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!