Perissodactyla (Rhinocerotidae and Equidae) from Kanapoi

Disruption of trait-environment relationships in African megafauna occurred in the middle Pleistocene

Mammalian megafauna have been critical to the functioning of Earth's biosphere for millions of years. However, since the Plio-Pleistocene, their biodiversity has declined concurrently with dramatic environmental change and hominin evolution. While these biodiversity declines are well-documented, their implications for the ecological function of megafaunal communities remain uncertain. Here, we adapt ecometric methods to evaluate whether the functional link between communities of herbivorous, eastern African megafauna and their environments (i.e., functional trait-environment relationships) was disrupted as biodiversity losses occurred over the past 7.4 Ma. Herbivore taxonomic and functional diversity began to decline during the Pliocene as open grassland habitats emerged, persisted, and expanded. In the mid-Pleistocene, grassland expansion intensified, and climates became more variable and arid. It was then that phylogenetic diversity declined, and the trait-environment relationships of herbivore communities shifted significantly. Our results divulge the varying implications of different losses in megafaunal biodiversity. Only the losses that occurred since the mid-Pleistocene were coincident with a disturbance to community ecological function. Prior diversity losses, conversely, occurred as the megafaunal species and trait pool narrowed towards those adapted to grassland environments.

Ancient and modern genomes unravel the evolutionary history of the rhinoceros family

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros

Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa's Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.

The environments of Australopithecus anamensis at Allia Bay, Kenya: A multiproxy analysis of early Pliocene Bovidae

Australopithecus anamensis, among the earliest fully bipedal hominin species, lived in eastern Africa around 4 Ma. Much of what is currently known about the paleoecology of A. anamensis comes from the type locality, Kanapoi, Kenya. Here, we extend knowledge of the range of environments occupied by A. anamensis by presenting the first multiproxy paleoecological analysis focusing on Bovidae excavated from another important locality where A. anamensis was recovered, locality 261-1 (ca. 3.97 Ma) at Allia Bay, East Turkana, Kenya. Paleoenvironments are reconstructed using astragalar ecomorphology, mesowear, hypsodonty index, and oxygen and carbon isotopes from dental enamel. We compare our results to those obtained from Kanapoi. Our results show that the bovid community composition is similar between the two fossil assemblages. Allia Bay and Kanapoi bovid astragalar ecomorphology spans the spectrum of modern morphologies indicative of grassland, woodland, and even forest-adapted forms. Dietary reconstructions based on stable isotopes, mesowear, and hypsodonty reveal that these bovids' diet encompassed the full C₃ to C₄ dietary spectrum and overlap in the two data sets. Our results allow us to confidently extend our reconstructions of the paleoenvironments of A. anamensis at Kanapoi to Allia Bay, where this pivotal hominin species is associated with heterogeneous settings including habitats with varying degrees of tree cover, including grasslands, bushlands, and woodlands.