Statistical estimates of hominin origination and extinction dates: A case study examining the Australopithecus anamensis–afarensis lineage

Using machine learning on new feature sets extracted from three-dimensional models of broken animal bones to classify fragments according to break agent

Distinguishing agents of bone modification at paleoanthropological sites is an important means of understanding early hominin evolution. Fracture pattern analysis is used to help determine site formation processes, including whether hominins were hunting or scavenging for animal food resources. Determination of how these behaviors manifested in ancient human sites has major implications for our biological and behavioral evolution, including social and cognitive abilities, dietary impacts of having access to in-bone nutrients like marrow, and cultural variation in butchering and food processing practices. Nevertheless, previous analyses remain inconclusive, often suffering from lack of replicability, misuse of mathematical methods, and/or failure to overcome equifinality. In this paper, we present a new approach aimed at distinguishing bone fragments resulting from hominin and carnivore breakage. Our analysis is founded on a large collection of scanned three-dimensional models of fragmentary bone broken by known agents, to which we apply state of the art machine learning algorithms. Our classification of fragments achieves an average mean accuracy of 77% across tests, thus demonstrating notable, but not overwhelming, success for distinguishing the agent of breakage. We note that, while previous research applying such algorithms has claimed higher success rates, fundamental errors in the application of machine learning protocols suggest that the reported accuracies are unjustified and unreliable. The systematic, fully documented, and proper application of machine learning algorithms leads to an inherent reproducibility of our study, and therefore our methods hold great potential for deciphering when and where hominins first began exploiting marrow and meat, and clarifying their importance and influence on human evolution.

Reappraising the palaeobiology of Australopithecus

The naming of Australopithecus africanus in 1925, based on the Taung Child, heralded a new era in human evolutionary studies and turned the attention of the then Eurasian-centric palaeoanthropologists to Africa, albeit with reluctance. Almost one hundred years later, Africa is recognized as the cradle of humanity, where the entire evolutionary history of our lineage prior to two million years ago took place-after the Homo-Pan split. This Review examines data from diverse sources and offers a revised depiction of the genus and characterizes its role in human evolution. For a long time, our knowledge of Australopithecus came from both A. africanus and Australopithecus afarensis, and the members of this genus were portrayed as bipedal creatures that did not use stone tools, with a largely chimpanzee-like cranium, a prognathic face and a brain slightly larger than that of chimpanzees. Subsequent field and laboratory discoveries, however, have altered this portrayal, showing that Australopithecus species were habitual bipeds but also practised arboreality; that they occasionally used stone tools to supplement their diet with animal resources; and that their infants probably depended on adults to a greater extent than what is seen in apes. The genus gave rise to several taxa, including Homo, but its direct ancestor remains elusive. In sum, Australopithecus had a pivotal bridging role in our evolutionary history owing to its morphological, behavioural and temporal placement between the earliest archaic putative hominins and later hominins-including the genus Homo.

An updated analysis of hominin phylogeny with an emphasis on re-evaluating the phylogenetic relationships of Australopithecus sediba

The discovery and description of Australopithecus sediba has reignited the debate over the evolutionary history of the australopiths and the genus Homo. It has been suggested that A. sediba may be an ancestor of Homo because it possesses a mosaic of derived Homo-like and primitive australopith-like traits. However, an alternative hypothesis proposes that the majority of the purported Homo-like craniodental characters can be attributed to the juvenile status of the type specimen, MH1. We conducted an independent character assessment of the craniodental morphology of A. sediba, with particular emphasis on evaluating whether the ontogenetic status of MH1 may have affected its purported Homo-like characteristics. In doing so, we have also expanded fossil hypodigms to incorporate the new Australopithecus anamensis cranium from Woranso-Mille (MRD-VP-1/1), as well as recently described Paranthropus robustus cranial remains from Drimolen (DNH 7, DNH 155). Morphological character data were analyzed using both standard parsimony and Bayesian techniques. In addition, we conducted a series of Bayesian analyses constrained to evaluate the hypothesis that Australopithecus africanus and A. sediba are sister taxa. Based on the results of the parsimony and Bayesian analyses, we could not reject the hypothesis that A. sediba shares its closest phylogenetic affinities with the genus Homo. Therefore, based on currently available craniodental evidence, we conclude that A. sediba is plausibly the terminal end of a lineage that shared a common ancestor with the earliest representatives of Homo. We caution, however, that the discovery of new A. sediba fossils preserving adult cranial morphology or the inclusion of postcranial characters may ultimately necessitate a re-evaluation of this hypothesis.

Hominins likely occupied northern Europe before one million years ago

Our understanding of when hominins first reached northern Europe is dependent on a fragmented archaeological and fossil record known from as early as marine isotope stage (MIS) 21 or 25 (c. 840 or 950 thousand years ago [Ka]). This contrasts sharply with southern Europe, where hominin occupation is evidenced from MIS 37 to 45 (c. 1.22 or 1.39 million years ago [Ma]). Northern Europe, however, exhibits climatic, geological, demographic, and historical disadvantages when it comes to preserving fossil and archaeological evidence of early hominin habitation. It is argued here that perceived differences in first occupation timings between the two European regions needs to be revised in light of these factors. To enhance this understanding, optimal linear estimation models are run using data from the current fossil and artefact record. Results suggest northern Europe to have first been occupied as early as 1.16 Ma, or as late as 913 Ka. These timings could represent minimum date expectations and be extended through future archaeological and fossil discoveries.

The Australopithecus assemblage from Sterkfontein Member 4 (South Africa) and the concept of variation in palaeontology

Interpreting morphological variation within the early hominin fossil record is particularly challenging. Apart from the fact that there is no absolute threshold for defining species boundaries in palaeontology, the degree of variation related to sexual dimorphism, temporal depth, geographic variation or ontogeny is difficult to appreciate in a fossil taxon mainly represented by fragmentary specimens, and such variation could easily be conflated with taxonomic diversity. One of the most emblematic examples in paleoanthropology is the Australopithecus assemblage from the Sterkfontein Caves in South Africa. Whereas some studies support the presence of multiple Australopithecus species at Sterkfontein, others explore alternative hypotheses to explain the morphological variation within the hominin assemblage. In this review, I briefly summarize the ongoing debates surrounding the interpretation of morphological variation at Sterkfontein Member 4 before exploring two promising avenues that would deserve specific attention in the future, that is, temporal depth and nonhuman primate diversity.

Baboon perspectives on the ecology and behavior of early human ancestors

For more than 70 y researchers have looked to baboons (monkeys of the genus Papio ) as a source of hypotheses about the ecology and behavior of early hominins (early human ancestors and their close relatives). This approach has undergone a resurgence in the last decade as a result of rapidly increasing knowledge from experimental and field studies of baboons and from archeological and paleontological studies of hominins. The result is a rich array of analogies, scenarios, and other stimuli to thought about the ecology and behavior of early hominins. The main intent here is to illustrate baboon perspectives on early hominins, with emphasis on recent developments. This begins with a discussion of baboons and hominins as we know them currently and explains the reasons for drawing comparisons between them. These include occupation of diverse environments, combination of arboreal and terrestrial capabilities, relatively large body size, and sexual dimorphism. The remainder of the paper illustrates the main points with a small number of examples drawn from diverse areas of interest: diet (grasses and fish), danger (leopards and crocodiles), social organization (troops and multilevel societies), social relationships (male–male, male–female, female–female), communication (possible foundations of language), cognition (use of social information, comparison of self to others), and bipedalism (a speculative developmental hypothesis about the neurological basis). The conclusion is optimistic about the future of baboon perspectives on early hominins.

Plio-Pleistocene environmental variability in Africa and its implications for mammalian evolution

We have developed an Africa-wide synthesis of paleoenvironmental variability over the Plio-Pleistocene. We show that there is strong evidence for orbital forcing of variability during this time that is superimposed on a longer trend of increasing environmental variability, supporting a combination of both low- and high-latitude drivers of variability. We combine these results with robust estimates of mammalian speciation and extinction rates and find that variability is not significantly correlated with these rates. These findings do not currently support a link between environmental variability and turnover and thus fail to corroborate predictions derived from the variability selection hypothesis.

Understanding the climatic drivers of environmental variability (EV) during the Plio-Pleistocene and EV’s influence on mammalian macroevolution are two outstanding foci of research in African paleoclimatology and evolutionary biology. The potential effects of EV are especially relevant for testing the variability selection hypothesis, which predicts a positive relationship between EV and speciation and extinction rates in fossil mammals. Addressing these questions is stymied, however, by 1) a lack of multiple comparable EV records of sufficient temporal resolution and duration, and 2) the incompleteness of the mammalian fossil record. Here, we first compile a composite history of Pan-African EV spanning the Plio-Pleistocene, which allows us to explore which climatic variables influenced EV. We find that EV exhibits 1) a long-term trend of increasing variability since ∼3.7 Ma, coincident with rising variability in global ice volume and sea surface temperatures around Africa, and 2) a 400-ky frequency correlated with seasonal insolation variability. We then estimate speciation and extinction rates for fossil mammals from eastern Africa using a method that accounts for sampling variation. We find no statistically significant relationship between EV and estimated speciation or extinction rates across multiple spatial scales. These findings are inconsistent with the variability selection hypothesis as applied to macroevolutionary processes.

Mosaic habitats at Woranso-Mille (Ethiopia) during the Pliocene and implications for Australopithecus paleoecology and taxonomic diversity

Many important Pliocene hominin specimens have been recovered from Woranso-Mille, a paleontological research area in the Afar region of Ethiopia, including the complete cranium of Australopithecus anamensis, a partial skeleton of Australopithecus afarensis, mandibular and maxillary elements representing a new species, Australopithecus deyiremeda, and a partial foot of an as-yet-unnamed species. Woranso-Mille is the only site, so far, to have reported the co-existence of more than one early hominin species between 3.8 and 3.3 Ma and the temporal overlap between A. anamensis and A. afarensis. Thus, the site has important implications for our understanding of the paleoecology and taxonomic diversity of early hominins and their ecological niche. This paper explores the paleohabitats of Woranso-Mille through its faunal community ecological structure and taxonomic composition using correspondence analysis and Forbes modified similarity index. The results suggest that Pliocene Woranso-Mille was a mosaic of different habitat types, with riparian woodland and floodplain grassland along rivers draining into a lake, along with less mesic habitats such as woodland, grassland, and shrubland. The apparent high level of vegetation heterogeneity may have promoted dietary specializations and niche differentiation among the different Australopithecus species at Woranso-Mille and allowed for their co-existence at the site.

Estimating origination times from the early hominin fossil record

The age of the earliest recovered fossil evidence of a hominin taxon is all too often equated with that taxon's origination. However, the earliest known fossil record nearly always postdates, sometimes by a substantial period of time, the true origination of a taxon. Here we evaluate the first appearance records of the earliest potential hominins (Sahelanthropus, Ardipithecus, Orrorin), as well as of the genera Australopithecus, Homo, and Paranthropus, to illustrate the considerable uncertainty regarding the actual timing of origin of these taxa. By placing confidence intervals on the first appearance records of early hominin taxa, we can better evaluate patterns of hominin diversity, turnover, and potential correlations with climatic and environmental changes.

Relative tooth size, Bayesian inference, and Homo naledi

OBJECTIVES

Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins.

MATERIALS AND METHODS

After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference.

RESULTS

Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo.

DISCUSSION

Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

Rethinking the ecological drivers of hominin evolution

A central goal of paleoanthropology is understanding the role of ecological change in hominin evolution. Over the past several decades researchers have expanded the hominin fossil record and assembled detailed late Cenozoic paleoclimatic, paleoenvironmental, and paleoecological archives. However, effective use of these data is precluded by the limitations of pattern-matching strategies for inferring causal relationships between ecological and evolutionary change. We examine several obstacles that have hindered progress, and highlight recent research that is addressing them by (i) confronting an incomplete fossil record, (ii) contending with datasets spanning varied spatiotemporal scales, and (iii) using theoretical frameworks to build stronger inferences. Expanding on this work promises to transform challenges into opportunities and set the stage for a new phase of paleoanthropological research.

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.

Statistical inference of earlier origins for the first flaked stone technologies

Identifying when hominins first produced Lomekwian, Oldowan, and Acheulean technologies is vital to multiple avenues of human origins research. Yet, like most archaeological endeavors, our understanding is currently only as accurate as the artifacts recovered and the sites identified. Here we use optimal linear estimation (OLE) modelling to identify the portion of the archaeological record not yet discovered, and statistically infer the date of origin of the earliest flaked stone technologies. These models provide the most accurate framework yet for understanding when hominins first produced these tool types. Our results estimate the Oldowan to have originated 2.617 to 2.644 Ma, 36,000 to 63,000 years earlier than current evidence. The Acheulean's origin is pushed back further through OLE, by at least 55,000 years to 1.815 to 1.823 Ma. We were unable to infer the Lomekwian's date of origin using OLE, but an upper bound of 5.1 million years can be inferred using alternative nonparametric techniques. These dates provide a new chronological foundation from which to understand the emergence of the first flaked stone technologies, alongside their behavioral and evolutionary implications. Moreover, they suggest there to be substantial portions of the artifact record yet to be discovered.