Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata

Molecular investigations have gathered a diverse set of mammals-predominantly African natives like elephants, hyraxes, and aardvarks-into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.

The virtual brain endocast of Trogosus (Mammalia, Tillodontia) and its relevance in understanding the extinction of archaic placental mammals

After successfully diversifying during the Paleocene, the descendants of the first wave of mammals that survived the end-Cretaceous mass extinction waned throughout the Eocene. Competition with modern crown clades and intense climate fluctuations may have been part of the factors leading to the extinction of these archaic groups. Why these taxa went extinct has rarely been studied from the perspective of the nervous system. Here, we describe the first virtual endocasts for the archaic order Tillodontia. Three species from the middle Eocene of North America were analyzed: Trogosus hillsii, Trogosus grangeri, and Trogosus castoridens. We made morphological comparisons with the plaster endocast of another tillodont, Tillodon fodiens, as well as groups potentially related to Tillodontia: Pantodonta, Arctocyonidae, and Cimolesta. Trogosus shows very little inter-specific variation with the only potential difference being related to the fusion of the optic canal and sphenorbital fissure. Many ancestral features are displayed by Trogosus, including an exposed midbrain, small neocortex, orbitotemporal canal ventral to rhinal fissure, and a broad circular fissure. Potential characteristics that could unite Tillodontia with Pantodonta, and Arctocyonidae are the posterior position of cranial nerve V3 exit in relation to the cerebrum and the low degree of development of the subarcuate fossa. The presence of large olfactory bulbs and a relatively small neocortex are consistent with a terrestrial lifestyle. A relatively small neocortex may have put Trogosus at risk when competing with artiodactyls for potentially similar resources and avoiding predation from archaic carnivorans, both of which are known to have had larger relative brain and neocortex sizes in the Eocene. These factors may have possibly exacerbated the extinction of Tillodontia, which showed highly specialized morphologies despite the increase in climate fluctuations throughout the Eocene, before disappearing during the middle Eocene.

Brawn before brains in placental mammals after the end-Cretaceous extinction

Mammals are the most encephalized vertebrates, with the largest brains relative to body size. Placental mammals have particularly enlarged brains, with expanded neocortices for sensory integration, the origins of which are unclear. We used computed tomography scans of newly discovered Paleocene fossils to show that contrary to the convention that mammal brains have steadily enlarged over time, early placentals initially decreased their relative brain sizes because body mass increased at a faster rate. Later in the Eocene, multiple crown lineages independently acquired highly encephalized brains through marked growth in sensory regions. We argue that the placental radiation initially emphasized increases in body size as extinction survivors filled vacant niches. Brains eventually became larger as ecosystems saturated and competition intensified.

The impact of locomotion on the brain evolution of squirrels and close relatives

How do brain size and proportions relate to ecology and evolutionary history? Here, we use virtual endocasts from 38 extinct and extant rodent species spanning 50+ million years of evolution to assess the impact of locomotion, body mass, and phylogeny on the size of the brain, olfactory bulbs, petrosal lobules, and neocortex. We find that body mass and phylogeny are highly correlated with relative brain and brain component size, and that locomotion strongly influences brain, petrosal lobule, and neocortical sizes. Notably, species living in trees have greater relative overall brain, petrosal lobule, and neocortical sizes compared to other locomotor categories, especially fossorial taxa. Across millions of years of Eocene-Recent environmental change, arboreality played a major role in the early evolution of squirrels and closely related aplodontiids, promoting the expansion of the neocortex and petrosal lobules. Fossoriality in aplodontiids had an opposing effect by reducing the need for large brains.

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size.

Brain evolution in Proboscidea (Mammalia, Afrotheria) across the Cenozoic

As the largest and among the most behaviourally complex extant terrestrial mammals, proboscideans (elephants and their extinct relatives) are iconic representatives of the modern megafauna. The timing of the evolution of large brain size and above average encephalization quotient remains poorly understood due to the paucity of described endocranial casts. Here we created the most complete dataset on proboscidean endocranial capacity and analysed it using phylogenetic comparative methods and ancestral character states reconstruction using maximum likelihood. Our analyses support that, in general, brain size and body mass co-evolved in proboscideans across the Cenozoic; however, this pattern appears disrupted by two instances of specific increases in relative brain size in the late Oligocene and early Miocene. These increases in encephalization quotients seem to correspond to intervals of important climatic, environmental and faunal changes in Africa that may have positively selected for larger brain size or body mass.

Light and scanning electron microscopy of the olfactory mucosa in the rufous sengi (Elephantulus rufescens)

Sengis are eutherian insectivores belonging to superorder Afrotheria, a recently defined clade of mammals that diverged from other placentals over 100 million years ago. In this study, a histological and ultrastructural analysis was carried out on the olfactory mucosa (OM) of the rufous sengi (Elephantulus rufescens) and the data were compared with those reported earlier in the dog (Canis familiaris) and the sheep (Ovis aries), whose dietary lifestyles are carnivorous and herbivorous, respectively. Qualitatively, the microstructure of the sengi's OM was basically similar to that of the other eutherian mammals except for differences in the pattern of cilia projection from the dendritic knobs of the olfactory receptor neurons (ORNs) and distribution of Bowman's glands within the lamina propria of the OM. On morphometry, significant differences (p < .05) were recorded with respect to olfactory epithelial (OE) thickness between the sengi (65.4 ± 2.6 μm) and the other species. ORN packing density and cilia number/ORN knob varied markedly only between the sengi (73.8 ± 5.4 mm^-2  × 10³ and 15 ± 4, respectively) and the sheep. No remarkable differences were noted in regard to ORN bundle diameters between sengis (62.7 ± 12.5 μm) and the other species. The observed differences in OM structural refinement may be attributed to olfactory function demand levels related to feeding lifestyles and ecology. Myrmecophagous insectivory, social monogamy, absentee maternal care and exposed sheltering habits are behavioural features that may warrant substantial OM modification in sengis.

Synchrotron scanning reveals the palaeoneurology of the head-butting Moschops capensis (Therapsida, Dinocephalia)

Dinocephalian therapsids are renowned for their massive, pachyostotic and ornamented skulls adapted for head-to-head fighting during intraspecific combat. Synchrotron scanning of the tapinocephalid Moschops capensis reveals, for the first time, numerous anatomical adaptations of the central nervous system related to this combative behaviour. Many neural structures (such as the brain, inner ear and ophthalmic branch of the trigeminal nerve) were completely enclosed and protected by bones, which is unusual for non-mammaliaform therapsids. The nearly complete ossification of the braincase enables precise determination of the brain cavity volume and encephalization quotient, which appears greater than expected for such a large and early herbivore. The practice of head butting is often associated with complex social behaviours and gregariousness in extant species, which are known to influence brain size evolution. Additionally, the plane of the lateral (horizontal) semicircular canal of the bony labyrinth is oriented nearly vertically if the skull is held horizontally, which suggests that the natural position of the head was inclined about 60–65°to the horizontal. This is consistent with the fighting position inferred from osteology, as well as ground-level browsing. Finally, the unusually large parietal tube may have been filled with thick conjunctive tissue to protect the delicate pineal eye from injury sustained during head butting.

The mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) compared with the brain of the extant African elephant (Loxodonta africana)

This study presents the results of an examination of the mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) recovered from the Yakutian permafrost in Siberia, Russia. This unique specimen (from 39,440-38,850 years BP) provides the rare opportunity to compare the brain morphology of this extinct species with a related extant species, the African elephant (Loxodonta africana). An anatomical description of the preserved brain of the woolly mammoth is provided, along with a series of quantitative analyses of various brain structures. These descriptions are based on visual inspection of the actual specimen as well as qualitative and quantitative comparison of computed tomography imaging data obtained for the woolly mammoth in comparison with magnetic resonance imaging data from three African elephant brains. In general, the brain of the woolly mammoth specimen examined, estimated to weigh between 4,230 and 4,340 g, showed the typical shape, size, and gross structures observed in extant elephants. Quantitative comparative analyses of various features of the brain, such as the amygdala, corpus callosum, cerebellum, and gyrnecephalic index, all indicate that the brain of the woolly mammoth specimen examined has many similarities with that of modern African elephants. The analysis provided here indicates that a specific brain type representative of the Elephantidae is likely to be a feature of this mammalian family. In addition, the extensive similarities between the woolly mammoth brain and the African elephant brain indicate that the specializations observed in the extant elephant brain are likely to have been present in the woolly mammoth.