Speciation in the deep: genomics and morphology reveal a new species of beaked whale Mesoplodon eueu

Abstract

The deep sea has been described as the last major ecological frontier, as much of its biodiversity is yet to be discovered and described. Beaked whales (ziphiids) are among the most visible inhabitants of the deep sea, due to their large size and worldwide distribution, and their taxonomic diversity and much about their natural history remain poorly understood. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari's beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous peoples of the lands from which the species holotype and paratypes were recovered. Mitogenome and ddRAD-derived phylogenies demonstrate reciprocally monophyletic divergence between M. eueu and True's beaked whale (M. mirus) from the North Atlantic, with which it was previously subsumed. Morphometric analyses of skulls also distinguish the two species. A time-calibrated mitogenome phylogeny and analysis of two nuclear genomes indicate divergence began circa 2 million years ago (Ma), with geneflow ceasing 0.35-0.55 Ma. This is an example of how deep sea biodiversity can be unravelled through increasing international collaboration and genome sequencing of archival specimens. Our consultation and involvement with Indigenous peoples offers a model for broadening the cultural scope of the scientific naming process.

Keywords: Mesoplodon eueu; Mesoplodon mirus; Ramari's beaked whale; True's beaked whale; biodiversity; taxonomy.

Figure 1.

Sampling locations in the NA (black circles) and SH (yellow circle). Global map viewed as a Spilhaus projection that shows the connectedness of the ocean, with sampling locations and distribution of Mesoplodon mirus and proposed species M. eueu shown by the key (sourced from [3,11]), with the artist's impression of the species in top right. Credit: Vivian Ward, University of Auckland.

Figure 2.

Deep genetic divergence between M. mirus (black) and M. eueu (yellow). (a) ddRAD-based phylogenetic tree on 17 217 SNPs, with 95% bootstrap support indicated by black boxes; (b) inset showing ddRAD-based admixture plot of M. mirus and M. eueu, based on 15 761 SNPs variable in these two species. (c) Mitogenome phylogenetic tree with 95% HPDs indicated by black boxes. (d) hPSMC analysis of nuclear genomes from one specimen each from USA and South Africa showing the end of gene flow between the Northern Hemisphere and SHs estimated at 0.35–0.55 Ma. The black line is the hPSMC result from our observed data and the grey lines represent the simulations closest to the real data without overlapping it, following Li and Durbin [22]. Holotype samples in (a) and (c) indicated with yellow and black stars.

Figure 3.

Historical effective population sizes of M. mirus (black) and M. eueu (yellow) over time. Pairwise sequential Markovian coalescent reconstruction of the two species effective population sizes from 20 000 to 3 million years before present, assuming a generation span of 25.9 years [26] and a mutation rate [27,28] of 2.3 × 10^–8. The dark single line represents the median and the lighter lines represent 100 bootstrap.

Figure 4.

Skull and morphological distinctiveness of M. eueu shown by holotype (NMNZ MM003000). (a) Skull in dorsal (left), ventral (centre) and left lateral (right) view (b) periotic in dorsal (left) and ventral (right) view; (c) tympanic bulla in dorsal (left) and ventral (right) view; (d) mandible in dorsal (top) and lateral (bottom) view; (e) mandibular tusks in medial (left) and lateral (right) view. (f) PCA of cranial and mandibular measurements showing clear separation between M. eueu from the SH and M. mirus from the NA. Percentages next to principal components (PCs) denote the total variance explained. Filled stars are holotypes and hollow stars paratypes. (Online version in colour.)