Convergence of Afrotherian and Laurasiatherian Ungulate-Like Mammals: First Morphological Evidence from the Paleocene of Morocco

Stripe and spot selection in cusp patterning of mammalian molar formation

Tooth development is governed largely by epithelial-mesenchymal interactions and is mediated by numerous signaling pathways. This type of morphogenetic processes has been explained by reaction-diffusion systems, especially in the framework of a Turing model. Here we focus on morphological and developmental differences between upper and lower molars in mice by modeling 2D pattern formation in a Turing system. Stripe vs. spot patterns are the primary types of variation in a Turing model. We show that the complexity of the cusp cross-sections can distinguish between stripe vs. spot patterns, and mice have stripe-like upper and spot-like lower molar morphologies. Additionally, our computational modeling that incorporates empirical data on tooth germ growth traces the order of cusp formation and relative position of the cusps in upper and lower molars in mice. We further propose a hypothetical framework of developmental mechanism that could help us understand the evolution of the highly variable nature of mammalian molars associated with the acquisition of the hypocone and the increase of lophedness.

Petrosal and bony labyrinth morphology of the stem paenungulate mammal (Paenungulatomorpha) Ocepeia daouiensis from the Paleocene of Morocco

Based on high-resolution computed tomography, we describe in detail the petrosal and inner ear anatomy of one of the few known African stem paenungulates (Paenungulatomorpha), Ocepeia daouiensis from the Selandian of the Ouled Abdoun phosphate basin (Morocco). The petrosal of Ocepeia displays some remarkable, probably derived features (among eutherians) such as relatively small pars cochlearis, pars canalicularis labyrinth (including small semicircular canals), a large wing-like pars mastoidea, a large and inflated tegmen tympani, and the dorsoventral orientation of the large canal for the ramus superior. The presence of small semicircular canals in Ocepeia is an interesting shared trait with tenrecoidean afrotherians. Otherwise, and consistent with a general primitive skull morphology, the middle ear and labyrinth of Ocepeia daouiensis is characterised by many plesiomorphic traits close to the eutherian generalised plan. This adds to the rather generalised morphology of the earliest crown paenungulates such as Eritherium, Phosphatherium and Seggeurius to support an ancestral paenungulatomorph morphotype poorly derived from the eutherian pattern. As a result, Ocepeia provides key morphological and fossil data to test phylogenetic relationships of the Afrotheria (including Paenungulatomorpha) at the placental root mostly inferred from molecular studies.

Out of Africa: A New Afrotheria Lineage Rises From Extinct South American Mammals

The South American native ungulates (SANUs) are usually overlooked in Eutherian phylogenetic studies. In the rare studies where they were included, the diversity of SANUs was underrated, keeping their evolutionary history poorly known. Some authors recognized the SANUs as a monophyletic lineage and formally named it Meridiungulata. Here, we recognized and defined a new supraordinal lineage of Eutheria, the Sudamericungulata, after performing morphological phylogenetic analyses including all lineages of SANUs and Eutheria. The SANUs resulted as non-monophyletic; thus, Meridiungulata is not a natural group; Litopterna and “Didolodontidae” are Panameriungulata and closer to Laurasiatheria than to other “Meridiungulata” (Astrapotheria, Notoungulata, Pyrotheria, and Xenungulata). The other “Meridiungulata” is grouped in the Sudamericungulata, as a new monophyletic lineage of Afrotheria Paenungulata, and shared a common ancestor with Hyracoidea. The divergence between the African and South American lineages is estimated to Early Paleocene, and their interrelationships support the Atlantogea biogeographic model. Shortly afterward, the Sudamericungulata explosively diversified in its four lineages. Confronting the Sudamericungulata evolutionary patterns and the Cenozoic natural events (such as tectonics and climatic and environmental changes, among others) helps to unveil a new chapter in the evolution of Gondwanan Eutheria, as well as the natural history of South America during the Cenozoic.

Developmental influence on evolutionary rates and the origin of placental mammal tooth complexity

Interactions during development among genes, cells, and tissues can favor the more frequent generation of some trait variants compared with others. This developmental bias has often been considered to constrain adaptation, but its exact influence on evolution is poorly understood. Using computer simulations of development, we provide evidence that molecules promoting the formation of mammalian tooth cusps could help accelerate tooth complexity evolution. Only relatively small developmental changes were needed to derive the more complex, rectangular upper molar typical of early placental mammals from the simpler triangular ancestral pattern. Development may therefore have enabled the relatively fast divergence of the early placental molar dentition.

Development has often been viewed as a constraining force on morphological adaptation, but its precise influence, especially on evolutionary rates, is poorly understood. Placental mammals provide a classic example of adaptive radiation, but the debate around rate and drivers of early placental evolution remains contentious. A hallmark of early dental evolution in many placental lineages was a transition from a triangular upper molar to a more complex upper molar with a rectangular cusp pattern better specialized for crushing. To examine how development influenced this transition, we simulated dental evolution on “landscapes” built from different parameters of a computational model of tooth morphogenesis. Among the parameters examined, we find that increases in the number of enamel knots, the developmental precursors of the tooth cusps, were primarily influenced by increased self-regulation of the molecular activator (activation), whereas the pattern of knots resulted from changes in both activation and biases in tooth bud growth. In simulations, increased activation facilitated accelerated evolutionary increases in knot number, creating a lateral knot arrangement that evolved at least ten times on placental upper molars. Relatively small increases in activation, superimposed on an ancestral tritubercular molar growth pattern, could recreate key changes leading to a rectangular upper molar cusp pattern. Tinkering with tooth bud geometry varied the way cusps initiated along the posterolingual molar margin, suggesting that small spatial variations in ancestral molar growth may have influenced how placental lineages acquired a hypocone cusp. We suggest that development could have enabled relatively fast higher-level divergence of the placental molar dentition.

Testing the occurrence of convergence in the craniomandibular shape evolution of living carnivorans

Convergence consists in the independent evolution of similar traits in distantly related species. The mammalian craniomandibular complex constitutes an ideal biological structure to investigate ecomorphological dynamics and the carnivorans, due to their phenotypic variability and ecological flexibility, offer an interesting case study to explore the occurrence of convergent evolution. Here, we applied multiple pattern‐based metrics to test the occurrence of convergence in the craniomandibular shape of extant carnivorans. To this aim, we tested for convergence in many dietary groups and analyzed several cases of carnivoran convergence concerning either ecologically equivalent species or ecologically similar species of different body sizes described in the literature. Our results validate the occurrence of convergence in ecologically equivalent species in a few cases (as well as in the case of giant and red pandas), but almost never support the occurrence of convergent evolution in dietary categories of living carnivorans. Therefore, convergent evolution in this clade appears to be a rare phenomenon. This is probably the consequence of a complex interplay of one‐to‐many, many‐to‐one, and many‐to‐many relationships taking place between ecology, biomechanics, and morphology.

A new early Eocene deperetellid tapiroid illuminates the origin of Deperetellidae and the pattern of premolar molarization in Perissodactyla

Deperetellidae is a clade of peculiar, Asian endemic tapiroids from the early and middle Eocene. The previously published material mainly comprises maxillae, mandibles, and some postcranial elements. However, the absence of cranial materials and primitive representatives of the deperetellids obscures their phylogenetic relationships within Tapiroidea. Furthermore, derived deperetellids have completely molarized premolars, but the pattern of their evolution remains unclear. Here, we report a nearly complete skull and some carpals of a new basal deperetellid tapiroid, Irenolophus qii gen. et sp. nov., from the late early Eocene of the Erlian Basin, Inner Mongolia, China. We suggest that deperetellids (along with Tapiridae) probably also arose from some basal 'helaletids', based on the reduced, flat, lingually depressed metacones on the upper molars, the trend towards the bilophodonty on the lower molars, and a shallow narial notch with the premaxilla in contact with the nasal. The molarization of the premolars in Deperetellidae from Irenolophus through Teleolophus to Deperetella was initiated and gradually enhanced by the separation between the paraconule and the protocone. That pattern differs from the protocone-hypocone separation in helaletids, tapirids, and most rhinoceroses, and the metaconule-derived pseudohypocone in amynodontids. However, the specific relationship of deperetellids within Tapiroidea and the roles of different patterns of premolar molarization in perissodactyl evolution need further and comprehensive study.

The phylogeny of desmostylians revisited: proposal of new clades based on robust phylogenetic hypotheses

Background

Desmostylia is a clade of extinct aquatic mammals with no living members. Today, this clade is considered belonging to either Afrotheria or Perissodactyla. In the currently-accepted taxonomic scheme, Desmostylia includes two families, 10 to 12 genera, and 13–14 species. There have been relatively few phylogenetic analyses published on desmostylian interrelationship compared to other vertebrate taxa, and two main, alternative phylogenetic hypotheses have been proposed in previous studies. One major problem with those previous studies is that the numbers of characters and OTUs were small.

Methods

In this study, we analyzed the phylogenetic interrelationship of Desmostylia based on a new data matrix that includes larger numbers of characters and taxa than in any previous studies. The new data matrix was compiled mainly based on data matrices of previous studies and included three outgroups and 13 desmostylian ingroup taxa. Analyses were carried out using five kinds of parsimonious methods.

Results

Strict consensus trees of the most parsimonious topologies obtained in all analyses supported the monophyly of Desmostylidae and paraphyly of traditional Paleoparadoxiidae. Based on these results, we propose phylogenetic definitions of the clades Desmostylidae and Paleoparadoxiidae based on common ancestry.

Improvements in the fossil record may largely resolve current conflicts between morphological and molecular estimates of mammal phylogeny

Phylogenies of mammals based on morphological data continue to show several major areas of conflict with the current consensus view of their relationships, which is based largely on molecular data. This raises doubts as to whether current morphological character sets are able to accurately resolve mammal relationships. We tested this under a hypothetical 'best case scenario' by using ancestral state reconstruction (under both maximum parsimony and maximum likelihood) to infer the morphologies of fossil ancestors for all clades present in a recent comprehensive DNA sequence-based phylogeny of mammals, and then seeing what effect the subsequent inclusion of these predicted ancestors had on unconstrained phylogenetic analyses of morphological data. We found that this resulted in topologies that are highly congruent with the current consensus phylogeny, at least when the predicted ancestors are assumed to be well preserved and densely sampled. Most strikingly, several analyses recovered the monophyly of clades that have never been found in previous morphology-only studies, such as Afrotheria and Laurasiatheria. Our results suggest that, at least in principle, improvements in the fossil record-specifically the discovery of fossil taxa that preserve the ancestral or near-ancestral morphologies of the nodes in the current consensus-may be sufficient to largely reconcile morphological and molecular estimates of mammal phylogeny, even using current morphological character sets.

Early African Fossils Elucidate the Origin of Embrithopod Mammals

Modern mammals rapidly evolved in the early Cenozoic in all continental provinces, including in Africa, with one of the first placental branches, the Afrotheria [1, 2]. Afrotherian evolution is at the origin of the major radiation of African ungulate-like mammals, including extant hyrax, elephant, and sea cow orders, which all belong to the Paenungulata. The paenungulate radiation also includes the extinct order Embrithopoda of uncertain interordinal relationships, which is best known for the giant and strangely specialized Oligocene genus Arsinoitherium. The Ouled Abdoun basin, Morocco, yielded exceptional Paleocene-Eocene fossils documenting the early paenungulate evolution [3-8]. Here we report two new small Ypresian species, Stylolophus minor n.g., n.sp. and cf. Stylolophus sp., which are the earliest and most primitive embrithopods. The cladistic analysis relates the Embrithopoda to crown paenungulates as the stem-group of the Tethytheria, which makes crown tethytherians restricted to extant elephant and sea cow orders. The Embrithopoda is therefore an early tethytherian offshoot predating the elephant and sea cow divergence. The resulting phylogeny supports a strictly African early radiation of the paenungulates excluding the Phenacolophidae and Anthracobunia. It sustains an at least early Paleocene African origin of the Embrithopoda. The unique tooth pattern of the embrithopods (hyperdilambdodont and pseudolophodont molars) is resolved as evolving early and directly from the dilambdodont (W-shaped labial molar crests) ancestral paenungulate morphotype. The specialized upper molar morphology with two transverse crests is convergent and non-homologous in embrithopods and crown Tethytheria. These convergences for specialized folivorous diet were driven by free herbivorous African niches in the early Paleogene.

Chitinase genes (CHIAs) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals

The end-Cretaceous extinction led to a massive faunal turnover, with placental mammals radiating in the wake of nonavian dinosaurs. Fossils indicate that Cretaceous stem placentals were generally insectivorous, whereas their earliest Cenozoic descendants occupied a variety of dietary niches. It is hypothesized that this dietary radiation resulted from the opening of niche space, following the extinction of dinosaurian carnivores and herbivores. We provide the first genomic evidence for the occurrence and timing of this dietary radiation in placental mammals. By comparing the genomes of 107 placental mammals, we robustly infer that chitinase genes (CHIAs), encoding enzymes capable of digesting insect exoskeletal chitin, were present as five functional copies in the ancestor of all placental mammals, and the number of functional CHIAs in the genomes of extant species positively correlates with the percentage of invertebrates in their diets. The diverse repertoire of CHIAs in early placental mammals corroborates fossil evidence of insectivory in Cretaceous eutherians, with descendant lineages repeatedly losing CHIAs beginning at the Cretaceous/Paleogene (K/Pg) boundary as they radiated into noninsectivorous niches. Furthermore, the timing of gene loss suggests that interordinal diversification of placental mammals in the Cretaceous predates the dietary radiation in the early Cenozoic, helping to reconcile a long-standing debate between molecular timetrees and the fossil record. Our results demonstrate that placental mammal genomes, including humans, retain a molecular record of the post-K/Pg placental adaptive radiation in the form of numerous chitinase pseudogenes.

Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades

Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia. Selection and timetree analyses further reveal that ucp1 inactivations temporally correspond with strong secondary reductions in metabolic intensity in xenarthrans and pangolins, or in six other lineages coincided with a ~30 million-year episode of global cooling in the Paleogene that promoted sharp increases in body mass and cladogenesis evident in the fossil record. Our findings also demonstrate that members of various lineages (for example, cetaceans, horses, woolly mammoths, Steller's sea cows) evolved extreme cold hardiness in the absence of UCP1-mediated thermogenesis. Finally, we identify ucp1 inactivation as a historical contingency that is linked to the current low species diversity of clades lacking functional UCP1, thus providing the first evidence for species selection related to the presence or absence of a single gene product.