Phylogenomics of the world's otters
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Phylogenomics of the world's otters. / de Ferran, Vera; Figueiró, Henrique Vieira; Trindade, Fernanda de Jesus; Smith, Oliver; Sinding, Mikkel-Holger S.; Trinca, Cristine S.; Lazzari, Gabriele Zenato; Veron, Géraldine; Vianna, Juliana A.; Barbanera, Filippo; Kliver, Sergei; Serdyukova, Natalia; Bulyonkova, Tatiana; Ryder, Oliver A.; Gilbert, M. Thomas P.; Koepfli, Klaus-Peter; Eizirik, Eduardo.
In: Current Biology, Vol. 32, No. 16, 2022, p. 3650-3658.e4.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Phylogenomics of the world's otters
AU - de Ferran, Vera
AU - Figueiró, Henrique Vieira
AU - Trindade, Fernanda de Jesus
AU - Smith, Oliver
AU - Sinding, Mikkel-Holger S.
AU - Trinca, Cristine S.
AU - Lazzari, Gabriele Zenato
AU - Veron, Géraldine
AU - Vianna, Juliana A.
AU - Barbanera, Filippo
AU - Kliver, Sergei
AU - Serdyukova, Natalia
AU - Bulyonkova, Tatiana
AU - Ryder, Oliver A.
AU - Gilbert, M. Thomas P.
AU - Koepfli, Klaus-Peter
AU - Eizirik, Eduardo
N1 - Publisher Copyright: © 2022 Elsevier Inc.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Carnivora
KW - comparative genomics
KW - conservation genomics
KW - evolutionary genomics
KW - genealogical discordance
KW - genomic diversity
KW - historical demography
KW - Mammalia
KW - phylogenetics
KW - species delimitation
U2 - 10.1016/j.cub.2022.06.036
DO - 10.1016/j.cub.2022.06.036
M3 - Journal article
C2 - 35779528
AN - SCOPUS:85136093686
VL - 32
SP - 3650-3658.e4
JO - Current Biology
JF - Current Biology
SN - 0960-9822
IS - 16
ER -
ID: 319884457