Thursday, 7 December 2017

Coverage in The New Scientist

Our recent study, in review and available as a pre-print, has been covered by The New Scientist online and in print Magazine issue 3155, published 9 December 2017 (author: Michael Le Page)

https://www.newscientist.com/article/mg23631554-700-lizards-reevolved-eggs-after-2-million-years-of-live-births/

This study, led by Hans Recknagel, used high resolution genomics of 200,000 loci informed by our new high quality genome (Yurchenko et al. in prep) to resolve the phylogeny of the Zootoca vivipara species complex - or the Eurasian common lizard. This lizard species has egg-laying and live-bearing lineages but it has not been at all clear how and in what order the different reproductive modes evolved from the oviparous ancestry. Our topology is consistent with a single origin of viviparity from oviparity, and then a re-evolution of viviparity. While this remains to be assessed with more detailed experiments (in the works!), ours is the most robust and data-rich tackling of this long-standing question.

Tuesday, 22 August 2017

New preprint: population genomics to discriminate salmon louse populations despite high gene flow

New paper available as a preprint on biorxiv with Arne Jacobs and IBAHCM colleague Martin Llewellyn (and other great sea louse collaborators) on
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Arne Jacobs, Michele De Noia, Kim Praebel, √ėyvind Kanstad-Hanssen, Marta Paterno, Dave Jackson, Philip McGinnity, Armin Sturm, Kathryn R. Elmer, Martin S. Llewellyn

http://www.biorxiv.org/content/early/2017/08/21/179218

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Lepeophtheirus salmonis is the predominant species that occurs in the Northern Hemisphere. Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic L. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC = 0.018, p<0.0001) and only one significant pairwise FST comparison was observed (Scotland vs Kenmare Bay, (FST = 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc = 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081-0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest that L. salmonis SNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

Tuesday, 1 August 2017

New paper: rare but significant colocalisation and synteny of ecologically relevant QTL in salmonids

The organization of functional regions within genomes has important implications for the evolutionary potential of species. We compared the distribution of nearly a thousand ecologically relevant QTL within and across six salmonids (Arctic charr, Atlantic salmon, lake whitefish, rainbow trout, chinook salmon, coho salmon ) to understand their distribution across the genome. Using a novel analytical framework for comparative mapping and significance testing, we identified synteny blocks and co-localized clusters for phenotypic traits across and within species. Specifically, only two or three pairs of traits were significantly co-localized in three species (lake whitefish, coho salmon, and rainbow trout). These findings suggest genetic linkage between traits within species is relatively rare, advancing our understanding of the renowned ecological and phenotypic variability in salmonid fishes.

This project was a collaboration based on an idea hatched by Kathryn, consultation and insights from Karim in Edinburgh Genomics as an expert on genetic mapping in salmonids, detailed literature review and database building by Robyn during her MVLS-DTP mini-project, clever analytical approaches by Mel co-housed in Maths & Stats, and most importantly outstanding analysis, synthesis and drafting by Arne. Well done team!

We hope the database is of use to other salmonid researchers, as it can be supplemented as new information arises. All information is shared in the supplementary material of the paper.

Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR (2017) Significant synteny and co-localization of ecologically relevant quantitative trait loci across salmonid species. Genetics, early online

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!