Elmer Lab

Welcome to Li Chao, a visiting PhD student from Jun ZHAO's lab at the South China Normal University. Li Chao is here with a scholarship to work on conservation genetics and genomics projects about rare fishes.

Arne Jacobs wrote a great blog post for Nature Ecology and Evolution 'behind the paper' about our recent whitefish study. Find it here https://natureecoevocommunity.nature.com/users/194393-arne-jacobs/posts/41623-reversing-speciation-reversal-rapid-niche-expansion-in-european-whitefish-following-ecosystem-recovery Arne and Kathryn on the early morning sampling run Jasminca getting serious about sampling Hendrick and Arne sampling Madeleine and Arne giving a seminar to Konstanz Limnologie

Our paper is out, which finds the genetic basis of traits underpinning very rapid ecological expansion in a whitefish species and shows how fish biodiversity can recover after pollution clean-up. These findings demonstrate the potential of functional diversity to re-emerge rapidly following habitat restoration. However, this potential for recovery is likely contingent on genetic architecture, ecological context, and evolutionary history. Jacobs, A., M. Carruthers, R. Eckmann, E. Yohannes, C. E. Adams, J. Behrmann-Godel, and K. R. Elmer, 2018 Rapid niche expansion by reuse of genetic material after ecosystem recovery . Nature Ecology and Evolution online early: 1-13. See our 'behind the scenes'  post here A full-text view-only version  is available with SharedIt at: https://rdcu.be/bcmD6 This paper is highlighted by the University of Glasgow Media Office News at https://www.gla.ac.uk/news/headline_624145_en.html **** Press release **** Scientists find clu...

A new paper, published with a wonderful large set of collaborators, resolves the influence of postglacial dynamics and climatic oscillations on the genetic diversity of the Algerian salamander. This species is highly variable in colouration and some populations are of conservation concern. Dinis M, Merabet K, Martinez-Freiria F, Steinfartz S, Vences M, Burgon JD, Elmer KR, Donaire D, Hinckley A, Fahd S, Joger U, Fawzi A, Slimani T, Velo-Anton G (2018) Allopatric diversification and evolutionary melting pot in a North African Palearctic relict: The biogeographic history of Salamandra algira . Molecular Phylogenetics and Evolution , in press, The paper is currently freely available here: https://authors.elsevier.com/c/1XvLg3m3nMuJY1 And then soon will be fully open access, thanks to RCUK and Uni Glasgow. Abstract North Africa is a climatically and topographically complex region with unique biotic assemblages resulting from the combination of multiple biogeographic realms. Here, ...

New paper, in press with Systematics and Biodiversity " Hierarchies of evolutionary radiation in the world’s most species rich vertebrate group, the Neotropical Pristimantis leaf litter frogs " Emily Waddell & Marco Crotti, Stephen C Lougheed, David Cannatella, Kathryn R Elmer In this paper we add a number of new specimens to the mix in this highly diverse yet deeply cryptic group of frogs. Using molecular techniques we show that several of these are new species and we also contribute new diversity to known species. We then analyse the rate and pattern of evolution across the entire phylogeny. We suggest that these 'higher evolutionarily significant units' might be a useful way of grouping and investigating diversification patterns in these famously diverse species. This was part of Emily's MRes project which she conducted in our group. In fact this project started as part of my PhD work, then was added to in later research with Dave Cannatella and the A...

Congratulations to two of the lab's recent PhD graduates, Hans Recknagel ("Environmental constraints and genetic basis for the evolution of viviparity") and Arne Jacobs ("The population genomic origins of ecological specialisation in salmonid fishes"), both (*both!*) of whom were nominated by their respective examining committees for the university's top honours - the thesis prize. This ranks them in the top 5% of theses examined at the University of Glasgow in the academic year. Fantastic work!

Congratulations to Hans Recknagel for his talk in the Hamilton symposium at ESEB/Evolution in Montpellier, Aug 2018. Hans gave a fantastic talk in a really competitive line up of outstanding PhD projects from around the world. It was a great honour to be shortlisted. ps - there was more than one other person in the audience of that HUGE theatre, just that I was up near the front.

Well done to Team Lizard 2017, who have had their paper on a rare but pervasive colour polymorphism in common lizards published! The summer field team of University of Glasgow Zoology undergrads, a masters and a PhD student analysed and drafted this paper from the field site, documenting melanic common lizards in the Alps. There is also the possibility melanism is sex biased, as only females were found, but given how rare these specimens are it is difficult to draw conclusions on that and more sampling will be needed. Paper is out in Herpetology Notes  2018 Melanism in common lizards (Squamata: Lacertidae: Zootoca vivipara): new evidence for a rare but widespread ancestral polymorphism by Hans Recknagel, Megan Layton, Ruth Carey, Henrique Leitão, Mark Sutherland, Kathryn R Elmer https://www.biotaxa.org/hn/article/view/33903 Abstract. The presence of a dark-coloured body colouration polymorphism (melanism) is a pervasive phenomenon in the animal kingdom, particularly in...

Our paper on the evolution of oviparity and viviparity, as inferred from phylogenomics, is now fully available in the journal Molecular Phylogenetics and Evolution at   https://doi.org/10.1016/j.ympev.2018.05.029 Common lizards break Dollo’s law of irreversibility: genome-wide phylogenomics support a single origin of viviparity and re-evolution of oviparity Well done to Hans, who led this work as part of his PhD 'Trees through time', a Lord Kelvin Adam Smith Interdisciplinary grant from the University of Glasgow and into the NERC grant. This research was earlier covered by New Scientist  here  when the ms was a preprint.

I was recently in Duluth and presented our work on parallel evolution and population genomics in Arctic charr (largely from our preprint available here ) at a plenary for the International Charr Symposium. Well done to the organisers, it was a very interesting and well attended congress. And we had a truly American experience ...

Congratulations to Arne who defended his thesis on "The population genomic origins of ecological specialisation in salmonid fishes". He was examined by Paul Johnson (IBAHCM) and Craig Primmer (Helsinki) with Martin Llewellyn as convenor. Arne did an excellent job -- well done!

Welcome to our FSBI Intern Tie Caribe, who has a busy summer ahead of lab work, husbandry, and and learning lots of new science! Congratulations on a successful award.

We welcome our summer project Masters students Allan Campbell, John Smout and Melissa Raske who are all working on molecular biotech projects, either in the field using in situ, rapid assessment with tests of the cool new qPCR-on-an-iPhone from biomeme, linking candidate genetic variants with local environments, or doing tissue-specific ecological transcriptomics in the lab. They have in intensive but exciting few months ahead!

Congratulations to Hans, who successfully defended (="viva") his thesis on 22 April. With many thanks to the examiners and convenor, it was an interesting discussion and an exceptional thesis. Hans' research is on the ecology and evolution of reproductive modes, primarily using squamates as a model. His project was funded by an interdisciplinary Lord Kelvin-Adam Smith project with Kathryn Elmer (IBAHCM) and Nick Kamenos (Geography). There was also a pic of a lovely leaping lizard cake, but it is all gobbled up ...

A big congratulations to Madeleine for a successful PhD viva on her project on ecological transcriptomics and adaptive divergences in salmonid fishes! And here she is celebrating with a delicious charr cake. (tasted better than that sounds)

Congrats to James Burgon for a very successful viva / PhD thesis defence for his project on 'how the salamander got his spots' on March 19th. And his colleagues made him a lovely thematic cake!

Parallel evolution by non-parallel routes is a major fascination of mine. Here we have a pre-print submitted (and ms in the appropriate pipelines) about how such parallel evolution can happen, overcoming non-parallel backgrounds. The transcriptome! This is the outcome of a major group effort, including two PhD theses and many many years' worth of sampling ... Preprint at https://www.biorxiv.org/content/early/2018/02/14/265272.article-info Abstract:  Quantifying the extent to which evolution is predictable is critical to understanding biodiversity origins and its responses to future environmental challenges 1,2 . Replicate, or parallel, phenotypic evolution has been found in classic examples such as anole lizards, stickleback fishes, salmonid fishes, and cichlid fishes 3-8 and reflects similar adaptive outcomes. However it is not well understood if, how, and at what rate ecologically relevant phenotypic evolution can overcome the heterogeneous genetic backgro...

Very few fishes are colony breeding and so those that do are particularly interesting. In the clear waters of crater lake Apoyo, famous for its sympatric speciation of cichlids, the ‘short’ Midas cichlid have dense seasonal aggregations that breed and care for their young in beds of Chara algae. We wondered, why are they doing this? How does it relate to their family structures? Are males or females breeding where they were born or near their kin? We suspected that, given that the young babies are reared and tended in close proximity and with lots of brood swapping, that siblings might set up breeding territories close to each other. However, by sampling breeding pairs for genetic relatedness within and across multiple colonies, we discovered that there is no local genetic association. Nor does the biology differ, as patters are the same for males nor females. Our results suggest that strong philopatry or spatial assortative mating are unlikely to explain the rapid speciation pro...

Recently published collaboration with our group and Glasgow Polyomics, including the efforts of masters and PhD student researchers. De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species Madeleine Carruthers, Andrey A. Yurchenko, Julian J. Augley, Colin E. Adams, Pawel Herzyk and Kathryn R. Elmer The paper is available open access at BMC Genomics, 19, 32.  Annotated transcript sequences are available from NCBI or from Kathryn by email. Abstract Background: Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de...