Seals are diphyletic. Goodbye Pinnipedia!

This split has been suspected or imagined for quite some time…
…but never documented with fossil taxa in phylogenetic analysis until today in the large reptile tree (LRT 1040 taxa; subset Fig. 1).

Seals are diphyletic.
These marine Carnivora had two terrestrial origins. Phoca is an earless seal (family: Phocidae) derived from a sister to Paleaosinopa. On the other hand, Zalophus is an eared seal (family: Otariidae) derived from a sister to Hyopsodus and Miacis. Thus the clade Pinnipedia is no longer monophyletic. The last common ancestor of seals in the LRT is the extant common raccoon, Procyon.  Doubtless a similar form that lived closer to the Cretaceous was the actual last common ancestor. Both clades of seals (that’s what we’ll still call them forever) adapted to water in similar, but not identical ways (see below).

Molecular evidence
According to Wikipedia: “While seals were historically thought to have descended from two ancestral lines, molecular evidence supports them as a monophyleticlineage (descended from one ancestral line). Pinnipeds belong to the order Carnivora and their closest living relatives are bears and musteloids (weasels, raccoons, skunks, and red pandas), having diverged about 50 million years ago.”  Of course, if the sister taxa that split seals are extinct (fossil taxa) as they are here, then molecular studies cannot service this issue or answer this question.

Earlier hypotheses
imagined otariids descended from bears and phocids descended from mustelids (weasels). Below are some of those earlier, mostly molecular studies and their intrinsic problems.

1. Arnason et al. 2006. Molecular study. Outgroups include bears, minks other Carnivora and no fossil taxa.
2. Flynn et al. 2005. Molecular study of the Carnivora. Outgroups include no fossil taxa.
3. Higdon et al. 2007. Molecular study of the Pinnipedia. Outgroups include bears and dogs and no fossil taxa.
4. Hunt and Barnes 1994. Skull base comparisons link seals to bears, not otters and ferrets.
5. Lento GM et al. 1995. Molecular study found pinnipeds derived from the bear/raccoon/panda radiation. Outgroups include no fossil taxa.
6. Sato JJ, et al. 2006. Molecular study allies pinnipeds with otters and ferrets. Outgroups include no fossil taxa.

Issues: Palaeosinopa
was considered a non-Eutherian placental mammal. Here it nests within Carnivora without a priori assumptions clouding the selection of the inclusion group.

Issues: Hyopsodus
was considered an odd-toed ungulate that was swift and lived in burrows. Here it nests within Carnivora without a priori assumptions clouding the selection of the inclusion group.

What about Enaliarctos?
Found in Late Oligocene strata, this earliest otariid (Fig. 6; Mitchell and Tedford 1973) nests between Zalophus and Hyopsodus in the LRT.

What about Puijula?
Pujilia darwini (Rybczynski, Dawson and Tedford 2009; Late Oligocene 23 mya;1m in length) was originally considered an extinct species of seal based chiefly on skull and tooth traits. Here in the LRT it nests at the base of the clade that produced phocid seals, not otarid seals. It was derived from a sister to Mustela the river otter and lived in and near high Arctic lakes.

Differences
According to Wikipedia: “Otariids use their front limbs primarily to propel themselves through the water, while phocids and walruses use their hind limbs. Otariids and walruses have hind limbs that can be pulled under the body and used as legs on land. By comparison, terrestrial locomotion by phocids is more cumbersome. Otariids have visible external ears, while phocids and walruses lack these.”

By the way,
moving one seal next to the other in the LRT adds 14 steps.

You might remember
the LRT for all of its faults (the list grows shorter every day) was able to similarly separate toothed whales (Odontoceti) from baleen whales (Mysticeti) and document they each had separate terrestrial ancestors, tenrecs and desmostylians respectively. Given the overall similarity of Otariids to Phocids, their separation in the LRT is another demonstration of the acuity and authority of large gamut phylogenetic analyses.

By the way, since this is science…
this is something anyone can do. Repeat the experiment if you have doubts, and let me know what you get. Apparently earlier workers were excluding pertinent outgroup taxa from their analyses, and this is something we’ve seen over and over again. That’s what set the stage for ReptileEvolution.com and this blog.

References
Arnason U, et al. (6 other authors) 2006. Pinniped phylogeny and a new hypothesis for their origin and dispersal. Molecular Phylogenetics and Evolution. 41 (2): 345–54.
Flynn JJ, Finarelli JA, Zehr S, Hsu J and Nedbal MA 2005. Molecular phylogeny of the Carnivora (Mammalia): Assessing the impact of increased sampling on resolving enigmatic relationships. Systematic Biology. 54 (2): 317–37.
Higdon JW, Bininda-Emonds OR, Beck RM and Ferguson SH 2007. Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset. BMC Evolutionary Biology. 7: 216.
Hunt RM Jr and Barnes LG 1994. Basicranial evidence for ursid affinity of the oldest pinnipeds. Proceedings of the San Diego Society of Natural History. 29: 57–67.
Lento GM, Hickson RE, Chambers GK and Penny D 1995. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Molecular Biology and Evolution. 12(1): 28–52.
Mitchell E and Tedford RH 1973. The enaliarctinae a new group of extinct aquatic carnivora and a consideration of the origin of the otariidae. Bulletin of the American Museum of Natural History 151:284 pp.
Orlov YA 1933. Semantor macrurus (ordo Pinnipedia, Fam. Semantoridae Fam. nova) aus den Neogen-Ablagerungen Westsibiriens. Trudy Paleontologicheskii Institut Akademiia Nauk SSSR 2, 249-253.
Rybczynski N, Dawson MR. and Tedford RH 2009. A semi-aquatic Arctic mammalian carnivore from the Miocene epoch and origin of Pinnipedia. Nature 458, 1021–1024.
Sato JJ, et al. (7 other authors) 2006. Evidence from nuclear DNA sequences sheds light on the phylogenetic relationships of Pinnipedia: Single origin with affinity to Musteloidea. Zoological Science. 23 (2): 125–46.

wiki/Pinniped
wiki/Enaliarctos
wiki/Phoca
wiki/Zalophus
wiki/Hyopsodus
wiki/Palaeosinopa

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