A Total Evidence Phylogenetic Analysis of Pinniped Phylogeny and the Possibility of Parallel Evolution Within a Monophyletic Framework

Abstract

In the present study, a series of phylogenetic analyses of morphological, molecular, and combined morphological-molecular datasets were conducted to investigate the relationships of 23 extant and 44 fossil caniforme genera, in order to test the phylogenetic position of putative stem pinniped Puijila within a comprehensive evolutionary framework. With Canis as an outgroup, a Bayesian Inference analysis employing tip-dating of a combined molecular-morphological (i.e., Total Evidence) dataset recovered a topology in which musteloids are the sister group to a monophyletic pinniped clade, to the exclusion of ursids, and recovered Puijila and Potamotherium along the stem of Pinnipedia. A similar topology was recovered in a parsimony analysis of the same dataset. These results suggest the pinniped stem may be expanded to include additional fossil arctoid taxa, including Puijila, Potamotherium, and Kolponomos. The tip-dating analysis suggested a divergence time between pinnipeds and musteloids of ∼45.16 million years ago (Ma), though a basal split between otarioids and phocids is not estimated to occur until ∼26.52 Ma. These results provide further support for prolonged freshwater and nearshore phases in the evolution of pinnipeds, prior to the evolution of the extreme level of aquatic adaptation displayed by extant taxa. Ancestral character state reconstruction was used to investigate character evolution, to determine the frequency of reversals and parallelisms characterizing the three extant clades within Pinnipedia. Although the phylogenetic analyses did not directly provide any evidence of parallel evolution within the pinniped extant families, it is apparent from the inspection of previously-proposed pinniped synapomorphies, within the context of a molecular-based phylogenetic framework, that many traits shared between extant pinnipeds have arisen independently in the three clades. Notably, those traits relating to homodonty and limb-bone specialization for aquatic locomotion appear to have multiple origins within the crown group, as suggested by the retention of the plesiomorphic conditions in early-diverging fossil members of the three extant families. Thus, while the present analysis identifies a new suite of morphological synapomorphies for Pinnipedia, the frequency of reversals and other homoplasies within the clade limit their diagnostic value.

Mind the Outgroup and Bare Branches in Total-Evidence Dating: a Case Study of Pimpliform Darwin Wasps (Hymenoptera, Ichneumonidae)

“…In practice, however, most of the recent TED studies included one to a handful of outgroup taxa, which are thus severely underrepresented compared to the ingroup, both in terms of morphological characters and fossils ( Ronquist et al 2012a ; Arcila et al 2015 ; Dornburg et al 2015 ; Close et al 2016 ; Lee 2016 ; Kittel et al 2016 ; Herrera and Davalos 2016 ; Bannikov et al 2017 ; Wang et al 2018 ; Paterson et al 2020 ). The reasons for including these outgroups, despite their potentially negative effects, is seldom reported in these studies and might vary between authors.…”

Feeding in marine mammals: An integration of evolution and ecology through time

“…The sea otter is the only extant marine mammal that employs a crushing biting strategy. In the past, the durophagous niche was occupied by the phocid Hadrokirus (Amson and de Muizon, 2014) and aquatic bear/pinnipedimorph Kolponomos (Tseng et al, 2016;Paterson et al, 2020). Marine mammals that employ a crushing biting strategy FIGURE 2.…”

“…Stem pinnipedimorphs are mostly reconstructed as having had an ancestral coastal marine habitat as is characteristic of most extant taxa (Appendix 5). Since the fossil Puijila is now identified as a pinnipedimorph (Paterson et al, 2020) a lacustrine ancestral habitat is also indicated. The stem otariid Eotaria is reconstructed as having had a pelagic marine habitat.…”

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

“…However, loss of these receptors occurred independently in the ancestors of the reciprocally monophyletic Phocidae (seals) and Otaroidea (Otariidae [sea lions, fur seals] + Odobenidae [walruses]) rather than in the common ancestor of Pinnipedia [100]. Numerous morphological features related to raptorial feeding and hydrodynamic locomotion also appear to have evolved independently in the three extant families of Pinnipedia [101]. In Cetacea, multiple cranial and postcranial specializations for an aquatic lifestyle (e.g., shortened humerus, loss of radial tuberosity, reduction/loss of hindlimbs, posterior migration of the blowhole, cranial 'telescoping') evolved convergently in odontocetes and mysticetes [1,102,103].…”