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Investigating the genomic basis of discrete phenotypes using a Pool-Seq-only approach: New insights into the genetics underlying colour variation in diverse taxa
Stockholm University, Faculty of Science, Department of Zoology. Pennsylvania State University, USA.
Stockholm University, Faculty of Science, Department of Zoology.
Stockholm University, Faculty of Science, Department of Zoology.
Number of Authors: 4
2017 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 26, no 19, 4990-5002 p.Article in journal (Refereed) Published
Abstract [en]

While large-scale genomic approaches are increasingly revealing the genetic basis of polymorphic phenotypes such as colour morphs, such approaches are almost exclusively conducted in species with high-quality genomes and annotations. Here, we use Pool-Seq data for both genome assembly and SNP frequency estimation, followed by scanning for F-ST outliers to identify divergent genomic regions. Using paired-end, short-read sequencing data from two groups of individuals expressing divergent phenotypes, we generate a de novo rough-draft genome, identify SNPs and calculate genomewide F-ST differences between phenotypic groups. As genomes generated by Pool-Seq data are highly fragmented, we also present an approach for super-scaffolding contigs using existing protein-coding data sets. Using this approach, we reanalysed genomic data from two recent studies of birds and butterflies investigating colour pattern variation and replicated their core findings, demonstrating the accuracy and power of a Pool-Seq-only approach. Additionally, we discovered new regions of high divergence and new annotations that together suggest novel parallels between birds and butterflies in the origins of their colour pattern variation.

Place, publisher, year, edition, pages
2017. Vol. 26, no 19, 4990-5002 p.
Keyword [en]
adaptive variation, colour patterns, genome, nonmodel organisms, Pool-Seq
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-148850DOI: 10.1111/mec.14205ISI: 000413375500011PubMedID: 28614599OAI: oai:DiVA.org:su-148850DiVA: diva2:1159673
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2017-11-23Bibliographically approved

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CiteExportLink to record
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