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

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, 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.]

Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum

“…This timing is about 2-3 Myr more recent than those proposed by McGowen et al 17 and Steeman et al 1 . It is worth mentioning that recent estimates proposed by McGowen et al 86 included four of the six porpoise species and were more in line with our estimates. The increase of the genetic information, node calibrations and number of sequences per species are known to influence phylogenetic inferences and divergence time estimates 6,87,88 .…”

The complete mitochondrial genome of the critically endangered Atlantic humpback dolphin, Sousa teuszii (Kükenthal, 1892)

“…Based on pairwise comparisons, the S. teuszii mitogenome is 1.9% divergent from S. chinensis and $3% divergent from other delphinine dolphins. Results here mirror those of Horreo (2019); however, the mitogenomic phylogeny of Delphinidae differs significantly from nuclear phylogenies, which place Sousa in a more basal position within the subfamily Delphininae (McGowen et al 2019).…”

Losing Genes: The Evolutionary Remodeling of Cetacea Skin

“…Yet, gene loss has now been described in many types of organisms, including protists, fungi, plants and animals. In Cetacea, the emergence of genome sequences in various species allowed in the past decade the identification of ancestral events of gene inactivation underscoring various lineage-specific phenotypic adaptations (e.g., McGowen et al, 2014McGowen et al, , 2020Sharma et al, 2018). Here, we review the contribution of gene loss in the molecular make-up of the unique skin phenotype of this iconic group of marine mammals -the skin lossOme.…”