Elmer Lab

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 lon...

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, Øyvind 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 populati...

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 insight...

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 .

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 .  image from Oliver Hooker

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...

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!

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.

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.

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!