Conflict Resolution for Mesozoic Mammals: Reconciling Phylogenetic Incongruence Among Anatomical Regions

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. Excluding these character complexes brought agreement between anatomical regions and improved the confidence in tree topology. These results emphasize the importance of considering and ameliorating major sources of bias in morphological data, and we anticipate that these will be valuable for confidently integrating morphological and molecular data in phylogenetic and dating analyses.

The making of calibration sausage exemplified by recalibrating the transcriptomic timetree of jawed vertebrates

“…Celik and Phillips (2020) called Juramaia “purportedly Jurassic” without comment and found middling support for a sister-group relationship to Theria as a whole, noting that this agreed with earlier doubts (e.g. by Sweetman et al, 2017).…”

“…While the oldest uncontested metatherians are only some 110 Ma old (Bi et al, 2018), Mao et al (2019: fig. S9) and Celik and Phillips (2020) have returned Sinodelphys (of the same age as Eomaia and Acristatherium , slightly younger than Ambolestes ) to its status as the oldest known metatherian. If this holds and if Juramaia has the same age instead of being Jurassic or is not a therian, and if further Durlstotherium and Durlstodon can be disregarded, virtually no ghost lineage is required at the base of Metatheria.…”

“…M), neither option having strong support by its own criteria; judging from the dashes in their fig. 2 and S1, Celik and Phillips (2020) may have found the same result using an improved version of the same matrix, but they did not publish their most parsimonious trees. For comparisons between the methods as applied to paleontological datasets, see the references cited under node 102 (above).…”

“…The phylogenetic position of Haramiyida, a clade that reaches beyond these ages into the Late Triassic, has been controversial; Celik and Phillips (2020) have presented a strong argument that it lies well outside Mammalia, which is one of the two positions found in previous analyses.…”

“…While the oldest uncontested metatherians are only some 110 Ma old (Bi et al, 2018), Mao et al (2019: fig. S9) and Celik and Phillips (2020) have returned Sinodelphys (of the same age as Eomaia and Acristatherium, slightly younger than Ambolestes) to its status as the oldest known metatherian.…”