Thursday, July 21, 2016

Online course on Metabarcoding


If I remember correctly I had mentioned this here and there - in collaboration the the University of Guelph Open Ed department we are developing a distance education course on metabarcoding. I am happy to report that the development is in its final stages and the first course will be held from October 3 to 28, 2016 - registration is open

This 4-week, web-based course will provide an overview of the state of current technology and the various platforms used. The course consists of a series of online lectures and research exercises introducing different aspects of metabarcoding and environmental DNA research. We will also touch on the suite of bioinformatics tools available for sequence analysis and data interpretation.

We tried to cover as much as possible given the online format and the limited time participants usually have available to do such training. The course is designed for four weekly instructional hours. The current plan is to run the course once a year.

And now on to the next - there will be another such announcement coming soon for yet another course (Regulatory and Forensic Applications of DNA Barcoding).  

Wednesday, July 20, 2016

All the lonely sequences. Where do they all come from?

Comparative phylogeography across a large number of species allows investigating community-level processes at regional and continental scales. An effective approach to such studies would involve automatic retrieval of georeferenced sequence data from nucleotide databases (a first step towards an ‘automated phylogeography’).

A team of researchers from Austria, Germany and Italy evaluated the geographical information available in GenBank accessions of tetrapods. They were particularly interesting in exploring temporal and geographical patterns, and wanted to quantify data available for automated phylogeography. 

The study began with about 1.1M accessions representing over 20,000 species but these impressive numbers shrank quite rapidly. Not unexpectedly, only 6.2% (some 70,000) of the retrieved GenBank submissions actually reported geographical coordinates and, even more concerning, the colleagues didn't noted any increase in recent years. The team also made an attempt to increase this number by developing scripts that assign geographical coordinates from textual context (e.g. keywords in publication, country information and so on). This geocoding raised the number of georeferenced accessions to 15.1%.

What I find most remarkable is that BOLD accessions, which represent only 3.4% of the analysed data, contributed a large portion of the total georeferenced (including accessions with geocoding) sequences (20.2%), and about half (47.3%) of the originally georeferenced accessions. This is not surprising as the DNA barcoding community naturally sees the value in sharing this information and BOLD supports as part of its metadata package. Actually, it is at least partially enforced as it is not possible to generate records on BOLD without basic information on the country of origin. The same requirement is part of the to-dos in order to obtain the BARCODE keyword for a GenBank record. Furthermore, researchers are always encouraged to provide lat/lon information to BOLD. Interestingly, tetrapod barcoding data are likely rather small in comparison with other datasets, e.g. fish or arthropods. A similar analysis of the latter should provide even higher proportions because the amount of fully geo-references records of insects on BOLD should reach 4 Million. 

The authors try to answer the question why so many date are submitted without detailed georeferencing and they come up with three of them:

(1) genuine lack of precise geographical information;
(2) unwillingness to reveal sensitive data (e.g. for samples from threatened species or populations); (3) lack of interest and awareness about the potential importance of direct georeferencing of data deposited in nucleotide databases for large-scale reanalysis of sequence data

I am afraid that (3) accounts for most cases. The vast majority of modern field collections use GPS data and the percentage of sensitive data is very small. Often, GPS data are still used but the precise location is masked by manually decreasing the GPS precision (cutting off some decimals or seconds/minutes does the trick). It is far too easy to just submit sequences with the minimum requirement for metadata to the INDSC databases. Only community efforts with agreed upon standards (such as barcoding campaigns and projects, e.g. iBOL) can lead to an improvement unless GenBank and Co want to change their rules.

Although geocoding offers a partial solution to the scarcity of direct georeferencing, the amount of data potentially useful for automated phylogeography is still limited. Strong underrepresentation of hard-to-access areas suggests that sampling logistics represent a main hindrance to global data availability. We propose that, besides enhancing georeferencing of genetic data, future research agendas should focus on collaborative efforts to sample genetic diversity in biodiversity-rich tropical areas.

Tuesday, July 19, 2016

Postdoctoral Research Fellow - DNA Metabarcoring of Herbivore Diet


Postdoctoral Research Fellow in DNA Metabarcoring of Herbivore Diet


A three year position as postdoctoral research fellow available available at Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo.

Within the framework of the position duties may be assigned. The position is available from September 2016. No one can be appointed for more than one fixed-term period at the same institution.

Project description

We generate DNA based diet data and study species and human interactions of the reindeer - one of the last remnants of the Beringian megafauna in the Arctic, keystone species, with high cultural and economic value for indigenous residents. Using DNA metabarcoding we analyze geographic, climatic and seasonal patterns of reindeer diet variation in different socio-economic settings. We will study diet overlap and infer trophic interactions with other herbivore species in the Arctic, such as geese, ptarmigan (Svalbard) and rodents (Finnmark). Our study will test whether reindeer diet changes correlate with warmer/longer summers or variation in population density. We integrate this ecosystem-based information with socio-economic data and local knowledge of reindeer herders to apply adaptive governance for developing co-management actions and implementation of alternative reindeer husbandry practices and mitigation measures for climate and/or land use change. The project is closely linked to the PhyloAlps (LECA, CNRS, Grenoble), ECOGEN (Tromsø University Museum) and REINCLIM (NTNU, Trondheim) projects. Project partners: CEU (Budapest, Hungary) and James Hutton Institute (Aberdeen, Scotland) provide necessary expertise on socio-economic and adaptive governance approaches.

Qualifications:

The Faculty of Mathematics and Natural Sciences has a strategic ambition of being a leading research faculty. Candidates for these fellowships will be selected in accordance with this, and expected to be in the upper segment of their class with respect to academic credentials.

Applicants must hold a PhD-degree in Biology (or other corresponding education equivalent to a Norwegian doctoral degree). Additionally some years of post-doctoral research experience or research experience at this level are considered an advantage. In particular, research experience in DNA metabarcoding including data processing from high-throughput sequencing and bioinformatic analyses, herbivore diet analyses, as well as experience/knowledge of herbivore and arctic community ecology, arctic biodiversity, molecular biology and biostatistics are very relevant. Experience in field work in arctic/boreal regions and student supervision are a strong asset.

The candidate will be hosted by the Centre for Ecological and Evolutionary Synthesis (CEES) at the Dept. of Biosciences and work on the NCR funded research grant to Galina Gusarova, project nr257642 entitled REININ - Reindeer interactions from plants and birds to humans: balancing the odds of climate change. The work will be done in close collaboration with research teams from the linked projects. The candidate will be engaged in field collecting, laboratory and data analyses stages of the project with the focus on DNA metabarcoding/metagenomics and ecological data analyses and interpretations.

We seek a highly motivated, enthusiastic person with the ambition to push research and methodology frontier and publish papers in leading international journals, and in possession of good interpersonal skills and willingness to work in close collaboration with others.

The main purpose of post-doctoral research fellowships is to qualify researchers for work in top academic positions within their disciplines.

Please also refer to the regulations pertaining to the conditions of employment for post-doctoral fellowship positions.

A good command of English is required.

Salary:
Position code 1352, NOK 486,100 – 567,100 per year, (Pay Grade: 57 – 65) depending on qualifications and seniority.  

The application (Reference number: 2016/8420) must include:

  • Application letter including a statement of interest, describing how your background and previous experience relate to the project in general, and how your skills fit into the framework outlined for the postdoc
  • CV (summarizing education, positions, pedagogical experience, administrative experience and other relevant activities)
  • Copies of educational certificates, transcript of records, letters of recommendationA complete list of publications and unpublished work, and up to 5 academic papers that the applicant wishes to be considered by the evaluation committee
  • Names and contact details of 2-3 references (name, relation to candidate, e-mail and telephone number)

Please remember that all documents should be in English or a Scandinavian language.

Application deadline: 15 August, 2016

In accordance with the University of Oslo’s equal opportunities policy, we invite applications from all interested individuals regardless of gender or ethnicity.

UiO has an agreement for all employees, aiming to e.g. secure rights to research results.


Contacts:
Dr. Galina Gusarova
Questions regarding Easycruit, contact HR Officer Torunn Standal Guttormsen
Telephone: +47 22 85 42 72

Monday, July 18, 2016

World's greatest concentration of endemic mammals

Tree-mouse, Credit: Larry Heaney
Luzon is the largest island in the Philippines; at about 103,000 square kilometers, it's the 15th largest island in the world. The island has never been connected to any continental land which means that a lot of its biodiversity has been isolated, like the animals that live in Hawaii. But Luzon is much larger and at least five times older than the oldest island in Hawaii, and so has had time for the few species that arrived from the Asian mainland to evolve and diversify greatly.

On islands, we sometimes see an acceleration of evolution. Animals are closed off from the rest of the world in places where there are few or no predators or competitors. This enables them to branch out into special adaptations, eventually forming new species. And not only is the island of Luzon isolated, but it's covered in mountains. Mountaintops form "sky islands", little pockets of distinctive habitat that the animals further adapt to.

A team of American and Filipino authors have studied the mammalian fauna of Luzon Island over 15-years and summarized their findings in a new paper. They showed that out of 56 species of non-flying mammal species that are now known to live on the island, 52 are endemic. Of those 56 species, 28 were discovered during the course of the project. 

We started our study on Luzon in 2000 because we knew at the time that most of the native mammal species on the island were unique to the island, and we wanted to understand why that is the case. We did not expect that we would double the number already known.

Among the 28 new species discovered by the team are four species of tiny tree-mice with whiskers so long they reach nearly to their ankles, and five species of mice that look like shrews and feed primarily on earthworms. Most of the new species live in tropical cloud forest high in the mountains, where frequent typhoons can drop four or five meters of rain per year.

All 28 of the species we discovered during the project are members of two branches on the tree of life that are confined to the Philippines. There are individual mountains on Luzon that have five species of mammals that live nowhere else. That's more unique species on one mountain than live in any country in continental Europe. The concentration of unique biodiversity in the Philippines is really staggering.

We reject the general assumption that mammals on tropical oceanic islands are sufficiently well known that analysis and modeling of the dynamics of species richness may be conducted with precision. In the development of conceptual biogeographic models and implementation of effective conservation strategies, existing estimates of species richness, levels of endemism, and the number of subcenters of endemism should be actively reassessed and verified through robust field, museum, and laboratory studies.



Friday, July 15, 2016

Amazonian tree diversity - 300 more years of work

...we need far better data on the geographic ranges and abundances of tropical tree species to finally put the “how many species?” question to rest. It seems to me that our priorities are misplaced. We spend many billions of dollars to look for extra-terrestrial life but far less to understand life and its distribution on our own planet. (SP Hubbell)

There are more different tree species in the Amazon rainforest than anywhere else on earth, but the exact number has long been a mystery. In 2013, scientists estimated that the number of species was around 16,000. However, no one had ever counted them all up nor been able to describe them all.

In a new study, the same scientists delved into museum collections from around the world to confirm just how many tree species have been recorded for the Amazon region so far and how many have yet to be discovered. The study relied upon the digitization of museum collections data, photographs and digital records of the specimens housed in museum collections that are shared worldwide through aggregator sites like IDigBio.

We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families.


The researchers interpret this to mean that their earlier estimate of 16,000 species is valid, and that about 4,000 Amazonian trees remain to be discovered and described. There is a bit of a problem though. The colleagues also state that since 1900, between fifty and two hundred new trees have been discovered in the Amazon every year. Based on the new results this would mean that it will take us more than 300 years to discover the rest. It is likely that some of them will be gone by the time we would be able to find them. According to the authors if deforestation were to increase to levels of the early 2000s, most of the rare - and possibly unknown - species in eastern and southern Amazonia would face threat of extinction.


The colleagues have some suggestion to speed up the process a bit:
  • Digitize all Amazonian herbarium specimens as there might be up to 50% of the undiscovered species hiding in some collections.
  • Support and develop taxonomic and floristic expertise
  • Accelerate and facilitate information exchange on Amazonian trees
  • More focus on Amazonian research
  • Target geographic areas where collection effort is low and expected diversity is high
  • Embrace new technologies (they explicitly include DNA barcoding in this)





Thursday, July 14, 2016

Underwater microscopy

Benthic Underwater Microscope
Many important biological processes in the ocean take place at microscopic scales, but when researchers remove organisms from their native habitats to study them under laboratory conditions, much of the information and its context are lost.

Colleagues from the Scripps Institution of Oceanography in San Diego have developed a new type of underwater microscope to image marine microorganisms in their natural settings without disturbing them. The Benthic Underwater Microscope, or BUM, is a two-part system.  An underwater computer with a diver interface tethered to a microscopic imaging unit allows researchers to study marine subjects at nearly micron resolution. The instrument has a high magnification lens, a ring of focused LED lights for fast exposures, fluorescence imaging capabilities, and a flexible tunable lens, similar to the human eye, to change focus for viewing structures in 3-D.

To test the new technology's ability to capture small-scale processes the imaging system was used to view millimeter-sized coral polyps off the coast of Israel in the Red Sea, and off Maui, Hawaii. During the experiments in the Red Sea, the researchers set up the BUM to capture the interactions of two corals species placed close to each other. The images revealed processes in which corals emit string-like filaments that secrete enzymes from their stomach cavity to wage a chemical turf battle to destroy the tissue of other species in a competition for seafloor space. 

The team also looked at temporal processes such as the algal colonization and overgrowth of bleaching corals. Off Maui they followed one of the largest coral-bleaching events on record, which occurs when single-celled algae that live inside the coral polyp eject themselves during high ocean temperature events. Recently bleached corals are still alive, but in their weakened state can be rapidly invaded and overgrown by filamentous turf algae. Using the microscope, the research team observed a previously unreported honeycomb pattern of initial algal colonization and growth in areas between the individual coral polyps during coral bleaching.

This underwater microscope is the first instrument to image the seafloor at such small scales. The system is capable of seeing features as small as single cells underwater. This instrument is a part of a new trend in ocean research to bring the lab to the ocean, instead of bringing the ocean to the lab.


Wednesday, July 13, 2016

Biodiversity and evolution

Pseudomonas fluorescens, bacterial species used
There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns.

Past studies on ecosystem changes showed both increase and decrease of the net number of new species evolving. In other words evolution can slow down as the result of increased competition for existing niches or the same competition can actually cause adaptive radiation. 

In a new study colleagues from France and Germany explored the evolutionary dynamics of a bacterial species growing in communities with varying levels of biodiversity especially looking at the effects of higher biodiversity. The controlled environment and experimental conditions allowed them to probe into the potential reasons for the contrasting results of prior research.

They found that higher biodiversity stimulates the evolution of species especially under resource constraints:

High functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. 

The study shows that extinctions not only have an effect to current ecosystem functions but also slow down evolutionary diversification. The authors also believe that as a consequence of the nested structure and compartmentalization of many food webs, higher functional diversity fosters the evolution of new species even at high species richness.