Multiple fossil calibrations, nuclear loci and mitochondrial genomes provide new insight into biogeography and divergence timing for true seals (Phocidae, Pinnipedia)

Abstract

Aim To better understand the historical biogeography of the true seals, Phocidae, by combining nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) in a divergence time analysis using multiple fossil calibrations.Location Arctic, Antarctic, Pacific and Atlantic Oceans, Lake Baikal, Caspian Sea.Methods Fifteen nuclear genes totalling 8935 bp plus near-complete mitochondrial genome sequences were used in a Bayesian divergence time analysis, incorporating eight soft-bound fossil calibrations across the phylogeny. All species of true seals were included, plus the walrus, three otariids and seven carnivore outgroups. The majority of the nuclear sequences and four phocid mitochondrial genomes (plus three non-phocid mitochondrial genomes) were newly generated for this study using DNA extracted from tissue samples; other sequences were obtained from GenBank.Results Using multiple nuclear genes and multiple fossil calibrations resulted in most divergence time estimations within Phocidae being much more recent than predicted by other molecular studies incorporating only mtDNA and using a single calibration point. A new phylogenetic hypothesis was recovered for the Antarctic seals.Main conclusions Incorporating multiple nuclear genes and fossil calibrations had a profound effect on the estimated divergence times. Most estimated divergences within Phocinae (Arctic seals) correspond to Arctic oceanic events and all occur within the last 12 Myr, a time when the Arctic and Atlantic oceans were freely exchanging and perennial Arctic sea ice existed, indicating that the Arctic seals may have had a longer association with ice than previously thought. The Monachinae ('southern' seals) split from the Phocinae c. 15 Ma on the eastern US coast. Several early trans-Atlantic dispersals possibly occurred, leaving no living descendants, as divergence estimates suggest that the Monachus (monk seal) species divergences occurred in the western Atlantic c. 6 Ma, with the Mediterranean monk seal ancestor dispersing afterwards. The tribes Lobodontini (Antarctic seals) and Miroungini (elephant seals) are also estimated to have diverged in the eastern Atlantic c. 7 Ma and a single Lobodontini dispersal to Antarctica occurred shortly afterwards. Many of the newly estimated dates are used to infer how extinct lineages/taxa are allied with their living relatives.

Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates

“…The resolution to this problem depends to some degree on what should be done with Phoca ( sensu lato ), which varies regularly between being recognized as a single genus (for example, [13,57]), as four separate genera (for example, [14,53,58]) or some intermediate solution (for example, [54]). Given the relative divergence times inferred in this and other studies (for example, [49,50,59]), we would argue that Histriophoca and Pagophilus should remain as distinct genera, with both Halichoerus and Pusa being subsumed with Phoca . In the latter case, the designation of subgenera within Phoca is difficult due to the paraphyly of Pusa , unless one is willing to subsume Halichoerus within the subgenus Pusa .…”

Life in the Aftermath of Mass Extinctions

“…A relatively minor extinction event overall ($15% loss of shelly marine invertebrates [2]), the EOT also showed strange ecosystems within the first million years likely due to prevailing environmental conditions [101,102]. After the EOT many clades diversified that are still dominant today: diatoms radiated [103], ancient whales (archaeocetes) were replaced by modern whales (odontocetes and mysticetes) [104], and pinnipeds (i.e., seals, sea lions, and walruses) diverged from other mammalian carnivores [105].…”

Bioenergetics model for estimating food requirements of female Pacific walruses Odobenus rosmarus divergens

“…Like otariids, odobenids do not undergo extreme seasonal fasting periods related to breeding, lactating, and molting as do phocids, but rather these events occur over a longer time span and are combined with regular feeding (Fay 1982, Kovacs & Lavigne 1992. Furthermore, recent genetics studies have demonstrated that odobenids are more closely related to otariids than to phocids (Schröder et al 2009, Agnarsson et al 2010, Fulton & Strobeck 2010.…”