[MARMAM] Publication of new paper: Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence Capture

Michael McGowen 1mmcgowen1 at gmail.com
Mon Oct 21 13:46:29 PDT 2019


Publication of new paper in Systematic Biology:

Phylogenomic Resolution of the Cetacean Tree of Life Using Target Sequence
Capture

Michael R McGowen, Georgia Tsagkogeorga,  Sandra Álvarez-Carretero, Mario
dos Reis, Monika Struebig,  Robert Deaville, Paul D Jepson, Simon
Jarman, Andrea
Polanowski, Phillip A Morin,
Stephen J Rossiter


Abstract:
The evolution of cetaceans, from their early transition to an aquatic
lifestyle to their subsequent diversification, has been the subject of
numerous studies. However, while 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 ∼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 dataset for cetaceans, spanning 6,527,596
aligned base pairs 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 Delphininae.
We carried out Bayesian estimation of species divergence times using
MCMCTree, and compared our complete dataset to a subset of clocklike genes.
Analyses using the complete dataset consistently showed less variance in
divergence times than the reduced dataset. In addition, integration of new
fossils (e.g., Mystacodon selenensis) indicate that the diversification of
Crown Cetacea began before the Late Eocene and the divergence of Crown
Delphinidae as early as the Middle Miocene.


https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syz068/5601630


------

Michael McGowen, PhD

Research Zoologist and Curator of Marine Mammals

Curator-in-Charge, Division of Mammals

Department of Vertebrate Zoology

National Museum of Natural History

Smithsonian Institution

10th St & Constitution Ave. NW

Washington, DC 20560 USA

+1 (202) 633-1292

mcgowenm at si.edu

1mmcgowen1 at gmail.com
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