I'm honoured to have been awarded the Zoological Society of London Scientific Medal for 2023.
Monday 2 October 2023
Welcome to our new PhD student Molly Uzzell, who has been awarded a position in the NorthWestBio Doctoral Training programme. Molly's project, co-supervised with Isabella Capellini in QU Belfast, will be on pre- & post-zygotic reproductive isolation in lizards, and the effects of hybridisation on reproductive success. Molly has been with us as a volunteer since undergrad, then honours and masters - looking forward to the next phase!
Saturday 30 September 2023
I'm thrilled to share that we have had a Pushing the Frontiers grant funded by NERC. The project is with co-Is Mike Ritchie and Oscar Gaggiotti at St Andrews, Maureen Bain in Glasgow, and Project Partners Jean-François Le Galliard and Pierre de Villemereuil in France and Hans Recknagel in Slovenia. This will support 4 years of research on sex-specific fitness landscapes in oviparous-viviparous lizards.
Sunday 1 January 2023
Monday 31 January 2022
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 suggests that different fish populations of varying sizes will respond differently to fishing selection at the genetic level. Furthermore, as a population is fished over time, the genes under selection may change as the population diminishes. This could have repercussions on population resilience. This study highlights the importance of selection but also environmental and density effects on harvested fish populations.
Tuesday 2 November 2021
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.
Thursday 21 October 2021
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
Monday 13 September 2021
We are back in the field and setting up a new experiment on reproductive mode evolution! Delays due to covid are behind us and I'm thrilled to be at CNRS Station for Theoretical and Experimental Ecology and starting our collaboration with ecology legend Jean Clobert.
First lizard pots are ready and lizards are arriving this week!
This is a NERC funded project with Maureen Bain and Jean Clobert, and the collaboration of Hans Recknagel and new postdoc Morgane Bonade, to dig deeper into the functional development of oviparity in ancestral and derived lineages. Through this experiment we will directly tackle the thorny issue of putative reversal to oviparity ... do lizards break Dollo's Law?
Also perfect timing for some momentum, as our major paper on functional genomics of oviparity vs viviparity is in press. Free online at https://rdcu.be/cy5S2
more new soon!
Sunday 5 September 2021
Recently published in the Journal of Evolutionary Biology -
Evolutionary origins of viviparity consistent with palaeoclimate and lineage diversification
It has long been argued that the origin of viviparity is related to cold climatic conditions. However this is challenging to disentangle correlation from causation, and response from cause. Also many studies have examined particular species groups but we have lacked the data so far to estimate a time tree in context of climate. Here led by Hans Recknagel in his interdisciplinary PhD studentship, we showed that stable and long-lasting cold climatic conditions are correlated with transitions to viviparity across squamates. Interestingly, this correlation of parity mode and palaeoclimate is mirrored by background diversification rate in squamates. Further, exploring patterns by simulations of a binary trait also showed a similar association with palaeoclimate. Overall this suggests that vivparity evolution cannot be separated from squamate lineage diversification. We suggest that parity mode transitions depend on environmental and intrinsic effects and that background diversification rate may be a factor in trait diversification more generally.
Ultimately we need more genome-informed and mechanistic information about the basis of viviparity to better retrace its evolution, but these data are lacking.
Friday 27 November 2020
We were recently awarded a three year NERC grant to study the evolution and development of reproductive modes, with common lizards as a model organism
Check back early January if you are interested - we will be advertising for a postdoc soon!
Reproductive mode evolution and reversal demonstrate the genetic toolkits of egg-laying and live-bearing
Abstract: Laying eggs or giving birth to live young are two fundamentally different ways for females to produce their offspring. All birds, crocodilians, turtles, monotreme mammals (such as duck-billed platypus), and many lizards and snakes are egg-laying, as were most dinosaurs. In contrast, all placental mammals (like humans), marsupials, and some lizards and snakes are live-bearing. From studying embryos we know that many molecular and developmental aspects of these reproductive modes arose deep within the tree of life. For example, ancient egg-making structures are still retained within mammalian placenta, and the genes activated by pregnancy in lizards are the same as those activated by pregnancy in mammals and seahorses. Yet, clearly, substantial reproductive differences evolved between species; though it is not known how or why because the core genetic controls of these reproductive modes remain unknown. This major and obvious gap in our biological knowledge has persisted into the genomic era - where we can now study the entire DNA sequence of an organism - because we lacked an informative experimental model. Simply put, to test the genetic basis of traits that differ, the definitive experiment is to make a cross between the two different types. In the case of reproductive mode this is usual not possible, because species are too divergent to successfully breed. For example, no one can make a genetic cross of a platypus and a snake to test if the 'egg making DNA' is the same in both species.
Our proposal seeks to shed light on the genetic basis of these fundamental reproductive traits using an exceptional species: the humbly-named 'common lizard'.
To test long-standing ideas about the genetic basis of fundamental reproductive traits, we plan to do controlled functional studies of the different types found within these lizards and hybrid experimental crosses. By comparing the two lineages of egg-laying lizards we will be able to identify the genes necessary for egg-laying. This is due to the fact that the core genes should be found in the genomes of both and, if they are shared, these genes should be expressed in similar places and times. Mismatches will be evident and point to different bases. Then we will use computational approaches to reconstruct the phylogenetic tree of the 'egg-laying' (and 'live-bearing') genes across the history of the entire species and if oviparity evolved once or multiple times. This will reveal how changes in a species' DNA give rise to changes in reproductive mode. Because of the ancient origins and sharing of reproductive genes across species, the lessons learned from these lizards will provide new and valuable insights into the biology, reproductive health, and evolution of all vertebrates.
PI: Kathryn R Elmer (IBAHCM)
co-I Maureen Bain (IBAHCM-Vet School)
Project Parter: Jean Clobert (CNRS Moulis)
Tuesday 3 November 2020
from his time as a visiting PhD student in our lab group, Li Chao has published an excellent paper on cryptic diversity and its taxonomic implications.
Cryptic species in White Cloud Mountain minnow, Tanichthys albonubes: Taxonomic and conservation implications
Molecular Phylogenetics and Evolution
Chao Li, Shuying Jiang. Kevin Schneider. Jinjin Jin, Hungdu Lin, JunjieWang, Kathryn R.Elmer, Jun Zhao
Abstract: Cryptic species describe two or more species that had mistakenly been considered to be a single species, a phenomenon that has been found throughout the tree of life. Recognizing cryptic species is key to estimating the real biodiversity of the world and understanding evolutionary processes. Molecular methods present an unprecedented opportunity for biologists to question whether morphologically similar populations are actually cryptic species. The minnow Tanichthys albonubes is a critically endangered freshwater fish and was classified as a second-class state-protected animal in China. Previous studies have revealed highly divergent lineages with similar morphological characters in this species. Herein, we tested for cryptic species across the ranges of all known wild populations of this minnow. Using multilocus molecular (one mitochondrial gene, two nuclear genes and 13 microsatellite loci) and morphological data for 230 individuals from eight populations, we found deep genetic divergence among these populations with subtle morphological disparity. Morphological examination found variance among these populations in the number of branched anal-fin rays. Based on genetic data, we inferred eight monophyletic groups that were well supported by haplotype network and population clustering analyses. Species delimitation methods suggested eight putative species in the T. albonubes complex. Molecular dating suggested that these cryptic species diverged in the period from the Pliocene to the Pleistocene. Based on these findings, we propose the existence of seven cryptic species in the T. albonubes complex. Our results highlight the need for a taxonomic revision of Tanichthys. What is more, the conservation status of and conservation strategies for the T. albonubes complex should be reassessed as soon as possible.
New paper: Intraspecific variation and structuring of phenotype in a lake-dwelling species are driven by lake size and elevation
Research from now-FSBI PhD student Peter Koene, from his masters project in Glasgow -
Tuesday 21 July 2020
Tuesday 14 April 2020
Sunday 1 March 2020
Burgon, J.D., Vieites, D.R., Jacobs, A., Weidt, S.K., Gunter, H.M., Steinfartz, S., Burgess, K., Mable, B.K. and Elmer, K.R., 2020. Functional colour genes and signals of selection in colour polymorphic salamanders. Molecular Ecology. in press online early
Sunday 26 January 2020
Li, C., Wang, J., Chen, J., Schneider, K., Veettil, R.K., Elmer, K.R. and Zhao, J., 2020. Native bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix populations in the Pearl River are threatened by Yangtze River introductions as revealed by mitochondrial DNA. Journal of Fish Biology. in press online early
Culturally and economically important fishes with conservation challenges due to people stocking fry and building dams.
Bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix have been two economically important aquaculture species in China for centuries. In the past decades, bighead and silver carp have been introduced from the Yangtze River to many river systems in China, including the Pearl River, in annual, large‐scale, stocking activities to enhance wild fisheries. Nonetheless, few studies have assessed the ecological or genetic impacts of such introductions on native conspecific fish populations. An mtDNA D‐loop segment of 978 bp from 213 bighead carp samples from 9 populations and a 975 bp segment from 204 silver carp samples from 10 populations were obtained to evaluate genetic diversity and population integrity. Results from a haplotype network analysis revealed that most haplotypes of the Pearl River clustered with those of Yangtze River origin and only a small proportion were distinct, suggesting that both the native Pearl River bighead and silver carp populations are currently dominated by genetic material from the Yangtze River. The genetic diversity of Pearl River populations is high in both species because of this inter‐population gene flow, but the diversity of native Pearl River populations is low. To preserve the native genetic diversity, stocking of non‐native fingerlings should cease immediately and native Pearl River bighead and silver carp fish farms should be established. This research demonstrates the danger to native biodiversity across China because of the substantial, ongoing stock‐enhancement activities without prior genetic assessment.
Sunday 5 January 2020
Schneider, K., Adams, C.E. and Elmer, K.R., 2019. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC genomics, 20(1), pp.1-23.
open access paper available here
Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup.
All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling.
Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
Sunday 1 December 2019
McLennan, D., Recknagel, H., Elmer, K.R. and Monaghan, P., 2019. Distinct telomere differences within a reproductively bimodal common lizard population. Functional Ecology, 33(10), pp.1917-1927.
Open access full article here
Different strategies of reproductive mode, either oviparity (egg‐laying) or viviparity (live‐bearing), will be associated with a range of other life‐history differences that are expected to affect patterns of ageing and longevity. It is usually difficult to compare the effects of alternative reproductive modes because of evolutionary and ecological divergence. However, the very rare exemplars of reproductive bimodality, in which different modes exist within a single species, offer an opportunity for robust and controlled comparisons.One trait of interest that could be associated with life history, ageing and longevity is the length of the telomeres, which form protective caps at the chromosome ends and are generally considered a good indicator of cellular health. The shortening of these telomeres has been linked to stressful conditions; therefore, it is possible that differing reproductive costs will influence patterns of telomere loss. This is important because a number of studies have linked a shorter telomere length to reduced survival. Here, we have studied maternal and offspring telomere dynamics in the common lizard (Zootoca vivipara). Our study has focused on a population where oviparous and viviparous individuals co‐occur in the same habitat and occasionally interbreed to form admixed individuals. While viviparity confers many advantages for offspring, it might also incur substantial costs for the mother, for example require more energy. Therefore, we predicted that viviparous mothers would have relatively shorter telomeres than oviparous mothers, with admixed mothers having intermediate telomere lengths. There is thought to be a heritable component to telomere length; therefore, we also hypothesized that offspring would follow the same pattern as the mothers. Contrary to our predictions, the viviparous mothers and offspring had the longest telomeres, and the oviparous mothers and offspring had the shortest telomeres. The differing telomere lengths may have evolved as an effect of the life‐history divergence between the reproductive modes, for example due to the increased growth rate that viviparous individuals may undergo to reach a similar size at reproduction.
Wednesday 17 July 2019
Project: The lake-dwelling salmonid fish, the Arctic charr (Salvelinusalpinus) is highly diverse both in phenotype and genotype. This takesthe form of substantial variation within and between lakes; in someplaces the latter being expressed as eco-morphologically distinctand reproductively isolated sympatric polymorphisms. In addition thespecies is of high conservation value in the UK. This project willuse high-resolution population genomic techniques to resolve questionsabout the phylogenetic similarities between allopatric and sympatricpopulations to inform the taxonomic position of the species and to helpidentify units that may require conservation protection. Samples from a wide range of populations from across Scotland andoutgroups are already available, and there may be the opportunity tocollect more.
The project is supported in part by Scottish Natural Heritage and theoutcomes of this PhD will have direct relevance for national freshwaterconservation and management.
Funding: The project is fully funded for 3 years: stipend (salary)of pounds 14,500 per year, university fees at UK/EU rate, and consumablescosts. **Anyone from the EU/UK is eligible for the full funding**
The successful candidate for this project is likely to be someone with astrong theoretical background in evolution and/or population genetics andwho can show evidence of practical laboratory and analytical experiencein an appropriate field.
You will join a collegial and motivated research team with PhDstudents, postdocs and technician support studying evolution andadaptation in natural environments, especially with a focus on fishesand herps. Prof. Adams studies fish biology and trophic ecology and isDirector of the Scottish Centre for Ecology and the Natural Environment(SCENE) on Loch Lomond. Dr. Elmer is interested in the genetics ofbiodiversity and ecological diversification and based in the EvolutionaryAnalysis Group. Both faculty are in the Institute of Biodiversity,Animal Health & Comparative Medicine, which is part of the College ofMedical, Veterinary and Life Sciences at the University of Glasgow,Scotland. You can find more about our activities and interests here:https://www.gla.ac.uk/researchinstitutes/bahcm/staff/kathrynelmer/http://elmerlab.blogspot.comhttps://www.gla.ac.uk/researchinstitutes/bahcm/staff/colinadams/
The project is also co-supervised by Colin Bean (Scottish Natural Heritage)and will work closely with collaborators in Ireland (P. Prodohl) The University of Glasgow ranks in the world's top 100 universities andIBAHCM is an outstanding research institution with many opportunitiesfor collaboration and discussion in a supportive and productiveenvironment. Glasgow is a lively cultural city on the doorstep of thebeautifully rugged Scottish Highlands.
Deadline for applications is 14 August 2019All applications must be made through the website strictly by the deadline.
start date 1 Oct 2019
Please find more details and the application herehttps://www.findaphd.com/phds/project/the-adaptive-diversity-of-arctic-charr-salvelinus-alpinus-in-scotland/?p110955
Informal inquiries to Kathryn Elmer or Colin Adams in advance of the deadline are welcome.