Plio-Pleistocene East African Pulsed Climate Variability and Its Influence on Early Human Evolution

The evolving three-dimensional landscape of human adaptation

Over the past 3 million years, humans have expanded their ecological niche and adapted to more diverse environments. The temporal evolution and underlying drivers behind this niche expansion remain largely unknown. By combining archeological findings with landscape topographic data and model simulations of the climate and biomes, we show that human sites clustered in areas with increased terrain roughness, corresponding to higher levels of biodiversity. We find a gradual increase in human habitat preferences toward rough terrains until about 1.1 million years ago (Ma), followed by a 300 thousand-year-long contraction of the ecological niche. This period coincided with the Mid-Pleistocene Transition and previously hypothesized ancestral population bottlenecks. Our statistical analysis further reveals that from 0.8 Ma onward, the human niche expanded again, with human species (e.g., H. heidelbergensis, H. neanderthalensis, and H. sapiens) adapting to rougher terrain, colder and drier conditions, and toward regions of higher ecological diversity.

Plant wax biomarkers in human evolutionary studies

Plant wax biomarkers are an innovative proxy for reconstructing vegetation composition and structure, rainfall intensity, temperature, and other climatic and environmental dynamics. Traditionally used in earth sciences and climate studies from "off-site" ocean and lake records, biomarker research is now incorporated in archeology and paleoanthropology to answer questions relating to past human-environment interactions and human evolution. Biomarker research is generating new and exciting information on the ecological context in which Homo and its closest relatives evolved, adapted, and invented stone tool technologies. In this review, we examine plant wax biomarkers and their use in reconstructing past plant landscapes and hydroclimates. We summarize the applications of plant wax molecular proxies in archeological research, assess challenges relating to taphonomy, consider the role of modern plant ecosystems in interpreting ancient habitats, and examine case studies conducted at key paleoanthropological locations in eastern and southern Africa and Europe.

Complexities of assessing palaeocave stratigraphy: reconstructing site formation of the ∼2.61 Ma Drimolen Makondo fossil site

Palaeocave sites in South Africa are world renowned repositories for palaeontological and archaeological material, dating from the terminal Pliocene to the Early Pleistocene. Due to their antiquity, complex karstification history and multifaceted infilling phases, palaeocave sites are notoriously difficult to contextualise. Further to this, 19th century lime-mining and diverse excavation and sampling techniques, have complicated stratigraphic interpretations of fossil-bearing deposits within the region. Locating and assessing newly discovered, minimally disturbed palaeocave sites allow for contextual information to be gathered with greater confidence and can aid in constructing a more robust understanding of the South African fossil record. Here, we use Drimolen Makondo; a minimally lime-mined ∼2.61 Ma palaeontological site, to apply a series of in-depth stratigraphic and micromorphological studies. Contextual data presented within this study, testifies to a relatively rapid infill with greater fluvial activity when compared to adjacent deposits at the younger ∼2.04-1.95 Ma Drimolen Main Quarry. The quantity of articulated macromammalian remains, high density of micromammalian remains and pollen identified, also highlights Drimolen Makondo as a key site for ongoing palaeoenvironmental studies at the Pliocene to Pleistocene transition in South Africa.

New mitogenomic lineages in Papio baboons and their phylogeographic implications

OBJECTIVES

Incomplete and/or biased sampling either on a taxonomic or geographic level can lead to delusive phylogenetic and phylogeographic inferences. However, a complete taxonomic and geographical sampling is often and for various reasons impossible, particularly for widespread taxa such as baboons (Papio spp.). Previous studies on baboon phylogeography identified several sampling gaps, some of which we fill by investigating additional material including samples from museum specimens.

MATERIALS AND METHODS

We generated 10 new mitochondrial genomes either via conventional PCR and subsequent Sanger sequencing from two blood samples or via high-throughput shotgun sequencing from degraded DNA extracted from eight museum specimens. Phylogenetic relationships and divergence times among baboon lineages were determined using maximum-likelihood and Bayesian inferences.

RESULTS

We identified new mitochondrial lineages in baboons from Central Africa (Chad, the Central African Republic), from the Mahale, and the Udzungwa Mountains (Tanzania), with the latter likely representing a case of mitochondrial capture from sympatric kipunjis (Rungwecebus kipunji). We also found that the mitochondrial clades of olive baboons found in Ivory Coast and Tanzania extend into Niger and the Democratic Republic of Congo, respectively. Moreover, an olive baboon from Sierra Leone carries a mitochondrial haplotype usually found in Guinea baboons, suggesting gene flow between these two species.

DISCUSSION

The extension of the geographic sampling by including samples from areas difficult to visit or from populations that are most likely extirpated has improved the geographic and temporal resolution of the mitochondrial phylogeny of baboons considerably. Our study also shows the great value of museum material for genetic analyses even when DNA is highly degraded.

Contemporaneity of Australopithecus, Paranthropus, and early Homo erectus in South Africa

Understanding the extinction of Australopithecus and origins of Paranthropus and Homo in South Africa has been hampered by the perceived complex geological context of hominin fossils, poor chronological resolution, and a lack of well-preserved early Homo specimens. We describe, date, and contextualize the discovery of two hominin crania from Drimolen Main Quarry in South Africa. At ~2.04 million to 1.95 million years old, DNH 152 represents the earliest definitive occurrence of Paranthropus robustus, and DNH 134 represents the earliest occurrence of a cranium with clear affinities to Homo erectus These crania also show that Homo, Paranthropus, and Australopithecus were contemporaneous at ~2 million years ago. This high taxonomic diversity is also reflected in non-hominin species and provides evidence of endemic evolution and dispersal during a period of climatic variability.

Multiple radiations of spiny mice (Rodentia: Acomys) in dry open habitats of Afro-Arabia: evidence from a multi-locus phylogeny

Background

Spiny mice of the genus Acomys are distributed mainly in dry open habitats in Africa and the Middle East, and they are widely used as model taxa for various biological disciplines (e.g. ecology, physiology and evolutionary biology). Despite their importance, large distribution and abundance in local communities, the phylogeny and the species limits in the genus are poorly resolved, and this is especially true for sub-Saharan taxa. The main aims of this study are (1) to reconstruct phylogenetic relationships of Acomys based on the largest available multilocus dataset (700 genotyped individuals from 282 localities), (2) to identify the main biogeographical divides in the distribution of Acomys diversity in dry open habitats in Afro-Arabia, (3) to reconstruct the historical biogeography of the genus, and finally (4) to estimate the species richness of the genus by application of the phylogenetic species concept.

Results

The multilocus phylogeny based on four genetic markers shows presence of five major groups of Acomys called here subspinosus, spinosissimus, russatus, wilsoni and cahirinus groups. Three of these major groups (spinosissimus, wilsoni and cahirinus) are further sub-structured to phylogenetic lineages with predominantly parapatric distributions. Combination of alternative species delimitation methods suggests the existence of 26 molecular operational taxonomic units (MOTUs), potentially corresponding to separate species. The highest genetic diversity was found in Eastern Africa. The origin of the genus Acomys is dated to late Miocene (ca. 8.7 Ma), when the first split occurred between spiny mice of eastern (Somali-Masai) and south-eastern (Zambezian) savannas. Further diversification, mostly in Plio-Pleistocene, and the current distribution of Acomys were influenced by the interplay of global climatic factors (e.g., Messinian salinity crisis, intensification of Northern Hemisphere glaciation) with local geomorphology (mountain chains, aridity belts, water bodies). Combination of divergence dating, species distribution modelling and historical biogeography analysis suggests repeated “out-of-East-Africa” dispersal events into western Africa, the Mediterranean region and Arabia.

Conclusions

The genus Acomys is very suitable model for historical phylogeographic and biogeographic reconstructions of dry non-forested environments in Afro-Arabia. We provide the most thorough phylogenetic reconstruction of the genus and identify major factors that influenced its evolutionary history since the late Miocene. We also highlight the urgent need of integrative taxonomic revision of east African taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1380-9) contains supplementary material, which is available to authorized users.

U-Pb-dated flowstones restrict South African early hominin record to dry climate phases

The Cradle of Humankind (Cradle) in South Africa preserves a rich collection of fossil hominins representing Australopithecus, Paranthropus and Homo¹. The ages of these fossils are contentious^2-4 and have compromised the degree to which the South African hominin record can be used to test hypotheses of human evolution. However, uranium-lead (U-Pb) analyses of horizontally bedded layers of calcium carbonate (flowstone) provide a potential opportunity to obtain a robust chronology⁵. Flowstones are ubiquitous cave features and provide a palaeoclimatic context, because they grow only during phases of increased effective precipitation^6,7, ideally in closed caves. Here we show that flowstones from eight Cradle caves date to six narrow time intervals between 3.2 and 1.3 million years ago. We use a kernel density estimate to combine 29 U-Pb ages into a single record of flowstone growth intervals. We interpret these as major wet phases, when an increased water supply, more extensive vegetation cover and at least partially closed caves allowed for undisturbed, semi-continuous growth of the flowstones. The intervening times represent substantially drier phases, during which fossils of hominins and other fossils accumulated in open caves. Fossil preservation, restricted to drier intervals, thus biases the view of hominin evolutionary history and behaviour, and places the hominins in a community of comparatively dry-adapted fauna. Although the periods of cave closure leave temporal gaps in the South African fossil record, the flowstones themselves provide valuable insights into both local and pan-African climate variability.

Progressive aridification in East Africa over the last half million years and implications for human evolution

Evidence for Quaternary climate change in East Africa has been derived from outcrops on land and lake cores and from marine dust, leaf wax, and pollen records. These data have previously been used to evaluate the impact of climate change on hominin evolution, but correlations have proved to be difficult, given poor data continuity and the great distances between marine cores and terrestrial basins where fossil evidence is located. Here, we present continental coring evidence for progressive aridification since about 575 thousand years before present (ka), based on Lake Magadi (Kenya) sediments. This long-term drying trend was interrupted by many wet-dry cycles, with the greatest variability developing during times of high eccentricity-modulated precession. Intense aridification apparent in the Magadi record took place between 525 and 400 ka, with relatively persistent arid conditions after 350 ka and through to the present. Arid conditions in the Magadi Basin coincide with the Mid-Brunhes Event and overlap with mammalian extinctions in the South Kenya Rift between 500 and 400 ka. The 525 to 400 ka arid phase developed in the South Kenya Rift between the period when the last Acheulean tools are reported (at about 500 ka) and before the appearance of Middle Stone Age artifacts (by about 320 ka). Our data suggest that increasing Middle- to Late-Pleistocene aridification and environmental variability may have been drivers in the physical and cultural evolution of Homo sapiens in East Africa.

Sporadic sampling, not climatic forcing, drives observed early hominin diversity

The role of climate change in the origin and diversification of early hominins is hotly debated. Most accounts of early hominin evolution link observed fluctuations in species diversity to directional shifts in climate or periods of intense climatic instability. None of these hypotheses, however, have tested whether observed diversity patterns are distorted by variation in the quality of the hominin fossil record. Here, we present a detailed examination of early hominin diversity dynamics, including both taxic and phylogenetically corrected diversity estimates. Unlike past studies, we compare these estimates to sampling metrics for rock availability (hominin-, primate-, and mammal-bearing formations) and collection effort, to assess the geological and anthropogenic controls on the sampling of the early hominin fossil record. Taxic diversity, primate-bearing formations, and collection effort show strong positive correlations, demonstrating that observed patterns of early hominin taxic diversity can be explained by temporal heterogeneity in fossil sampling rather than genuine evolutionary processes. Peak taxic diversity at 1.9 million years ago (Ma) is a sampling artifact, reflecting merely maximal rock availability and collection effort. In contrast, phylogenetic diversity estimates imply peak diversity at 2.4 Ma and show little relation to sampling metrics. We find that apparent relationships between early hominin diversity and indicators of climatic instability are, in fact, driven largely by variation in suitable rock exposure and collection effort. Our results suggest that significant improvements in the quality of the fossil record are required before the role of climate in hominin evolution can be reliably determined.

Modelling the role of groundwater hydro-refugia in East African hominin evolution and dispersal

Water is a fundamental resource, yet its spatiotemporal availability in East Africa is poorly understood. This is the area where most hominin first occurrences are located, and consequently the potential role of water in hominin evolution and dispersal remains unresolved. Here, we show that hundreds of springs currently distributed across East Africa could function as persistent groundwater hydro-refugia through orbital-scale climate cycles. Groundwater buffers climate variability according to spatially variable groundwater response times determined by geology and topography. Using an agent-based model, grounded on the present day landscape, we show that groundwater availability would have been critical to supporting isolated networks of hydro-refugia during dry periods when potable surface water was scarce. This may have facilitated unexpected variations in isolation and dispersal of hominin populations in the past. Our results therefore provide a new environmental framework in which to understand how patterns of taxonomic diversity in hominins may have developed.

Water is a fundamental resource, but its role in hominin evolution is not well explored. Here, the authors use a combination of groundwater, climate and agent-based models to show that groundwater availability may be critical to past patterns of taxonomic diversity in hominin development in East Africa.

A spring forward for hominin evolution in East Africa

Groundwater is essential to modern human survival during drought periods. There is also growing geological evidence of springs associated with stone tools and hominin fossils in the East African Rift System (EARS) during a critical period for hominin evolution (from 1.8 Ma). However it is not known how vulnerable these springs may have been to climate variability and whether groundwater availability may have played a part in human evolution. Recent interdisciplinary research at Olduvai Gorge, Tanzania, has documented climate fluctuations attributable to astronomic forcing and the presence of paleosprings directly associated with archaeological sites. Using palaeogeological reconstruction and groundwater modelling of the Olduvai Gorge paleo-catchment, we show how spring discharge was likely linked to East African climate variability of annual to Milankovitch cycle timescales. Under decadal to centennial timescales, spring flow would have been relatively invariant providing good water resource resilience through long droughts. For multi-millennial periods, modelled spring flows lag groundwater recharge by 100 s to 1000 years. The lag creates long buffer periods allowing hominins to adapt to new habitats as potable surface water from rivers or lakes became increasingly scarce. Localised groundwater systems are likely to have been widespread within the EARS providing refugia and intense competition during dry periods, thus being an important factor in natural selection and evolution, as well as a vital resource during hominin dispersal within and out of Africa.

Early human speciation, brain expansion and dispersal influenced by African climate pulses

Early human evolution is characterised by pulsed speciation and dispersal events that cannot be explained fully by global or continental paleoclimate records. We propose that the collated record of ephemeral East African Rift System (EARS) lakes could be a proxy for the regional paleoclimate conditions experienced by early hominins. Here we show that the presence of these lakes is associated with low levels of dust deposition in both West African and Mediterranean records, but is not associated with long-term global cooling and aridification of East Africa. Hominin expansion and diversification seem to be associated with climate pulses characterized by the precession-forced appearance and disappearance of deep EARS lakes. The most profound period for hominin evolution occurs at about 1.9 Ma; with the highest recorded diversity of hominin species, the appearance of Homo (sensu stricto) and major dispersal events out of East Africa into Eurasia. During this period, ephemeral deep-freshwater lakes appeared along the whole length of the EARS, fundamentally changing the local environment. The relationship between the local environment and hominin brain expansion is less clear. The major step-wise expansion in brain size around 1.9 Ma when Homo appeared was coeval with the occurrence of ephemeral deep lakes. Subsequent incremental increases in brain size are associated with dry periods with few if any lakes. Plio-Pleistocene East African climate pulses as evinced by the paleo-lake records seem, therefore, fundamental to hominin speciation, encephalisation and migration.

Dynamics of green Sahara periods and their role in hominin evolution

Astronomically forced insolation changes have driven monsoon dynamics and recurrent humid episodes in North Africa, resulting in green Sahara Periods (GSPs) with savannah expansion throughout most of the desert. Despite their potential for expanding the area of prime hominin habitats and favouring out-of-Africa dispersals, GSPs have not been incorporated into the narrative of hominin evolution due to poor knowledge of their timing, dynamics and landscape composition at evolutionary timescales. We present a compilation of continental and marine paleoenvironmental records from within and around North Africa, which enables identification of over 230 GSPs within the last 8 million years. By combining the main climatological determinants of woody cover in tropical Africa with paleoenvironmental and paleoclimatic data for representative (Holocene and Eemian) GSPs, we estimate precipitation regimes and habitat distributions during GSPs. Their chronology is consistent with the ages of Saharan archeological and fossil hominin sites. Each GSP took 2–3 kyr to develop, peaked over 4–8 kyr, biogeographically connected the African tropics to African and Eurasian mid latitudes, and ended within 2–3 kyr, which resulted in rapid habitat fragmentation. We argue that the well-dated succession of GSPs presented here may have played an important role in migration and evolution of hominins.