Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation

Fritjof Lammers,Moritz Blumer,Maria A Nilsson,Cornelia Rücklé

doi:10.1186/s13100-018-0143-2

Abstract

BackgroundBaleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes.ResultsIn eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions.ConclusionsWhole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species.

Highlights

Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious
While some studies showed that the only extant species of gray whales (Eschrichtius robustus) is phylogenetically placed within rorquals [6,7,8], others placed the gray whale as a sister group to rorquals, which was expected given its different morphology and feeding behaviour [5, 9]
The bowhead whale is a natural outgroup to rorquals and gray whales, we focused on calling non-reference insertions in the 11 baleen whales to obtain an ascertainment bias free marker set for rorquals and gray whales

Summary

Introduction

Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. Whole-genome sequencing (WGS) of most extant baleen whale species suggested that the rapid radiation of rorquals might represent a hard polytomy [10]. TEs evolve neutrally and occur interspersed throughout the genome They avoid potentially biased phylogenetic signals from gene tree error or linkage disequilibrium that can occur in sequence-based multi-locus analyses [12]. TE insertions are virtually homoplasy-free because parallel insertions in the large genomic space are very rare [11] They are less prone to reversals or mutational saturation that can affect SNV-based phylogenetic inference [11]

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Conclusion