Friday, 21 July 2017

New paper: Resolving the history of fire salamanders

In a recent paper, Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches, we used three large-scale molecular datasets to identify the evolutionary relationships in salamanders. To date these have been effectively unresolvable as there was never sufficient data for the deeper nodes. Here we found that ddRADseq and RNAseq nuclear data -- both using thousands of loci -- resolved the same phylogenetic topologies of all the species involved. However full mitogenome data suggested a slightly different history of the Salamandra atra-lanzai-corsica species. We suggest this may be because of ancient introgression of mitochondrial genomes. Importantly, our study shows that SNPs from ddRADseq (now using illumina NextSeq) can also be used to tackle deeper evolutionary relationships, perhaps just as well (and for less cost) as transcriptomes. The Glasgow portion of this work was led by PhD student James Burgon.

Tuesday, 20 June 2017

New paper: fish ecomorphological variability associated with lake environment

A new paper is published, with an analysis led by Hans Recknagel and in collaboration with SCENE researchers Oliver Hooker and Colin Adams. We examined ecomorphological variability of Arctic charr in populations across 30 lakes in Scotland and Northern Ireland. As a summary univariate measure for complex trophic diversity in these fishes, we used maximum, minimum, mean and variance in head depth. We found that the extent of variability of head depth is closely associated with the physical lake environment - in particular 'ecosystem size', which is a combination of lake size, depth, volume, and littoral zone. There was no association of head depth with biotic community of other fishes in the lake, abundance of charr in the lake, nor charr genetic diversity.

Recknagel, H., Hooker, O., Adams, C. E., & Elmer, K. R. 2017. Ecosystem size predicts eco-morphological variability in a postglacial diversification. Ecology and Evolution. online early 

image from Oliver Hooker

Monday, 29 May 2017

New paper: Vision genes in fishes

New paper from work done in Konstanz and now led by Julian Torres-Dowdall, "Rapid and parallel adaptive evolution of the visual system of Neotropical Midas cichlid fishes" in the journal Molecular Biology and Evolution

This study represented an excellent combination of field experiments for collections and detailed characterisation of environment, sequencing the full complement of opsin genes and expression, and assessing the structures of the eye.

Abstract: Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted towards shorter wavelengths compared to the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution.

Finalist for PhD student Hamilton Award

PhD student Arne Jacobs has been selected as a finalist for the Hamilton Award for Outstanding Student Presentation. Check out his work and the other exciting finalists at the Evolution meeting in Portland!

Thursday, 11 May 2017

Congrats to Paige!

Congratulations to summer-2016 FSBI Intern and subsequent Honours student with our group  - Paige Robinson - who has been offered (and accepted) a PhD position through NERC iCASE on fish epigenetic research at the University of Exeter.

Monday, 27 March 2017

Margaret Savigear Lecture Series

Kathryn was invited to present at the Margaret Savigear Annual Lecture series at the University of Sheffield. She presented on "Parallel evolution and its alternatives" with a discussion of ecological 'omics and the diversification of fishes.



Wednesday, 25 January 2017

Congrats to Arne for 'best student' award

Congratulations to Arne Jacobs for winning the 'best PhD report in the Institute' for his end of 2nd year write-up. This was awarded at the IBAHCM annual Away Day. And now on track for a productive push through to finishing his PhD next year!

Thursday, 24 November 2016

New funding for genome finishing

We have just been awarded pilot Facilities and Technology funding from the NERC Biomolecular Analysis Facility (NBAF). This project will explore using the new PacBio Sequel platform for extra-long sequencing reads for hybrid assembly, gap-closing, and high quality finishing of the Zootoca vivipara genome. Not only is this species fascinating for is bimodal live-bearing-egg-laying reproduction, but it is also a high priority species for Genome 10K. We look forward to sharing our final genome with the international community soon!

Friday, 16 September 2016

New paper: Linkage of adaptive traits

We studied the genomic organisation of ecologically relevant traits in Midas cichlids.

Fruciano, Carmelo, Paolo Franchini, Viera Kovacova, Kathryn R. Elmer, Frederico Henning & Axel Meyer. 2016. Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nature Communications 7, Article number: 12736 (2016) doi:10.1038/ncomms12736

Abstract
Our understanding of how biological diversity arises is limited, especially in the case of speciation in the face of gene flow. Here we investigate the genomic basis of adaptive traits, focusing on a sympatrically diverging species pair of crater lake cichlid fishes. We identify the main quantitative trait loci (QTL) for two eco-morphological traits: body shape and pharyngeal jaw morphology. These traits diverge in parallel between benthic and limnetic species in the repeated adaptive radiations of this and other fish lineages. Remarkably, a single chromosomal region contains the highest effect size QTL for both traits. Transcriptomic data show that the QTL regions contain genes putatively under selection. Independent population genomic data corroborate QTL regions as areas of high differentiation between the sympatric sister species. Our results provide empirical support for current theoretical models that emphasize the importance of genetic linkage and pleiotropy in facilitating rapid divergence in sympatry.

Tuesday, 30 August 2016

Welcome to new postdoc A. Yurchenko

WELCOME to new our Postdoc, Andrey Yurchenko who joins us from the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg. Andrey has outstanding expertise in genome bioinformatics and also a strong history in organismal biology (including catching fish!). He will be working with Kathryn Elmer, Rod Page and Maureen Bain on the ‘Major evolutionary transitions’ NERC project.

Tuesday, 12 July 2016

Kathryn awarded membership to the Royal Society of Edinburgh's Young Academy of Scotland

Kathryn Elmer is very pleased to have been awarded a membership to the Royal Society of Edinburgh's Young Academy of Scotland. YAS "fosters interdisciplinary activities among emerging leaders from the disciplines of science and humanities, the professions, the arts, business and civil society". I am very much looking forward to all the new ideas and colleagues brought together by working with YAS.

Congratulations to Kevin on his recent success

Kevin Schneider successfully gained a full scholarship from the Fisheries Society of the British Isles to fund his PhD research on comparative ecological genomics of salmonid fishes. Kevin will start his PhD this autumn, working with Kathryn Elmer and Colin Adams. Congratulations to Kevin on winning such a competitive scholarship.

Welcome to the new summer students

We are happy to host an enthusiastic new bunch of summer students this year. Welcome to Kevin Schneider, who is on an ERASMUS-funded internship who recently finished his Masters in Austria, Marco Crotti, who recently finished his Masters at the Natural History Museum London, Peter Koene, a second year undergraduate student here in Glasgow getting some hands on skills in molecular work, and third year student Paige Robinson who received FSBI internship funding.

Tuesday, 10 May 2016

Welcome and congrats to new intern Paige

Congratulations to Glasgow undergraduate student Paige Robinson for her successful award of an FSBI Internship with our group for summer 2016. Looking forward to some fascinating comparative population genetics of Scottish fishes!

Friday, 15 April 2016

New paper: ecological genomics of salmonid fishes

Spanning recent studies on salmonid fishes across the globe, Elmer summarises some of the key lessons learned on life history tactics, ecological speciation, and stock integrity by using genomic tools. For those readers new to ecological genomics, this paper clearly describes some of the key modern techniques and how they can be applied to questions about your study species in the wild. Also included is some ‘best practices’ advice for field biologists, so that the hard work that goes into ecological and fisheries collections can also have a long future in genomic applications.

Elmer KR (2016) Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes:
a perspective for charr. Hydrobiologia, online early doi: 10.1007/s10750-015-2614-5, 18.

The paper is available freely and open access from Hydrobiologia


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.