SVP abstracts 2017: Are pinnipeds (seals/sea lions) monophyletic?

Earlier the large reptile tree (LRT, 1050 taxa) invalidated the former clade Pinnipedia (seals and kin) as it split it into two clades, each derived from separate terrestrial limbed ancestors. Now comes this well written abstract from Paterson et al. 2017 that brings up all the right questions. The question is, did it have the right outgroups? I like how they say they are going to test tradition with genes and fossils. Unfortunately, they might lack a few pertinent outgroup taxa.

Figure 1. Phoca the phocid seal is most closely related to Palaeosinopa of all tested taxa.

Figure 1. Phoca the phocid seal is most closely related to Palaeosinopa of all tested taxa.

From the Paterson et al. abstract:
“Monophyly of pinnipeds is well-established. However, it is difficult to reconcile a monophyletic origin of pinnipeds with the disparate locomotor modes and associated skeletal morphologies observed between the extant families. Furthermore, the fossil record suggests many of the conventional pinniped synapomorphies arose independently, as many are not present in fossil taxa (Eotaria, Prototaria, Devinophoca) that have been firmly established as early-diverging crown members of the three extant families (e.g., homodont dentition, loss of fossa muscularis, reduction of nasolabialis fossa, loss of M2/m2, fusion of tibia and fibula, reduction of fossa for teres femoris).

“Herein, we test the hypothesis that otarioids (otariids + odobenids) and phocids share a common ancestor that was not yet fully aquatic. In the present analysis, a total evidence approach was employed to investigate the relationships of 19 extant and 37 fossil caniforme genera. Our analysis sampled five genes totalling 5490 bp and 184 morphological characters, sampled relatively evenly across morphological partitions (cranial, dental, postcranial). With Canis as an outgroup, Bayesian inference produced strong support for a monophyletic origin of pinnipeds, and recovered Puijila and Potamotherium as early-diverging pinnipedimorphs

(Ursidae(Musteloidea(Potamotherium(Puijila(Enaliarctos, (Desmatophocidae(Phocidae,(Odobenidae, Otariidae)))))))). Similar results were obtained from Bayesian and parsimony analyses of a morphology-only data set, a cranial-only data set, a craniodental-only data set, and a post-cranial-only data set. Bayesian inference of morphology-only partitions recovered Mustelavus and a sister grouping of Allocyon + Kolponomos along the stem to later-diverging pinnipedimorphs. The parsimony analysis recovered 20 synapomorphies of Potamotherium + Puijila + Pinnipedimorphs, and nine synapomorphies for a crown group Pinnipedia, to the exclusion of the pinnipedimorphs. In spite of a reinterpretation of the plesiomorphic state of many previously proposed pinniped synapomorphies, there remain more than enough pinniped synapomorphies to exclude the semi-aquatic  pinnipedimorphs, thereby challenging our hypothesis of a dual origin of flippers. However, this may be an artifact of a Bayesian model of morphological inference which, among other limitations, cannot model direction evolution, and thus, may be incapable of capturing parallel evolution in such a context.”

Figure 3. Zalophus, an otariid seal, is most closely related to Hyoposodus among tested taxa in the LRT

Figure 2. Zalophus, an otariid seal lion, is most closely related to Hyoposodus among tested taxa in the LRT. Seals and sea lions are incredibly alike. It’s a tribute to the authority of the LRT that it was able to separate these two clades, both derived from distinct and different terrestrial ancestors.

I don’t have their complete taxon list. 
If it includes the pertinent taxa that split the Pinnipedia, then we’ll have to reexamine the data. If not, it’s still worth comparing.

Their choice of
Canis (the wolf/dog) as an outgroup is a weakness. They should have let a large gamut of mammals decide the outgroup(s) for pinnipeds. I don’t see Palaeosinopa in their published taxon list, but it might be in there somewhere. In the LRT it nests with phocids, like Phoca and the limbed carnivore, PujiliaI don’t see Miacis and Hyopsodus in their taxon list. In the Paterson et al. study Enaliarctos nests basal to all extant pinnipeds, but in the LRT, Enaliarctos nests with Miacis, Hyopsodus and Zalophus, the California sea lion, an otariid. So, it looks like taxon exclusion is present here, yet again. Paterson et al. appear to be missing some pertinent outgroups. The last common ancestor of seals and sea lions goes back to something like Herpestes, the mongoose, and/or Procyon, the raccoon.

Seals and sea lions are incredibly alike.
It’s a tribute to the authority of the LRT that it was able to separate these two clades, both derived from distinct and different terrestrial ancestors.

References
Paterson RS et al. 2017. The evolution of pinnipeds from a terrestrial ancestor: the possibility of parallel evolution within a monophyletic framework. SVP abstracts 2017.

Advertisements

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).

Figure 1. Subset of the LRT focusing on Carnivora and the diphyletic nesting of seals, derived from separate terrestrial ancestors. Moving one seal next to the others adds 14 steps.

Figure 1. Subset of the LRT focusing on Carnivora and the diphyletic nesting of seals, derived from separate terrestrial ancestors. Moving one seal next to the others adds 14 steps.

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).

Figure 1. Phoca the phocid seal is most closely related to Palaeosinopa of all tested taxa.

Figure 1. Phoca the phocid seal is most closely related to Palaeosinopa of all tested taxa.

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.

Figure 3. Zalophus, an otariid seal, is most closely related to Hyoposodus among tested taxa in the LRT

Figure 3. Zalophus, an otariid seal, is most closely related to Hyopsodus among tested taxa in the LRT

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.

Figure 1. Palaeosinopa, complete and largely articulated. Body length about 50 cm. Tail adds 35 cm. From Rose and Koenigswald 2005.

Figure 4. Palaeosinopa, complete and largely articulated. Body length about 50 cm. Tail adds 35 cm. From Rose and Koenigswald 2005. This taxon nests with Phoca in the LRT.

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.

Figure 1. Hyopsodus as originally reconstructed (below) and as reconstructed here above in two views. This former condylarth now nests with dogs.

Figure 5. Hyopsodus as originally reconstructed (below) and as reconstructed here above in two views. This former condylarth now nests with dogs.

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.

Figure 6. Enaliarctos nests between Zalophus and Hyopsodus in the LRT.

Figure 6. Enaliarctos nests between Zalophus and Hyopsodus in the LRT. The long bone around the knees is a baculum, or penis bone, found only in males.

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.

Figure 6. Pujilia was considered a basalmost pinniped, but here nests at the base on only the phocids, not the otarids.

Figure 6. Pujilia was considered a basalmost pinniped, but here nests at the base on only the phocids, not the otarids.

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

/tetrapod-zoology/pinnipeds-descended-from-one-ancestral-line-not-two/

Speaking of taeniodont origins, there’s another candidate: Cimolestes

Yesterday we looked at the origin of taeniodonts, like Stylinodon. and found it nested with Mustela the mink and Phoca the seal. Other workers (Lillegraven 1969, Rook and Hunter 2013) indicated that Cimolestes (Fig.1, Late Cretaceous) was a suitable ancestor to the taeniodonts. So, let’s look at Cimolestes and compare it to related taxa.

Figure 1. Cimolestes mandible from Lillegraven 1969 compared to a phylogenetically basal eutherian the marsupial without a pouch, Monodelphis, the basal tenrec, Maelestes and Cimolestes. All have a slender mandible.

Figure 1. Cimolestes mandible from Lillegraven 1969 compared to a phylogenetically basal eutherian the marsupial without a pouch, Monodelphis, the basal tenrec, Maelestes and Cimolestes. All have a slender mandible without the anterior depth found in Stylinodon, Mustela and Martes in figure 2.

In comparison
Cimolestes is more like the basal eutherians Monodelphis and Maeilestes (Fig. 1) in having a rather slender mandible with incisors anterior to the canines. By contrast, the carnivores Martes, the martin, and Mustela (Fig. 2), and the taeniodonts, Wortmania (Fig. 3) and Stylinodon have a robust mandible, deep anteriorly with canines to the anterior and incisors between them.

Figure 2. Martes, the extant martin, and Mustela, the extant mink or polecat mandibles. Both are deeper in front, more like the taeniodont, Stylinodon.

Figure 2. Martes, the extant martin, and Mustela, the extant mink or polecat mandibles. Both are deeper in front, more like the taeniodont, Stylinodon. Note the number of teeth varies among these closely related taxa.

Lillegraven 1969 wrote: “A smaller carnivorous species described as new of Cimolestes probably represents a primitive stage in the development of miacids, and subsequently fissiped and pinniped carnivores.” Well, we’re all in the same ballpark and thinking along similar lines. Not sure where Cimolestes nests in the LRT yet. Not much is known of it, other than jaw fragments.

Figure 6. Wortmania as drawn freehand by Schoch compared to bones Photoshopped together.

Figure 6. Wortmania as drawn freehand by Schoch compared to bones Photoshopped together.

References
Lillegraven JA 1969. Latest Cretaceous mammals of upper part of Edmonton formation of Alberta, Canada, and review of marsupial-placental dichotomy in mammalian evolution. Article 50 (Vertebrata 12) The U. of Kansas Paleontological Contributions. 122pp.
Rook DL and Hunter JP 2013. rooting around the eutherian family tree: the origin and relations of the Taeniodonta. Journal of Mammal Evolution. DOI 10.1007/s10914-013-9230-9

wiki/Cimolestes

Stylinodon may be a giant herbivorous mink

In 1873 
O. C. Marsh 1874) found an extinct Eocene (50.3 to 40.4 Ma) mammal “of great interest. The lower molar teeth, all essentially alike, and inserted in deep sockets” were the most striking feature. He named it Stylodon mirus (Figs. 1,2). All the teeth grew with “persistent pulps” and had a thin layer of enamel. The specimen was considered close to Toxodon with some edentate affinities (Marsh 1897). Stylinodon was placed under the family Stylinodontidae and the order Tillodontia. According to Schoch 1986 (first issue of JVP!) its ancestors were like Onychodectes.

Stylinodon mirus (Marsh 1874; middle Eocene, 45 mya; Figs. 1-2) was originally considered a taeniodont, perhaps derived from Onychodectes. Here it nests with Mustela, the living European mink, among the Carnivora. There were twice as many molars (4), each with a single root, as in the two double rooted molars of the mink. Large claws and certain forelimb traits indicate that Stylinodon was a digger, not a cursor.

The present nesting
of Stylinodon mirus (YPM VP 011095, Marsh 1874; Figs. 1, 2) in the Carnivora occurred when I realized it was a poor fit at the base of the Condylarthra/Paenungulata, despite its herbivorous dentition and tusk-like teeth (canines, not incisors).

Figure 1. Stylinodon skull. Note the transverse premaxilla, a trait of the Carnivora.

Figure 1. Stylinodon skull. Note the transverse premaxilla, a trait of the Carnivora.

Distinct from condylarths
Stylinodon has a transverse premaxilla, essentially invisible in lateral view. The lower canine is the anteriormost tooth on the dentary. These traits are shared with other members of the Carnivora. In the present taxon list Stylinodon shares more traits with Mustela, the European mink (Fig. 1) despite the loss of molar cusps and increase in size. They both were diggers. Together they nest with Phoca, the seal, and Palaeosinopa, the amphibious piscivore, all derived from a sister to Procyon, the omnivorous raccoon (Fig. 2).

Figure 1. Stylinodon compared to Mustela, the European mink to scale.

Figure 2 Stylinodon compared to Mustela, the European mink to scale.

As in the earlier issue
with indricotheres, related taxa can have distinctively different types of teeth, one more reason to not weight dental traits too heavily, unless that’s all you have.

Figure 2. Mustela the European mink is an extant relative to Stylinodon.

Figure 3. Mustela the European mink is an extant relative to Stylinodon.

Mustela lutreola (Linneaus 1761; extant European mink; up to 43cm in length) is a fast and agile animal related to weasels and polecats. Mustela lives in a burrow, but it also swims and dives skilfully. It is able to run along stream beds, and stay underwater for one to two minutes. Mustela is derived from a sister to Phoca and other seals, all derived from a sister to Procyon. With this close relationship, Stylinodon (Fig. 2 a giant weasel with simple teeth.

Schoch and Lucas 1981
and Schoch 1983 considered Stylinodon and kin derived from a sister to the long-legged basal condylarth, Onychodectes. The large reptile tree (LRT, Fig. 2) does not support that nesting. Onychodectes has a long premaxilla lacking in taeniodonts.

Figure 2. Subset of the LRT showing the Carnivora nesting at the base of the Eutheria (placental mammals).

Figure 4. Subset of the LRT showing the Carnivora nesting at the base of the Eutheria (placental mammals).

Schoch and Lucas 1981
determined that Stylinodon had two upper incisors (one lower), a giant canine, four premolars and three molars, as in Onychodectes. That may be so, but the premolars and molars look alike.

 

Figure 6. Wortmania as drawn freehand by Schoch compared to bones Photoshopped together.

Figure 6. Wortmania as drawn freehand by Schoch compared to bones Photoshopped together.

Wortmania (Hay 1899, Williamson and Brusatte 2013; above) and Psittacotherium (Cope 1862; below) are related to Stylinodon. All are among the largest taxa in the early post-Cretaceous, derived from smaller weael-like basal mammals in the Cretaceous.

Figure 7. Psittacotherium in various views.

Figure 6.  Psittacotherium in various views. Overall it is elongated to more closely match related taxa.

It is rare but not unheard of
for members of the Carnivora to become omnivores and herbivores. Think of the giant panda and certain viverrids. Now the stylinodontid taeniodonts join their ranks.

References
Linneaus C von 1761. xxx
Marsh OC 1874. Notice of new Tertiary mammals 3. American Journal of Science. (3) 7i: 531-534.|
Marsh OC 1897. The Stylinodontia, a suborder of Eocene Edentates. The American Journal of Science Series 4 Vol. 3:137-146.
Rook DL and Hunter JP 2013. Rooting Around the Eutherian Family Tree: the Origin and Relations of the Taeniodonta. Journal of Mammalian Evolution: 1–17.
Schoch RM and Lucas SG 1981. The systematics of Stylinodon, an Eocene Taeniodont (Mammalia) from western North America. Journal of Vertebrate Paleontology 1(2):175-183.
Schoch RM 1983. Systematics, functional morphology and macroevolution of the extinct mammalian order Taeniodonta. Peabody Museum of Natural History Bulletin 42: 307pp. 60 figs. 65 pls.

 

 

 

wiki/Stylinodon
wiki/Mustela

The laughing hyena (Crocuta crocuta) is a ‘CatDog’

Traditionally
hyenas, like Crocuta crocuta (spotted or laughing hyaena, Kaup 1828, Erxleben 1777; up to 160 cm in length, Pliocene, 10 mya to present; Figs. 1,2), have been nested with palm civets, like Nandinia, and mongooses, like Herpestes. I hate to keep doing this, but adding Crocuta to the large reptile tree (LRT) nests this hyena rather strongly between dogs, like Canis (Fig. 3) and cats, like the African lion, Panthera leo (African lion, Linneaus 1758; up to 250 cm in length (sans tail), Pliocene, 10 mya to present; Fig. 4). So the hyena is something of a CatDog (see way below, Fig. 5). It is not a basal member of the Carnivora.

Figure 1. Crocuta skull is quite similar to that of Canis, its sister in the LRT. But also similar to Panthera, its other sister in the LRT.

Figure 1. Crocuta skull is quite similar to that of Canis, its sister in the LRT. But also similar to Panthera, its other sister in the LRT.

And it’s easy to see why hyenas nest with dogs.
There is even a clade of widely recognized dog-like hyenas among fossil taxa. Wikipedia reports, “Although phylogenetically they are closer to felines and viverrids, hyenas are behaviourally and morphologically similar to canines in several aspects” So most workers consider this convergent evolution. Having examined the characters in detail, I call this nothing but rather typical evolution and sisterhood. There are only a few traits that separate the three sisters.

Figure 3. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2)

Figure 2. Crocuta (hyena) skeleton. Note similarities to Canis (figure 2). Note the shorter torso and more robust limbs, perhaps the most obvious differences between hyenas and their sisters, cats and dogs.

From the  website of the
IUCN Hyaena Specialist Group “Although extant hyenas are rather dog-like in many aspects of their appearance, the family Hyaenidae actually belongs to the Carnivore suborder Feliformia, which also contains cats, mongooses, civets, and allies.”

Figure 3. Canis lupus, the wolf, nests as a sister to Crocuta in the LRT.

Figure 3. Canis lupus, the wolf, nests as a sister to Crocuta in the LRT.

Contra that hypothesis of relationships,
the LRT nests civets, mongooses, moles, raccoons, seals and allies as basal carnivores. Cats, dogs and  hyenas nest as derived carnivores and sisters to the extinct taxa, Miacis and Hyopsodus.

Figure 1. Panthera leo skull and skeleton. This taxon nests basal to hyenas + wolves.

Figure 4. Panthera leo skull and skeleton. This taxon nests basal to hyenas + wolves. Note the relatively large scapula and slender limbs with retractable claws.

Perhaps more reasons to distrust DNA studies
The IUCN website notes: “Fossil data suggest that members of the family Hyaenidae last shared a common ancestor with their Feliform sister taxon in the Oligocene, around 25 million years ago (MYA) (Werdelin & Solounias 1991), and recent molecular data suggest this divergence occurred even earlier, approximately 29 MYA (Koepfli et al. 2006). The molecular data further suggest that the sister group to the Hyaenidae is a Feliform clade containing the mongooses (family Herpestidae) and the fossa (genus Cryptoprocta), a small, civet-like Malagasy carnivore that was assigned to the family Viverridae until quite recently (Yoder et al. 2003).”

Sisters to the dog-cat split, Miacis and Hyopsodus, 
were found in Late Paleocene to Late Eocene strata. So phylogenetic bracketing pushes the cat-dog + hyena split back to that era.

Figure 4. CatDog is a cartoon character that in no way resembles the extant hyena.

Figure 5. CatDog is a cartoon character that in no way resembles the extant hyena.

The cartoon
CatDog is a animated television character (Fig. 5) with two heads that in no way resembles the extant hyena. As you might imagine, they often want to go their separate ways and this leads to frustration and fun.

While we’re on the subject of hyenas…
Proteles crostata (aardwolf; Fig. 6; Sparrman 1783; extant), is in the same family as hyenas, according to Wikipedia. And it is, in a way… except the LRT nests this long-legged termite-eater closer to Canis than Crocuta.

Figure 6. The extant aardwolf, Proteles, nests as a sister to Canis in the LRT and this clade is a sister to Crocuta, the hyena. Note the tiny teeth, except for the large canines, of this long-legged termite eater.

Figure 6. The extant aardwolf, Proteles, nests as a sister to Canis in the LRT and this clade is a sister to Crocuta, the hyena. Note the tiny teeth, except for the large canines, of this long-legged termite eater.

And this footnote:
The weasel or stoat (Mustela erminea; Linneaus 1758) nests basal to all six above named taxa in the LRT, derived from a sister to the raccoon (Procyon).

References
Erxleben J 1777. Systema regni animalis.
Kaup JJ 1828. Über Hyaena, Uromastix, Basiliscus, Corthaeolus, Acontias. Isis 21, columns 1144–1150.
Linnaeus C von 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.
Sparman A 1783. 

wiki/Canis
wiki/Carnivora
wiki/Crocuta
wiki/Hyena
wiki/Panthera
wiki/Aardwolf

Phylogeny of the Carnivora – its topsy-turvy!

The large reptile tree
(LRT) presents a novel topology for many clades within the Reptilia. Among them is the Carnivora (Fig.1). The LRT uses fossil taxa and, you’ll note by comparison, is virtually upside-down (topsy-turvy, backwards) when it comes to trees recovered in molecular studies. That major difference MIGHT be traced to the choice of outgroup, as you will see…

Figure 1. Carnivora subset of the LRT with Monodelphis, a basal placental, as the outgroup, not Manis the pangolin.

Figure 1. Carnivora subset of the LRT with Monodelphis, a basal placental, as the outgroup, not Manis the pangolin.

Using molecular phylogenetics
(no fossils) Eizirik et al 2010 recovered a cladogram of the Carnivora that used Manis, the pangolin (Fig. 2), as the outgroup. Does this surprise you? …especially considering the fact that Manis has bounced around various nodes on the mammal family tree for decades. …and since it is toothless! And since it has scales instead of hair! etc. etc.

Figure 2. Manis, the Chinese Tree Pangolin along with other views of other pangolins

Figure 2. Manis, the Chinese Tree Pangolin along with other views of other pangolins

That, in itself, is very strange
to have a highly derived taxon used as a plesiomorphic outgroup. By contrast, in the LRT the outgroup is Monodelphis (Fig. 3), a tiny very plesiomorphic, opossum-like basal placental with origins in the Jurassic. And it has teeth!  And hair!

Figure 4. Entire skeleton of Monodelphis from Digimorph.org and used with permission.

Figure 3. Entire skeleton of Monodelphis from Digimorph.org and used with permission. This little taxon makes a great outgroup for the Carnivora that will flip topologies on their head when employed.

Using a pangolin as the outgroup
the Eizirik team recovered a basal split between feliforms and caniforms.

Feiliforms include Nandinia, then a split between cats and civets + hyenas + mongooses + fossas.

Caniforms include a basal split between wolves and bears + seals + raccoons + minks. Essentially these topologies are quite similar to the LRT, only in the opposite order with cats and dogs nesting in basal nodes, while minks and mongooses nest in derived nodes.

Notice the relatively flipped topologies
Can we blame this on the choice of an outgroup? On the lack of fossil taxa? On the inadequacies of DNA analyses across large clades? Or a little of all three?

Note that
Talpa, the extant Eastern mole, and Mondelphis, the extant gray short-tailed opossum were excluded a priori from the Eizirik study, but revealed by the large gamut analysis of the LRT, which minimizes a priori assumptions such as these.

Also using molecules
Wesley-Hunt and Flynn 2005 found a similar topology to the Eizirik study, turning the order recovered by the LRT on its head, with opossum-like carnivores (civets, minks) in derived nodes. This study used a variety of outgroups (Manis, ElephasLoxodonta, Equus, Bos, Sus, Homo) rather than Monodelphis. Results did not change the topology within the Carnivora.

Now is a good time to ask yourself,
Why did they use such silly, useless and obviously wrong outgroups rather than seek the one true plesiomorphic outgroup?

This is exactly why
this blog and ReptileEvolution.com were created — to throw back the curtain on such odd practices, methods and choices — AND produce viable alternative answers. These are experiments you can repeat yourself, BTW.

Let’s not forget
moles (Fig. 3) are carnivores, too!

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

References
Eizirik E, Murphy WJ, Koepfli KP, Johnson WE, Dragoo JW and O’Brien SJ 2010. Pattern and timing of the diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. Molecular Phylogenetics and Evolution 56:49–63.
Wesley-Hunt GD and Flynn JJ 2005. Phylogeny of the Carnivores. Journal of Systematic Palaeontology. 3:1–28.

LRT news: Moles are mongoose sisters and members of the order Carnivora.

Now the order Scoricomorpha is breaking up in the LRT.
Wikipedia reports, “The order Soricomorpha (“shrew-form”) is a taxon within the class of mammals. In the past it formed a significant group within the former order Insectivora. Traditionally the clade includes:

  1. Soricidea – several types of shrews
  2. Talpidaemoles
  3. SolenodontidaeSolenodon
  4. Nesophontidae – West Indian shrews
  5. Heterosoricidae – several taxa only an expert would recognize

Earlier we looked at shrews and apatemyids.

Figure 1. Herpestes, the Egyptian mongoose, nests in the LRT with Talpa the Eastern mole.

Figure 1. Herpestes, the Egyptian mongoose, nests in the LRT with Talpa the Eastern mole.

Adding the Egyptian mongoose
Herpestes (Figs. 1, 3), to the large reptile tree (LRT, not yet updated), finding better data for Talpa (Figs. 2, 4) the Eastern mole, and changing all the matrix scores that needed changing resulted in a taxon shift. Talpa moved to become a sister to Herpestes within the Carnivora. Solenodon and Scutisorex (a shrew) remained behind within the clade Glires (rabbits and rodents and their kin including multituberculates). Moles were never a good fit here. Glires all have very large gnawing incisors. Carnivora are known for their large canines and tiny nipping incisors.

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Figure 2. Talpa the Eastern mole nests in the LRT with Herpestes the mongoose.

Both Herpestes and Talpa
are derived from a sister to Protictis, known at present by an anterior skull fragment.

Figure 3. Herpestes skull. Note the complete postorbital ring, a rare trait in the Carnivora.

Figure 3. Herpestes skull. Note the complete postorbital ring, a rare trait in the Carnivora.

In figure 4 (below)
you can see where the initial confusion arose. The drawing makes it look like the premaxilla covers the anterior rostrum like a nose cone. That would make the largest teeth incisors. And the large ones should be the medial ones, if moles were related to shrews. But when you look at the bones, you’ll see the incisors are tiny and the premaxilla is short enough to be considered ‘transverse’ like most carnivores. And don’t those canines look like real carnivore canines.

Figure 4. Talpa skull. If you look closely you can see the tiny orbit completely surrounded by bone. Note the transverse premaxilla and large canines in the colorful lateral view. This is in contrast to the drawing below it that appears to indicate a longer premaxilla that would have included the long caniniform teeth. The palate view confirms the small transverse premaxilla.

Figure 4. Talpa skull. If you look closely you can see the tiny orbit completely surrounded by bone. Note the transverse premaxilla and large canines in the colorful lateral view. This is in contrast to the drawing below it that appears to indicate a longer premaxilla that would have included the long caniniform teeth. The palate view confirms the small transverse premaxilla.

There’s more of course…
Herpestes and Talpa share a humerus longer than the femur, a tibia longer than the femur, and a postorbital ring where the frontal produces a process that meets a process arising from the jugal. This trait arises several times within the Mammalia by convergence. Mongooses live in burrows and use their claws principally for digging. So do moles. Mongooses eat a variety of vertebrates and invertebrates. Some kill snakes. Moles eat earthworms, other inverts and buried nuts. The mongoose can survive snake venom. The mole produces venom to paralyze worms for later consumption.

Herpestids nest between
cat-like and raccoon/dog-like carnivores in the LRT. Golden moles, like Chrysocloris, have large incisors and nest within Glires.

This appears to be the first time
Talpa has been nested within Carnivora and was only made possible by the inclusion of Herpestes. The other carnivores so far tested did not share so many traits. I’ll put up the latest version of the reptile cladogram when things settle down and stop shifting around so much in the Mammalia. Getting closer every day. About a dozen new taxa will appear then.