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.

Tuesday, 22 August 2017

New preprint: population genomics to discriminate salmon louse populations despite high gene flow

New paper available as a preprint on biorxiv with Arne Jacobs and IBAHCM colleague Martin Llewellyn (and other great sea louse collaborators) on
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach
Arne Jacobs, Michele De Noia, Kim Praebel, √ėyvind Kanstad-Hanssen, Marta Paterno, Dave Jackson, Philip McGinnity, Armin Sturm, Kathryn R. Elmer, Martin S. Llewellyn

http://www.biorxiv.org/content/early/2017/08/21/179218

Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Lepeophtheirus salmonis is the predominant species that occurs in the Northern Hemisphere. Dispersal of sea lice between marine aquaculture sites and geographic regions is thought to occur rapidly via planktonic transport of larvae. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic L. salmonis, frustrating efforts to track louse populations, improve targeted control measures and understand local adaption to environmental conditions. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland (N=2, 27 individuals), Scotland (N=1, 11 individuals) and North Norway (N=1, 12 individuals). Weak global structure (FSC = 0.018, p<0.0001) and only one significant pairwise FST comparison was observed (Scotland vs Kenmare Bay, (FST = 0.018, p<0.0001)) using all 1286 SNPs. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment (DAPC assignment probability = 1), increased global Fsc = 0.098, (p<0.0001) and resulted in pairwise comparisons that all showed highly significant Fst-values (range = 0.081-0.096, p<0.0001). Out of 19 SNPs found to be under directional selection between populations, 12 corresponded to the discriminatory SNPs identified using random forest. Taken together our data suggest that L. salmonis SNP diversity exists with which it is possible to discriminate differences between nearby populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

Tuesday, 1 August 2017

New paper: rare but significant colocalisation and synteny of ecologically relevant QTL in salmonids

The organization of functional regions within genomes has important implications for the evolutionary potential of species. We compared the distribution of nearly a thousand ecologically relevant QTL within and across six salmonids (Arctic charr, Atlantic salmon, lake whitefish, rainbow trout, chinook salmon, coho salmon ) to understand their distribution across the genome. Using a novel analytical framework for comparative mapping and significance testing, we identified synteny blocks and co-localized clusters for phenotypic traits across and within species. Specifically, only two or three pairs of traits were significantly co-localized in three species (lake whitefish, coho salmon, and rainbow trout). These findings suggest genetic linkage between traits within species is relatively rare, advancing our understanding of the renowned ecological and phenotypic variability in salmonid fishes.

This project was a collaboration based on an idea hatched by Kathryn, consultation and insights from Karim in Edinburgh Genomics as an expert on genetic mapping in salmonids, detailed literature review and database building by Robyn during her MVLS-DTP mini-project, clever analytical approaches by Mel co-housed in Maths & Stats, and most importantly outstanding analysis, synthesis and drafting by Arne. Well done team!

We hope the database is of use to other salmonid researchers, as it can be supplemented as new information arises. All information is shared in the supplementary material of the paper.

Jacobs A, Womack R, Chen M, Gharbi K, Elmer KR (2017) Significant synteny and co-localization of ecologically relevant quantitative trait loci across salmonid species. Genetics, early online

Friday, 21 July 2017

New paper: Resolving the history of fire salamanders

In a recent paper, Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches, we used three large-scale molecular datasets to identify the evolutionary relationships in salamanders. To date these have been effectively unresolvable as there was never sufficient data for the deeper nodes. Here we found that ddRADseq and RNAseq nuclear data -- both using thousands of loci -- resolved the same phylogenetic topologies of all the species involved. However full mitogenome data suggested a slightly different history of the Salamandra atra-lanzai-corsica species. We suggest this may be because of ancient introgression of mitochondrial genomes. Importantly, our study shows that SNPs from ddRADseq (now using illumina NextSeq) can also be used to tackle deeper evolutionary relationships, perhaps just as well (and for less cost) as transcriptomes. The Glasgow portion of this work was led by PhD student James Burgon.

Tuesday, 20 June 2017

New paper: fish ecomorphological variability associated with lake environment

A new paper is published, with an analysis led by Hans Recknagel and in collaboration with SCENE researchers Oliver Hooker and Colin Adams. We examined ecomorphological variability of Arctic charr in populations across 30 lakes in Scotland and Northern Ireland. As a summary univariate measure for complex trophic diversity in these fishes, we used maximum, minimum, mean and variance in head depth. We found that the extent of variability of head depth is closely associated with the physical lake environment - in particular 'ecosystem size', which is a combination of lake size, depth, volume, and littoral zone. There was no association of head depth with biotic community of other fishes in the lake, abundance of charr in the lake, nor charr genetic diversity.

Recknagel, H., Hooker, O., Adams, C. E., & Elmer, K. R. 2017. Ecosystem size predicts eco-morphological variability in a postglacial diversification. Ecology and Evolution

image from Oliver Hooker

Monday, 29 May 2017

New paper: Vision genes in fishes

New paper from work done in Konstanz and now led by Julian Torres-Dowdall, "Rapid and parallel adaptive evolution of the visual system of Neotropical Midas cichlid fishes" in the journal Molecular Biology and Evolution

This study represented an excellent combination of field experiments for collections and detailed characterisation of environment, sequencing the full complement of opsin genes and expression, and assessing the structures of the eye.

Abstract: Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted towards shorter wavelengths compared to the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution.

Finalist for PhD student Hamilton Award

PhD student Arne Jacobs has been selected as a finalist for the Hamilton Award for Outstanding Student Presentation. Check out his work and the other exciting finalists at the Evolution meeting in Portland!

Thursday, 11 May 2017

Congrats to Paige!

Congratulations to summer-2016 FSBI Intern and subsequent Honours student with our group  - Paige Robinson - who has been offered (and accepted) a PhD position through NERC iCASE on fish epigenetic research at the University of Exeter.

Monday, 27 March 2017

Margaret Savigear Lecture Series

Kathryn was invited to present at the Margaret Savigear Annual Lecture series at the University of Sheffield. She presented on "Parallel evolution and its alternatives" with a discussion of ecological 'omics and the diversification of fishes.



Wednesday, 25 January 2017

Congrats to Arne for 'best student' award

Congratulations to Arne Jacobs for winning the 'best PhD report in the Institute' for his end of 2nd year write-up. This was awarded at the IBAHCM annual Away Day. And now on track for a productive push through to finishing his PhD next year!

Thursday, 24 November 2016

New funding for genome finishing

We have just been awarded pilot Facilities and Technology funding from the NERC Biomolecular Analysis Facility (NBAF). This project will explore using the new PacBio Sequel platform for extra-long sequencing reads for hybrid assembly, gap-closing, and high quality finishing of the Zootoca vivipara genome. Not only is this species fascinating for is bimodal live-bearing-egg-laying reproduction, but it is also a high priority species for Genome 10K. We look forward to sharing our final genome with the international community soon!

Friday, 16 September 2016

New paper: Linkage of adaptive traits

We studied the genomic organisation of ecologically relevant traits in Midas cichlids.

Fruciano, Carmelo, Paolo Franchini, Viera Kovacova, Kathryn R. Elmer, Frederico Henning & Axel Meyer. 2016. Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish. Nature Communications 7, Article number: 12736 (2016) doi:10.1038/ncomms12736

Abstract
Our understanding of how biological diversity arises is limited, especially in the case of speciation in the face of gene flow. Here we investigate the genomic basis of adaptive traits, focusing on a sympatrically diverging species pair of crater lake cichlid fishes. We identify the main quantitative trait loci (QTL) for two eco-morphological traits: body shape and pharyngeal jaw morphology. These traits diverge in parallel between benthic and limnetic species in the repeated adaptive radiations of this and other fish lineages. Remarkably, a single chromosomal region contains the highest effect size QTL for both traits. Transcriptomic data show that the QTL regions contain genes putatively under selection. Independent population genomic data corroborate QTL regions as areas of high differentiation between the sympatric sister species. Our results provide empirical support for current theoretical models that emphasize the importance of genetic linkage and pleiotropy in facilitating rapid divergence in sympatry.