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 melania.cristescu@mcgill.ca

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 miriam.schmidt@uni-due.de. For questions please contact florian.leese@uni-due.de.

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.

Friday, January 29, 2016

Barcodes to validate mitogenomic data

Mitogenomic data are increasingly used in many fields of biology especially since new sequencing technology enabled us to retrieve them rather easy and at low cost. However, very often with increasing numbers the chance for the occurrence of erroneous data increases as well. Over the years I came across a couple of fish mitogenomes that were assigned to the wrong species likely due to initial mis-identification. 

A new paper in Mitochondrial DNA - the journal that probably publishes most of the current papers on newly sequences mitogenomes - shows another case of such a erroneous assignment, this time for a bat sequence. However, the authors don't stop there, they actually propose some best practices for future studies to implement some sort of quality control. Some of the proposed standards are pretty common withing the DNA barcoding community and others actually suggest to use DNA barcoding to confirm the identity of a species.

Here is what the authors propose:

Proposed guidelines for accurately reporting new mitogenomes

(1) Provide detailed information on the origin of the sample used for mitogenome sequencing.

(2) Conduct a phylogenetic analysis of the new mitogenome in the context of closely related species.

(3) Provide a barcoding identification assessment of the sample thanks to a ML tree based on the closest available sequences.

There is much more detail on each of the three points in the paper and I hope it will be used as quality control standard for Mitogenome Announcement publications in Mitochondrial DNA and elsewhere. 

Thursday, January 28, 2016

What's in fish feed?

One of today's most popular sources of protein is seafood. The demand is constantly increasing and as a consequence almost half of the seafood we eat comes from aquaculture. In fact seafood farming is the fastest growing food production system in the world. It is expected to exceed the production of beef, pork or poultry within the next decades. Aquaculture is also portrait as a method to harvest seafood without further impact on biodiversity probably even reducing the pressure on natural populations. However, the industry heavily depends on marine captured fishes as main nutrient source, e.g. fishmeal.

Fishmeal is a commercial product made from both the whole fishes and their bones and offal from processed fish in order to provide the farmed fish species with natural high quality proteins. The fishmeal industry relies greatly on a “hunting-and-gathering” technique. Cooking, pressing, drying and grinding the fish make fishmeal. As a result, about one-fourth of the seafood harvested from the wild is consumed in fishmeal or other products, not for human consumption. It seems to be a global trend to produce fishmeal using fish processing waste; for example, in Spain and in United Kingdom accounted for 100 and 84% of total fishmeal production respectively. Currently about 25% of the world's fishmeal is generated from fish processing wastes. The proportion is expected to increase, given the growth of aquaculture.

The future expansion of aquaculture may be constrained by the dependence on such low value/trash fish and the impact on natural populations of fish. Therefore, it is very important to have tools in place to monitor fishmeal composition. Obviously, DNA Barcoding lends itself to such investigations but the product in question has been heavily processed which would exclude a conventional Sanger-based sequencing approach.

This is why a group of Egyptian researchers used the metabarcoding approach, applying the Roche/454 platform, to determine fish species composition of fish feeds used in local aquaculture. Their results are concerning as about 46% of all fish species detected are either overexploited or populations are in strong decline. In addition all products contained iridescent shark (Pangasianodon hypophthalmus), an endangered species. 

Interestingly, there are fishmeal products that are incorporated into the diet of herbivorous fishes such as tilapia and carp. The study shows that these products differ in species composition from the those used in fish feed for carnivorous species. However, my first question would be why we are feeding fishmeal to herbivorous species in the first place?

In this scenario, an aquaculture regulatory framework in the countries concerned with fish feed production and trading, including Egypt, should be established in order to regulate fisheries and aquaculture sustainability and to protect biodiversity. Finally, we strongly recommend the introduction of NGS technologies as a tool for fish feed inspections in order to balance/regulate the fish feed productions for sustaining both animal and human life.