Phylogenomics of the world’s otters

Ferran, Vera de; Figueiró, Henrique V.; Trindade, Fernanda J.; Smith, Oliver; Sinding, Mikkel‐Holger S.; Trinca, Cristine Silveira; Lazzari, Gabriele Zenato; Veron, Géraldine; Vianna, Juliana A.; Barbanera, Filippo; Kliver, Sergei; Serdyukova, Natalia A.; Bulyonkova, Tatiana; Ryder, Oliver A.; Gilbert, Martin; Koepfli, Klaus‐Peter; Eizirik, Eduardo

doi:10.1016/j.cub.2022.06.036

Cited by 20 publications

(14 citation statements)

References 60 publications

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“…Low genetic diversity is often accompanied by an elevated inbreeding level ( 39 , 40 ). The genomic inbreeding coefficients (F ROH ) of the eight recognized pangolin species range from 2.32% for the White-bellied pangolin to 34.03% for the Malayan pangolin, with an average of 13.96%.…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis reveals a cryptic pangolin species

Gu,

Wu,

Yang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Eight extant species of pangolins are currently recognized. Recent studies found that two mitochondrial haplotypes identified in confiscations in Hong Kong could not be assigned to any known pangolin species, implying the existence of a species. Here, we report that two additional mitochondrial haplotypes identified in independent confiscations from Yunnan align with the putative species haplotypes supporting the existence of this mysterious species/population. To verify the new species scenario we performed a comprehensive analysis of scale characteristics and 138 whole genomes representing all recognized pangolin species and the cryptic new species, 98 of which were generated here. Our morphometric results clearly attributed this cryptic species to Asian pangolins ( Manis sp.) and the genomic data provide robust and compelling evidence that it is a pangolin species distinct from those recognized previously, which separated from the Philippine pangolin and Malayan pangolin over 5 Mya. Our study provides a solid genomic basis for its formal recognition as the ninth pangolin species or the fifth Asian one, supporting a new taxonomic classification of pangolins. The effects of glacial climate changes and recent anthropogenic activities driven by illegal trade are inferred to have caused its population decline with the genomic signatures showing low genetic diversity, a high level of inbreeding, and high genetic load. Our finding greatly expands current knowledge of pangolin diversity and evolution and has vital implications for conservation efforts to prevent the extinction of this enigmatic and endangered species from the wild.

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Section: Resultsmentioning

confidence: 99%

Genomic analysis reveals a cryptic pangolin species

Gu,

Wu,

Yang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…The colored circles represent presence of results from DNA, RNA, or enzymatic tests; no circle means there are no data to report. Phylogenetic relationships shown are based on data from previously published work ( Esselstyn et al 2017 ; Swanson et al 2019 ; McGowen et al 2020 ; de Ferran et al 2022 ). Silhouette images are from Phylopic (CC BY‐SA 3.0).…”

Section: Resultsmentioning

confidence: 99%

Reduction ofParaoxonaseExpression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Graham

Jamison

Bustos

et al. 2023

Molecular Biology and Evolution

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Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages - Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best correlated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

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Section: Resultsmentioning

confidence: 99%

Reduction ofParaoxonaseexpression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization

Graham

Jamison

Bustos

et al. 2022

Preprint

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Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of function; loss of protein function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages - Pon1 became a pseudogene at least six times independently in aquatic and semiaquatic mammals with clear genetic lesions, such as stop codons and frameshifts. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and blood plasma activity across four major aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We also observed in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing for accumulation of disrupting mutations. The recurrent and rapid loss of Pon1 even suggests that it is adaptive in aquatic mammals. Accordingly, we examined diving and dietary traits across pinniped species as potential driving forces of Pon1 loss. We found that loss is best correlated with diving activity and is likely the result of selective pressures associated with hypoxia and hypoxia-induced inflammation.

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Phylogenomics of the world’s otters

Cited by 20 publications

References 60 publications

Genomic analysis reveals a cryptic pangolin species

Genomic analysis reveals a cryptic pangolin species

Reduction ofParaoxonaseExpression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Reduction ofParaoxonaseexpression followed by inactivation across independent semiaquatic mammals suggests stepwise path to pseudogenization

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