Monday, February 29, 2016

CBD GTI Training Course on Rapid Identification of Invasive Alien Species is back

In 2015 The Secretariat of the Convention on Biological Diversity launched a capacity-building “training for trainers” course in DNA Barcoding available to interested Parties to the Convention. With generous financial support from the Government of Japan, the Secretariat will support a second round of the training course in 2016 on the application of DNA barcoding in the detection and monitoring of priority invasive alien species, pests and zoonotic disease vectors for interested Parties. This course will provide opportunities for Parties to develop national capacity in the detection and management of invasive alien species, pests and disease vectors that threaten habitats, ecosystems or the health of plants, animals and humans. 
The training course has two major components: an 8-week online distance education course on DNA barcoding methodological approaches and technologies, and a 4-week hands-on training course in standard DNA barcoding protocols for selected trainees at the Biodiversity Institute of Ontario, University of Guelph, Canada.  Applicants should be nominated by the National Focal Point for the Convention on Biological Diversity. National Focal Points are encouraged to consult with the national or regional plant protection organization (NPPO or RPPO) to recommend appropriate individuals to take the training course. The course is open to additional self-funded experts from countries that are not eligible for SCBD financial support.

The call for applications was announced last week on the CBD GTI website. For inquiries on eligibility, selection criteria, and application procedure, please contact the CBD Secretariat.

As per usual the online training component of this course is open to everyone else. This particular run of the course is exceptional as it draws in such a huge international audience which is a great learning environment. So mark your calendar - the online course starts April 11th, 2016.

Thursday, February 25, 2016

Spider evolution

Spiders are an ancient and diverse group comprising over 45,000 described species with probably three times as many awaiting discovery. In addition to their remarkable diversity, ecology, and abundance, spiders are known for some extraordinary compounds, such as venoms and silks. Although few spider venoms are dangerous to humans, they potentially hold some medical promise as insecticides and therapeutics. And, no other animal can claim a more varied and elegant use of silk a super strong material we are started to explore more in order to use it to create biometic material such as artificial nerve constructs, implant coatings, and drug delivery systems.

Despite all that, our understanding of spider evolution was rather poor. The orb web, the spiral wheel shaped web made by many spider species, was once considered "the crowning achievement of aerial spiders" and consequently researchers believed it to have evolved independently at least twice across the group's evolutionary history. However, studies in the 1980s suggested the opposite and many colleagues concluded that the orb web and the taxa that spin it all shared a common ancestor. 

Well, this thought will likely change once again. Colleagues in the US conducted a massive phylogenetic study of spiders using next generation sequencing technologies. Perhaps I should start calling them HTS - High Throughput Sequencing which seems to become the new standard. The researchers generated a genomic data set composed of nearly 3,400 genes for 70 spider taxa that represented a wide breadth of the order's diversity. The resulting phylogenetic tree confirms earlier suspicions that all orb weaving spiders are, in fact, not closely related to one another. Although these data could be interpreted to mean that the orb web evolved more than once the team finds this hypothesis highly unlikely. 

Our results are relatively clear that while orb weaving taxa are not as closely related as previously thought, our data do support the notion that the orb web itself has evolved only once. What we are calling the "ancient origin hypothesis" for the web, simply means that the largest branch on the spider tree of life had an ancestor that constructed an orb web but most of its descendants abandoned it for other more seemingly more lucrative prey hunting strategies.

Further diversification analyses actually showed that the mostly ground-dwelling, web-less spiders diversified faster than orb weavers. Molecular dating estimates show a major increase in biomass of non-flying insects during the Cretaceous Terrestrial Revolution 125–90 million years ago favoring diversification of spiders that feed on running rather than flying prey. 

A very interesting read and as it has been noted by a couple of colleagues via Twitter that the new PeerJ graphical abstracts (image above) are pretty cool, too.

Wednesday, February 24, 2016

Freshwater biodiversity boosts global food security

Inland waters are the most threatened systems globally, with dams, water extraction, pollution and invasive species as well as overharvesting of the fisheries themselves recognised as some of the biggest threats. It is imperative that the relationships we explored should be considered within freshwater and fisheries management; the protection and conservation of species diversity in freshwater systems is a win-win outcome for human food security and conservation efforts to preserve freshwater ecosystems.

At least two billion people depend directly on inland freshwaters for the provision of food. However, despite thousands of freshwater species contributing to food security, the relationship between biodiversity and yield remains poorly understood.

A new study from the University of Southampton and the International Union for Conservation of Nature (IUCN) now shows that freshwater environments with a greater fish biodiversity have higher-yielding and less variable fisheries. Using datasets from the Food and Agriculture Organization of the United Nations (FAO) and IUCN covering 100 countries in Africa, Europe and parts of Asia, the researchers have conducted the first large-scale test of the impact of freshwater biodiversity on fishery yields and the variability of yield over time.

After taking into account other factors that would be expected to have an effect on yield, such as fishing effort, the size of lakes, and temperature and precipitation, the colleagues found that fisheries with a higher number of species are also producing higher yields. In addition, they showed that in regions with a higher number of fish species there was also more stability in the year to year yield. Countries with such strong relationships were Tanzania, Democratic Republic of Congo, Vietnam and Thailand.

The results suggest that fish biodiversity may deliver benefits for human well being. As such, these results provide a powerful argument for placing biodiversity conservation centrally within fisheries management, particularly in countries with the highest yielding inland fisheries as these also tend to have high freshwater biodiversity.

Beyond food security, the researchers say that understanding the degree to which biodiversity underpins freshwater fisheries has particular policy relevance because freshwater systems are of major importance for the conservation of biodiversity. Freshwater habitats are disproportionately species rich given that they cover only 0.8% of the Earth's surface but contain 10% of all species described to date and as many as a third of all vertebrates.

Tuesday, February 23, 2016

The root cause of tropical forest diversity

Oreomunnea mexicana Photo: James Dalling
Tropical forests are renowned for their high diversity, yet in many sites a single tree species accounts for the majority of the individuals in a stand. An explanation for these monodominant forests remains elusive, but may be linked to mycorrhizal symbioses.

The types of beneficial fungi that associate with tree roots can alter the fate of a patch of tropical forest, boosting plant diversity or, conversely, giving one tree species a distinct advantage over many others. A new study sought to explain this phenomenon that occurs in some tropical forests: Small patches of "monodominant forest," where one species makes up more than 60 percent of the trees, form islands of low diversity in the otherwise highly diverse tropical forest growing all around them. These patches dominated by a single species are rare but understanding how monodominant forests arise and persist could help explain how tropical forests otherwise maintain their remarkable diversity.

The new study focused on mountain forests in Panama that harbor hundreds of tree species, but which include small patches dominated by the tree species Oreomunnea mexicana. A team of US researchers focused on two types of fungi that form symbiotic relationships with trees: arbuscular mycorrhizas and ectomycorrhizas. Arbuscular mycorrhizas grow inside the roots of many different tree species, supplying phosphorus to their tree hosts. Ectomycorrhizas grow on the surface of tree roots and draw nitrogen from the soil, some of which they exchange for sugars from the trees. Ectomycorrhizas cooperate with only a few tree species, 6 % or less, of those that grow in tropical forests.

The researchers tested three hypotheses to explain the high abundance of Oreomunnea. First, they tested the idea that Oreomunnea trees are better able to resist species-specific pathogens than trees growing in more diverse forest areas. They actually found the opposite: The trees suffered more from pathogen infection when grown in soil from the same species than in soil from other species.

The researchers next tested whether mature Oreomunnea trees supported nearby Oreomunnea seedlings by sending sugars to them via a shared network of ectomycorrhizal fungi. But they found no evidence of cooperation between the trees.

In a third set of experiments, the team looked at the availability of nitrogen inside and outside the Oreomunnea patches. They found three-fold higher soil nitrate and ammonium concentrations outside than inside Oreomunnea-dominated forest and a correlation between soil nitrate and Oreomunnea abundance in plots.

Ectomycorrhizal fungi make some of their nitrogen available to the trees while starving other plants and soil microbes of this essential nutrient. The lack of adequate nitrogen means bacteria and fungi are unable to break down organic matter in the soil, causing most other trees to suffer because they depend on the nitrogen supplied by the microbial decomposers.

Monday, February 22, 2016

Bird identification - use your phone

Researchers of the Jena University in Germany have developed an algorithm that allows the software to memorize the appearance of a variety of animal and plant species and thereby developing the ability to discriminate between them. The visual fine-grained project not only aims to develop a new precise way of pattern recognition but also to deliver the parameter the software develops during the learning process.

The algorithm uses deep learning and big data methods for pattern recognition and by including images of many different perspectives it can recognize e.g. birds and dogs even while they move.

The algorithm we developed is able to automatically distinguish between different types of birds, flowers, dog breeds, and in general very similar object categories. It is based on computer vision and machine learning techniques that learn the appearance of object categories from a given set of images together with their annotations. Very recent ideas from the deep learning area allow for estimating very complex visual models and boost the recognition performance up to 82% for a dataset with 200 different bird categories. 

One potential outcome would be an app that would enable all of us to identify species in the field as using only a cell phone camera. There is already one less versatile one available. The Merlin app, a tool used in North American to identify birds now lets you upload an image of a bird that you’ve photographed, and if the photo shows one of the supported species, it returns the correct species in the top 3 results, 90% of the time. It currently supports 400 species in North America and needs good photographs of the animal. 

Friday, February 19, 2016

MIDORI Prize for Biodiversity nominations

Maybe you know of somebody who should be nominated.  The AEON Environmental Foundation opened nominations a few days ago for the MIDORI Prize for Biodiversity 2016:

The MIDORI Prize, a biennial international prize, was established by the Foundation in 2010 in order to extend the developmental influence of individuals’ efforts to various projects relating to biodiversity throughout the world, and to raise awareness about biodiversity.  In 2009, the Foundation established “The Japan Awards for Biodiversity,” a domestic prize.  This prize is also biennial and these two prizes are awarded alternately.  This year marks the fourth time that the MIDORI Prize has been presented.

The aim of the MIDORI Prize is to honor distinguished individuals who have made outstanding contributions to the conservation and sustainable use of biodiversity.  Each prize winner is awarded a wooden plaque, a commemorative gift and a monetary prize of 100,000 US dollars.

The conservation of biodiversity and the prevention of climate change are two of the greatest challenges of our time. In order to achieve the Aichi Biodiversity Targets during the United Nations Decade on Biodiversity 2011-2020, AEON Environmental Foundation will make further efforts in support of biodiversity issues through conducting various projects including award-presenting activities.

Period of Nomination: 15 February – 30 June

Award Ceremony:
The Prize will be awarded at a special ceremony organized in conjunction with the thirteenth meeting of the Conference of the Parties to the Convention on Biological Diversity (COP 13) in Cancún, Mexico in December 2016.  Following the Award Ceremony, the Winners’ Forum will be held in Tokyo, Japan, in the same month of the year.

Thursday, February 18, 2016

DNA Barcoding to fight song bird slaughter

I don't know if you ever heard of Ambelopoulia, which is a traditional dish of grilled, pickled or boiled songbirds served on Cyprus. I find the idea of such a dish disgusting to begin with but what is really concerning is that the birds are caught by using non-selective methods such as mist nets and limesticks during the migration period in autumn but also in the spring. Trappers mainly target blackcaps but also other birds such as bee-eaters and shrikes. In contrast the list of trapped bird species is over 150 species long and includes 78 species listed as threatened by BirdLife International and the EU Birds Directive. According to Birdlife Cyprus over 1.5 million migrating songbirds are killed annually, and the number is increasing each year.

To be clear, this practice is outlawed by the EU and national legislation but it is a highly lucrative local commodity which means it is secretly served and birds are obtained through black market sources. Once prepared it is very difficult to determine what bird was actually used. However, DNA Barcoding is the new hope for the song birds. A new project aims to establish the method as a test if restaurant owners are trying to pass off illegally trapped birds as chicken or other legal species.

The project is a three-year collaboration between researchers at the University of Pisa, Italy, and the University of Cyprus, Nicosia, as well as the Ministry of the Interior's Cyprus Game and Fauna Service and the conservation group BirdLife Cyprus. So far, the team's unpublished work has shown that sequences from COI are enough to distinguish 81 bird species. This worked even when the DNA was extracted from meat baked at 90 °C, and cooked with salt or vinegar — a method that matches local gastronomy but that could degrade the DNA. 

With the help of their colleagues in Pisa, the team at the University of Cyprus was able to set up a laboratory to conduct DNA Barcoding on site. Furthermore, as part of the project two game-service officers were trained to enable them to testify on DNA evidence in court cases. This approach seems to be successful as the method has already been used in two pending court cases.

It is encouraging that methods such as DNA Barcoding can actually help to make a difference in such cases. However, lets be clear on that - the real change will only happen if humans start to develop respect for the species they share the planet with. We are not talking about a crucial source for food without the local human population can't obtain essential nutrients. This is an example for something completely unnecessary only maintained illegally because there are enough people that pay good money to have this dish. It reminds me a lot of the shark-fin soup that has no nutritional value and is still served with the excuse that it is an old deeply rooted tradition in local culture which is also a pro argument for Ambelopoulia. Well, I am curious if someone asked the younger generation about that kind of tradition. I met and talked with a number of students (school and university) who all reject these kinds of dishes, that are part of their respective culture, for what they are - unnecessary, brainless slaughter of animals. There is hope.

Wednesday, February 17, 2016

Archea from Hell

Microorganisms that live below the surface of the earth remain one of the last great areas of exploration. Organisms that live there have not been cultured in the laboratory and therefore their lifestyles are unknown.

An international team from the University of Texas, Uppsala University, UNC Chapel Hill, and the University of Bremen, have discovered how microorganisms, first discovered in a South African gold mine at a depth of about 3 km, are able to make a living in the absence of oxygen and light.

In order to understand these elusive organisms, the colleagues sequenced the genomes of several species. They were able to determine how these microbes should be classified and what physiological tricks they use to thrive under these extreme conditions with temperatures of up to 80°C. These organisms live in areas devoid of oxygen and the researchers suggest that they are able to survive by using carbon monoxide for energy production. The chemical pathways the cells use to metabolize carbon monoxide are unique and have not seen anywhere else before.

As this new group of microbes is specialized for survival beneath the surface, the colleagues called them Hadesarchaea, after the ancient Greek god of the underworld. As its name suggests, the Hadesarchaea belong to  the archaea, a relatively unknown group of microorganisms. Archaea were discovered only some 40 years ago, by Carl Woese. They were initially classified as bacteria, but this classification is outdated. From an evolutionary perspective, both groups differ more from each other than a human does from a tree. Many species in this group have been found thriving in acidic hot springs and salt likes, environments that would be uninhabitable to most other life forms. To date, archaea remain poorly studied in comparison to bacteria and other life forms, such as animals and plants.

Tuesday, February 16, 2016

Workshop announcement

Workshop on the application of genomic tools for biomonitoring of marine environments

Rapidly increasing impact of industrial activities on marine biodiversity strongly affects marine ecosystem health and services. Yet, the growing demand for measuring and mitigating these impacts can hardly be satisfied by classical monitoring based on morphological species identification. New genomic tools based on the analysis of environmental DNA (eDNA) could potentially overcome these limitations, but their application for biomonitoring is still very limited. The main objective of the workshop is to examine the effectiveness of the eDNA method for seabed monitoring from ecological, legal and socio-economic perspectives. 

The workshop will discuss the need to modify regulatory requirements and legal instruments for incorporating eDNA data into biotic indices. The participants will also learn about the advantages and challenges of using eDNA to explore biodiversity and to value ecosystem services. The event will bring together molecular biologists, ecologists, environmental managers, and policy makers interested in integrating genomic tools in environmental impact assessment of industrial activities in marine environments.

The workshop is a part of the project funded by the Swiss Network for International Studies, in collaboration among others with the International Seabed Authority, Scripps Institution of Oceanography, Environmental Law Institute, and Federal Institute of Water (EAWAG), Switzerland. Among the participants there are specialists of the environmental impact assessment in the deep-sea and coastal areas as well as the representatives of environmental agencies and international organisations involved in the conservation of marine environment, such as UNEP, IUCN, CIESM, and JRC.

The workshop is free and open to everyone. You are very welcome to take part in this unique event and if you wish to make a presentation of any project related to the topics of metabarcoding and marine biomonitoring.

Please do not hesitate to contact Jan Pawlowski for further information and registration.

Friday, February 12, 2016

Darwin Day

Image courtesy Alex Smith, showing the
UoG Cannon Old Jeremiah today
For those of you who might not know by now, Darwin Day is a celebration to commemorate the anniversary of the birth of Charles Darwin on 12 February 1809. It became a global celebration of science and reason with a multitude of events around the world. Today we are celebrating Darwin's 217th birthday but also intellectual bravery, perpetual curiosity,hunger for truth (International Darwin Day Foundation).

For those of you who have an hour to spare here is a very good BBC documentary about Charles Darwin. It was produced to mark the bicentenary of Darwin's birth back in 2009 and is presented by the great David Attenborough (yes, I am a great admirer):

Happy Birthday, Charles Darwin.

Wednesday, February 10, 2016

Two openings (PhD and PostDoc)

Announcements from the Metabarcoding website:

Deciphering genome skimming data over a broad taxonomic scale (the PhyloAlps data) to study the dynamic of the organelle genome evolution.

**A PhD position is open at LECA - Grenoble - France.**

Candidates will have to apply for a PhD Fellowship competitive exam organized by the "Ecole Doctorale Chimie et Sciences du Vivant" PhD school of the Grenoble Alpes University.

The competitive exam is open to students holding a master degree in science.

Candidates must have broad interests and training in evolution and by the development of new data analysis methods able to deal with high-throughput genomic data. This PhD project has to be considered as a true bioinformatic project covering biological topics but also requiring computer science developments. Therefore, to allow big-data analysis, candidates must have very strong abilities in bioinformatics including programming.

This PhD project proposes to use an unprecedented data set of several thousands of data of low coverage shotgun genome sequencing to study the evolutionary dynamics of organelle genome in plants. Interesting avenues for research could be explored by the candidate. Among them, the genetic transfers between the nuclear, the mitochondrial and the chloroplastic genomes and the impact of the repeated sequences on the dynamic of evolution are particularly promising. A third important topic that could be explored by the candidate is conducting a formal test of whether circular topology classically considered for plants’ chloroplast genomes can be considered true for all plant clades. The results will be put in relation with the phylogeny and the ecological characteristics of plant species considered in order to test whether some of the observed genomic properties can be associated to specific clades and to particular environments and species life-history traits.

Data sources :
The PhD project will be mainly based on the PhyloAlps sequencing initiative, which is currently producing a large dataset of genomic data constituted by a low coverage genome sequencing for each species of plant belonging the european Alpine Flora. This initiative will yield about 6,000 sequenced specimens, which can used to obtain the complete sequence of the organelle genome for each species sequenced. This project will also be within a framework of international collaborations including the Nowegian Barcode of Life (NorBOL) initiative that will provide similar data for about 2,000 additional specimens belonging the arctic flora.

Contact :

ECOGEN - Ecosystem change and species persistence over time: a genome-based approach


Main Goal: Develop high taxonomic resolution ancient environmental DNA methods in order to evaluate how drivers of change (human, climate, biota) affect species persistence and ecosystem tipping points in arctic-alpine biomes

Sub goals:

  1. Improve methods for full genome analyses of environmental DNA.
  2. Compile palaeo data to plan a balanced design of climatic and human impacts.
  3. Do full genome analyses of lake cores to obtain information on past presence and abundance of vascular plant species and key herbivores?
  4. Identify biotic drivers and disentangle their effects from human land use and climate change on ecosystem resilience and ecosystem services.
  5. Estimate species persistence across periods of changes and identify factors causing extinction.
  6. Provide methods and knowledge to inform species conservation and ecosystem management.

We are seeking a research fellow that will join a cross-disciplinary team (ecology, palaeoecology, genetics, archaeology, geology, niche modelling) working in two geographical regions (Norway and the Alps). We will expand our knowledge on past vascular plant and animal diversity and abundance at a taxonomic depth that has not been possible until now due to methodological limitations. We expect to disentangle the effects of past human land-use (hunting, husbandry, burning, agriculture), climate change, and biota on species and ecosystem changes and thereby be able to answer questions central to our understanding of our biological resources, such as the level of persistence of species and resilience of ecosystems to environmental drivers, the extinction risk of species, and the capacity of mountain landscape to buffer against these changes. By identifying drivers of shifts in ecosystem services through time, we may inform future management.
The successful candidate will work on development of improved technology. The most recent applications of ancient plant DNA analyses are largely developed by our team (Taberlet et al. 2007, Sønstebø et al. 2010, Yoccoz et al. 2012, Willerslev et al. 2014). For vascular plants, the 50-100 base pair long P6 loop region of the chloroplast trnL (UAA) intron is used in a PCR based method (Taberlet et al. 2007), which allows identification of all plant families, most genera (>75%), and one third of the species (Sønstebø et al. 2010). When applied to modern lake sediments, half of the species present within 2 m of lakes were detected (Alsos et al. In prep.). Our recent study of an 8500 year old core from Svalbard show that the method detect all except two genera identified in a macrofossil study from the same lake (Alsos et al. 2015). Overall, 1.2 times more taxa of vascular plants were identified with ancient DNA than macrofossils, and the number of taxa identified per sample was 2.7 times higher for the former. Thus, DNA analyses of Holocene lake sediment can reveal the presence of rare taxa and thereby allow for a better estimation of species persistence. Further, the method is now resource-efficient and repeatable, and it can be extended to any group of organisms, given that a DNA reference library and adequate primers are developed . It also allows for semi-quantitative interpretations based on the number of PCR repeats where taxa are identified (Pansu et al. 2015). We will do minor optimization of these applications and analyse all samples for vascular plants and key herbivores.... [for the remainder of the text and the citations follow this linked text].
Contact : Prof. Inger Greve Alsos
Tromsø University Museum
NO-9037 Tromsø

Tuesday, February 9, 2016

eDNA use in the Tropics

The best method for managing the spread of invasive aquatic species is through the prevention of new incursions, rather than post-infestation eradication. To avoid widespread establishment of invasive species it is crucial to detect infestations early when their density is lowest. Recent advances in our understanding of the movement of environmental DNA (eDNA) and particle size through streams and capture methods continue to validate and optimize the reliability of eDNA techniques for detecting the presence of low-density aquatic species, including invasive species.

eDNA allows us to detect the presence of organisms without direct observation. Plants and animals shed cellular material into their surrounding environment, and this material can be collected and analyzed. Traces of DNA extracted from environmental samples can be used to determine if a target species has been in the vicinity of a sampling site.

There have been a number of studies with promising results especially with respect to the detection of invasive fish species. The most advanced field of study deals with the ongoing invasion of the Great Lakes by Asian Carp. However, most studies were conducted in temperate regions and not in tropical freshwater environments which come with additional challenges such as high turbidity, higher temperatures and higher ultra-violet light intensity most of which can have a profound destructive effect on eDNA. 

A new study from Australia put some of the parameters to the test. The researchers used Mozambique tilapia (Oreochromis mossambicus) as a detection model for the effect of modifications of conventional eDNA protocols for use in tropical environments.

Large–pore filters (20 μm) were effective in filtering turbid waters and retaining sufficient eDNA, whilst achieving filtration times of 2-3 minutes per 2-L sample. High water temperatures, often experienced in the tropics (23, 29, 35 °C), did not affect eDNA degradation rates, although high temperatures (35 °C) did significantly increase fish eDNA shedding rates.  We established a minimum detection limit for tilapia (1 fish/ 0.4 megalitres/ after 4 days) and found that low water flow (3.17 L/s) into ponds with high fish density (>16 fish/ 0.4 megalitres) did not affect eDNA detection. These results demonstrate that eDNA technology can be effectively used in tropical ecosystems to detect invasive fish species.

The only thing I don't understand is the use of 16S rRNA as marker system for this study. It is a rather unusual choice as it is not very commonly used for fish. Earlier studies that looked into 16S as a potential marker for a microarray based identification system showed that it is not very suitable for this purpose, one problem being the secondary structure of the molecule. There are also not as many sequences available as for COI barcodes or even cytb. It is fairly easy to find sequences that help with qPCR probe design for tilapia as this species has been subject to thorough analysis over the years but in order to go after real invaders one would need to move to a different system. Luckily, most of the suggested protocol changes and amendments are not with respect to the choice of markers which makes this a minor issue.

Monday, February 8, 2016

Molecular scatology

The Semipalmated Sandpiper (Calidris pusilla) is an Arctic-breeding shorebird that undergoes a long-distance fall migration to wintering grounds in South America. Much of the population is thought to complete this migration with a single stop in the Bay of Fundy, Canada. While in the region, these birds feed extensively on infaunal prey found on intertidal mudflats.

Earlier morphological analysis of stomach contents had led researchers to believe that Semipalmated Sandpipers in the Bay of Fundy rely on an amphipod species called Corophium volutator as their major food source. However, a new study by researchers of the University of New Brunswick shows that the sandpipers' diet is far more general than previously thought. 

The colleagues used molecular scatology through metabarcoding, in other words they used Next Generation Sequencing to barcode carefully selected and sampled bird droppings.

The results show that the birds also feed on freshwater insects that wash down onto the beach in streams, eggs of ocean-going fish deposited on the shore by tides, and organisms that live in the beach's intertidal zone, among those Corophium volutator. This broader diet may increase their exposure to pesticides and other toxins, in addition to making the birds more resilient to changes in their habitat, such as those due to climate change.

Current Semipalmated Sandpiper conservation efforts in the Bay of Fundy focus on beach and intertidal habitats, neglecting terrestrial, pelagic, and freshwater systems that may not only supply nutrients, but harmful chemicals or pesticides as well. Future studies need to explore this possibility, attempting to determine if bioaccumulation of harmful toxins from multiple ecosystems in the Semipalmated Sandpipers are having any negative impacts upon this species.

Friday, February 5, 2016

What happened around 14,500 years ago?

We uncovered a completely unknown chapter of human history: a major population turnover in Europe at the end of the last Ice Age.

A European research team pieced together a piece of missing history by reconstructing the mitochondrial genomes of 55 hunter-gatherer individuals who lived in Italy, Germany, Belgium, France, the Czech Republic, and Romania 35,000 to 7,000 years ago.

Their results show that the mitochondrial DNA of three individuals who lived in present-day Belgium and France before the coldest period in the last Ice Age, the Last Glacial Maximum, belonged to haplogroup M, which was thought to be absent in modern Europeans but is extremely common in modern Asian, Australasian, and Native American populations.

This had previously led to the theory that non-African people dispersed on multiple occasions to spread across Eurasia and Australasia. The colleagues think that the discovery of this maternal lineage in Europe suggests instead that all non-Africans dispersed rapidly from a single population, at a time they place around 50,000 years ago. The M haplogroup disappeared from Europe when the Last Glacial Maximum began around 25,000 years ago. Hunter-gatherer populations retreated to the south into a number of putative refugia, and the resulting bottleneck caused the loss of this haplogroup.

The researchers say their biggest surprise, however, was evidence of a major turnover of the population in Europe around 14,500 years ago, as the climate began to warm. Our model suggests that during this period of climatic upheaval, the descendants of the hunter-gatherers who survived through the Last Glacial Maximum were largely replaced by a population from another source. The exact origin for this population is unknown, although the inferred demographic history  suggests that it descended from another, separate Last Glacial Maximum refugium.

Wednesday, February 3, 2016

Postdoctoral Position in Bioinformatics and Environmental Genomics

And another one - this time a PostDoc position at McGill University. Not bad at all either :-)

We invite applicants for a two-year postdoctoral position in Bioinformatics and Environmental Genomics at McGill University, Biology Department. 

The position will be funded by the WSP and the Mitacs Accelerate program. WSP is one of the world's leading engineering professional services consulting firmsm. It provides services to transform the built environment and restore the natural environment, with expertise ranging from environmental remediation to urban planning, from engineering iconic buildings to designing sustainable transport networks, and from developing the energy sources of the future to enabling new ways of extracting essential resources. The Biology department offers a highly collaborative environment and excellent ecological-genomics facilities and experimental stations .

The Postdoctoral Fellow will be involved in developing tools for assessing biodiversity and will use next-generation sequencing of environmental samples collected from a diversity of impacted aquatic habitats (ponds, streams, lakes, rivers). The candidate will have the opportunity to work closely with the WSP team of scientists and other industrial, governmental and academic partners. The candidate will compare results from traditional sampling techniques with biodiversity estimates based on refined metabarcoding approaches to describe the fish and invertebrate diversity within a diversity of impacted aquatic habitats. The candidate will be also involved in long-term and highly replicated laboratory and field experiments on the effect of multiple stressors on the structure and function of aquatic communities. 

Experience with next generation sequencing or sequence data and related bioinformatics / computational / programming skills is strongly desired. Familiarity with one or more of the following would be an advantage: genomics, phylogenetic analyses, genome evolution / programming language (R/Unix/Python or Perl). Experience working with aquatic organisms is an asset. The candidate should have a good publication record and the ability to work well in a collaborative research environment.

The position is for one year, but can be renewed for a second year and can begin as early as March 2016. Interested applicants should send their CV, a brief statement of research interest,

For more information and inquiries about the position please contact Melania Cristescu at

PhD position in Metabarcoding

I just got this announcement for an opening (PhD position) at the University of Duisburg-Essen. So, if you are a student considering doing your PhD and are interested in Metabarcoding, this is a great opportunity as these guys are doing some pretty cool things:

We are one of the youngest universities in Germany and think in terms of possibilities, not limitations. In the heart of the Ruhrregion, we develop ideas of the future at our 11 faculties. We are strong in research and teaching, live diversity, support potential and are highly committed to an educational equality that has earned this name.

The University of Duisburg-Essen (Campus Essen) Centre for Water and Environmental Research (ZWU) Aquatic Ecosystem Research Group (AG Leese) offers

1 PhD position, Doktorandenstelle (f/m)
(Part-time 55%; salary equivalent TV-L 13)
in Genetic Monitoring / Metabarcoding
(BMBF German Barcode of Life 2 subproject)

The group of Prof. Florian Leese is interested in developing new molecular approaches to assess the
ecological status of aquatic ecosystems. Specifically, we develop and apply DNA metabarcoding to
monitor changes in stream communities under environmental stressors. Furthermore, we utilize genomewide markers and perform transcriptional profiling to understand population and organismal responses to multiple stressors. As part of a recently granted subproject within the large collaborative German Barcode of Life Project (GBOL2, funded by the Federal Ministry of Education and Research, BMBF), we want to bring DNA metabarcoding of freshwater invertebrates to the application stage. In cooperation with our collaborators at the Zoological Research Museum Alexander Koenig (Bonn, Germany), the candidate will conduct collect samples, perform experiments, generate and analyse next-generation sequencing data on whole communities (amplicon sequencing). Further reading: Elbrecht & Leese, PLoS ONE 2015; Macher et al., Ecological Indicators, 2016. 

The successful candidate (f/m) will hold a Master in Biology, Chemistry or Bioinformatics and has good experience in molecular lab work. Furthermore, he/she has experience and strong interest in a
programming or scripting language (e.g. R, C, Python). Candidates will benefit from the international and interdisciplinary research environment at the research group, the GBOL2 project and the ZWU. Excellent high-throughput genomics and bioinformatics equipment are available in the newly equipped labs.

The position will start as soon as possible initially for 2,5 years.
Deadline: 29. February 2016

Please send applications as a single pdf file with reference code 42-16 to For questions please contact

The University Duisburg-Essen aims at promoting the diversity of its membersApplications from disabled or equivalents according to § 2 Abs. 3 SGB IX are encouraged. The University Duisburg-Essen has been awarded for its effort to promote gender equality with the "Total-EQuality-Award". It aims at increasing the share of women in the scientific personnel and therefore explicitly encourages women to apply. Women will be preferentially considered when equally qualified according to the state equality law.

Tuesday, February 2, 2016

Grade 8 scientists and lionfish diet

For a number of years a marine invasion has been happening in the western Atlantic. In the mid-1980s some lionfish (Pterois volitans) were released in Florida. Since then, they have become established in >4 million km2 of the western Atlantic, Caribbean, and Gulf of Mexico.

The problem is that these invasive lionfish reach higher densities and larger sizes than in their native range (Indonesia). Their hunting method is unlike that of any Atlantic predator as they use prey herding to catch fish and crustaceans which they ingest as a whole (prey can be half their own body size).  This has an immense impact on the native reef fish populations in the western Atlantic. Furthermore, little is known of how lionfish numbers are kept stable within their native range. For a long time the problem was the lack of an in-depth understanding of their diet which in turn would help to assess the impact on the native species. Given their hunting mode, lionfish could prey on most fish species within their gape size limits and as a matter of fact the studies showed that they are generalists as many invasive species. Their impact is devastating because of the large number of interspecific interactions they can create or disrupt, particularly in species-rich ecosystems like coral reefs.

Only taxonomically well-resolved diet information combined with prey availability data can help to identify the species most at risk from lionfish predation. Over the last couple of years a number of studies utilized DNA Barcoding of lionfish stomach content, some of those were done here at our facility. Some of my coauthors went further and tried to identify general traits of prey that predict vulnerability to predation, and examine diet selection at different spatial scales. Their work confirmed that lionfish have a voracious appetite and will eat almost any fish smaller than they are, but it also shows that they do have their favorites. 

There is much more work that needs to be done in order better understand this rapid invasion and find ways to efficiently fight it. However, it seems we got some help. Students at Woodlawn Beach Middle School in Florida are now participating in a research project by the Gulf Islands Research and Education Center, a partnership between the University of West Florida and the Gulf Islands National Seashore, to try to determine what the lionfish are eating and how much of an impact that is having on the local ecosystem. Their teacher received a grant to bring DNA analysis into the classroom and the students are analyzing stomach content pretty much the same way as we did. Here is a newspaper article (make sure you check out the video on page 2 of it).

Monday, February 1, 2016

Liverworts and hornworts

Although Charles Darwin himself intended to compile a complete catalog of all known plant species more than a century ago, such is yet to be realized. An international research team now present the first ever worldwide checklist of hornworts and liverworts, prepared as a part of the Global Strategy for Plant Conservation aiming to list the whole plant kingdom by 2020.

Both liverworts and hornworts are of critical biological and ecological value, and an important component of the vegetation in many regions of the world. Liverworts, for example, are so widespread that can be found all the way from coastal Antarctica to the tundra of the Northern hemisphere and from the quite dry areas of Australia to the rainforest of Amazonia. Growing almost everywhere, they have turned into a microhabitat for a myriad of organisms such as single-celled eukaryotes, protozoa, and a wide range of invertebrates.

Moreover, both liverworts and hornworts play a vital role in the global carbon and carbon dioxide cycle. In the past they have even been used as climate change indicators and could be used as such to track potential signs of global warming in future.

The new database includes over 25,000 publications, almost 39,000 published names, and over 700,000 geographical observations. In summary they authors have assembled names for 7486 valid species in 398 genera representing 92 families from the two phyla.

The broader accessibility to the wealth of auxiliary data will help augment monographic and revisionary work for many taxonomic groups, aid in identifying the need for increased floristic and survey work in many regions throughout the world, and have broad implications and applications beyond taxonomic research such as conservation science. However, such an effort can only be successful if it comes with sustained funding and infrastructure rather than depending on an ad hoc commitment by a few individuals, however dedicated.

Time to build a full barcode reference library.