Tip dating supports novel resolutions of controversial relationships among early mammals

Jurassic shuotheriids show earliest dental diversification of mammaliaforms

Shuotheriids are Jurassic mammaliaforms that possess pseudotribosphenic teeth in which a pseudotalonid is anterior to the trigonid in the lower molar, contrasting with the tribosphenic pattern of therian mammals (placentals, marsupials and kin) in which the talonid is posterior to the trigonid1-4. The origin of the pseudotribosphenic teeth remains unclear, obscuring our perception of shuotheriid affinities and the early evolution of mammaliaforms1,5-9. Here we report a new Jurassic shuotheriid represented by two skeletal specimens. Their complete pseudotribosphenic dentitions allow reidentification of dental structures using serial homology and the tooth occlusal relationship. Contrary to the conventional view1,2,6,10,11, our findings show that dental structures of shuotheriids can be homologized to those of docodontans and partly support homologous statements for some dental structures between docodontans and other mammaliaforms6,12. The phylogenetic analysis based on new evidence removes shuotheriids from the tribosphenic ausktribosphenids (including monotremes) and clusters them with docodontans to form a new clade, Docodontiformes, that is characterized by pseudotribosphenic features. In the phylogeny, docodontiforms and 'holotherians' (Kuehneotherium, monotremes and therians)13 evolve independently from a Morganucodon-like ancestor with triconodont molars by labio-lingual widening their posterior teeth for more efficient food processing. The pseudotribosphenic pattern passed a cusp semitriangulation stage9, whereas the tribosphenic pattern and its precursor went through a stage of cusp triangulation. The two different processes resulted in complex tooth structures and occlusal patterns that elucidate the earliest diversification of mammaliaforms.

The decline and fall of the mammalian stem

The mammalian crown originated during the Mesozoic and subsequently radiated into the substantial array of forms now extant. However, for about 100 million years before the crown's origin, a diverse array of stem mammalian lineages dominated terrestrial ecosystems. Several of these stem lineages overlapped temporally and geographically with the crown mammals during the Mesozoic, but by the end of the Cretaceous crown mammals make up the overwhelming majority of the fossil record. The progress of this transition between ecosystems dominated by stem mammals and those dominated by crown mammals is not entirely clear, in part due to a distinct separation of analyses and datasets. Analyses of macroevolutionary patterns tend to focus on either the Mammaliaformes or the non-mammalian cynodonts, with little overlap in the datasets, preventing direct comparison of the diversification trends. Here I analyse species richness and biogeography of Synapsida as a whole during the Mesozoic, allowing comparison of the patterns in the mammalian crown and stem within a single framework. The analysis reveals the decline of the stem mammals occurred in two discrete phases. The first phase occurred between the Triassic and Middle Jurassic, during which the stem mammals were more restricted in their geographic range than the crown mammals, although within localities their species richness remained at levels seen previously. The second phase was a decline in species richness, which occurred during the Lower Cretaceous. The results show the decline of stem mammals, including tritylodontids and several mammaliaform groups, was not tied to a specific event, nor a gradual decline, but was instead a multiphase transition.

Middle ear innovation in Early Cretaceous eutherian mammals

The middle ear ossicles in modern mammals are repurposed from postdentary bones in non-mammalian cynodonts. Recent discoveries by palaeontological and embryonic studies have developed different models for the middle ear evolution in mammaliaforms. However, little is known about the evolutionary scenario of the middle ear in early therians. Here we report a detached middle ear preserved in a new eutherian mammal from the Early Cretaceous Jehol Biota. The well-preserved articulation of the malleus and incus suggest that the saddle-shaped incudomallear joint is a major apomorphy of Early Cretaceous eutherians. By contrast to the distinct saddle-like incudomallear articulation in therians, differences between the overlapping versus the half-overlapping incudomallear joints in monotremes and stem mammals would be relatively minor. The middle ear belongs to the microtype by definition, indicating its adaptation to high-frequency hearing. Current evidence indicates that significant evolutionary innovations of the middle ear in modern therians evolved in Early Cretaceous.

Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches

There have been multiple published phylogenetic analyses of platyrrhine primates (New World monkeys) using both morphological and molecular data, but relatively few that have integrated both types of data into a total evidence approach. Here, we present phylogenetic analyses of recent and fossil platyrrhines, based on a total evidence data set of 418 morphological characters and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies, using undated and tip-dating approaches in a Bayesian framework. We compare the results of these analyses with molecular scaffold analyses using maximum parsimony and Bayesian approaches, and we use a formal information theoretic approach to identify unstable taxa. After a posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with recent molecular analyses and support largely similar relationships, with strong support for Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine, and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater Antilles. They also suggest that the fossil Proteropithecia may not be closely related to pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa. Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8-27.0 Ma) age for crown Platyrrhini, congruent with recent molecular clock analyses.

A new mammal from the Lower Cretaceous Jehol Biota and implications for eutherian evolution

Here we report on a new Early Cretaceous eutherian represented by a partial skeleton from the Jiufotang Formation at Sihedang site, Lingyuan City, Liaoning Province that fills a crucial gap between the earliest eutherians from the Yixian Formation and later Cretaceous eutherians. The new specimen reveals, to our knowledge for the first time in eutherians, that the Meckelian cartilage was ossified but reduced in size, confirming a complete detachment of the middle ear from the lower jaw. Seven hyoid elements, including paired stylohyals, epihyals and thyrohyals and the single basihyal are preserved. For the inner ear the ossified primary lamina, base of the secondary lamina, ossified cochlear ganglion and secondary crus commune are present and the cochlear canal is coiled through 360°. In addition, plesiomorphic features of the dentition include weak conules, lack of pre- and post-cingula and less expanded protocones on the upper molars and height differential between the trigonid and talonid, a large protoconid and a small paraconid on the lower molars. The new taxon displays an alternating pattern of tooth replacement with P3 being the last upper premolar to erupt similar to the basal eutherian Juramaia. Parsimony analysis places the new taxon with Montanalestes, Sinodelphys and Ambolestes as a sister group to other eutherians. This article is part of the theme issue 'The impact of Chinese palaeontology on evolutionary research'.

Distributions of extinction times from fossil ages and tree topologies: the example of mid-Permian synapsid extinctions

Given a phylogenetic tree that includes only extinct, or a mix of extinct and extant taxa, where at least some fossil data are available, we present a method to compute the distribution of the extinction time of a given set of taxa under the Fossilized-Birth-Death model. Our approach differs from the previous ones in that it takes into account (i) the possibility that the taxa or the clade considered may diversify before going extinct and (ii) the whole phylogenetic tree to estimate extinction times, whilst previous methods do not consider the diversification process and deal with each branch independently. Because of this, our method can estimate extinction times of lineages represented by a single fossil, provided that they belong to a clade that includes other fossil occurrences. We assess and compare our new approach with a standard previous one using simulated data. Results show that our method provides more accurate confidence intervals. This new approach is applied to the study of the extinction time of three Permo-Carboniferous synapsid taxa (Ophiacodontidae, Edaphosauridae, and Sphenacodontidae) that are thought to have disappeared toward the end of the Cisuralian (early Permian), or possibly shortly thereafter. The timing of extinctions of these three taxa and of their component lineages supports the idea that the biological crisis in the late Kungurian/early Roadian consisted of a progressive decline in biodiversity throughout the Kungurian.

The evolution of anteriorly directed molar occlusion in mammals

In non-mammalian synapsids and early mammals, evolutionary transformations in the feeding and hearing apparatuses are posited to have been prerequisites for the radiation of extant mammals. Unlike most vertebrates, including many early synapsids, mammals have precise dental occlusion, a lower jaw composed of one bone, and middle ear ossicles derived from ancestral jaw bones. We illuminate a related functional transition: therian mammals (eutherians and metatherians) evolved anteriorly directed chewing strokes, which are absent in other synapsid lineages. Anteriorly directed jaw movement during occlusion necessitates anteriorly directed muscle force vectors, and we posit that a shift in muscle orientation is reflected in the fossil record by the evolutionary appearance of a posteriorly positioned angular process in cladotherians (therians and their close kin). Anteriorly directed occlusion might have been absent in earlier synapsids because of the presence of attached middle ear elements in the posterior region of the jaw that prohibited the posterior insertion of jaw musculature. These changes to the masticatory apparatus in cladotherians are likely to have permitted the evolution of novel masticatory movements, including grinding in both the anterior and medial directions (e.g. rodents and ungulates, respectively). Thus, this evolutionary transition might have been a crucial prerequisite for the dietary diversification of therians.

Fossoriality and evolutionary development in two Cretaceous mammaliamorphs

Mammaliamorpha comprises the last common ancestor of Tritylodontidae and Mammalia plus all its descendants¹. Tritylodontids are nonmammaliaform herbivorous cynodonts that originated in the Late Triassic epoch, diversified in the Jurassic period^2-5 and survived into the Early Cretaceous epoch^6,7. Eutriconodontans have generally been considered to be an extinct mammalian group, although different views exist⁸. Here we report a newly discovered tritylodontid and eutriconodontan from the Early Cretaceous Jehol Biota of China. Eutriconodontans are common in this biota⁹, but it was not previously known to contain tritylodontids. The two distantly related species show convergent features that are adapted for fossorial life, and are the first 'scratch-diggers' known from this biota. Both species also show an increased number of presacral vertebrae, relative to the ancestral state in synapsids or mammals^10,11, that display meristic and homeotic changes. These fossils shed light on the evolutionary development of the axial skeleton in mammaliamorphs, which has been the focus of numerous studies in vertebrate evolution^12-17 and developmental biology^18-28. The phenotypes recorded by these fossils indicate that developmental plasticity in somitogenesis and HOX gene expression in the axial skeleton-similar to that observed in extant mammals-was already in place in stem mammaliamorphs. The interaction of these developmental mechanisms with natural selection may have underpinned the diverse phenotypes of body plan that evolved independently in various clades of mammaliamorph.

Jaw shape and mechanical advantage are indicative of diet in Mesozoic mammals

Jaw morphology is closely linked to both diet and biomechanical performance, and jaws are one of the most common Mesozoic mammal fossil elements. Knowledge of the dietary and functional diversity of early mammals informs on the ecological structure of palaeocommunities throughout the longest era of mammalian evolution: the Mesozoic. Here, we analyse how jaw shape and mechanical advantage of the masseter (MAM) and temporalis (MAT) muscles relate to diet in 70 extant and 45 extinct mammals spanning the Late Triassic-Late Cretaceous. In extant mammals, jaw shape discriminates well between dietary groups: insectivores have long jaws, carnivores intermediate to short jaws, and herbivores have short jaws. Insectivores have low MAM and MAT, carnivores have low MAM and high MAT, and herbivores have high MAM and MAT. These traits are also informative of diet among Mesozoic mammals (based on previous independent determinations of diet) and set the basis for future ecomorphological studies.