventional silicon integrated circuits.

The researchers took a single DNA molecule constructed from just 11 base pairs and connected it to an electronic circuit only a few nanometers in size. When they measured the current through the molecule, it did not show any special behavior. However, when layers of a coralyne were inserted between layers of DNA, the behavior of the circuit changed drastically. Coralyne is a small crescent-shaped molecule that is among a group of molecules known to preferentially intercalate DNA triplexes over duplexes and to increase the thermal stability of triplex DNA . In the case of the diode experiment the current jumped to 15 times larger negative vs. positive voltages--a necessary feature for a nano diode.

In summary, we have constructed a molecular rectifier based on intercalating specific, small molecules into designed DNA strands. Not only do these results offer a new method for studying the DNA–molecule interaction, they also suggest a novel strategy for engineering molecular electronic elements based on a specifically designed functional DNA complex.

Stop doesn't always mean stop

This illustrates the ease by which the genetic code may evolve new coding schemes, possibly aiding organisms to adapt to changing environments, and show the genetic code is much more flexible than previously thought.

In 2014 researchers from the Joint Genome Institute and Yale University found out that some organisms interpret the one of three "stop" codons which terminate translation to mean anything but. In a computational study they scanned several trillion base pairs of metagenomic data and revealed a large number of stop codon reassignments in bacteria and bacteriophages. In some of those organisms, the three-letter codon UGA, which normally signals the end of a protein-coding gene, is hijacked to code for a the rarely encoded amino acid called selenocysteine.

The same team now discovered that some microorganisms actually recognize more than one codon for selenocysteine. From approximately 6.4 trillion bases of metagenomic sequences and 25,000 microbial genomes, the team identified several species that recognize the stop codons UAG and UAA, in addition to 10 sense codons, as acceptable variants for the selenocysteine codon UGA.

What about eukaryotic organisms? Although we found nine tRNASec variants of algal origin, they need further validation, because they are almost identical to canonical tRNASec species. A similar search of 92 mammalian genomes (215 Gbp) and of the Drosophila melanogaster genome (139 Mbp) showed no exception to the use of UGA as the Sec codon. Whether this is related to the necessity of selenoproteins in high-level redox signaling pathways or due to the sophisticated backup systems remains to be investigated. However, in the lower eukaryote Euplotes crassus UGA serves both as a Cys and also as a SECIS-dependent Sec codon