Phylogenomics of the world's otters
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Current Biology |
| Vol/bind | 32 |
| Udgave nummer | 16 |
| Sider (fra-til) | 3650-3658.e4 |
| Antal sider | 13 |
| ISSN | 0960-9822 |
| DOI | |
| Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:
We thank Prof. A.A. Khan (Zoology Department, Ghazi University, Dera Ghazi Khan, Pakistan) and Prof. T.M. Ansari (Institutional Research Ethical Committee of Bahauddin Zakariya University, Multan, Pakistan) for access to samples; Alexander Migura for help; the Smithsonian Institution High Performance Cluster (SI/HPC) for access to computational resources; and Drs. A.R. Percequillo, F.R. Santos, and S.L. Bonatto for constructive comments on a previous version of this manuscript (part of V.d.F.’s doctoral dissertation at PPG-EEB/PUCRS). Credits for the otter illustrations in the figures are to Toni Llobet in Handbook of the Mammals of the World, Vol. 1. Carnivores. Financial support for this study was provided by the Office of Naval Research Global (award N62909-15-1-N107 to E.E.), CNPq (grants 141172/2017-7 and 309068/2019-3 awarded to V.d.F. and E.E. respectively), the PUCRS/CAPES-PrInt Program (fellowship 88887.370464/2019-00 awarded to V.d.F.), and ANID - MILENIO (ICN2021_044 and ICN2021_002 awarded to J.A.V.). This study is a contribution of the National Institute of Science and Technology in Ecology, Evolution and Biodiversity Conservation (INCT-EECBio), supported by MCTIC/CNPq (proc. 465610/2014-5) and FAPEG (proc. 201810267000023). Conceptualization, E.E. K.-P.K. and V.d.F.; data curation, V.d.F. H.V.F. and F.d.J.T.; formal analysis, V.d.F. H.V.F. F.d.J.T. and S.K.; funding acquisition, E.E. K.-P.K. and M.T.P.G.; investigation, V.d.F. O.S. M.-H.S.S. and G.Z.L.; methodology, V.d.F. H.V.F. O.S. M.-H.S.S. K.-P.K. and E.E.; project administration, E.E. and K.-P.K.; resources, C.S.T. G.V. J.A.V. F.B. N.S. T.B. O.A.R. and M.T.P.G.; supervision, E.E. K.-P.K. and M.T.P.G.; writing – original draft, V.d.F. E.E. and K.-P.K.; writing – review & editing, H.V.F. F.d.J.T. O.S. M.-H.S.S. C.S.T. G.Z.L. G.V. J.A.V. F.B. S.K. N.S. T.B. O.A.R. and M.T.P.G. The authors declare no competing interests.
Funding Information:
We thank Prof. A.A. Khan (Zoology Department, Ghazi University, Dera Ghazi Khan, Pakistan) and Prof. T.M. Ansari (Institutional Research Ethical Committee of Bahauddin Zakariya University, Multan, Pakistan) for access to samples; Alexander Migura for help; the Smithsonian Institution High Performance Cluster (SI/HPC) for access to computational resources; and Drs. A.R. Percequillo, F.R. Santos, and S.L. Bonatto for constructive comments on a previous version of this manuscript (part of V.d.F.’s doctoral dissertation at PPG-EEB/PUCRS). Credits for the otter illustrations in the figures are to Toni Llobet in Handbook of the Mammals of the World, Vol. 1. Carnivores. Financial support for this study was provided by the Office of Naval Research Global (award N62909-15-1-N107 to E.E.), CNPq (grants 141172/2017-7 and 309068/2019-3 awarded to V.d.F. and E.E., respectively), the PUCRS /CAPES-PrInt Program (fellowship 88887.370464/2019-00 awarded to V.d.F.), and ANID - MILENIO ( ICN2021_044 and ICN2021_002 awarded to J.A.V.). This study is a contribution of the National Institute of Science and Technology in Ecology, Evolution and Biodiversity Conservation (INCT-EECBio), supported by MCTIC / CNPq (proc. 465610/2014-5 ) and FAPEG (proc. 201810267000023 ).
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© 2022 Elsevier Inc.
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