More and more human genomic data has become available in recent years by the improvement of DNA sequencing technologies. These data provide abundant genetic variation information which is an important resource to help us to understand the evolutionary history of humans. In this thesis I evaluated the performance of the Approximate Bayesian Computation (ABC) approach for inferring demographic parameters for large-scale population genomic data. According to simulation results, I can conclude that the ABC approach will continue to be a useful tool for analysing realistic genome-wide population-genetic data in the post-genomic era. Secondly, I implemented the ABC approach to estimate the pre-historic events connected with the “Bantu-expansion”, the spread of peoples from West Africa. The analysis based on genetic data with a large number of loci support a rapid population growth in west Africans, which lead to their concomitant spread to southern and eastern Africa. Contrary to hypotheses based on language studies, I found that Bantu-speakers in south Africa likely migrated directly from west Africa, and not from east Africa. Thirdly, I evaluated Thomson's estimator of the time to most recent common ancestor (TMRCA). It is robust to different recombination rates and the least-biased compared to other commonly used approaches. I used the Thomson estimator to infer the genome-wide distribution of TMRCA for complete human genome sequence data in various populations from across the world and compare the result to simulated data. Finally, I investigated and analysed the effects of selection and demography on genetic polymorphism patterns. In particular, we could detect a clear signal in the distribution of TMRCA caused by selection for a constant-size population. However, if the population was growing, the signal of selection will be difficult to detect under some circumstances. I also discussed and gave a few suggestions that might lead to a more realistic path of successful identification of genes targeted by selection in large-scale genomic data.

Population Genetics has led to countless numbers of fruitful studies of evolution, due to its abilities for prediction and description of the most important evolutionary processes such as mutation, genetic drift and selection. The field is still growing today, with new methods and models being developed to answer questions of evolutionary relevance and to lift the veil on the past of all life forms. In this thesis, I present a modest contribution to the growth of population genetics. I investigate different questions related to the dynamics of populations, with particular focus on studying human evolution. I derive an upper bound and a lower bound for FST, a classical measure of population differentiation, as functions of the homozygosity in each of the two studied populations, and apply the result to discuss observed differentiation levels between human populations. I introduce a new criterion, the Gain of Informativeness for Assignment, to help us decide whether two genetic markers should be combined into a haplotype marker and improve the assignment of individuals to a panel of reference populations. Applying the method on SNP data for French, German and Swiss individuals, I show how haplotypes can lead to better assignment results when they are supervised by GIA. I also derive the population size over time as a function of the densities of cumulative coalescent times, show the robustness of this result to the number of loci as well as the sample size, and together with a simple algorithm of gene-genealogy inference, apply the method on low recombining regions of the human genome for four worldwide populations. I recover previously observed population size shapes, as well as uncover an early divergence of the Yoruba population from the non-African populations, suggesting ancient population structure on the African continent prior to the Out-of-Africa event. Finally, I present a case study of human adaptation to an arsenic-rich environment.

Key insights into the evolutionary origins of human social behavior can be gained via study of our closest living relatives, bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Despite being equally related to humans, these two species differ importantly in aspects of their morphology, physiology, behavior, and cognition. Morphological comparisons reveal numerous traits in bonobos that can be viewed as paedomorphic, or juvenile, relative to chimpanzees. Meanwhile, comparisons of endocrinology in the two species suggest that aspects of steroid physiology have changed significantly in bonobos in line with their reductions in male mating competition. Based on this evidence, I tested the hypothesis that behavioral and cognitive differences between bonobos and chimpanzees derive from changes in their 1) developmental trajectories of behavioral and cognitive traits and 2) neuroendocrine influences on behavior and cognition. I tested this hypothesis by studying semi free-ranging populations of bonobos and chimpanzees. First, I found that bonobos retained juvenile levels of food sharing and social inhibition into adulthood, leading them to differ from chimpanzees in these traits as adults. Second, I found that bonobos showed muted elevations in their levels of testosterone from infancy to adulthood in comparison to chimpanzees, suggesting that numerous aspects of development differ between these two species. Third, I found that male bonobos and chimpanzees differ in their immediate neuroendocrine shifts surrounding competition, implicating changes in proximate mechanisms influencing social behavior between the two species. Fourth, I found that patterns of cognitive development in these two apes differed significantly from those of human children. These results provide substantial support for my hypothesis that phenotypic differences between bonobos and chimpanzees evolved via shifts in bonobo development and neuroendocrine physiology. More broadly, they illustrate how behavioral and cognitive evolution can occur through changes in ontogenetic trajectories and neuroendocrine mechanisms. These findings thus show the merits of integrating ultimate and proximate levels of analysis in studies of the evolution of human behavior and cognition. / Human Evolutionary Biology

Throwing with power and accuracy is a uniquely human behavior and a potentially important mode of early hunting. Chimpanzees, our closest living relatives, do occasionally throw, although with much less velocity. At some point in our evolutionary history, hominins developed the ability to produce high performance throws. The anatomical changes that enable increased throwing ability are poorly understood and the antiquity of this behavior is unknown. In this thesis, I examine how anatomical shifts in the upper body known to occur during human evolution affect throwing performance. I propose a new biomechanical model for how humans amplify power during high-speed throwing using elastic energy stored and released in the throwing shoulder. I also propose and experimentally test a series of functional hypotheses regarding how four key shifts in upper body anatomy affect throwing performance: increased torso rotational mobility, laterally oriented shoulders, lower humeral torsion, and increased wrist hyperextensability. These hypotheses are tested by collecting 3D body motion data during throws performed by human subjects in whom I varied anatomical parameters using restrictive braces to examine their effects on throwing kinematics. These data are broken down using inverse dynamics analysis into the individual motions, velocities, and forces acting around each joint axis. I compare performance at each joint across experimental conditions to test hypotheses regarding the relationship between skeletal features and throwing performance. I also developed and tested a method for predicting humeral torsion using range of motion data, allowing me to calculate torsion in my subjects and determine its effect on throwing performance. My results strongly support an important role for elastic energy storage in powering humans’ uniquely rapid throwing motion. I also found strong performance effects related to anatomical shifts in the torso, shoulder, and arm. When used to interpret the hominin fossil record, my data suggest high-speed throwing ability arose in a mosaic-like fashion, with all relevant features first present in Homo erectus. What drove the evolution of these anatomical shifts is unknown, but as a result the ability to produce high-speed throws was available for early hunting and likely provided an adaptive advantage in this context. / Anthropology

All human societies process their food extensively by thermal and non-thermal means. This feature distinguishes us from other species, and may even be compulsory given that humans are biologically committed to an energy-rich diet that is easy to chew and digest. Yet the energetic consequences of food processing remain largely unknown. This dissertation tests the fundamental hypothesis that thermal and non-thermal processing lead to biologically relevant increases in energy gain from protein-rich meat and starch-rich tubers, two major caloric resources for modern and ancestral humans that present divergent structural and macronutrient profiles. The energetic consequences of food processing are evaluated using three indices of energy gain, each of which account for costs not currently captured by conventional biochemical assessments of dietary energy value. Chapter 2 investigates the effects of cooking and pounding on net energy gain as indexed by changes in body mass, controlling for differences in food intake and activity level. Chapter 3 examines the effect of cooking and pounding on diet-induced thermogenesis, the metabolic cost of food digestion. Chapter 4 considers the effort required to engage in food processing, arguing that the advantageous ratio of benefit to cost has likely had important effects on human life history. By each of these definitions of energy gain, food processing is shown to have substantial energetic significance. Overall, energetic gains due to thermal processing exceeded those of non-thermal processing, consistent with recent proposals that the adoption of cooking had a particularly important influence on human biology. Gains due to food processing were observed in both meat and tuber substrates, supporting a transformative role for habitual food processing in the evolution and maintenance of the human energy budget. / Human Evolutionary Biology

<p>Humans are champions of prosociality. Across different cultures and early in life, humans routinely engage in prosocial behaviors that benefit others. Perhaps most strikingly, humans are even prosocial toward strangers (i.e. xenophilic). This is an evolutionary puzzle because it cannot be explained by kinship theory, reciprocal altruism or reputation. The parochialism hypothesis proposes that this extreme prosociality is unique to humans, is motivated by unselfish motivation and evolved through group selection made possible by human culture and warfare. The first impression hypothesis, on the other hand, proposes that xenophilia can evolve to promote the selfish benefits that accrue from extending one's social network. It predicts that 1) nonhuman species can evolve prosociality toward strangers when the benefit of forming new relations is higher than the cost, 2) the motivation for prosociality can be selfish, and 3) encounters with strangers can be a positive social event since strangers represent potential social partners. This dissertation presents three sets of experiments designed to test these predictions with bonobos (Pan paniscus), a species known for reduced xenophobia. These experiments showed, first, that bonobos voluntarily shared monopolizable food with a stranger and helped the stranger to obtain out-of-reach food. Second, the observed prosociality was driven by a selfish motivation to initiate an interaction with the stranger in close proximity and an other-regarding motivation to benefit the stranger. Third, an involuntary yawning task and a voluntary choice task show converging results that bonobos attribute positive valence to completely unknown strangers by default. These experiments support the three core predictions of the first impression hypothesis and challenge the view that intergroup competition is crucial to the origin of prosociality toward strangers in our species. Instead, the first impression hypothesis proposes that xenophilia in bonobos is probably an adaptation to initiating non-kin cooperation. Because female bonobos are highly cooperative even though they are the dispersing sex, xenophilia might function to quickly establish cooperative relationships with new immigrants. This suggests that xenophilia and reciprocity are likely two complementary aspects of non-kin cooperation: the former explains its initiation while the latter explains its maintenance. Similarly, xenophilia in humans is likely a result of the increasing need for cooperation among non-kin due to enhanced fission-fusion dynamics, population expansion, obligate cooperative foraging and greater dependence on cultural knowledge.</p> / Dissertation

This dissertation begins with a comprehensive review of the evolutionary biological debate over the evolution of altruism and a discussion of how various models of mechanism have influenced the models of circumstance that paleoanthropologists continue to use in reconstructing details about the level of cooperation displayed by early hominin societies. The remainder of the dissertation concerns itself with systematically exposing previously unquestioned assumptions to potential falsification as well as with exploring some new scenarios concerning the evolution and landscape archaeology of Plio-Pleistocene hominin food sharing, all via a null agent-based model called SHARE. This heuristic model was built to address two major questions: (1) What range of ecological and social conditions facilitates the evolution of food sharing in artificial Plio-Pleistocene hominin populations and (2) Is food sharing at central places necessary for the formation of the so-called "scatter and patches" archaeological landscapes that are characteristic of the Plio-Pleistocene record in East Africa? In answer to the first question, population-level genetic results collected from artificial societies of hominin agents demonstrate that the so-called transitional zone of ecological patchiness can facilitate the evolution of altruistic food sharing in mixed starting populations, even if foragers lack the ability to remember past interactions or to avoid social cheaters. In answer to the second question, ecological patchiness can affect the movements of simple foragers such that the artificial archaeological landscapes they create display the same spatial signature that characterizes observed Oldowan landscapes. That is, in ecological conditions marked by fragmented food resources, archaeological landscapes composed of both concentrated patches and diffuse scatters can form as a result of solitary foragers using simple routes that are in no way tethered to culturally-defined and culturally-maintained central places. In the end, SHARE provides new hypotheses about how ecological patchiness could have influenced both the evolution of altruistic food sharing and the structure of Lower Paleolithic archaeological landscapes. The latter can be tested in the field by looking at the relationship between artifact density and the paleoenvironmental characteristics of locales both in which artifacts are abundant and from which they are conspicuously absent.

The series of papers in this dissertation are aimed at testing evolutionary hypotheses concerning the adaptive advantages of religious values or experiences, a gender difference in purpose in life and the evolutionary relationship between deception and self-deception. Explanations are argued for in terms of their consequences for evolutionary fitness contributing to individual survival within the human species. Darwin's theory of natural selection within the framework of evolutionary psychology provides the theoretical background for the study. In psychology as well as in other social sciences, Darwinian theories of natural and sexual selection have been undergoing a revival with a significant upsurge of an interest in evolutionary psychology as a unifying paradigm for the understanding of human functioning as a living organism, optimising its fitness to survive the exigencies of environmental and social selection pressures. The broad or covering hypothesis addressed is that religious values or experiences, purpose in life, deception and self-deception each involve a kind of consciousness or strategic cognitive process that has evolved through the operation of natural selection due to its importance and worth for the survival of the individual. The study is empirical, conducted by using the technique of secondary analysis on the data yielded by the World Values Survey collected in 43 countries in its second wave of 1990 to 1993 as well as on a South African dataset containing variables of interest to the second and third papers of this dissertation. National aggregate data has been obtained from the United Nations Development Reports for the corresponding years under study. Findings showed a significantly positive relationship between religious values and evolutionary fitness promoting factors derived by factor analysis; a significantly greater purpose in life in females as compared to males; and a significantly positive relationship between deception and self-deception. However, the relationship between deception and evolutionary fitness promoting factors, derived by factor analysis, was inconclusive. / Thesis (M.Sc.)-University of Natal, 1999.

Despite most educated people now accepting Darwinian explanations for human physical evolution, many of these same people remain reluctant to accept similar accounts of human behavioural or cognitive evolution. Leftists in particular often assume that our evolutionary history now has little bearing on modern human social behaviour, and that cultural processes have taken over from the biological imperatives at work elsewhere in nature. The leftist view of human nature still largely reflects that of Karl Marx, who believed that our nature is moulded solely by prevailing social and cultural conditions, and that, moreover, our nature can be completely changed by totally changing society. Ethical philosopher Peter Singer challenges this leftist view, arguing that the left must replace its non-Darwinian view of an infinitely malleable human nature with the more accurate scientific account now made possible by modern Darwinian evolutionary science. Darwinism, Singer suggests, could then be used as a source of new ideas and new approaches that could revive and revitalise the egalitarian left. This thesis defends and develops Singer’s arguments for a Darwinian left. It shows that much modern leftist opposition to evolutionary theory is misguided, and that Darwinism does not necessarily have the egregious political implications so often assumed by the egalitarian left – even in such controversial areas as possible ‘biological’ differences between the sexes or between different human populations.

The following research paper was concerned with five basic objectives:(1) outlining the major theoretical and methodological approaches used in the reconstruction of early hominid social behavior/social structure as a context in which to view Richard Wrangham's and Michael Ghiglieri's phylogenetic models of stem-hominid social structure.(2) examining Wrangham's and Ghiglieri's models of stem-hominid and chimpanzee social structure.(3) indicating how theoretical and methodological aspects of structure essentially represent an extension of the theoretical and methodological approaches the same researchers applied to their models of chimpanzee social structure.(4) addressing the theoretical and methodological deficiences of Wrangham's and Ghiglieri's models of chimpanzee social structure.(5) providing suggestions for improved phylogenetic models of early hominid social structure.The first objective was achieved by: (a) reviewing Tooby and Devore's (1986) and Wrangham's (1986) evaluations of the major theoretical approaches and methodologies used in the reconstruction of hominid social behavior/structure (b) defining, classifying and evaluating Wrangham's and Ghiglieri's phylogenetic approaches within this context.The second objective was accomplished by outlining, analyzing, and comparing/contrasting Wrangham's and Ghiglieri's phylogenetic models of stem-hominid social structure (i.e.Wrangham 1986; Ghiglieri 1987, 1989) and Wrangham's and Ghiglieri's models of chimpanzee social structure (i.e. Wrangham 1975, 1979; Ghiglieri 1984, 1985, 1987, 1989).The third objective was achieved by recognizing how Wrangham and Ghiglieri used/stressed principles and concepts derived from evolutionary biology and/or behavioral ecology to develop their models of stem-hominid and chimpanzee social structure. This analysis showed that Wrangham's models of social structure were more favorably inclined toward the method of behavioral ecology than Ghiglieri's models, which favored a sociobiological paradigm. Furthermore, although neither researcher relied exclusively on the above theoretical approaches, the main thrust of their argument often centered around it. For instance, Wrangham's analysis of chimpanzee social structure (Wrangham 1975, 1979) indicated that the ultimate cause of that structure was ecological i.e., patchy food distribution leads to wide female dispersal for optimal foraging efficiency, which in turn favors a male kin breeding group that can maintain a territority that includes several individual female ranges. In contrast, Wrangham's phylogenetic model of the social structure of the stem-hominid (Wrangham, 1986) suggested that phylogenetic inertia may be partially responsible for the shared social features found among African Hominoidea. However, in the same work, Wrangham also suggested that further socioecological analysis of African apes may indicate whether food distribution and its effects on female dispersion/association may partially explain conservative African ape social features.Ghiglieri's phylogenetic model of the stem-hominid (1987, 1989), on the other hand, explained the conservative social features of bonobos, common chimpanzees, and hominids to be primarily a product of phylogenetic inertia and sexual selection. Furthermore, for Ghiglieri the most important sexual selection variable was a male communal reproductive strategy. This, according to Ghiglieri, is the ultimate cause of social structure. Notably, Ghiglieri (1984, 1985) had earlier stressed the overiding importance of a male communal reproductive strategy but was less dogmatic in his insistence that chimpanzees had essentially solved their ecological problems (e.g. that they had solved the food distribution problem by fusion-fission sociality; predators were never a real problem). Nevertheless, Ghiglieri's earlier position similarily expressed the idea that a communal reproductive strategy constituted the ultimate cause of social structure.The fourth objective was accomplished by presentation of an alternative model of chimpanzee social behavior which suggested that structure; the effect of phylogenetic inertia on social structure; chimpanzee social structure is the combined product of ecological and sexual selection forces: female optimal foraging, male mating strategies, and predator pressure. The model was considered by the author to be unique in that it integrated essential aspects of both Wrangham's and Ghiglieri's models and, in addition, provided support for Alexander's (1974) contention that predation pressure is an ultimate cause of ape social structure. The model also outlined scenarios for the evolution of chimpanzee group._ extensibility (fusion-fission sociality) and the capacity for warfare among chimpanzees.The last objective was achieved by a discussion of the implications that the author's model had for phylogenetic models of stem-hominid social structure. In this discussion the author reviewed the following issues as they related to the phylogenetic reconstruction of hominid social structure: the role of phylogeny and/or ecology in the causation of social encountered when using a phylogenetic referential model for the personal biases that enter into phylogenetic econstructions; pitfalls reconstruction of early hominid social evolution; the significance of chimpanzee models of social structure.The importance of the preceding study lay in its ability to stimulate improved conceptual models of African hominoid social structure. / Department of Anthropology