Resources

In addition to those outcomes from new research findings and commitment to openly accessible primary data from our research, one of my favourite aspects of science is putting together and sharing new tools, databases, and archives - from our team to the world.

Here is a partial list of tools and archives generated and made available:

Salmonid QTLs extracted from broad thorough review and their locations mapped to Atlantic salmon
Supplementary material in Genetics paper
(Update on this coming soon from S. Fenton!)

R script for resampling to test QTL co-localisation relative to background expectations
Supplementary material in Genetics paper

Four transcriptomes of salmonid species
Available through our BMC Genomics paper

Database of pregnancy genes in viviparous squamates and mammals (and seahorse)
Supplementary material in Nature Eco Evo paper

Chromosome-level and annotated reference genome of common lizard Zootoca vivipara
Accessible from GBE paper

Reference genome of Midas cichlid  (now superseded by later work)
Accessible from Nature Comms paper

New  approach, protocol, and efficacy evaluation of ddRADseq using ion-Proton
Accessible from Molecular Ecology Resources paper

Methodology for getting double duty from epigenetic and genomic RAD datasets
Explained in Methods in Ecology & Evolution paper

New microsatellite loci for Pristimantis leaf litter frogs and tested across related species
Described here Molecular Ecology Notes

High density linkage maps for Midas cichlids (and very early adoption of RADseq and with optimised protocol for cichlidsd)
Available here Genome Biol Evol paper

Field-based, rapid genotyping for parity mode and sex in squamates coming soon!



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 in a collaboration with Amelie Crespel and Shaun Killen, we brought some genomics to an applied evolutionary question - is there evolutionary response to fisheries harvesting? We suspected that forces like size-selective harvest can have impact but what about environmental or demographic context? Open access paper here ! Crespel A, Schneider K, Miller T, Rácz A, Jacobs A, Lindström J, Elmer KR, Killen SS (2021) Genomic basis of fishing-associated selection varies with population density. Proc Natl Acad Sci U S A, 118, e2020833118. Significance: Fisheries-associated selection is recognized as one of the strongest potential human drivers of contemporary evolution in natural populations. The results of this study show that while simulated commercial fishing techniques consistently remove fish with traits associated with growth, metabolism, and social behavior, the specific genes under fishing selection differ depending on the density of the targeted population. This finding suggest
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Welcome to new lab members!

We welcome two new lab members for autumn 2021 - postdoc Morgane Bonade and PhD student Nic Strowbridge.  Morgane is working on the project 'do common lizards break Dollo's Law' by reversing back to oviparity? This is a NERC funded project that tests functionally - using genetic crosses, RNAseq, and phylogeny - some hypotheses put forward in our phylogenomic reconstruction that suggested reversal (open access paper here in MPE ).  Nic is an IAPETUS2 doctoral training programme student working on convergent evolution of colouration and toxicity defence in salamanders, in collaboration with Mike Ritchie at St Andrews.
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New paper: Functional genetic basis of reproductive mode

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Our paper on the genetic basis of parity mode is now published. The functional genetic architecture of egg-laying and live-bearing reproduction in common lizards H. Recknagel, M. Carruthers, A. Yurchenko, M. Nokhbatolfoghahai, N.A. Kamenos, M.M. Bain, K.R. Elmer Nature Ecology and Evolution 2021 SharedIt link:  https://rdcu.be/cy5S2 All amniotes reproduce either by egg-laying (oviparity), which is ancestral to vertebrates, or by live-bearing (viviparity), which has evolved many times independently. However, the genetic basis of these parity modes has never been resolved and consequently its convergence across evolutionary scales is currently unknown. Here we leveraged natural hybridisations between oviparous and viviparous common lizards (Zootoca vivipara) to describe the functional genes and genetic architecture of parity mode and its key traits, eggshell and gestation length, and compared our findings across vertebrates. In these lizards, parity trait genes were associated with prog
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