Friday, 7 December 2018

Arne wrote a lovely 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

Wednesday, 7 November 2018

PhD opportunities in Institute of Biodiversity and with national and international collaborators

PhD Opportunities for autumn 2019 start


Currently I have three well funded, multidisciplinary PhD studentship projects available in the IAPETUS NERC-funded doctoral training programme.  As far as I know, these are the only ecological and evolutionary genomics projects on offer from Glasgow!

We are seeking ambitious and creative researchers with a keen interest in evolution and environment and excellent academic records. You will join an active, productive, and collegial research team in the Evolutionary Analysis Group of the Institute of Biodiversity, Animal Health and Comparative Medicine. PhD students in my group have an excellent record of high quality publications and strong international profiles (see some examples on the blog News page).

These projects also have outstanding opportunities to conduct research with co-supervisors on the projects, including other parts of Uni Glasgow, St Andrew's University in Scotland, Peterborough and Lancaster in England, and Spain.

Closing 18 January 2019. 

Please see
IAP2-18-04: Environmental and genomic associations with colour and toxicity: biological insights for newt species of conservation concern (CASE Partner project)
with Oscar Gaggiotti (St Andrews) and Laurence Jarvis (Froglife) as co-supervisors and with input from Karl Burgess (Glasgow Metabolomics)


IAP2-18-05: From molecules to populations: the genomic legacy of historic pollution on freshwater fish (CASE Partner project)
with Steve Lofts (CEH Lancaster) and Willie Yeomans (Clyde River Foundation)


IAP2-18-06: Genetic mechanisms of amphibian colour pattern and toxicity in the natural environment
with Oscar Gaggiotti (St Andrews) as co-supervisor and input from Karl Burgess (Glasgow Metabolomics) and David Vieites (Museo Nacional de Ciencias Naturales, Madrid)

Eligibility

All applicants need to meet NERC’s eligibility criteria to be considered for an IAPETUS studentship and these are detailed in NERC’s current studentship handbook.  

(Unfortunately ...) IAPETUS is only able to consider applications from Home/European Union candidates. International candidates are not eligible to be considered and where an candidate from another EU country has not been resident in the UK for 3 years or more prior to the commencement of their studies with IAPETUS, they will only be eligible for a fees-only studentship.  

IAPETUS is looking for candidates with the following qualities and backgrounds:  

A first or 2:1 undergraduate degree, or have relevant comparable experience;  
In addition, candidates may also hold or be completing a Masters degree in their area of proposed study or a related discipline; &  
An outstanding academic pedigree and research potential, such as evidenced through the publication of articles, participation in academic conferences and other similar activities.


Funding Notes

IAPETUS’ postgraduate studentships are tenable for between 3 and 4 years, depending on the doctoral research project the student is studying and provides the following package of financial support:  

A tax-free maintenance grant set at the UK Research Council’s national rate, which in 2019/20 is £14,999 (pending confirmation).  
Full payment of their tuition fees at the Home/EU rate; &  
Access to extensive research support funding.  
Part-time award-holders are funded for between six (6) and eight (8) years and receive a maintenance grant at 50% of the full-time rate.


Application Process

Prospective students must apply to the University of Glasgow Graduate School (College of Medical, Veterinary and Life Sciences) via the postgraduate student applications system. 

Deadline: Friday 18th January 2019 at 4 pm (GMT).

In the application, students need to specify clearly that they wish to be considered for an IAPETUS2 studentship and state the research project (s) that they wish to be considered for (can only choose ONE).

Prospective students must provide/attach the following documentation/information to their application: 
a) Current CV. 
b) A cover letter written by the prospective student, no greater than 2 sides in length, detailing their reasons for applying and why they have selected the project that they wish to conduct. 
c) Two (or more) references, avoiding any references from any members of the supervisory team that are part of the research project that they wish to conduct. 
d) Full transcripts of previous qualifications obtained to date. 

The successful applicant will proceed to a competitive selection interview at the IAPETUS2 Studentships Panel on Wednesday 20th February 2019. 

Informal inquiries in advance to Kathryn Elmer are encouraged.

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.



Wednesday, 26 September 2018

Joseph Black Medal & Hird Prize PhD nominations - congrats to Hans and to Arne

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!

Sunday, 26 August 2018

Congratulations to Hans for being shortlisted for the Evolution Hamilton symposium

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.

Friday, 24 August 2018

New paper: Melanic common lizards

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 reptiles. We provide the first reporting of melanic individuals in a subspecies of common lizards, Zootoca vivipara carniolica or the Eastern oviparous lineage. Two melanic females were found out of 194 individuals collected. Melanic females did not differ in size or weight from non-melanic females. No melanic individuals were found (N = 134) in the nearby viviparous population. Melanism has been reported in related lineages of Z. vivipara, so the discovery in this sister to all other lineages suggests that it is an ancestral polymorphism. The frequency of melanism varies but other studies also find it is usually very rare (<3%) and may be sex-biased. The processes mediating advantages and disadvantages of melanism in Z. vivipara are unclear and require more research.


Monday, 13 August 2018

New paper: Lizards break Dollo's Law?

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.



This research was earlier covered by New Scientist here when the ms was a preprint.


Sunday, 1 July 2018

Plenary talk: Charr Symposium USA

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 ...

Thursday, 7 June 2018

Congratulations to Dr. Arne Jacobs

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!

Friday, 18 May 2018

Welcome to FSBI Intern Tie

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.

Friday, 11 May 2018

Welcome to the new summer Masters students

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!

Thursday, 3 May 2018

Congratulations to Dr. Hans Recknagel!

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 ...



Wednesday, 11 April 2018

Congratulations to Dr Madeleine Carruthers!

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)




Monday, 9 April 2018

Congratulations to Dr James Burgon!

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!

Wednesday, 7 March 2018

New pre-print on Arctic charr parallel evolution

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 challenges1,2. Replicate, or parallel, phenotypic evolution has been found in classic examples such as anole lizards, stickleback fishes, salmonid fishes, and cichlid fishes3-8 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 backgrounds that are pervasive in natural populations. To test evolutionary predictability in a Holarctic ‘natural experiment’, we used genome-informed single nucleotide polymorphism data, transcriptome-wide gene expression comparisons, and eco-morphology analysis within and across lakes and evolutionary lineages of a freshwater salmonid fish, Arctic charr (Salvelinus alpinus). We found significant parallel evolution in replicate specialist ‘ecotypes’ for adaptive morphological traits associated with foraging. This predictability overcomes pervasive population-specific variation caused by complex demographic histories, differing genomic divergence in response to selection, and non-parallel genetic associations with ecotype. Remarkably the functional molecular bases to ecotypes, inferred from gene expression and biological pathways, were extensively and significantly shared across ecotype replicates. Our findings suggest that parallel evolution by non-parallel evolutionary routes is possible when the regulatory molecular phenotype compensates for divergent histories.    


Thursday, 1 February 2018

New paper: Colony breeding cichlids have itchy feet

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 processes associated with cichlids in Nicaraguan Lake Apoyo.

This was a collaboration between behavioural ecologist Topi Lehtonen, cichlid evolutionary biologist Axel Meyer, and evolutionary biologist Kathryn Elmer, now at IBAHCM Glasgow. A Uni Glasgow Honours student with Kathryn, Meri Lappalainen, also contributed to this work and is an author.

This paper is published open access in Scientific Reports at doi:10.1038/s41598-018-19266-5

Midas cichlids
crater lake Apoyo

Wednesday, 31 January 2018

New paper: transcriptome resources for salmonids

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 novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date.
Results: We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210 M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, and low confidence transcripts. The final assemblies consisted of 36,505 protein-coding transcripts for Atlantic salmon, 35,736 for brown trout, 33,126 for Arctic charr, and 33,697 for European whitefish and are made publicly available. Assembly completeness was assessed using three approaches, all of which supported high quality of the assemblies: 1) ~78% of Actinopterygian single-copy orthologs were successfully captured in our assemblies, 2) orthogroup inference identified high overlap in the protein sequences present across all four species (40% shared across all four and 84% shared by at least two), and 3) comparison with the published Atlantic salmon genome suggests that our assemblies represent well covered (~98%) protein-coding transcriptomes. Thorough comparison of the generated assemblies found that 84-90% of transcripts in each assembly were orthologous with at least one of the other three species. We also identified 34-37% of transcripts in each assembly as paralogs. We further compare completeness and annotation statistics of our new assemblies to available related species.
Conclusion: New, high-confidence protein-coding transcriptomes were generated for four ecologically and economically important species of salmonids. This offers a high quality pipeline for such complex genomes, represents a valuable contribution to the existing genomic resources for these species and provides robust tools for future investigation of gene expression and sequence evolution in these and other salmonid species.

Thursday, 7 December 2017

Coverage in The New Scientist

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 long-standing question.