False positives in an LRT subset lacking fossil taxa

I think you’ll find this phylogenetic experiment both
gut-wrenching and extremely illuminating. While reading this, keep in mind the importance of having/recovering the correct outgroup for every clade and every node. That can only be ascertained by including a wide gamut of taxa—including fossils. Adding taxa brings you closer and closer to echoing actual events in deep time while minimizing the negative effects of not including relevant/pertinent taxa.

Today you’ll see
what excluding fossil taxa (Fig. 1) will do to an established nearly fully resolved cladogram, the large reptile tree (LRT, 1318 taxa). Earlier we’ve subdivided the LRT before, when there were fewer taxa in total. Here we delete all fossil taxa (except Gephyrostegus, a basal amniote used to anchor the cladogram because PAUP designates the first taxon the outgroup).

PAUP recovers 250+ trees
on 264 (~20%) undeleted extant taxa.

  1. Overall lepidosaurs, turtles, birds and mammals nest within their respective clades.
  2. Overall lepidosaurs nest with archosaurs and turtles with mammals, contra the LRT, which splits turtles + lepidosaurs and mammals + archosaurs as a basal amniote dichotomy.
  3. Overall mammals are not the first clade to split from the others, contra traditional studies. All pre-mammal amniotes in the LRT are extinct.
  4. Within lepidosaurs, the highly derived horned lizards and chameleons are basal taxa, contra the LRT, which nests Iguana as a basal squamate.
  5. Within lepidosaurs, geckos no longer nest with snakes, contra the LRT.
  6. Crocodiles nest with kiwis, as in the LRT, but it is still amazing that PAUP recovered this over such a large phylogenetic distance.
  7. Within aves, so few taxa are fossils in the LRT that the tree topology is very close to the original.
  8. Within mammals marsupials no longer nest between monotremes and placentals
  9. …and because of this carnivores split off next.
  10. Contra the LRT, hippos are derived from the cat and dog clade, all derived from weasels.
  11. Within mammals odontocetes no longer nest with tenrecs.
  12. Within mammals mysticetes nest with odontocetes, no longer nest with hippos.
  13. Contra the LRT, whales are derived from manatees and elephants.
Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

Figure 1. Subset of the LRT focusing on Amniota (=Reptilia) with all fossil taxa deleted. Gephyrostegus, a Westphalian fossil is included as the outgroup.

BTW,
here are the results based on using the basal fish, Cheirolepis, as an outgroup:

    1. The caecilian, Dermophis, nests as the basalmost tetrapod.
    2. Followed by the frog and salamander.
    3. Squamates branch off next with legless lizards and burrowing snakes at a basalmost node. Terrestrial snakes are derived from burrowing snakes. Gekkos split next followed by varanids and skinks. Another clade begins with the tegu and Lacerta, followed by iguanids. Sphenodon nests between the horned lizards, Moloch and Phyrnosoma + the chameleon.
    4. Turtles split off next with the soft-shell turtle, Trionyx, at the base.
    5. One clade of mammals split off next with echidnas first, then elephant shrews and tenrecs, followed by a clade including the pangolin, seals and other basal carnivores. Cats and dogs split off next followed by hippos, then artiodactyls, perissodactyls, the hyrax, elephants, manatees, mysticetes and odontocetes.
    6. Another clade of mammals include edentates, followed by tree shrews and glires, followed by (colugos + bats) + primates, followed by another clade of basal carnivores, followed by marsupials.
    7. The final clade is Crocodylus + extant birds, which are not well resolved and split apart into two major clades with some subclades maintaining their topology while other clades split apart. So the archosaurs nest together.

This test emphasizes the need for the inclusion of fossil taxa in order to recover a gradual accumulation of traits at all nodes, which takes us closer to actual evolutionary patterns in deep time.

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The short-faced bear (Arctodus) is a giant wolverine in the LRT.

Yesterday we looked at three bears, Ursus, Arctodus (Fig. 1) and Ailuropoda (the polar bear, the short-faced bear and the panda bear). They do not form a single bear clade in the large reptile tree (LRT, 1299 taxa), but each is more closely related to small weasels and grew to bear-size by convergence.

For instance,
Arctodus is most closely related to today’s wolverine (Gulo gulo, Figs. 1, 2) among tested taxa, and the similarities are immediately apparent. Have they ever been tested together before? Let me know if this is so.

Figure 1. Arctodus (shor-faced bear) skeleton compared to the smaller Gulo (wolverine) skeleton. Both have similar proportions. Arctodus is larger than 3m, while Gulo is about 1m in length.

Figure 1. Arctodus (shor-faced bear) skeleton compared to the smaller Gulo (wolverine) skeleton. Both have similar proportions. Arctodus is larger than 3m, while Gulo is about 1m in length.

Arctodus simus (Leidy 1854; Cope 1874; up to 3 to 3.7m tall) is the extinct short-faced bear, one of the largest terrestrial mammalian carnivores of all time. Long limbs made it a fast predator. Being related to the wolverine made it short-tempered and dangerous.

Figure 2. Long-legged Gulo, the wolverine, is most similar to Arctodus, the short-faced bear in the LRT.

Figure 2. Long-legged Gulo, the wolverine, is most similar to Arctodus, the short-faced bear in the LRT. That’s a penile bone, not a prepubis.

Gulo gulo (Linneaus 1758; up to 110 cm in length) is the extant wolverine, a ferocious predator resembling a small bear. Note the tail length is midway between the long tail of weasels and the short tail of birds.

Figure 1. Subset of the LRT focusing on the Carnivora with tan tones on the bears newly added.

Figure 3. Subset of the LRT focusing on the Carnivora with tan tones on the bears newly added.

The red panda
(Ailurus) was also added to the LRT (Fig. 3) and, to no one’s surprise, nests with the raccoon, Procyon apart from the giant panda.

Figure 4. Gulo skull in lateral and dorsal views. Compare to Arctodus in figure 5.

Figure 4. Gulo skull in lateral and dorsal views. Compare to Arctodus in figure 5. The male skull has the larger and longer parasagittal crest.

The skulls of Gulo and Arctodus
(Figs. 4, 5) despite their size differences, are quite similar. Both display sexual dimorphism.

Figure 5. Arctodus (short-faced bear) skull in lateral view. Compare to figure 4.

Figure 5. Arctodus (short-faced bear) skull in lateral view. Compare to figure 4.

Taxon inclusion
sheds light on phylogenetic interrelationships.

If you have an interest in wolverine evolution,
I suggest you use the keyword “Gulo” or you’ll end up learning about Marvel’s superhero, also named Wolverine.

References
Cope ED 1879. The cave bear of California. American Naturalist 13:791.
Leidy 1854. Remarks on Sus americanus or Harlanus americanus, and on other extinct mammals. Proceedings of the Academy of Natural Sciences of Philadelphia 7:90.
Linnaeus C 1758. Systema naturæ per regna tria naturæ, secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis. Tomus I. Editio decima, reformata.

wiki/Gulo
wiki/Short-faced_bear

The most basal mammal in the LRT: Megazostrodon

I thought for many years
that Megazostrodon was known from only a fragment of skull, lacking both the anterior and posterior parts.

Then somehow this paper popped up on the Internet
Gow 1986 illustrated the skull of Megazostrodon (Fig. 1; BPI/1/4983; Crompton & Jenkins, 1968; Latest Triassic; 200 mya). Even without this skull data the large reptile tree (LRT, 1293 taxa) nested Megazostrodon at the base of the Mammalia. There is little  argument among paleontologists that this taxon is a close sister to the last common ancestor of all living mammals.

Often wrongly associated
with Morganucodon, the two are phylogenetically separated from one another by tiny Hadrocodium in the LRT. In Megazostrodon the zygomatic arch is straight (without the ascending arch). The skull lacks a sagittal crest.  As in modern marsupials, carnivores, primates and tree shrews the teeth have a standard incisor, canine, premolar and molar appearance. The permanent molars occlude precisely. Uniquely (as far as I know), the dentary has a coronoid boss and a coronoid process.

Figure 1. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here.

Figure 1. Megazostrodon skull in several views. Drawings from Gow 1986. Colors applied here. The upper molars are worn down.

The large reptile tree
(Fig. 2) presents a simple, validated topology of mammals and their ancestors based on hundreds of traits, very few of them dental. It differs in nearly every regard from the Close et al. 2015 study, which employs many dental taxa.

Figure 1. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

Figure 3. Subset of the LRT focusing on the Kynodontia and Mammalia. Non-eutherian taxa in red were tested in the LRT but not included because they reduce resolution. Eutherian taxa in red include a basal pangolin and derived xenarthran, clades that extend beyond the bottom of this graphic. The pink clade proximal to mammals was considered mammalian by Lautenschlager et al. due to a convergent mammalian-type jaw joint.

The first time I reconstructed Megazostrodon
(Fig. 4) the skull looked legit, and was approved by cynodont expert Jim Hopson, but it had some problems. I’m glad to finally get better data on this, that resolves scoring problems around this node.

Figure 1. Megazostrodon, an early mammal, along with Hadrocodium, a Jurassic tiny mammal.

Figure 4. Megazostrodon, an a Jurassic mammal, along with Hadrocodium, a Jurassic tiny mammal. The Megazostrodon skull shown here is not correct.

On a side note:
Wikipedia reports,Tinodon (Marsh 1887; YMP11843) is an extinct genus of Late Jurassic mammal from the Morrison Formation. It is of uncertain affinities, being most recently recovered as closer to therians than eutriconodonts but less so than allotherians.” 

Figure 1. Tinodon is best represented by an incomplete mandible with affinities to basal mammals.

Figure 5. Tinodon is best represented by an incomplete mandible with affinities to basal mammals and basal metatherians. Image from Morphobank.

Too few characters are present here
to add it to the large reptile tree, but if I have restored the missing parts correctly, then it is close to the base of the Mammalia and Theria near Megazostrodon.

References
Close RA, Friedman M. Lloyd GT and Benson RBJ 2015. Evidence for a mid-Jurassic adaptive radiation in mammals. Current Biology. 25 (16): 2137–2142. doi:10.1016/j.cub.2015.06.047PMID 26190074.
Crompton AW and Jenkins FA Jr 1968. Molar occlusion in late Triassic mammals, Biological Review, 43 1968:427-458.
Gow CE 1986. A new skull of Megazostrodon ( Mammalia, Triconodonta) from the Elliot Formation (Lower Jurassic) of Southern Africa. Palaeontologia Africana 26(2):13–22.
Marsh OC 1887. American Jurassic mammals. The American Journal of Science, series 3 33(196):327-348

wiki/Megazostrodon

 

Asioryctes: Re-restoring a pes, re-nesting a taxon

I should have noticed this pairing earlier.
Evidently it escaped everyone else’s notice, too. Asioryctes nemegetensis (Kielan-Jaworowska 1975, 1984; Figs. 1,2; middle Late Cretaceous, Djadokhta Formation, ~85 mya) is a good match for the living bandicoot, Perameles. Maga and Beck 2017 nested Asioryctes with the coeval Ukhaatherium, and the extant Perameles with another bandicoot, Echymipera.

FIgure 1. Skulls of Asioryctes, Perameles and Macrotis compared.

FIgure 1. Skulls of Asioryctes, Perameles and Macrotis compared. The overall shapes are similar, and so are the teeth, and other details. Historically the feet have been different, and that’s our starting point. 

Figure 2. Left: original restoration of Asioryctes pes. Colors added. Right: New restoration based on phylogenetic proximity to Perameles and other marsupial taxa with vestigial digit 1 and gracile digits 2 and 3 (grooming claws).

Figure 2. Left: original restoration of Asioryctes pes. Colors added. Right: New restoration based on phylogenetic proximity to Perameles and other marsupial taxa with vestigial digit 1 and gracile digits 2 and 3 (grooming claws). 

The first three taxa
are members of the large reptile tree (LRT, 1272 taxa), but the first two don’t nest together. The LRT now nests Asioryctes with Perameles and Macrotis, two extant bandicoots. Ukhaatherium nests with the basalmost members of Theria several nodes earlier.

One of the problems with this
is the original restoration of the Asioryctes pes, based on disarticulated parts (Kielan-Jaworowska 1975; Fig. 2). The REAL problem is no other mammal has gracile lateral metatarsals. Sans the pes, the skull nests with Perameles and Macrotis (Fig. 1), taxa with only a vestige pedal digit 1 and reduced digits 2 and 3.

Hmmm.
That opens up a possibility not foreseen by Kielan-Jaworowska.

A new restoration
of the illustrated elements (Fig. 2) identifies the slender metatarsals as 2 and 3. The tarsal elements are all present (contra Kielan-Jaworowska 1975) just reidentified here in accord with a standard bandicoot foot.

And… so… for the first time
we can see a predecessor taxon demonstrating a transitional morphology to the reduced pedal digits 1–3 seen in bandicoots and kangaroos.

References
Geoffrey Saint-Hilaire E 1803. Note sur les genres Phascolomis et Perameles, nouveaux genres d’animaux à bourse. Bulletin des Sciences par la Société Philomathique de Paris 80, 49–150.
Kielan-Jaworowska Z 1975. 
Preliminary description of two new eutherian genera from the Late Cretaceous of Mongolia. Palaeontologia Polonica 33:5-15.
Kielan-Jaworowska, Z 1984. Evolution of the therian mammals in the Late Cretaceous of Asia. Part VII. Synopsis. Palaeontologia Polonica 4:173-183. online pdf
Maga AM and Beck RMD 2017. Skeleton of an unusual, cat-sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44-43 million years ago) of Turkey. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181712

wiki/Asioryctes
wiki/Perameles
wiki/Macrotis

Mammal taxa: size categories

A few days ago, we looked at a revised and expanded cladogram of the Mammalia based on skeletal traits (distinct from and contra to a cladogram based on DNA). Yesterday we looked at the deep time chronology of mammals. Today we add size categories to the cladogram to indicate Cope’s Rule (size increase over time) and phylogenetic miniaturization (size decrease over time, Fig. 1).

Looking at various mammal taxa size categories:

Figure 2. Subset of the LRT focusing on mammals. Color bars indicate size categories.

Figure 2. Subset of the LRT focusing on mammals. Color bars indicate size categories. The general trend is toward larger taxa with only a few phylogenetic miniaturization reversals.

Some notes:

  1. Mouse-sized taxa are typical at the origin of the Mammalia and the Metatheria (Marsupialia) with a few taxa growing to cat-sized. The few human-sized taxa are wolf-like or kangaroos. The two cow-sized metatherians are giant wombats.
  2. Cat-sized taxa are typical at the origin of the Eutheria (placentals). Larger taxa do not appear until after the large dinosaurs became extinct. Note: during the Mesozoic some large pre-mammals, like Repenomamus, remained.
  3. There are no elephant-sized prototheres or metatheres.
  4. There are no mouse-sized taxa more derived than Maelestes and close kin.
  5. Phylogenetic miniaturization attends the origin of mammals, the origin of the Hadrocodium clade, and after the glyptodonts. Little to no evidence of miniaturization appears at the origin of metatherians and eutherians. Slight evidence of miniaturization also appears at Ocepeia (pre mysticetes), Cainotherium (pre-artiodactyls) and Ectocion (pre-hyrax/elephant/siren).

Much earlier we looked at birth types (helpless vs. able) in a previous cladogram of the Mammalia that is as up-to-date as this one, but the point is made. We also briefly looked at the flexible spinal column of basal mammals vs. the less flexible spine of derived mammals.

Cladogram of the Mammalia (subset of the LRT)

A summary today…
featuring a long cladogram (Fig. 1), a subset from the large reptile tree (LRT, 1259 taxa) focusing on the Mammalia. This is how this LRT subset stands at present. Not much has changed other than the few node changes from the past week.

The transition from Prototheria to Theria (Metatheria)
includes long-snouted taxa, like Ukhaatherium. Nearly all Prototheria are also long-snouted (Cifelliodon is the current sole exception).

The transition from Metatheria to Eutheria (simplified)
includes small omnivorous didelphids arising from the carnivorous/herbivorous split among larger metatherians. Basal Carnivora, the most basal eutherian clade, are also omnivores. Caluromys, the extant wooly opossum, has a pouch, but nests at the base of all placental taxa (the LRT tests only skeletal traits), so it represents the size and shape of the earliest placentals (contra O’Leary et al. 2013)… basically didelphids without pouches, and fewer teeth, generally (but not always).

Basal members of most placental clades
are all Caluromys-like taxa, with a rapid radiation in the Late Triassic/Early Jurassic generating most of the major placental clades in the LRT (Fig. 1). Larger members of each of these placental clades appeared in the fossil record only after the K-T extinction event. So hardy where these basal taxa, that many still live to this day.

As shown earlier, higher eutheria are born able to able to walk or swim. They are no longer helpless with arboreal parents (tree-climbing goats the exception). Basal eutherians reproduce more like their metatherian ancestors, with helpless infants.

Figure 1. Subset of the LRT focusing on mammals.

Figure 1. Subset of the LRT focusing on mammals. Extant taxa are colored. Thylacinus is recently extinct.

The latest competing study
(O’Leary et al. 2013, Fig. 2) recovers the highly specialized edentates, aardvarks, elephants and elephant shrews as the most primitive placentals. Carnivora + bats are quite derived in the O’Leary team cladogram, somehow giving rise to ungulates and whales. This is an untenable hypothesis. It doesn’t make sense. Evidently the O’Leary team had faith that smaller didelphid-like ancestors would fill in the enormous phylogenetic gaps in their cladogram. By contrast the LRT has all the operational taxonomic units (OTUs) it needs to produce a series of gradually accumulating derived traits between every taxon in its chart (Fig. 1). The LRT makes sense.

Figure 5. Simplified version of the O'Leary et al 2013 cladogram showing placental relations exploded after the K-T boundary.

Figure 5. Simplified version of the O’Leary et al 2013 cladogram showing placental relations exploded after the K-T boundary.

References
O’Leary, MA et al. 2013. The placental mammal ancestor and the post-K-Pg radiation of  placentals. Science 339:662-667. abstract
Wible JR, Rougier GW, Novacek MJ, Asher RJ 2007. Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary Nature 447: 1003-1006

https://pterosaurheresies.wordpress.com/2016/08/31/another-look-at-the-oleary-et-al-hypothetical-ancestor-of-placentals/

https://pterosaurheresies.wordpress.com/2013/02/15/post-k-t-explosion-of-placentals-oleary-et-al-2013/

ArchibaldEtAl.pdf
protungulatum-donnae website

Apatemys revisited with DGS

Another short one today
in which the skull elements of Apatemys chardini (Marsh 1872, Eocene, Figs. 1, 2) are restored to their in vivo positions as determined by molar occlusion and jaw glenoid insertion.

Figure 1. Apatemys skull traced and reconstructed using color overlays (DGS).

Figure 1. Apatemys skull traced and reconstructed using color overlays (DGS). Yes, quite a bit of the mandible appears to be hidden beneath the broken coronoid process. 

Apatemys chardini (Marsh 1872, Eocene, 50-33 mya) was a squirrel-lke arboreal herbivore with a massive skull. Here it nests between the much larger Trogosus and the more plesiomorphic, Tupaia, a tree shrew. Apatemys had long slender fingers, a long flexible lumbar region, and a long gracile tail.

This taxon also gives rise to the shrew Scutisorex (check out the similar teeth, for instance), and the former tenrecs, Limnogale and Potamogale. All three are extant.

Figure 1. Apatemys, only complete fossil skeleton of an apatemyid, turns out to be a basal shrew. So this clade is not extinct.

Figure 2. Apatemys, only complete fossil skeleton of an apatemyid, turns out to be a squirrel-like  basal shrew. So this clade is not extinct. 

References
Marsh OC 1872. Preliminary description of new Tertiary mammals. Part II. American Journal of Science 4(21):202-224.

wiki/Apatemyidae