Phylogenomics and adaptive evolution in stickleback fishes

• Main Author: Fang, Bohao
• Other Authors: Butlin, Roger, University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Research Programme, Doctoral Programme in Wildlife Biology, Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta, Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma, Helsingfors universitet, bio- och miljövetenskapliga fakulteten, Doktorandprogrammet i forskning om vilda organismer, Merilä, Juha, Momigliano, Paolo
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Helsingin yliopisto 2020
• Subjects: evolutionary biology; Arctic; Arctic Ocean; Pacific
• Online Access: http://hdl.handle.net/10138/320991

How predictable is evolution? There is no fully satisfactory answer to this 100-year old question yet. However, within the past two decades, much progress has been made towards unravelling various factors that influence the predictability of evolution. Much of this work has focused on the similarity of evolutionary responses in replicate populations of a given taxon that have independently colonised similar environments – a phenomenon known as parallel evolution. The fish species in the family Gasterosteidae (sticklebacks) have become popular models to study the repeatability of evolution. This thesis focuses on evolutionary history and parallel evolution in two ecologically similar and geographically co-distributed species in the family Gasterosteidae, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius). Freshwater populations of both species evolved similar phenotypic traits after marine ancestors independently colonised freshwater environments. A highly resolved phylogeny is a prerequisite for untangling the processes that have shaped the underlying genomic divergence, including natural selection and population demographic history. Therefore, my thesis begins by resolving the worldwide phylogenetic relationships and demographic history of both focal species, using state of the art phylogenomic analyses. The results indicate that extant three-spined stickleback populations originated from the Eastern Pacific in the late Pleistocene, and the Atlantic populations were colonised from the Pacific ancestors via the Arctic Ocean. In contrast, nine-spined sticklebacks have a more ancient history, diversifying in the late Pliocene, and their current distribution is the result of multiple waves of trans-Arctic colonisation from the Far East, with several divergent lineages having evolved across their geographic range. The thesis then moves on to investigate the genetic basis of parallel freshwater adaptation in each of the two species, using the information gained ...