Phylogenomics and pervasive genome-wide phylogenetic discordance among fin whales (Balaenoptera physalus)

Phylogenomics has the power to uncover complex phylogenetic scenarios
across the genome. In most cases, no single topology is reflected across
the entire genome as the phylogenetic signal differs among genomic regions
due to processes, such as introgression and incomplete lineage sorting.
Baleen whales are among the largest vertebrates on Earth with a high
dispersal potential in a relatively unrestricted habitat, the oceans. The
fin whale (Balaenoptera physalus) is one of the most enigmatic baleen
whale species, currently divided into four subspecies. It has been a
matter of debate whether phylogeographic patterns explain taxonomic
variation in fin whales. Here we present a chromosome-level whole genome
analysis of the phylogenetic relationships among fin whales from multiple
ocean basins. First, we estimated concatenated and consensus phylogenies
for both the mitochondrial and nuclear genomes. The consensus phylogenies
based upon the autosomal genome uncovered monophyletic clades associated
with each ocean basin, aligning with the current understanding of
subspecies division. Nevertheless, discordances were detected in the
phylogenies based on the Y chromosome, mitochondrial, autosomal genome and
X chromosome. Furthermore, we detected signs of introgression and
pervasive phylogenetic discordance across the autosomal genome. This
complex phylogenetic scenario could be explained by a puzzle of
introgressive events, not yet documented in fin whales. Similarly,
incomplete lineage sorting and a low phylogenetic signal could equally be
the mechanisms leading to such phylogenetic discordances. Our study
reinforces the pitfalls of relying on concatenated or single locus
phylogenies to determine taxonomic relationships below the species level
by illustrating the underlying nuances which some phylogenetic approaches
may fail to capture. We emphasize the significance of accurate taxonomic
delineation in fin whales by exploring crucial information revealed
through genome-wide assessments.