Wednesday, 25 November 2015

New position available: postdoctoral researcher in genome evolution

*Postdoc Opportunity Open to 7 March 2016*

We have an excellent opportunity for a postdoctoral researcher at the University of Glasgow’s Institute of Biodiversity, Animal Health & Comparative Medicine (IBAHCM) in the College of Medical, Veterinary and Life Sciences (MVLS), working in the Evolutionary Analysis Group and the research team of Kathryn Elmer (http://www.gla.ac.uk/researchinstitutes/bahcm/staff/kathrynelmer/).

We are seeking a motivated, creative and enthusiastic postdoctoral researcher for a project on ‘major evolutionary transitions’. The primary research effort will be on a NERC-funded project studying the molecular and genomic mechanisms underlying different reproductive modes (live-bearing vs egg-laying) in squamate lizards. Complementary projects on speciation, evolution and genomics in ‘ichs and herps’ are also possible.

Bioinformatic experience and expertise in whole genome analysis and NGS data is imperative, ideally with relevant experience contributing to genome assembly and a complex de novo genome project. Skills in quantitative trait mapping, comparative genomics, ecological and/or population genomics, and phylogenetics are also sought. Relevant molecular laboratory skills are desirable. Team working and positive attitude also a must. A track record of excellent genetic, evolutionary and/or ecological research is necessary, and on fishes and/or reptiles is a benefit. Candidates must have completed their PhD by the start of contract.

The position is for 1.5 years (with possibility for extension) and is funded through the NERC grant ‘Unravelling the genetics of a major evolutionary transition’ to Kathryn Elmer, Maureen Bain and Rod Page.

IBAHCM is a stimulating and interactive research environment with a wealth of opportunities for discussion, collaboration and cutting edge research in evolution, ecology, and disease. The University of Glasgow ranks in the world’s top 100 universities.  The city of Glasgow is lively and cultural, and sits on the doorstep of the great outdoors of the Scottish Highlands, islands, and coast.

The official job description and application requirements are available on the University of Glasgow homepage (under ‘current vacancies’; http://www.gla.ac.uk/about/jobs/vacancies/) at job reference 011679. Applicants must apply through that site.

Informal inquiries to K. Elmer welcome in advance. The position closes 7 March 2016.

Tuesday, 6 October 2015

New paper: how being gold colours the lives of fish

Can colour affect ecology and evolution, even within species? A recent publication of Kathryn Elmer with colleagues in University of Konstanz and the International Max Planck Research School found significant consequences of a colour dimorphism across ten populations of neotropical cichlid fishes. Named for King Midas, these Midas cichlid fishes are found in only two colour forms — all fishes start their life dark but in many species 5-20% of individuals lose their melanophores before adulthood and then become completely 'gold'. We found sympatric black- or gold-coloured individuals differed consistently in their ecology and morphology. Gold fishes were more typically ’snail-eaters’ and inhabit a lower trophic level, and this has some genetic basis.

H Kusche, KR Elmer & A Meyer, "Sympatric ecological divergence associated with a colour polymorphism” is published in the open access journal BMC Biology. doi:10.1186/s12915-015-0192-7




This was led by PhD student Henrik Kusche (now at Univ. Laval with L. Bernatchez) - see a great video about his IMPRS research here . Well done Henrik! 

Monday, 5 October 2015

PhD Position available in ecological genomics


A new PhD position is available in our group starting October 2016, which would be awarded through the competitive MVLS-Doctoral Training Programme. Please see our "Opportunities" page. 


Project: Comparative ecological genomics of environmental heterogeneity

PhD Project Summary:
Intrinsic factors such as genetics and extrinsic factors such as environment both influence a population’s contemporary patterns of diversity and adaptive potential. Quantifying the relative influence of those various factors is a major effort in biology,; it is fundamental to the mechanisms behind, the speed of, and the potential for evolution. Such patterns and processes have major implications for a range of issues in biomedical and biodiversity sciences.

This project will use advanced ecological and evolutionary genomics approaches in a rigorous comparative framework to assess the historical and contemporary patterns of diversity in Britain’s salmonid fishes. Based on new field collections, cutting edge high throughput genotyping approaches using next-generation sequencing will be used to infer the extent and organisation of genomic variability. The relative roles of environmental heterogeneity, ecological and morphological diversity, and genome-wide genetic diversity will be compared in a multispecies synthesis. The outcome will be a predictive framework for environmental heterogeneity in genomic and morphological evolutionary processes.

Salmonid fishes are of high economic, conservation, and natural history importance for Britain, but to date no relationship between environmental, genetic, and eco-morphological variability has been identified. Such a link is of key importance to preservation of biodiversity, its habitats, and the future of fisheries food security. This project is additionally supported by a Research Incentive Grant from the Carnegie Trust. Links with Scottish Natural Heritage or other charity/government bodies may also be possible.

Supervisors:
Dr Kathryn Elmer, Biodiversity, Animal Health and Comparative Medicine, University of Glasgow 
Prof Colin Adams, Biodiversity, Animal Health and Comparative Medicine, University of Glasgow

Monday, 21 September 2015

Welcome to the new cohort of Uni Glasgow Masters students!

Welcome to all the new Master's students (MRes and MSc) arriving to University of Glasgow.

We have range of exciting projects in the Quantitative Methods course and in the MRes! For example, how to individually identify a lizard based on colour patterns? Where around SCENE can we find lizards, and what are their reproductive traits like? (a project to live in that beautiful place!) How might they differ from alpine lizards (to live in the Alps!) What genes differ between adaptive radiations of fishes, and how can we track the genetic variation mining high throughput sequences? How is the genetic health of brown trout in the rivers around Glasgow?

Look forward to seeing you at the Session Opening party. Any questions about the projects on offer, please don't hesitate to ask.

Wednesday, 26 August 2015

New funding success: comparative population genomics in Scottish lakes

We thank the Carnegie Trust for the Research Incentive grant funding our project "Environmental and genomic drivers of diversity in Scottish fishes of high natural heritage value".

Scottish freshwater fishes harbour an exceptionally rich array of diversity within species and are regarded by scientists, government and society alike as having very high economic and natural heritage value, especially the loch-restricted salmonid species brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and powan (Coregonus lavaretus). All of these species are topics of biodiversity management conservation efforts and fundamental evolutionary biology and ecology research. In this project we aim to assess the roles of extrinsic and intrinsic factors influencing intraspecific diversity. This will be done in a comparative analysis across environments and species to identify the environmental, demographic and genomic facilitators of intraspecific, ecologically relevant morphological diversity. We aim to develop a predictive framework for the role of these factors in evolutionary processes and their importance for conservation and fisheries management.
This work will be done in cooperation with C. Adams.

Monday, 1 June 2015

FSBI Medal awarded to Kathryn Elmer

Thrilled to have been nominated for and now awarded the FSBI Medal for a young scientist 'deemed to have made exceptional advances in the study of fish biology', granted by the international society for fish biology based in the UK.

Friday, 8 May 2015

Congratulations to James

Congrats to James Burgon who has been awarded funding from the Systematics Research Fund  (Linnean Society of London and the Systematics Association) for his phylogenomics research on salamanders.

Congratulations to Heather

Congratulations to Heather McDevitt who has been awarded a Life Sciences Undergraduate Vacation Scholarship for her project on polymorphisms and genetics.

Monday, 30 March 2015

Speaker to the international charr symposium in Norway

See the coming conference in Tromso for a few fishy days of discussion and presentation about charr and their amazing diversity. I am very pleased be an invited speaker to talk about charr genomics and to meet up with some great colleagues and researchers in the land of the midnight sun! - Kathryn
   http://charr.akvaplan.com/program#monday-15th

Naturally Speaking - cutting edge research and ecology banter from the University of Glasgow

Kathryn Elmer and colleagues' work on parallel evolution of cichlid fishes is featured in the new Naturally Speaking podcast and blog in the article 'How many ways are there to make a fish?'
Check that and the other great entries for the research activities in our lab and in the Institute.

Friday, 20 March 2015

New methodology: ddRADseq for Ion Proton Ion Torrent sequencer

Using molecular markers in ecology and evolution is moving massively parallel. Not only can the new era of genotyping using next-generation sequencing give high resolution through generating thousands of markers but, with sufficient genomic knowledge, can be used to localize polymorphisms across the genome. Restriction site associated DNA sequencing (RADseq) of various different forms (see a very nice recent review of approaches here) is currently a major method of choice for researchers studying complex genomes and without requiring prior genomic resources.

We have recently developed a new genotyping-by-sequencing RAD sequencing approach for the Ion Torrent platform. The method can robustly generate thousands of loci using a modification of the ddRADseq protocol developed by Hopi Hoekstra's lab based on RADseq and applied on Ion Torrent/ Ion Proton/ Ion PGM semi-conductor sequencing.

The method is modular, has a low error rate, is economical, and importantly can be very fast. It is generally a low to medium through-put approach and so is likely especially suitable for researchers who have an Ion platform on hand. We have tested this method on a number of different non-model species that we are current interested in, such as common lizards, Arctic charr, European whitefish, and fire salamanders. The method can of course just as easily and successfully be applied to the so-called ‘model organisms’.

As recently presented at Population Genetics Group Sheffield, we offer a step-by-step bench protocol (in the manuscript Supporting Information) to anyone interested in trying the approach. Please be in touch if you have any questions.

Inherent to semiconductor sequencing, the reads generated by Ion Torrent differ in length around a median. We also provide a short Unix command in combination with an R script to maximize the number of base-pairs that will be retained for further analysis. Just like illumina-based RAD sequencing data, the reads can then be analyzed using customized RADSeq scripts or programs such as STACKS.

We ran the method with PI chips -- if Life Technologies releases the promised PII and PIII chips in the future, which should have the same chemistry and well technology so no need for new adapters, then the efficiency of this ddRADseq-ion method will increase many-fold.

The paper is in press with Molecular Ecology Resources. (IF = 5.626)

The work was supported by collaboration with Glasgow Polyomics, a University of Glasgow John Robertson Bequest grant, University of Glasgow start-up, and Wellcome Trust Institutional Strategic Support Fund Pilot funding from Glasgow Polyomics to KRE.

Paper:
Recknagel Hans, Jacobs Arne, Herzyk Pawel, Elmer Kathryn R (2015) Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with non-model organisms. Molecular Ecology Resources. in press.

Thursday, 12 February 2015

New paper: burbot subspecies at the contact zone

In a recent collaboration with the First Nations Gwich'in Renewable Resources Board, research about local fisheries of the Far North:

Hans Recknagel, Amy Amos & Kathryn R Elmer (2014) Morphological and ecological variation among populations and subspecies of Burbot (Lota lota) from the Mackenzie River Delta, Canada. CFN 128 (4)

The Mackenzie River Delta is a suture zone where many postglacial lineages come in contact as the Eurasian lineages reach east and south and North American lineages extended northward. We found considerable variability in ecological and morphological traits of burbot fishes in the region, and suggestion that that the different subspecies of burbot may exploit different niches. This is a new study following on earlier work that identified the first burbot subspecific contact zone and its asymmetric genetic admixture based on population genetics.

Quick dissemination of these findings were important because the Mackenzie River is under development pressure and decisions have to be made quickly by the local resources planners. The Gwich'in Renewables Resources Board had contacted us because were concerned at an increase in diseased fishes being caught in the area. Specifically, they wanted to identify if dispersal patterns might explain that worrying trend. Here we found that different communities of the Settlement Area probably have different subspecies of burbot, with the Eurasian subspecies being slightly different both genetically and phenotypically and restricted to the lower regions of the Mackenzie River Delta; thus they are probably not migrating to the higher reaches of the river.

We are very pleased that this work is published in Canada's flagship scientific natural history journal, with continuous publication since 1880 and now open access online. That means this collaborative work is accessible to all communities and resource planners, even in the most remote regions.

Wednesday, 11 February 2015

Lord Kelvin Adam Smith funding awarded to Watson & Elmer!


Our interdisciplinary project
“Convergence, connectivity, and continuity: Topological perspectives for mining novel biological information from ‘omics data”
and super-candidate Mel Chen from Australia have been awarded a Lord Kelvin Adam Smith PhD Scholarship from the University of Glasgow!

This research will bridge algebraic topology (L. Watson, Maths) and evolutionary biology (K. Elmer, IBAHCM). We look forward to welcoming Mel to Glasgow in the autumn.