Sero-genetic studies on the San of South West Africa.

The San, a physically, culturally and linguistically distinctive people, have been shown by archaeological records anciently to have inhabited the whole of Eastern and Southern Africa. They, in common with the Khoi, the other members of the Khoisan race, are confined now to Southern Africa and principally to Botswana and South West Africa, though a number are also found in Angola. Sero-genetic data concerning seven South West African groups are presented in this study, and confirm a shared overall genetic profile characteristic of the San in general, slightly different from that of the Khoi and in significant contrast with that of the Negroes.     

Middle and late Pleistocene faunas of Pinnacle Point and their paleoecological implications

The Western Cape region of South Africa is home to a unique type of mediterranean vegetation called fynbos, as well as some of the earliest sites of modern human occupation in southern Africa. Reconstructing the paleohabitats during occupations of these early anatomically modern Homo sapiens is important for understanding the availability of resources to the humans during the development of behaviors that are often considered advanced. These reconstructions are critical to understanding the nature of the changes in the environment and resources over time. Here we analyze the craniodental fossils of the larger mammals recovered from two Pleistocene assemblages in the Pinnacle Point complex, Mossel Bay, Western Cape Region, South Africa. We reconstruct the paleohabitats as revealed by multivariate analyses of the mammalian community structures. Pinnacle Point 30 is a carnivore assemblage and Pinnacle Point 13B includes early evidence of a suite of modern human behavior; together they present an opportunity to identify environmental change over time at a localized geographic scale. Further, this is the first such study to include dated Western Cape localities from Marine Isotope Stage 6, a time of environmental pressure that may have marginalized human populations. Results indicate that environmental change in the Western Cape was more complex than generalized C(4) grassland expansions replacing fynbos habitats during glacial lowered sea levels, and thus, resources available to early modern humans in the region may not have been entirely predictable.     

The biocultural evolution of Khoisan populations of Southern Africa

The research presented here offers new information on the recent evolution of Khoisan populations of southern Africa through the new study of Holocene skeletons. When combined with subfossil and historical remains, these archeological specimens provide a skeletal record for the last 5000–9000 years of southern African prehistory. Multivariate statistical analyses of cranial measurements were used to determine patterns of morphological variation in the skeletal record with which hypotheses of biocultural evolution were tested. These analyses yielded the following results. First, the traditional distinction between Bushmen and Hottentots holds for recent inland individuals. Second, there is a suggestion of a morphologically distinct San population living on the coast of South Africa. The idea of a “Strandloper” population suggested by early scholars is here revived. The third result is that there is little evidence of complete population succession on the coast of South Africa, suggesting that there were no massive population movements associated with the spread of Hottentot pastoralism throughout southern Africa.     

New founder haplotypes at the myotonic dystrophy locus in southern Africa.

The association between normal alleles at the CTG repeat and two nearby polymorphisms in the myotonin protein kinase gene, the Alu insertion/deletion polymorphism and the myotonic dystrophy kinase (DMK)(G/T) intron 9/HinfI polymorphism, has been analyzed in South African Negroids, a population in which myotonic dystrophy (DM) has not been described. South African Negroids have a CTG allelic distribution that is significantly different from that in Caucasoids and Japanese: the CTG repeat lengths of > or = 19 are very rare. The striking linkage disequilibrium between specific alleles at the Alu polymorphism (Alu(ins) and Alu(del)), the HinfI polymorphism (HinfI-1 and HinfI-2), and the CTG repeat polymorphism seen in Caucasoid (Europeans and Canadians) populations was also found in the South African Negroid population. Numerous haplotypes, not previously described in Europeans, were, however, found. It thus seems likely that only a small number of these "African" chromosomes were present in the progenitors of all non-African peoples. These data provide support for the "out of Africa" model for the origin of modern humans and suggest that the rare ancestral DM mutation event may have occurred after the migration from Africa, hence the absence of DM in sub-Saharan Negroid peoples.     

How large were the australopithecines?

Stature of the African early hominids is estimated from most of the available fragments of fossil long bones by means of regression analysis. The average height of the South African gracile australopithecines is predicted to be 145.1 cm (4′9″) where n = 4 and of the South African robust forms, 152.7 cm (5′) where n = 3. The East African early hominids are somewhat taller (x = 163.0 cm or 5′4″, where n = 7). Variability in stature is high even within the same site which is probably a reflection of fairly strong sexual dimorphism in body size. Evidence is presented which suggests that at least in one form of early hominid the size proportions of fore- and hindlimbs are different than in modern man. There is also evidence that average stature may have increased through time. The most significant of these findings is that the two forms of early hominids in South Africa are possibly more similar in stature than is usually cited. This does not imply necessarily that the two forms did not differ significantly in robustness or weight.     

mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans.

The intergenic COII/tRNA(Lys) 9-bp deletion in human mtDNA, which is found at varying frequencies in Asia, Southeast Asia, Polynesia, and the New World, was also found in 81 of 919 sub-Saharan Africans. Using mtDNA control-region sequence data from a subset of 41 individuals with the deletion, we identified 22 unique mtDNA types associated with the deletion in Africa. A comparison of the unique mtDNA types from sub-Saharan Africans and Asians with the 9-bp deletion revealed that sub-Saharan Africans and Asians have sequence profiles that differ in the locations and frequencies of variant sites. Both phylogenetic and mismatch-distribution analysis suggest that 9-bp deletion arose independently in sub-Saharan Africa and Asia and that the deletion has arisen more than once in Africa. Within Africa, the deletion was not found among Khoisan peoples and was rare to absent in western and southwestern African populations, but it did occur in Pygmy and Negroid populations from central Africa and in Malawi and southern African Bantu-speakers. The distribution of the 9-bp deletion in Africa suggests that the deletion could have arisen in central Africa and was then introduced to southern Africa via the recent "Bantu expansion."     

African Y chromosome and mtDNA divergence provides insight into the history of click languages

BACKGROUND: About 30 languages of southern Africa, spoken by Khwe and San, are characterized by a repertoire of click consonants and phonetic accompaniments. The Jumid R:'hoansi (!Kung) San carry multiple deeply coalescing gene lineages. The deep genetic diversity of the San parallels the diversity among the languages they speak. Intriguingly, the language of the Hadzabe of eastern Africa, although not closely related to any other language, shares click consonants and accompaniments with languages of Khwe and San. RESULTS: We present original Y chromosome and mtDNA variation of Hadzabe and other ethnic groups of Tanzania and Y chromosome variation of San and peoples of the central African forests: Biaka, Mbuti, and Lisongo. In the context of comparable published data for other African populations, analyses of each of these independently inherited DNA segments indicate that click-speaking Hadzabe and Jumid R:'hoansi are separated by genetic distance as great or greater than that between any other pair of African populations. Phylogenetic tree topology indicates a basal separation of the ancient ancestors of these click-speaking peoples. That genetic divergence does not appear to be the result of recent gene flow from neighboring groups. CONCLUSIONS: The deep genetic divergence among click-speaking peoples of Africa and mounting linguistic evidence suggest that click consonants date to early in the history of modern humans. At least two explanations remain viable. Clicks may have persisted for tens of thousands of years, independently in multiple populations, as a neutral trait. Alternatively, clicks may have been retained, because they confer an advantage during hunting in certain environments.     

Ancient Substructure in Early mtDNA Lineages of Southern Africa

Among the deepest-rooting clades in the human mitochondrial DNA (mtDNA) phylogeny are the haplogroups defined as L0d and L0k, which are found primarily in southern Africa. These lineages are typically present at high frequency in the so-called Khoisan populations of hunter-gatherers and herders who speak non-Bantu languages, and the early divergence of these lineages led to the hypothesis of ancient genetic substructure in Africa. Here we update the phylogeny of the basal haplogroups L0d and L0k with 500 full mtDNA genome sequences from 45 southern African Khoisan and Bantu-speaking populations. We find previously unreported subhaplogroups and greatly extend the amount of variation and time-depth of most of the known subhaplogroups. Our major finding is the definition of two ancient sublineages of L0k (L0k1b and L0k2) that are present almost exclusively in Bantu-speaking populations from Zambia; the presence of such relic haplogroups in Bantu speakers is most probably due to contact with ancestral pre-Bantu populations that harbored different lineages than those found in extant Khoisan. We suggest that although these populations went extinct after the immigration of the Bantu-speaking populations, some traces of their haplogroup composition survived through incorporation into the gene pool of the immigrants. Our findings thus provide evidence for deep genetic substructure in southern Africa prior to the Bantu expansion that is not represented in extant Khoisan populations.     

Did a discrete event 200,000-100,000 years ago produce modern humans?

Scenarios for modern human origins are often predicated on the assumption that modern humans arose 200,000-100,000 years ago in Africa. This assumption implies that something ‘special’ happened at this point in time in Africa, such as the speciation that produced Homo sapiens, a severe bottleneck in human population size, or a combination of the two. The common thread is that after the divergence of the modern human and Neandertal evolutionary lineages ∼400,000 years ago, there was another discrete event near in time to the Middle-Late Pleistocene boundary that produced modern humans. Alternatively, modern human origins could have been a lengthy process that lasted from the divergence of the modern human and Neandertal evolutionary lineages to the expansion of modern humans out of Africa, and nothing out of the ordinary happened 200,000-100,000 years ago in Africa.Three pieces of biological (fossil morphology and DNA sequences) evidence are typically cited in support of discrete event models. First, living human mitochondrial DNA haplotypes coalesce ∼200,000 years ago. Second, fossil specimens that are usually classified as ‘anatomically modern’ seem to appear shortly afterward in the African fossil record. Third, it is argued that these anatomically modern fossils are morphologically quite different from the fossils that preceded them.Here I use theory from population and quantitative genetics to show that lengthy process models are also consistent with current biological evidence. That this class of models is a viable option has implications for how modern human origins is conceptualized.     

Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola

Africa is the homeland of humankind and it is known to harbour the highest levels of human genetic diversity. However, many continental regions, especially in the sub-Saharan side, still remain largely uncharacterized (i.e. southwest and central Africa). Here, we examine the mitochondrial DNA (mtDNA) variation in a sample from Angola. The two mtDNA hypervariable segments as well as the 9-bp tandem repeat on the COII/tRNA^lys intergenic region have allowed us to allocate mtDNAs to common African haplogroups. Angola lies in the southern end of the putative western branch of the Bantu expansion, where it met the local Khoisan populations. Angolan mtDNA lineages show basically a Bantu substrate with no traces of Khoisan lineages. Roughly, more than half of the southwestern mtDNA pool can be assigned to west Africa, ~25% to central Africa and a significant 16% to east Africa, which points to the western gene pool having contributed most to the mtDNA lineages in Angola. We have also detected signals of extensive gene flow from southeast Africa. Our results suggest that eastern and western Bantu expansion routes were not independent from each other, and were connected south of the rainforest and along the southern African savannah. In agreement with historical documentation, the analysis also showed that the Angola mtDNA genetic pool shows affinities with the African lineages from Brazil, the main American destination of the slaves from Angola, although not all lineages in Brazil can be accounted for by the Angolan mtDNA pool.     

The dawn of human matrilineal diversity

The quest to explain demographic history during the early part of human evolution has been limited because of the scarce paleoanthropological record from the Middle Stone Age. To shed light on the structure of the mitochondrial DNA (mtDNA) phylogeny at the dawn of Homo sapiens, we constructed a matrilineal tree composed of 624 complete mtDNA genomes from sub-Saharan Hg L lineages. We paid particular attention to the Khoi and San (Khoisan) people of South Africa because they are considered to be a unique relic of hunter-gatherer lifestyle and to carry paternal and maternal lineages belonging to the deepest clades known among modern humans. Both the tree phylogeny and coalescence calculations suggest that Khoisan matrilineal ancestry diverged from the rest of the human mtDNA pool 90,000-150,000 years before present (ybp) and that at least five additional, currently extant maternal lineages existed during this period in parallel. Furthermore, we estimate that a minimum of 40 other evolutionarily successful lineages flourished in sub-Saharan Africa during the period of modern human dispersal out of Africa approximately 60,000-70,000 ybp. Only much later, at the beginning of the Late Stone Age, about 40,000 ybp, did introgression of additional lineages occur into the Khoisan mtDNA pool. This process was further accelerated during the recent Bantu expansions. Our results suggest that the early settlement of humans in Africa was already matrilineally structured and involved small, separately evolving isolated populations.     

Late archaic and modern Homo sapiens from Europe, Africa, and Southwest Asia: Craniometric comparisons and phylogenetic implications

The craniometric affinities among Neandertals. Upper Palcolithic Europeans, early anatomically modern Southwest Asians, and archaic and modern Africans are investigated using univariate and multivariate methods. For the first time, it is possible to analyse the North African finds Dar-es-Soltane 5, Nazlet Khater, and Wadi Kubbaniya. It was not possible to include the Neandertals from Central Europe due to their poor state of preservation. The results point to, first, a basic distinction between Neandertals on the one hand and modern humans from all geographic regions on the other, and, secondly, to great similarities between modern African and European populations. Late archaic sapiens specimens from Africa were more similar to Upper Paleolithic Europeans than were the Neandertals. The results do not support the hypothesis that a regional evolution giving rise to modern humans took place in Europe. The results are, however, consistent with the hypothesis that modern populations originated in Africa and spread to Europe from there.     

Genetic evidence and the modern human origins debate

A continued debate in anthropology concerns the evolutionary origin of 'anatomically modern humans' (Homo sapiens sapiens). Different models have been proposed to examine the related questions of (1) where and when anatomically modern humans first appeared and (2) the genetic and evolutionary relationship between modern humans and earlier human populations. Genetic data have been increasingly used to address these questions. Genetic data on living human populations have been used to reconstruct the evolutionary history of the human species by considering how global patterns of human variation could be produced given different evolutionary scenarios. Of particular interest are gene trees that reconstruct the time and place of the most recent common ancestor of humanity for a given haplotype and the analysis of regional differences in genetic diversity. Ancient DNA has also allowed a direct assessment of genetic variation in European Neandertals. Together with the fossil record, genetic data provide insight into the origin of modern humans. The evidence points to an African origin of modern humans dating back to 200,000 years followed by later expansions of moderns out of Africa across the Old World. What is less clear is what happened when these early modern humans met preexisting 'archaic human' populations outside of Africa. At present, it is difficult to distinguish between a model of total genetic replacement and a model that includes some degree of genetic mixture.     

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.     

The First Modern Human Dispersals across Africa

The emergence of more refined chronologies for climate change and archaeology in prehistoric Africa, and for the evolution of human mitochondrial DNA (mtDNA), now make it feasible to test more sophisticated models of early modern human dispersals suggested by mtDNA distributions. Here we have generated 42 novel whole-mtDNA genomes belonging to haplogroup L0, the most divergent clade in the maternal line of descent, and analysed them alongside the growing database of African lineages belonging to L0’s sister clade, L1’6. We propose that the last common ancestor of modern human mtDNAs (carried by “mitochondrial Eve”) possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations. Early modern human dispersals correlate with climate changes, particularly the tropical African “megadroughts” of MIS 5 (marine isotope stage 5, 135–75 ka) which paradoxically may have facilitated expansions in central and eastern Africa, ultimately triggering the dispersal out of Africa of people carrying haplogroup L3 ~60 ka. Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution.     

The number of vertebrae in the Southern African Negro,the American Negro and the Bushman (San)

The numbers of precoccygeal vertebrae (PCV) are compared in Southern African Negroes, Bushman (San) and American Negroes. The S.A. Negro and San males have an exceptionally high frequency of an increased total PCV number whilst the frequencies are significantly lower in a combined Caucasoid sample and the Mongoloid samples. The American Negro male, too, has a high frequency but not as high as in S.A. Negroes. The high frequency of increased PCV number in San, S.A. Negroes and American Negroes is in keeping with the view that the Khoisan peoples (here represented by the San), the Southern African Negroes and the African ancestors of American Blacks sprang from a common proto-negriform stock. Males have a significantly greater frequency of increased PCV to 30 or 31, whereas females are more likely to have a decreased number of 28 PCV. This sex difference is present in all the populations studied.     

Craniofacial diversity in earlyHomo and the affinities of the Sterkfontein Valley

The Sterkfontein Valley specimens SK 847 (Swartkrans Member 1) and Stw 53 (Sterkfontein Member 5) provide important evidence of earlyHomo in southern Africa. However, specific identity has been disputed, with that of SK 847 especially contentious. Opinions differ markedly as to whether the specimens are conspecific or not, whether they should be referred to East African earlyHomo species, or whether they represent new species. Morphometric analysis of facial dimensions reveals contrasting affinities for the two South African fossils, and so does not support claims for their conspecifity. Stw 53 is very like smaller East African crania referred toH. habilis, whereas SK 847 has a distinctive facial pattern. In some respects it resembles early AfricanH. erectus (=H. ergaster), but with a markedly more projecting mid-face, prominent zygomatic and unexpanded frontal region, all of which militate against inclusion in that species. The taxonomic implications of these contrasting facial affinities are briefly discussed.     

Correlations between flavonoid chemistry,anatomy and geography in the restionaceae

Comparisons of the flavonoid patterns in stems and inflorescences between Australasian and South African members of the Restionaceae indicate significant differences with geography. Nine of 14 Australasian species contain gossypetin or a related 8-hydroxyflavonoid and proanthocyanidins are uncommon. By contrast, the 33 South African taxa studied contain common flavonols, flavones and glycoflavones, while proanthocyanidins are present in 29. Two anatomically related South African genera, Chondropetalum and Elegia, contain, in addition, myricetin 3-galactoside, together with the 3-galactosides of the myricetin methyl ethers, larycitrin and syringetin. These results confirm the conclusions derived from anatomy that members of Hypolaena, Leptocarpus and Restio, genera represented in both Australia and South Africa, have the distinctive flavonoids characteristic of their geographic origin rather than of their systematic position. The family as a whole is different in flavonoid pattern from other monocotyledonous families with which it is sometimes associated.     

Deletion polymorphism in the human COL1A2 gene: genetic evidence of a non-African population whose descendants spread to all continents

We report the frequencies of a deletion polymorphism at the alpha 2 (1) collagen gene (COL1A2) and argue that this distribution has major implications for understanding the evolution of modern humans immediately after their exodus from sub-Saharan Africa as well as their subsequent spread to all continents. The high frequency of the deletion in non-African populations and its complete absence in sub-Saharan African groups suggest that the deletion event occurred just before or shortly after modern humans left Africa. The deletion probably arose shortly after the African exodus in a group whose descendants were among the ancestors of all contemporary populations, except for sub-Saharan Africans. This, of course, does not imply that there was a single migration out of Africa. The GM immunoglobulin haplotype GM*A,X G displays a similar distribution to that for the COL1A2 deletion, and these 2 polymorphisms suggest that the exodus from Africa may not have been a rapid dispersion to all other regions of the world. Instead, it may have involved a period of time for the savanna-derived gene pool to adapt to novel selective agents, such as bacteria, viruses, and/or environmental xenobiotics found in both animal and plant foods in their new environment. In this context these polymorphisms are indicators of the evolution that occurred before the diaspora of these populations to the current distribution of modern peoples.