Biogeographic and Evolutionary Implications of an Extinct Late Pleistocene Impala from the Lake Victoria Basin, Kenya

Estimation of site frequency spectra from low-coverage sequencing data using stochastic EM reduces overfitting, runtime, and memory usage

The site frequency spectrum is an important summary statistic in population genetics used for inference on demographic history and selection. However, estimation of the site frequency spectrum from called genotypes introduces bias when working with low-coverage sequencing data. Methods exist for addressing this issue but sometimes suffer from 2 problems. First, they can have very high computational demands, to the point that it may not be possible to run estimation for genome-scale data. Second, existing methods are prone to overfitting, especially for multidimensional site frequency spectrum estimation. In this article, we present a stochastic expectation-maximization algorithm for inferring the site frequency spectrum from NGS data that address these challenges. We show that this algorithm greatly reduces runtime and enables estimation with constant, trivial RAM usage. Furthermore, the algorithm reduces overfitting and thereby improves downstream inference. An implementation is available at github.com/malthesr/winsfs.

A Late Pleistocene human humerus from Rusinga Island, Lake Victoria, Kenya

In 2010, a hominin right humerus fragment (KNM-RU 58330) was surface collected in a small gully at Nyamita North in the Late Pleistocene Wasiriya Beds of Rusinga Island, Kenya. A combination of stratigraphic and geochronological evidence suggests the specimen is likely between ∼49 and 36 ka in age. The associated fauna is diverse and dominated by semiarid grassland taxa. The small sample of associated Middle Stone Age artifacts includes Levallois flakes, cores, and retouched points. The 139 mm humeral fragment preserves the shaft from distal to the lesser tubercle to 14 mm below the distal end of the weakly projecting deltoid tuberosity. Key morphological features include a narrow and weakly marked pectoralis major insertion and a distinctive medial bend in the diaphysis at the deltoid insertion. This bend is unusual among recent human humeri but occurs in a few Late Pleistocene humeri. The dimensions of the distal end of the fragment predict a length of 317.9 ± 16.4 mm based on recent samples of African ancestry. A novel method of predicting humeral length from the distance between the middle of the pectoralis major and the bottom of the deltoid insertion predicts a length of 317.3 mm ± 17.6 mm. Cross-sectional geometry at the midshaft shows a relatively high percentage of cortical bone and a moderate degree of flattening of the shaft. The Nyamita humerus is anatomically modern in its morphology and adds to the small sample of hominins from the Late Pleistocene associated with Middle Stone Age artifacts known from East Africa. It may sample a population closely related to the people of the out-of-Africa migration.

Evaluating the potential for tactical hunting in the Middle Stone Age: Insights from a bonebed of the extinct bovid, Rusingoryx atopocranion

The foraging behaviors of Middle Stone Age (MSA) early modern humans have largely been based on evidence from well-stratified cave sites in South Africa. Whereas these sites have provided an abundance of data for behavioral reconstruction that are unmatched elsewhere in Africa, they are unlikely to preserve evidence of the diversity of foraging strategies employed by MSA hunters who lived in a variety of ecological and landscape settings across the African continent. Here we describe the results of recent excavations at the open-air site of Bovid Hill at Wakondo, Rusinga Island, Kenya, which yielded 24 in situ MSA artifacts within an assemblage of bones comprised exclusively of the extinct alcelaphin bovid Rusingoryx atopocranion. The excavated faunal assemblage is characterized by a prime-age-dominated mortality profile and includes cut-marked specimens and an associated MSA Levallois blade-based artifact industry recovered from a channel deposit dated to 68 ± 5 ka by optically stimulated luminescence. Taphonomic, geologic, and faunal evidence points to mass exploitation of Rusingoryx by humans at Bovid Hill, which likely represents an initial processing site that was altered post-depositionally by fluvial processes. This site highlights the importance of rivers and streams for mass procurement in an open and seasonal landscape, and provides important new insights into MSA behavioral variability with respect to environmental conditions, site function, and tactical foraging strategies in eastern Africa. Bovid Hill thus joins a growing number of MSA and Middle Paleolithic localities that are suggestive of tactical hunting behaviors and mass capture of gregarious ungulate prey.

Continuous evolutionary change in Plio-Pleistocene mammals of eastern Africa

Much debate has revolved around the question of whether the mode of evolutionary and ecological turnover in the fossil record of African mammals was continuous or pulsed, and the degree to which faunal turnover tracked changes in global climate. Here, we assembled and analyzed large specimen databases of the fossil record of eastern African Bovidae (antelopes) and Turkana Basin large mammals. Our results indicate that speciation and extinction proceeded continuously throughout the Pliocene and Pleistocene, as did increases in the relative abundance of arid-adapted bovids, and in bovid body mass. Species durations were similar among clades with different ecological attributes. Occupancy patterns were unimodal, with long and nearly symmetrical origination and extinction phases. A single origination pulse may be present at 2.0-1.75 Ma, but besides this, there is no evidence that evolutionary or ecological changes in the eastern African record tracked rapid, 100,000-y-scale changes in global climate. Rather, eastern African large mammal evolution tracked global or regional climatic trends at long (million year) time scales, while local, basin-scale changes (e.g., tectonic or hydrographic) and biotic interactions ruled at shorter timescales.

Stable isotope paleoecology of Late Pleistocene Middle Stone Age humans from the Lake Victoria basin, Kenya

Paleoanthropologists have long argued that environmental pressures played a key role in human evolution. However, our understanding of how these pressures mediated the behavioral and biological diversity of early modern humans and their migration patterns within and out of Africa is limited by a lack of archaeological evidence associated with detailed paleoenvironmental data. Here, we present the first stable isotopic data from paleosols and fauna associated with Middle Stone Age (MSA) sites in East Africa. Late Pleistocene (∼100-45 ka, thousands of years ago) sediments on Rusinga and Mfangano Islands in eastern Lake Victoria (Kenya) preserve a taxonomically diverse, non-analog faunal community associated with MSA artifacts. We analyzed the stable carbon and oxygen isotope composition of paleosol carbonate and organic matter and fossil mammalian tooth enamel, including the first analyses for several extinct bovids such as Rusingoryx atopocranion, Damaliscus hypsodon, and an unnamed impala species. Both paleosol carbonate and organic matter data suggest that local habitats associated with human activities were primarily riverine woodland ecosystems. However, mammalian tooth enamel data indicate that most large-bodied mammals consumed a predominantly C4 diet, suggesting an extensive C4 grassland surrounding these riverine woodlands in the region at the time. These data are consistent with other lines of paleoenvironmental evidence that imply a substantially reduced Lake Victoria at this time, and demonstrate that C4 grasslands were significantly expanded into equatorial Africa compared with their present distribution, which could have facilitated dispersal of human populations and other biotic communities. Our results indicate that early populations of Homo sapiens from the Lake Victoria region exploited locally wooded and well-watered habitats within a larger grassland ecosystem.