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Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens)

Heredityvolume 120pages296309 (2018) | Download Citation

Abstract

The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.

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Acknowledgements

We would like to acknowledge Agri-Food and Veterinary Authority in Singapore, Subang Jaya Council, Dr. Sampath Seneviratne from the University of Colombo, University of Dhaka, Mfundo Tafeni from the Environmental Resource Management Department in Cape Town, Duncan Mitchell from Kenya, the Assistant Veterinary Officer, Meor Amri Md. Noor from the Penang Council, David Alila from Tanzania, Australian National Wildlife Collection and Western Australia Museum for providing specimens for DNA testing. We also thank Monash University Malaysia Genomics Facility for generating data used in this project; Dr. Han Ming Gan and Tan Mun Hua for their assistance with bioinformatics. We are also extremely grateful to Dr Collin Ryall, Prof Simon Ho, and The Persistence and Adaptation Research Team (PART) for their help in parts of this study. Funding for this study was provided by the Monash University Malaysia School of Science and Monash University Malaysia Tropical Medicine Biology Multidisciplinary Platform and the internal Monash sources, including PART research group funds. We would also like to acknowledge the Australian Government for granting the Endeavour Fellowship that has facilitated this study. The comments of three anonymous reviewers and the editorial process improved the manuscript.

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Affiliations

  1. School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia

    • Urszula Krzemińska
    • , Robyn Wilson
    • , Beng Kah Song
    • , Christopher M. Austin
    •  & Sadequr Rahman
  2. Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia

    • Urszula Krzemińska
    • , Robyn Wilson
    • , Beng Kah Song
    • , Christopher M. Austin
    •  & Sadequr Rahman
  3. Department of Genetics and Animal Breeding, Faculty of Animal Sciences, Warsaw University of Life Sciences SGGW, Warsaw, Poland

    • Urszula Krzemińska
  4. School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia

    • Hernán E. Morales
    • , Chris Greening
    • , Paul Sunnucks
    •  & Alexandra Pavlova
  5. Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE 405 30, Sweden

    • Hernán E. Morales
  6. Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA

    • Árpád S. Nyári
  7. School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia

    • Christopher M. Austin

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Correspondence to Urszula Krzemińska.

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DOI

https://doi.org/10.1038/s41437-017-0020-7