Chinese Amphibians

Since 2013, Cold Code, the initiative to barcode all amphibians and reptiles is working to assemble a DNA Barcode reference library. Cold Code is being coordinated out of the Kunming Institute of Zoology (KIZ), Chinese Academy of Sciences. To assure success, the project received start up funding. As a result, Cold Code offers to sequence the first 10 specimens of a species at no cost to an investigator but those requesting the service must submit relevant voucher data associated with the tissue samples. These data include but are not limited to species identification, collecting information locality (with GPS data), voucher specimen number (including image), collectors and steward of the data. 

The colleagues in China now presented some of their progress on amphibian barcoding. A new website, developed by the Kunming Institute of Zoology, provides information on Chinese amphibian species for herpetologists and the general public alike. As you can tell from the screenshot the site is in Chinese but Google translate does a fairly decent job to allow you to explore the site. 

The site currently holds 302 out of the 429 species of Chinese amphibians and according to the press releases all of them have a DNA Barcode. I am not sure if all these sequences are also on public databases such as BOLD or GenBank. The site has an ID engine (based on the BLAST algorithm) available but I wasn't able to access the reference library.

This is great progress for Cold Code and the website shows some very interesting creatures with detailed information on them.

Three steps for better protected areas

Achieving CBD's goals are imperative for nature and humanity, as people depend on biodiversity for important and valuable services. The scientific community now must step up and actively help governments identify what is need for their future protected area estates so they can achieve great conservation outcomes.

The Convention on Biological Diversity and its 193 signatory nations established 20 Aichi Biodiversity Targets organized under five strategic goals. Aichi Target 11 says: By 2020, at least 17 per cent of terrestrial and inland water, and 10 per cent of coastal and marine areas, especially areas of particular importance for biodiversity and ecosystem services, are conserved through effectively and equitably managed, ecologically representative and well connected systems of protected areas and other effective area-based conservation measures, and integrated into the wider landscapes and seascapes.

We are half way into this ten year plan, and progress towards the targets has been made, with 15.4% of the world’s terrestrial area and 8.4% of the marine realm covered by a Protected Area (PA) under national jurisdiction. Yet it is widely accepted that the overall PA estate is inefficient because PAs: are often poorly-located as well as poorly-managed; fail to capture important elements, functions and services of biodiversity; and, are failing to address continuing pressures such as outright habitat loss and resource exploitation, due to corruption, poor governance, or insufficient financial resources.

An international group of researchers has developed a three-point plan to ensure the world's protected areas meet these targets as they recognize that part of the current failure of the protected areas to stop the decline of biodiversity is partly to do with the lack of science available. The colleagues offer strategic guidance on the types of science needed to be conducted so PAs can be placed and managed in ways that support the overall goal to avert biodiversity loss. The three points of their solution are:

1. Establish ecologically sensible protected area targets to help prioritize important biodiversity areas and achieve ecological representation.
2. Identify clear, comparable performance metrics of ecological effectiveness so conservationists can assess progress toward the targets.
3. Identify metrics and report on the contribution of "other effective area-based conservation measures (OECMs) make toward the target.

You better know what bit you

King Cobra (Ophiophagus hannah)

Bites from venomous snakes are common in many parts of the world and a serious unresolved health problem to millions of people living in South and Southeast Asia, as well as Africa and Latin America. Although there are no reliable numbers at the global scale, it has been estimated that at least 421,000 cases of venom snakebites with up to 94,000 deaths occur worldwide each year. However, experts warn that these figures likely underestimate the real problem, which is believed to affect several million people bitten by venomous snakes annually and hundreds of thousands who die or survive disabled, suffering from amputation or deformed limbs as a result of unavailable or delayed treatment.

People bitten by snakes often do not seek treatment at a medical facility, and if they do, the vast majority don't take the snake with them although it is often killed. Of course they also can't identify the species that actually bit them. However, knowing the species of snake is critical to determining the best course of treatment. And even if the victims do everything right, the clinical personal does not necessarily have the expertise to identify the snake species.

Researchers from Thailand have now build a first DNA Barcode reference library for venomous snakes and one non-venomous snake (Python bivittatus bivittatus) found in Thailand. Based on their results they also developed species-specific multiplex PCR markers to allow for rapid delimitation of

eight groups of venomous snakes for which the Thai Red Cross keeps antivenom for clinical use. This assay could easily be applied to venom and saliva samples. If venom could be assigned to a particular species, doctors could quickly give anti-venom instead of waiting for clinical signs of poisoning, as it is current practice. This would also accelerate the transfer of patients to referral hospitals with intensive care units able to ensure adequate respiratory support. Such a test would be easy to administer in rural healthcare settings with limited resources.

This is a promising development in the search for an efficient means of examining snakebites, which could ensure the application of appropriate antivenom therapy. However, improvements in the sensitivity of markers, the limitation of locally restricted markers, and protocols for DNA isolation from a remnant swap are still required in order to produce an optimal and practical procedure for the delimitation of snake species.

Maine Barcode of Life Project

I have talked about this repeatedly - DNA Barcoding lends itself to education at various levels. Not only is the concept relatively simple to understand, but is also multidisciplinary and modular by nature. Schools, colleges and universities start embracing it more and more although the latter could do more for my taste. Very often it is independent organisations that take up the idea and offer it to students and/or teachers. A good example are our friends from Coastal Marine Biolabs in Ventura, California. 

Another rather new organisation that offers inroads to STEM (Science, Technology, Engineering and Math) education is iXplore, an independent, nonprofit organization with the goal to encourage students to pursue STEM degrees, to promote STEM awareness in the state of Maine, thereby expanding the skilled workforce supporting STEM-dependent business sectors.

Program participants contribute to the Maine Barcode of Life project using DNA Barcoding while working in a college biochemistry lab at the University of New England. Participants are introduced to molecular biology, ecology, and evolution concepts and develop lab skills such as centrifugation, electrophoresis, and polymerase chain reaction. Students learn to use computational biology and bioinformatics to analyze their DNA barcodes with tools embedded in the BOLD-Student Data Portal. 

This is a great trend which I hope will continue and include more fields of science. The more hands on the better and a little fun doesn't hurt either.

All photos were 'stolen' from Deborah Landry who runs iXplore.

There's excitement in the air with the sense of doing real science! I never thought I would be able to do this in high school.

Bugs on the rooftop

Nut weevil (Curculio nucum)

As temperature increases we see a corresponding change in the insect community, specifically for the resource specialists -- the insects that feed on only one species of plant. Earlier studies have confirmed that specialist species also respond rapidly to destruction of their habitats, so we are dealing with a very sensitive group of animals.

A volunteer registration of insects for 18 consecutive years on the roof of the Natural History Museum of Denmark in Copenhagen has revealed local insect community turnover due to climate change. 1543 different species of moths and beetles and more than 250,000 individuals have been registered over 18 years of monitoring. That corresponds to 42 % of all the species of moths in Denmark and 12 % of the beetles. More interestingly, the insect community has changed significantly during that period.

The nut weevil (Curculio nucum) is an example of a resource specialist, feeding only on hazel. It lives further north in Europe than its close relative the acorn weevil (Curculio glandium), which feeds only on acorns. While the nut weevil was only registered during the first half of the study, the acorn weevil appeared in the last part of the study, suggesting that specialist species are moving northwards in Europe. Using the entire dataset, the study was able to confirm this trend and highlights the increased pressure on the most northern species, which may be 'squeezed out' of their range in the long term.

We are likely to lose some specialist species as they retreat north, but more new specialist species will arrive from the south. This trend is theoretically expected but extremely rare to confirm with observations across this many species. Insects are often over-looked and under prioritised for long term studies.

It was two employees of the Natural History Museum of Denmark with extensive entomological expertise who collected and identified all the insects. The monitoring took place every week from 1992 to 2009 through spring, summer and autumn using a light trap at the roof of the museum. What started out as a hobby based on scientific curiosity, ended up in an extensive faunal and climate change study.

Some like it hot, some not

The great puzzle has been why some species of moth and butterflies have been increasing and spreading, whilst others have declined in the last 40 years. Now we know that most of the differences arise because each species responds in a different way to the climate. Some like it hot, some like it cold.  Some like it hot in winter but not in summer. Some like it wet in spring, others dry in the autumn.

It has been repeatedly shown that organismal response to climate change varies greatly from species to species. Furthermore, this variability has been regarded as very complex due to the number of biotic interactions. This in turn has led to concerns that predictions of responses are inherently uncertain.

Variation among species is attributed to differing sensitivity to climate change, and also because species vary in how much the climate has changed for them (their ‘exposure’). Sensitivity is a measure of how much species’ numbers change as a result of year-to-year changes in the weather because each species is sensitive to different aspects of the climate, such as winter temperature or summer rainfall.  

Researchers from the UK have now analysed how the abundance and distribution of 155 species of British butterflies and moths have changed since the 1970s. Using data collected by thousands of volunteers through ‘citizen science’ schemes, responses to recent climate change were seen to vary greatly from species to species.

It turns out that these 155 different species of butterflies and moth have almost 155 different ‘opinions’ on how much the climate has changed, and whether it has got better or worse.  Climate change is causing massive alterations to our wildlife.

Results show that species such as the treble brown spot moth (Idaea trigeminata) and the speckled wood butterfly (Pararge aegeria) which are sensitive to climate, and for which the climate has improved the most, have experienced the greatest increases in their distribution size and abundance. Conversely, other species, such as the grizzled skipper butterfly (Pyrgus malvae), the September thorn moth (Ennomos erosaria) and the mouse moth (Amphipyra tragopoginis), have experienced deteriorating climates resulting in declines in abundance and distribution size.

Species are sensitive to different aspects of the climate, which results in species being exposed to different levels of climate change. Nearly two-thirds of the changes in abundance can be explained by these species-specific differences. This means that their responses to climate change may be more predictable than previously recognised.

DNA Barcoding Intro Course offered again

Registration for the next offering of our DNA Barcoding course will open soon.

This course was developed together with our experts for distance education here at the UofG. It is an exclusively web-based course offered over an eight week period starting on February 8th 2016. On average, six to eight hours of study time are required each week to study the course material consisting of reading, audio and video material. Participants will have weekly assignments/quizzes and have plenty of opportunities to participate at discussions that are happening in designated chatrooms. The number of participants is limited to ensure adequate mentoring by the instructor (me).

Course Dates: February 8 to April 1, 2016

If you are interested please have a look at www.dnabarcodingcourses.com. The site details course content, tuition fees, requirements, etc. If you know somebody who might be interested please forward the information.