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

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. Look for PhD applications to Evolutionary Analysis. Include the IAPETUS2 project number and 'Supervisor: Elmer' in your application.
https://www.gla.ac.uk/postgraduate/research/evolutionaryanalysis/

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) reference letters (signed and on letterhead), 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 and into the NERC grant.



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 ...