Phylogenomics of the world's otters

Vera de Ferran, Henrique Vieira Figueiró, Fernanda de Jesus Trindade, Oliver Smith, Mikkel-Holger S. Sinding, Cristine S. Trinca, Gabriele Zenato Lazzari, Géraldine Veron, Juliana A. Vianna, Filippo Barbanera, Sergei Kliver, Natalia Serdyukova, Tatiana Bulyonkova, Oliver A. Ryder, M. Thomas P. Gilbert, Klaus-Peter Koepfli*, Eduardo Eizirik

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

23 Citations (Scopus)

Abstract

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1–5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.

Original languageEnglish
JournalCurrent Biology
Volume32
Issue number16
Pages (from-to)3650-3658.e4
Number of pages13
ISSN0960-9822
DOIs
Publication statusPublished - 2022

Bibliographical note

Publisher Copyright:
© 2022 Elsevier Inc.

Keywords

  • Carnivora
  • comparative genomics
  • conservation genomics
  • evolutionary genomics
  • genealogical discordance
  • genomic diversity
  • historical demography
  • Mammalia
  • phylogenetics
  • species delimitation

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