Célik and Phillips 2020 reshuffle basal mammal phylogeny by excluding traits (and taxa)

Célik and Phillips 2020 attempted to
understand the phylogenetic order of basal mammals by excluding traits. They wrote, “Excluding these character complexes brought agreement between anatomical regions and improved the confidence in tree topology.”

Those issues aside, taxon exclusion mars this study. 
The Célik and Phillips cladogram shuffled together unrelated taxa compared to the large reptile tree (LRT, 1737+ taxa). They cladogram (Fig. 1) mixed pre-mammals with placentals and marsupials chiefly due to taxon exclusion.

By employing so many taxa,
the LRT minimizes taxon exclusion and resolves such issues as the Multituberculata / Haramiyida problem. These taxa nest within Glires in the Placentalia in the LRT. Glires is not otherwise well represented in the Célik and Phillips cladogram.

Figure 1. Cladogram from Célik and Phillips 2020 with color overlay showing distribution of taxa in the LRT.

Figure 1. Cladogram from Célik and Phillips 2020 with color overlay showing distribution of taxa in the LRT.

From the abstract
“The evolutionary history of Mesozoic mammaliaformes is well studied. Although the backbone of their phylogeny is well resolved, the placement of ecologically specialized groups has remained uncertain. Functional and developmental covariation has long been identified as an important source of phylogenetic error, yet combining incongruent morphological characters altogether is currently a common practice when reconstructing phylogenetic relationships.”

“Ignoring incongruence may inflate the confidence in reconstructing relationships, particularly for the placement of highly derived and ecologically specialized taxa, such as among australosphenidans (particularly, crown monotremes), haramiyidans, and multituberculates. The alternative placement of these highly derived clades can alter the taxonomic constituency and temporal origin of the mammalian crown group.”

“Based on prior hypotheses and correlated homoplasy analyses, we identified cheek teeth and shoulder girdle character complexes as having a high potential to introduce phylogenetic error.

“We showed that incongruence among mandibulodental, cranial, and postcranial anatomical partitions for the placement of the australosphenidans, haramiyids, and multituberculates could largely be explained by apparently non-phylogenetic covariance from cheek teeth and shoulder girdle characters.”

Figure 1. Subset of the LRT focusing on basal placentals, including multituberculates.

Figure 3. Subset of the LRT focusing on basal placentals, including multituberculates.

Figure 3. Comparing multituberculate origins: Cziki-Sava et al. vs. LRT.

Figure 4. Comparing multituberculate origins: Cziki-Sava et al. vs. LRT.

Based on results recovered in the LRT,
I encourage Célik and Phillips to rerun their analysis with a far larger taxon list. A gradual accumulation of derived traits that mirrors evolutionary events will appear whenever taxon exclusion is minimized.


References
Célik MA and Phillips MJ 2020. Conflict Resolution for Mesozoic Mammals: Reconciling Phylogenetic Incongruence Among Anatomical Regions. Frontiers in Genetics 11: 0651
doi: 10.3389/fgene.2020.00651
https://www.frontiersin.org/articles/10.3389/fgene.2020.00651/full

Two papers in one: Haramiyidans and Juramaia

Part 1: King and Beck 2020
bring us their views (again), on ‘early mammal relationships‘. Let’s see how they stack up (again) against the validated (thanks to taxon inclusion) results of the large reptile tree (LRT, 1697+ taxa).

From their abstract:
“Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. Here, we apply Bayesian tip-dated phylogenetic methods [definition below] to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans.”

Bayesian tip-dated phylogenetic methods = online definition here.

You heard it here first
Earlier (2016) the LRT rejected a monophyletic Allotheria (separating Haramiavia (Fig. 1) and Thomasia), from Megaconus and all the multituberculates (Fig. 2). Haramiavia and Thomasia nest as pre-mammal synapsids (tritylodontids), not far from Pachygenelus. Several dozen nodes away, Megaconus and the multis nest within the placental clade Glires, at a node more highly derived than tree shrews, rodents and rabbits. So far that hypothesis of relationships has not been tested by other workers, despite several invitations to expand their taxon lists.

Figure 4. Haramiyava dentary showing what a more typical stem mammal dentary and teeth look like. Earlier studies linked this clade to multituberculates, but this dentary was cause to reject that association.

Figure 1. Haramiyava dentary showing what a more typical stem mammal dentary and teeth look like. Earlier studies linked this clade to multituberculates, but this dentary was cause to reject that association.

According to King and Beck 2020,
“Our analysis places Haramiyavia and Thomasia in a clade with tritylodontids, a result that may be the result of insufficient sampling of non-mammaliaform cynodont characters and taxa, and which we consider in need of further testing (see detailed discussion in the electronic supplementary material).” This confirms relationships first recovered by the LRT.

Figure 1. LRT taxa in the lineage of multituberculates arising from Carpolestes and Paulchoffatia.

Figure 2. LRT taxa in the lineage of multituberculates arising from Carpolestes and Paulchoffatia.

The authors continue,
“Our focal dataset was taken from Huttenlocker et al. 2018, which comprises 538 morphological characters scored for 125 mammaliaforms and non-mammaliaform cynodonts.

Unfortunately,
as I mentioned earlier, King and Beck still need to include extant mammals, like montoremes, marsupials, rodents and Daubentonia, rather than rely on fossil taxa exclusively. (See below).

Figure 1. Subset of the LRT focusing on Glires and subclades within.

Figure 3. Subset of the LRT focusing on Glires and subclades within.

Part 2: King and Beck 2020 report:
“A second taxon of interest is the eutherian Juramaia (Fig. 4) from the Middle–Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. We also test whether the Middle– Late Jurassic age of Juramaia is ‘expected’ given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia, but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age.”

Figure 2. Juramaia (Late Jurassic, 160 mya) is more completely known and nests between monotremes and therians (marsupials + placentals).

Figure 4. Juramaia (Late Jurassic, 160 mya) is more completely known and nests between monotremes and therians (marsupials + placentals).

By contrast In the LRT,
Juramaia is a basal protorothere, nesting between Megazostrodon + Sinodelphys and Chaoyangodens, all basal to the extant platypus and echidna in the LRT. Beck and King omit so many key taxa that they do not recover Prototheria, Metatheria and Eutheria.

The same authors publishing on a similar topic in 2019
were reviewed here. The following is one paragraph from that review: King and Beck 2019 bring us a new phylogenetic analysis restricted to Mesozoic mammals. This represents a massive case of taxon exclusion of basal mammals as demonstrated earlier here, because so many basal mammals are still alive! Think of all the tree shrews, arboreal didelphids, and nearly every little creeping taxon in Glires that nest basal to known Mesozoic mammals. You cannot restrict the taxon list to just those extremely rare Mesozoic mammals.

Colleagues: Please use extant mammals in your analyses!
They are guaranteed complete and articulated with soft tissues and gut contents. Figure out your cladogram with as many of these complete specimens as possible. Then… start adding crushed, incomplete and disarticulated fossil taxa. In other words, give yourself a basic education first. Establish a valid tree topology first. Don’t muddle through your studies with questionable traits based on fractured mandibles missing several teeth. As longtime readers know, a valid phylogenetic context is paramount for all further studies.


References
Huttenlocker AK, Grossnickle DM, Kirkland JI, Schultz JA and Luo Z-X 2018. Late-surviving stem mammal links the lowermost Cretaceous of North America and Gondwana. Nature 558, 108–112. 8. (doi:10.1038/s41586-018-0126-y);
King B and Beck R 2019. Bayesian Tip-dated Phylogenetics: Topological Effects, Stratigraphic Fit and the Early Evolution of Mammals. PeerJ
doi: http://dx.doi.org/10.1101/533885.
King B and Beck RMD 2020.
Tip dating supports novel resolutions of controversial relationships among early mammals. Proceedings of the Royal Society B 287: 20200943. http://dx.doi.org/10.1098/rspb.2020.0943

https://pterosaurheresies.wordpress.com/2019/02/07/taxon-exclusion-mars-mesozoic-mammal-study/

More evidence that euharamyidans are mislabeled Jurassic rodents

Figure 1. The Jurassic mammal Shenshou, which nests within Allotheria (Haramiyida + Mutituberculata) within the Mammalia, as I proposed based on the LRT without knowledge of this paper.

Figure 1. The Jurassic mammal Shenshou, which nests within Allotheria (Haramiyida + Mutituberculata) within the Mammalia, as I proposed based on the LRT without knowledge of this paper.

Euharamyidans include the squirrel-like Jurassic gliders
Shenshou (Figs. 1,2 ), Vilevolodon and Maiopatagium in the large reptile tree (LRT, 1265 taxa). These are sisters to the squirrel, Ratufa, the squirrel-like Paramys and two living rodents, Rattus and Mus (rat and mouse).

Mao et al. 2018 report, “The new evidence suggests presence of diphyodonty in euharamiyidans. While it will take time to amass data to resolve the discrepancy between competing phylogenetic hypotheses about ‘haramiyidans’, multituberculates, and/or allotherians, it is helpful to continue deepening our knowledge about the morphology of euharamiyidans. Our finding of potential diphyodonty in euharamiyidans provides an additional piece of evidence for mammalness of the peculiar group.”

Figure 2. Shenshou skull traced in colors.

Figure 2. Shenshou skull traced in colors.

Above:
The skull of Shenshou (Fig. 2), close to living squirrels. Evidently the molar cusps are convergent with those of Haramiyavia, but there are few other similarities.

Below:
Haramiyavia (Fig. 3), a pre-mammal cynodont with a small canine and large incisors not related to Shenshou. Note the dual articular/dentary jaw joint in Haramiyavia, missing (actually evolved into ear bones) in Shenshou. Such a jaw joint marks this taxon as a pre-mammal synapsid.

Figure 1. Haramiyavia reconstructed and restored. Missing parts are ghosted. Three slightly different originals are used for the base here. The last appears to be the least manipulated and it appears to fit the premaxilla better.  The fourth maxillary tooth appears to be a small canine. The groove on the dorsal premaxillary appears to be for the nasal, not the septomaxilla. Parts are taken from both mandibles

Figure 3. Haramiyavia reconstructed and restored. Missing parts are ghosted. Three slightly different originals are used for the base here. The last appears to be the least manipulated and it appears to fit the premaxilla better.  The fourth maxillary tooth appears to be a small canine. The groove on the dorsal premaxillary appears to be for the nasal, not the septomaxilla. Parts are taken from both mandibles

In the LRT, Haramyavia, a basal member of the Haramiyida
nests with other pre-mammals like Brasiliodon and Sinoconodon, hence: not related to euharamiyidans. Determining the clade based on traits (no matter what these traits may be) is the cause of the phylogenetic confusion based on tooth shape and replacement patterns, which can converge. Only a taxon’s placement on a cladogram can tell you what an animal really is. Sadly, that’s a current heresy, not widely appreciated.

According to Wikipedia
(ref below): Haramiyidans are a long lived lineage of mammaliaform cynodonts. Their teeth, which are by far the most common remains, resemble those of the multituberculates. However, based on Haramiyavia, the jaw is less derived; and at the level of evolution of earlier basal mammals like Morganucodon and Kuehneotherium, with a groove for ear ossicles on the dentary.[1] They are the longest lived mammalian clade of all time.”

As the LRT showed several years ago
the rodent-like Euharamiyidans (Fig. 1) nest with placental rodents in the clade Glires, not with the much more primitive pre-mammals like Haramiyavia (Fig. 3).

Mao et al. 2018 report, “presence of the diphyodont dentition alone is not diagnostic for mammals. This is because a diphyodont dentition exists not only in mammals but also in stem mammaliaforms, such as Morganucodon and docodonts, although there may be more than one replacement for the upper canine of Haldanodon (Martin et al., 2010b).”

By contrast, in the LRT
Morganucodon is a basal metatherian, not a stem mammaliaform. Which is one more reason why it has diphyodont dentition (milk teeth + permanent teeth). The late-surviving docodonts, Haldanodon and Castorocauda nest between the synapsids, Probainognathus and Pachygenelus in the LRT. Those four should be replacing all their teeth all the time. All four had a dual jaw joint that was not quite mammalian, but getting there!

Diphyodont dentition alone is diagnostic for mammals
because it implies toothless, milk-lapping/sucking hatchlings, (but be careful not to pull a Larry Martin here, because the LRT uses 231 traits and diphyodont dentition is not among them).

Among mammals
Mao et al. 2018 report, “tooth replacement is also complex among mammals. For instance, the molariform teeth of eutriconodonts show replacement and some species have the entire dentition replaced and show at least three tooth generations. Cheek tooth replacement is uncertain in “symmetrodontans”. In North American spalacotheriids deciduous canine and premolars were retained late in life and may never have been replaced; thus, their dentitions perhaps were monophyodont. This has been supported by the spalacolestine Lactodon from the Early Cretaceous Jehol Biota, in which there is no sign of cheek tooth replacement even though this taxon possesses deciduous-like antemolars. New CT scan data (unpublished) further confirmed that there is no tooth germ at any tooth locus, including incisors and canines, of Lactodon [= Lactodens”?]. Thus, presence of the diphyodonty in euharamiyidans, does not constitute a sufficient evidence for the group’s mammalian affinity.”

Let’s examine those arguments
in new light shed by the LRT.

  1. Eutriconodonts (Spinolestes, Gobiconodon and kin): These taxa do not nest within Mammalia in the LRT (contra Martin et al. 2015).
  2. Symmetrodontans (Zhangheotherium and kin): Zhangheotherium is a basal pangolin, hence the atavistic teeth, as in another placental clade, the archaeocete ‘whales’.
  3. Spalacotherids (Lactodon = Lactodens): Taxa like Lactodens nest within the prototheria in the LRT.

It always comes back down to phylogenetic analysis.
And the LRT answesr all such problems within its ken. The radiation of placental mammals was in the Early Jurassic based on the appearance of derived placental mammals in the Late Jurassic. Non-mammalian synapsids survived into the Middle Jurassic, so there was plenty of overlap.

Figure 4. Lactodens in situ. This Early Cretaceous protothere has tooth-lined jaws. At 72 dpi this is about 3x larger than life size.

Figure 4. Lactodens in situ. This Early Cretaceous protothere has tooth-lined jaws. At 72 dpi this is about 3x larger than life size.

PS. If you’re wondering about
Lactodens (= Lactodon; Fig. 4; Han and Meng 2018; Early Cretaceous) here it nests at the base of the echidna + platypus clade, two toothless (as adults) taxa. Perhaps that’s why the diphyodont dental rules start breaking down with this taxon, as described by Mao et al.

References
Mao F-Y et al. (5 co-authors) 2018. Evidence of diphyodonty and heterochrony for dental development in euharamiyidan mammals from Jurassic Yanliao Biota. Vertebrata PalAsiatica DOI: 10.19615/j.cnki.1000-3118.180803

https://en.wikipedia.org/wiki/Haramiyida