Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture.
Journal
Systematic biology
ISSN: 1076-836X
Titre abrégé: Syst Biol
Pays: England
ID NLM: 9302532
Informations de publication
Date de publication:
01 05 2020
01 05 2020
Historique:
received:
15
11
2018
revised:
02
10
2019
accepted:
06
10
2019
pubmed:
22
10
2019
medline:
15
12
2020
entrez:
22
10
2019
Statut:
ppublish
Résumé
The evolution of cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, although the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using nuclear loci. The combined application of high-throughput sequencing with techniques that target specific genomic sequences provide a powerful means of rapidly generating large volumes of orthologous sequence data for use in phylogenomic studies. To elucidate the phylogenetic relationships within the Cetacea, we combined sequence capture with Illumina sequencing to generate data for $\sim $3200 protein-coding genes for 68 cetacean species and their close relatives including the pygmy hippopotamus. By combining data from $>$38,000 exons with existing sequences from 11 cetaceans and seven outgroup taxa, we produced the first comprehensive comparative genomic data set for cetaceans, spanning 6,527,596 aligned base pairs (bp) and 89 taxa. Phylogenetic trees reconstructed with maximum likelihood and Bayesian inference of concatenated loci, as well as with coalescence analyses of individual gene trees, produced mostly concordant and well-supported trees. Our results completely resolve the relationships among beaked whales as well as the contentious relationships among oceanic dolphins, especially the problematic subfamily Delphinidae. We carried out Bayesian estimation of species divergence times using MCMCTree and compared our complete data set to a subset of clocklike genes. Analyses using the complete data set consistently showed less variance in divergence times than the reduced data set. In addition, integration of new fossils (e.g., Mystacodon selenensis) indicates that the diversification of Crown Cetacea began before the Late Eocene and the divergence of Crown Delphinidae as early as the Middle Miocene. [Cetaceans; phylogenomics; Delphinidae; Ziphiidae; dolphins; whales.].
Identifiants
pubmed: 31633766
pii: 5601630
doi: 10.1093/sysbio/syz068
pmc: PMC7164366
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
479-501Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of the Society of Systematic Biologists.
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