Friday, 27 November 2020

success with NERC standard grant and soon hiring

 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'. Native to all of Eurasia, including the British Isles, this species harbours a secret underneath its simple brown scales: some populations are egg-laying and others are live-bearing. Like all reptiles, egg-laying is the original, or ancestral, mode. This means that many millions of years ago all common lizard females laid eggs. Then, about three million years ago, some females discarded the egg-laying tactic; no longer encircling their embryos in eggshells, the females retained their babies inside their bodies until fully developed. Why and how this happened is not known, but is presumed to be an adaptation that allowed mothers to better protect their embryos from cold and challenging environments. Amazingly, evolutionary reconstructions suggest that another million years later, some common lizards abandoned the live-bearing strategy and reversed back to egg-laying. Today we have populations with the original egg-laying strategy (mostly in the Alps), the live-bearers (across most of Eurasia), and those few that reversed back to egg-laying from live-bearing (found in the Pyrenees). Importantly, because they are closely related, individuals from all of these populations can interbreed. 

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 make experimental crosses between them. 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. Then, using all the information we gain about how and where genes are active, we will use computational approaches to retrace the evolution of 'egg-laying' and 'live-bearing' genes across the history of the entire species. 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)

PhD opportunities for autumn 2021

 We have several PhD opportunities through competition in the IAPETUS programme. Please see Opportunities page

Tuesday, 3 November 2020

New paper: cryptic diversity in Chinese minnows

 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

https://doi.org/10.1016/j.ympev.2020.106950

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 - 

https://doi.org/10.1093/biolinnean/blaa137

Abstract

The fragmented, heterogeneous and relatively depauperate ecosystems of recently glaciated lakes present contrasting ecological opportunities for resident fish. Across a species, local adaptation may induce diverse and distinct phenotypic responses to various selection pressures. We tested for intraspecific phenotypic structuring by population in a common native lake-dwelling fish species across a medium-scale geographic region with considerable variation in lake types. We investigated potential lake-characteristic drivers of trophic morphology. Using geometric morphometric techniques, we quantified the head shapes of 759 adult brown trout (Salmo trutta L.) from 28 lakes and reservoirs across Scotland. Multivariate statistical analyses showed that almost all populations differed from one another. Trout from larger and deeper lakes had deeper, but shorter heads, and smaller eyes. Higher elevation lakes were associated with fish with shorter heads and jaws. Within-population shape variation also differed by population, and was positively correlated with lake surface area and depth. Trout within reservoirs differed subtly from those in natural lakes, having larger eyes, shorter jaws and greater variability. This study documents an extraordinary morphological variation between and within populations of brown trout, and demonstrates the role of the extrinsic environment in driving phenotypic structuring over a medium-scale and varied geographic area.

Tuesday, 21 July 2020

POSTDOC POSITION AVAILABLE

CLOSED 

Postdoc: UGlasgow.GenomicsReproductiveMode

We have a research opportunity open at the University of Glasgow's Institute of Biodiversity, Animal Health & Comparative Medicine (IBAHCM) working in the Evolutionary Analysis Group and the research team of Kathryn Elmer (http://www.gla.ac.uk/researchinstitutes/bahcm/staff/kathrynelmer/) in collaboration with Oscar Gaggiotti at University of St Andrews (https://risweb.st-andrews.ac.uk/portal/en/persons/oscar-eduardo-gaggiotti(43985656-390b-478e-b9a7-05fe88181e46).html_ The project is primarily based at Glasgow and research periods based at St Andrews are supported.

We are seeking a motivated, creative and enthusiastic postdoctoral researcher for a project on the genomic basis of oviparous and viviparous reproductive modes, funded by The Leverhulme Trust. This project will apply advanced statistical analyses to population-wide whole genome sequences to identify regions of the genome that show signals of response to selection, the molecular targets of that selection (genes, gene functions, and biological pathways), and genetic units fundamental to egg-laying vs live-bearing. The research model is the common lizard, which is a fascinating and unusual species because it is reproductively bimodal. 

A strong track record of genetic and evolutionary research is necessary, and on vertebrates is a benefit. Bioinformatic experience with NGS data and expertise in whole genome analysis is preferred. Skills in quantitative trait mapping, comparative genomics, ecological and/or population genomics, statistics, and phylogenetics are also valuable. Lab work and fieldwork skills are not strictly required but would be advantageous. Team working and positive attitude are a must. Candidates must have completed their PhD by the start of contract. International applicants will be eligible for a UK work visa. We welcome a diversity of applicants!

The position is for 3 years, with start date reasonably flexible. The position is open at grade 6 (early career postdoc) or grade 7 (experienced postdoc).

IBAHCM is a stimulating and interactive research environment with a wealth of opportunities for discussion, collaboration and cutting edge research in evolution, ecology, and disease. The University of Glasgow ranks in the world's top 100 universities.  The University and IBAHCM are both recognised with Athena SWAN awards. The city of Glasgow is lively and cultural, and sits on the doorstep of the great outdoors of the Scottish Highlands, islands, and coast.

The official job description and application requirements are available on the University of Glasgow homepage under current vacancies; http://www.gla.ac.uk/about/jobs/vacancies/ at job reference 039224

**The advertisement closes 7 August 2020.** 

Informal inquiries in advance are very welcome

Tuesday, 14 April 2020

New paper: Parallel evolution of Arctic charr across divergent lineages

"Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish" is in press with PLoS Genetics. data available on Enlighten. 

https://doi.org/10.1371/journal.pgen.1008658

Abstract
Understanding the extent to which ecological divergence is repeatable is essential for predicting responses of biodiversity to environmental change. Here we test the predictability of evolution, from genotype to phenotype, by studying parallel evolution in a salmonid fish, Arctic charr (Salvelinus alpinus), across eleven replicate sympatric ecotype pairs (benthivorous-planktivorous and planktivorous-piscivorous) and two evolutionary lineages. We found considerable variability in eco-morphological divergence, with several traits related to foraging (eye diameter, pectoral fin length) being highly parallel even across lineages. This suggests repeated and predictable adaptation to environment. Consistent with ancestral genetic variation, hundreds of loci were associated with ecotype divergence within lineages of which eight were shared across lineages. This shared genetic variation was maintained despite variation in evolutionary histories, ranging from postglacial divergence in sympatry (ca. 10-15kya) to pre-glacial divergence (ca. 20-40kya) with postglacial secondary contact. Transcriptome-wide gene expression (44,102 genes) was highly parallel across replicates, involved biological processes characteristic of ecotype morphology and physiology, and revealed parallelism at the level of regulatory networks. This expression divergence was not only plastic but in part genetically controlled by parallel cis-eQTL. Lastly, we found that the magnitude of phenotypic divergence was largely correlated with the genetic differentiation and gene expression divergence. In contrast, the direction of phenotypic change was mostly determined by the interplay of adaptive genetic variation, gene expression, and ecosystem size. Ecosystem size further explained variation in putatively adaptive, ecotype-associated genomic patterns within and across lineages, highlighting the role of environmental variation and stochasticity in parallel evolution. Together, our findings demonstrate the parallel evolution of eco-morphology and gene expression within and across evolutionary lineages, which is controlled by the interplay of environmental stochasticity and evolutionary contingencies, largely overcoming variable evolutionary histories and genomic backgrounds.

Sunday, 1 March 2020

New paper: Colour genes under selection in colourful salamanders


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

Led by PhD student James Burgon, this paper is a favourite! a project started with colleagues in Scotland, Germany and Spain, coming from plans that were long in the pipeline. A new set of colour candidate genes for amphibians.

Abstract
Colouration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we leverage insight from a highly colour‐variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs—ancestral black‐yellow striped, fully yellow, and fully brown—differed in pattern, visible colouration, and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However we identified 21 loci with genotype‐phenotype associations, several of which relate to known colour genes. Further, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to colouration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown, and black skin, 63 of which are candidate genes involved in animal colouration. The concordance across different statistical approaches and ‘omic datasets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1, and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.


Sunday, 26 January 2020

New paper: endemic fish diversity swamped by stocking

Work from Li Chao's research visit with us:
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.

Abstract
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

New paper: convergence in molecular signals of selection across genera

Paper led by PhD Student Kevin Schneider analysed all available transcriptome data for salmonids, to ask: at the molecular evolution level, what is similar about rapidly diversifying lake salmonids?

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

Abstract
Background
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.

Results
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.

Conclusions
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

New paper: telomere lengths differ between parity modes

We have a new collaborative paper out with Pat Monaghan and the telomeres lab. The dynamics of telomeres in lizards are really poorly understood. Here we brought together an evolutionary perspective, genetic and pedigree information, and an analysis of telomeres. Also cover image, a beautiful oviparous female and her clutch.

McLennan, D., Recknagel, H., Elmer, K.R. and Monaghan, P., 2019. Distinct telomere differences within a reproductively bimodal common lizard population. Functional Ecology33(10), pp.1917-1927.

Open access full article here 


ABSTRACT
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

fully funded PhD position available in charr population genomics

A competitive fully-funded PhD studentship is be available to studyadaptation and population genomics of Scotland's most variable fishthe Arctic charr -- with Colin Adams and Kathryn Elmer at the Universityof Glasgow, Scotland. We are looking for an enthusiastic evolutionarybiologist to join our team!
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.

Monday, 17 June 2019

Welcome to new summer interns!

We welcome our new summer interns!
Magdalena Butowska has just finished first year and will be working on molecular lab work of fish mtDNAs, morphometrics and plasticity;
Robbie Hussein has just finished second year and will be working on analysing whether pregnancy affects the running speed of lizards;
Giuditta Magian won a School of Life Sciences Undergraduate Vacation Scholarship after her third year and is busy working on Team Lizard-catching down in the Alps;
Tie Caribe just finished fourth year (whoop!) and was awarded an FSBI internship with Colin Adams. He will be doing some of his lab work up in the roof labs;
John Smout finished his Masters in Biotech last year, having done a project with us in the field then, and is also busy with Team Lizard this summer before he starts his PhD with MVLS in the autumn.


New paper: effect of conservation refugia on biodiversity

What is the impact of the 'refuge' or 'ark population' conservation measure on biodiversity? Masters/Honours student Peter Koene along with PhD student Marco Crotti have completed a project on how morphologies and plasticity change in new habitats and after population bottlenecks, studying powan or European whitefish (Coregonus lavaretus) here in Scotland.

Full paper is available here
"Differential selection pressures result in a rapid divergence of donor and refuge populations of a high conservation value freshwater fish Coregonus lavaretus (L.)"

J. Peter Koene, Marco Crotti, Kathryn R Elmer, Colin E Adams

Abstract
As a conservation measure to protect European whitefish in Scotland, a translocated popu-lation  was  established  in  Loch  Sloy  from  Loch  Lomond  stock  between  1988  and  1990.  Previous  study  has  assumed  that  current  morphological  differences  between  adults  from  the  donor  and  refuge  lakes  have  arisen  through  phenotypic  plasticity.  The  present  study  compared  the  morphologies  of  whitefish  at  three  life  stages:  alevins  and  fry  raised  in  a  common garden, and wild-caught adults. Alevins were clearly distinguishable by their lake of  origin.  Loch  Sloy  alevins  were  distinguishable  also  by  family,  although  this  was  not  the case for Loch Lomond. Differential allometric trajectories facilitated the persistence of morphological  differences  associated  with  lake  of  origin  through  the  fry  stage  into  adult-hood.  Overall,  the  whitefish  from  Loch  Lomond  displayed  morphologies  associated  with  pelagic  feeders,  while  the  more  robust  heads  and  ventrally  positioned  snouts  of  the  Loch  Sloy whitefish conformed to expectations for more benthic feeding habits. That differences between populations were present not only in wild adults, but also in alevins and fry from a common garden setup, strongly suggests that the divergence between populations is due to inheritance mechanisms, rather than differential plastic responses, and questions the effec-tiveness of translocation as a conservation measure.

Keywords   Whitefish · Conservation · Translocation · Divergence · Morphology

Monday, 13 May 2019

New paper: life-history trade-offs of oviparity and viviparity

Congratulations to Hans and our newest paper - "Differential reproductive investment in co-occurring oviparous and viviparous common lizards (Zootoca vivipara) and implications for life-history trade-offs with viviparity". A strength of this study is that it compares oviparity and viviparity reproduction from within the same geographic area and between sister lineages, therefore minimising the effects of environment and phylogeny.

The paper is available open access from here, in Oecologia
https://rdcu.be/bAGx7

Abstract
Live-bearing reproduction (viviparity) has evolved from egg-laying (oviparity) independently many times and most abun-dantly in squamate reptiles. Studying life-history trade-offs between the two reproductive modes is an inherently difficult task, as most transitions to viviparity are evolutionarily old and/or are confounded by environmental effects. The common lizard (Zootoca vivipara) is one of very few known reproductively bimodal species, in which some populations are oviparous and others viviparous. Oviparous and viviparous populations can occur in sympatry in the same environment, making this a unique system for investigating alternative life-history trade-offs between oviparous and viviparous reproduction. We find that viviparous females exhibit larger body size, smaller clutch sizes, a larger reproductive investment, and a higher hatching success rate than oviparous females. We find that offspring size and weight from viviparous females was lower compared to offspring from oviparous females, which may reflect space constraints during pregnancy. We suggest that viviparity in common lizards is associated with increased reproductive burden for viviparous females and speculate that this promoted the evolution of larger body size to create more physical space for developing embryos. In the context of life-history trade-offs in the evolution of viviparity, we suggest that the extent of correlation between reproductive traits, or differences between reproductive modes, may also depend on the time since the transition occurred.

However the parity mode of snow lizards is still not known.


Tuesday, 15 January 2019

common lizard, Zootoca vivipara, reference genome

Today we released a pre-print of our common lizard genome. Find details here
https://www.biorxiv.org/content/early/2019/01/15/520528

This is a Scottish lizard, from the Isle of Cumbrae - a member of the western viviparous clade. Her name is Vivacia.

Available upon request.


Thursday, 20 December 2018

Welcome to a new visiting research student

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.

Friday, 7 December 2018

"Behind the paper' blog by Arne

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

Tuesday, 4 December 2018

New paper published: Nature Ecology and Evolution on new diversity after ecosystem recovery

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 clue to ecosystem recovery after pollution 


Scientists find clue to ecosystem recovery after pollution

Scientists have discovered a fish species which significantly evolved and expanded its ecological toolset, after an effort was made to reduce pollution in its ecosystem.

The study, led by the University of Glasgow and the University of Konstanz and published in Nature Ecology and Evolution, found that the gangfisch – a European whitefish subspecies – expanded its genetic diversity after habitat loss and hybridization with other whitefish subspecies during eutrophication. This genetic mixing contributed to contemporary expansion of its ecological diversity after ecosystem recovery.

Eutrophication is a well-known water pollution problem caused by excess nutrient input from human activities, and it is recognised that such environmental degradation can result in dramatic losses of species and diversity. However, very little is known about if and how biodiversity can recover following ecosystem restoration.

By studying the gangfisch’s evolution in central Europe’s Lake Constance, the scientists have been able to contribute to understanding of how biodiversity can recover after an attempt is made to clean up an ecosystem.

Like many freshwater lakes, Lake Constance, one of the largest lakes in Europe, suffered from extreme eutrophication caused by high levels of nutrient pollution from agriculture and sewage during the mid-20th century. The consequent impact on water quality caused the collapse of natural habitats and resulted in the extinction of two of its five endemic whitefish subspecies.

But a concerted effort since the 1980s to reduce pollution enabled Lake Constance to revert rapidly to its pristine state.

In this study, the scientists studied the functional phenotypic and genomic diversity of whitefish in the lake to demonstrate the ability of biodiversity to re-emerge following such an ecosystem restoration.

The researchers found that, after the recovery of the ecosystem in Lake Constance, the gangfisch rapidly increased the range of its functional traits, namely its gill rakers, which are bony structures used by fish to filter feed plankton out of the water.

Dr Kathryn Elmer, from the University’s Institute of Biodiversity, Animal Health and Comparative Medicine, said; “We wanted to study biodiversity recovery after ecosystem remediation. What we found in our study was that the gangfisch evolved a greater range of gill raker number, to utilise a broader ecological position, than they did before the damage to its ecosystem. This happened in fewer than 10 generations and is amongst the fastest rates of evolution recorded in any animal system.

“While it’s an exciting discovery, this new diversity found in gangfisch is just within one species and does not replace the permanent loss of species caused by eutrophication”.

Dr Jasminca Behrmann-Godel from the Limnological Institute of the University of Konstanz adds; “Our findings demonstrate the potential of functional diversity to re-emerge rapidly following habitat restoration – and ecosystem remediation undoubtedly has almost immediate benefits for biodiversity – however this potential for recovery is likely contingent on the underlying genetics of the relevant traits, ecological context, and evolutionary history.”

The paper, ‘Rapid niche expansion by selection on functional genomic variation after ecosystem recovery’ is published in Nature Ecology and Evolution. The work was funded by Marie Curie CIG, the BBSRC, ERASMUS+, the Fisheries Society of the British Isles, and AFF from the University of Konstanz.

ENDS

Sunday, 14 October 2018

New paper: Geography and genetics in Salamandra algira - historical influences and contemporary patterns

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, we assess the role of climate in promoting intra-specific diversification in a Palearctic relict, the North African fire salamander, Salamandra algira, using a combination of phylogenetic and population genetic analyses, paleoclimatic modelling and niche overlap tests. We used mitochondrial DNA (Cyt-b), 9838 ddRADseq loci, and 14 microsatellite loci to characterize patterns of genetic diversity and population structure. Phylogenetic analyses recover two major clades, each including several lineages with mito-nuclear discordances suggesting introgressive patterns between lineages in the Middle Atlas, associated with a melting pot of genetic diversity. Paleoclimatic modelling identified putative climatic refugia, largely matching areas of high genetic diversity, and supports the role of aridity in promoting allopatric diversification associated with ecological niche conservatism. Overall, our results highlight the role of climatic microrefugia as drivers of populations’ persistence and diversification in the face of climatic oscillations in North Africa, and stress the importance of accounting for different genomic regions when reconstructing biogeographic processes from molecular markers.



Friday, 28 September 2018

New paper: Patterns and rates of diversification in Pristimantis leaf litter frogs

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 Amphibian Tree of Life project, and then finally more genes added and analyses updated by Glasgow masters students Emily Waddell and Marco Crotti. Well done team!





Some of those frogs were hard earned! Here's an image from a collecting party out for several days, in the rain,  in the upper Amazon of Ecuador ...


But other conditions were much more civilised. Here is how we processed frogs in style rather than in rain.