The disappearing San of southeastern Africa and their genetic affinities

Southern Africa was likely exclusively inhabited by San hunter-gatherers before ~2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (~1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists ~350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.     

Phylogeography and ethnogenesis of aboriginal Southeast Asians

Studying the genetic history of the Orang Asli of Peninsular Malaysia can provide crucial clues to the peopling of Southeast Asia as a whole. We have analyzed mitochondrial DNA (mtDNAs) control-region and coding-region markers in 447 mtDNAs from the region, including 260 Orang Asli, representative of each of the traditional groupings, the Semang, the Senoi, and the Aboriginal Malays, allowing us to test hypotheses about their origins. All of the Orang Asli groups have undergone high levels of genetic drift, but phylogeographic traces nevertheless remain of the ancestry of their maternal lineages. The Semang have a deep ancestry within the Malay Peninsula, dating to the initial settlement from Africa >50,000 years ago. The Senoi appear to be a composite group, with approximately half of the maternal lineages tracing back to the ancestors of the Semang and about half to Indochina. This is in agreement with the suggestion that they represent the descendants of early Austroasiatic speaking agriculturalists, who brought both their language and their technology to the southern part of the peninsula approximately 4,000 years ago and coalesced with the indigenous population. The Aboriginal Malays are more diverse, and although they show some connections with island Southeast Asia, as expected, they also harbor haplogroups that are either novel or rare elsewhere. Contrary to expectations, complete mtDNA genome sequences from one of these, R9b, suggest an ancestry in Indochina around the time of the Last Glacial Maximum, followed by an early-Holocene dispersal through the Malay Peninsula into island Southeast Asia.     

Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ~3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ~60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.     

The invasion of <Emphasis Type="Italic">Senecio pterophorus</Emphasis> across continents: multiple,independent introductions,admixture and hybridization

Senecio pterophorus (Compositae) is a perennial shrub native to eastern South Africa that was introduced into the Western Cape in South Africa and Australia approximately 100 years ago and into Europe (Italy and Spain) more than 25–30 years ago. In this study, the aims were to unravel the putative sources of the introduced populations and identify the changes in genetic diversity after invasion using molecular markers and phylogeographic and population genetic analyses. We sampled the entire area of distribution for S. pterophorus extensively. Based on the results, three lineages were established along a latitudinal and climatic gradient in the native range (south, central, central/north) with high levels of admixture. Multiple, independent introductions occurred in the four invaded ranges. The central/northern lineage (humid climate) was the primary source for all of the invaded regions (with drier climates), although a secondary role was revealed for the southern lineage in the Western Cape and the central/northern lineage in Australia and Spain. The genetic diversity was slightly lower in the Spanish and Australian populations than that in the native populations. A variety of demographic and genetic processes affected the amount and structure of genetic diversity in the invaded areas, including multiple introductions and admixture (Western Cape, Australia and Spain) as well as pre-invasive hybridization (Italy). The patterns of dispersion support a hypothesis of rapid evolution of S. pterophorus after invasion in response to novel climatic conditions.     

Indian Siddis: African descendants with Indian admixture

The Siddis (Afro-Indians) are a tribal population whose members live in coastal Karnataka, Gujarat, and in some parts of Andhra Pradesh. Historical records indicate that the Portuguese brought the Siddis to India from Africa about 300-500 years ago; however, there is little information about their more precise ancestral origins. Here, we perform a genome-wide survey to understand the population history of the Siddis. Using hundreds of thousands of autosomal markers, we show that they have inherited ancestry from Africans, Indians, and possibly Europeans (Portuguese). Additionally, analyses of the uniparental (Y-chromosomal and mitochondrial DNA) markers indicate that the Siddis trace their ancestry to Bantu speakers from sub-Saharan Africa. We estimate that the admixture between the African ancestors of the Siddis and neighboring South Asian groups probably occurred in the past eight generations (～200 years ago), consistent with historical records.     

Population structuring in mountain zebras (<Emphasis Type="Italic">Equus zebra</Emphasis>): The molecular consequences of divergent demographic histories

The endangered mountain zebra (Equus zebra) is endemic to the semi-arid inhospitable mountainous escarpments of southern Africa. The species is divided taxonomically into two geographically separated subspecies, each with differing recent population histories. In Namibia, Hartmann’s mountain zebra (E. z. hartmannae) is common and occurs in large free-ranging populations, whereas in South Africa, prolonged hunting and habitat destruction over the last 300 years has decimated populations of the Cape mountain zebra (E. z. zebra). In this study, we investigate the consequences of these divergent demographic histories for population genetic diversity and structure. We also examine the phylogeographic relationship between the two taxonomic groups. Genetic information was obtained at 15 microsatellite loci for 291 individuals from a total of 10 populations as well as 445 bp of the mitochondrial control region sequence data from 77 individuals. Both model-based and standard analytical approaches were used to examine the data. Both types of marker returned levels of diversity and structure that were consistent with population history. Low genetic variation within individual Cape mountain zebra populations, the characteristic indicator of population fragmentation and drift, was offset by moderate variation in the entire E. z. zebra sample. This implies that higher levels of diversity still exist within the Cape mountain zebra gene pool. A management strategy that entailed the mixing of aboriginal populations is therefore advocated in order to halt the further loss of Cape mountain zebra genetic diversity. Allele frequencies in Hartmann’s mountain zebra were relatively resilient to demographic fluctuations. Due to the high incidence of mitochondrial haplotype sharing between populations, the hypothesis that Cape and Hartmann’s mountain zebra mitochondrial lineages were reciprocally monophyletic was not supported. However, the presence of private alleles at nuclear loci rendered the two subspecies genetically distinct evolutionary significant units.     

Record of Blue tilapia Oreochromis aureus (Steindachner, 1864) in the Eerste River catchment,Western Cape province,South Africa

Oreochromis aureus was imported from Israel into South Africa in 1959 but data on its current status in South Africa are lacking. Genomic DNA was extracted and the COI gene amplified at the South African Institute for Aquatic Biodiversity. The identity of the sequences and specimens was determined using the Barcode of Life Data Systems and GenBank. Morphological and genetic assessment demonstrated that 11 specimens collected from two farm dams in the Eerste River System, Western Cape province, were Oreochromis aureus. A MaxEnt model compiled using global distribution, rainfall and temperature data predicted that large areas of southern Africa were climatically suitable for this species, indicating considerable invasion debt in southern Africa. As a result, surveys to assess for the extent of the invasion in South Africa and eradication of existing populations, if feasible, are recommended management actions.     

Genomic ancestry of North Africans supports back-to-Africa migrations

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from "back-to-Africa" gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.     

Coalescence methods reveal the impact of vicariance on the spatial genetic structure of Elephantulus edwardii (Afrotheria, Macroscelidea)

Within the Macroscelidea 15 species of elephant-shrews are recognized, of which nine occur in the southern African subregion. The Cape rock elephant-shrew (Elephantulus edwardii) is the only strictly endemic South African elephant-shrew species. Recent distribution data suggest that E. edwardii is continuously distributed from Namaqualand in the Western Cape Province to Port Elizabeth in the Eastern Cape Province. Molecular sequences from the mitochondrial cytochrome b gene and variable control region indicate significant substructure within the Cape rock elephant-shrew across its distribution. Our data unequivocally showed the presence of a northern Namaqua and central Fynbos clade with four evolutionary lineages identified within the latter. The geographical delimitation of the northern and central clades corresponds closely with patterns reported for other rock-dwelling vertebrate species, indicating a shared biogeographical history for these taxa in South Africa. A coalescent method revealed the effects of ancestral polymorphism in shaping the Namaqua and Fynbos populations since their divergence ~1.7 million years ago. Furthermore, our analyses uncovered a distinct Karoo lineage(s) that does not correspond to any of the previously described and/or currently recognized species, and we therefore argue for the possible recognition of a new sister taxon to E. edwardii. The taxonomic affinities of this clade were examined by sequencing corresponding regions from the type specimens of species described in the past, but which presently are synonimized within E. edwardii. Our results reveal the morphological misidentification of one of these types, accentuating the problems of field identification.     

The history of African gene flow into Southern Europeans, Levantines, and Jews

Previous genetic studies have suggested a history of sub-Saharan African gene flow into some West Eurasian populations after the initial dispersal out of Africa that occurred at least 45,000 years ago. However, there has been no accurate characterization of the proportion of mixture, or of its date. We analyze genome-wide polymorphism data from about 40 West Eurasian groups to show that almost all Southern Europeans have inherited 1%-3% African ancestry with an average mixture date of around 55 generations ago, consistent with North African gene flow at the end of the Roman Empire and subsequent Arab migrations. Levantine groups harbor 4%-15% African ancestry with an average mixture date of about 32 generations ago, consistent with close political, economic, and cultural links with Egypt in the late middle ages. We also detect 3%-5% sub-Saharan African ancestry in all eight of the diverse Jewish populations that we analyzed. For the Jewish admixture, we obtain an average estimated date of about 72 generations. This may reflect descent of these groups from a common ancestral population that already had some African ancestry prior to the Jewish Diasporas.     

POPULATION SIZE,DISTRIBUTION AND DISPERSAL OF KELP GULLS IN THE SOUTHWESTERN CAPE,SOUTH AFRICA

Steele, W.K. & Hockey, P.A.R. 1990. Population size, distribution and dispersal of Kelp Gulls in the southwestern Cape, South Africa. Ostrich 61:97-106.

There are indications that the Kelp Gull Larus dominicanus population of the southwestern Cape Province, South Africa, is increasing. It is proposed that decreased post-fledging mortality due to supplementary food from man's activities, at sites such as fishing harbours and refuse dumps, is likely to be the main cause of this population increase. Kelp Gulls aggregate, and juveniles (first-year birds) are disproportionately abundant, at sites where supplementary food is available. Juvenile dispersal from the two largest breeding colonies, 38 km apart, is in opposite directions.     

Extreme levels of intra-specific divergence among Cape Peninsula populations of the Cape galaxias,Galaxias zebratus Castelnau 1861, reveals a possible species complex

The Cape galaxias, Galaxias zebratus, is part of the paleao-endemic fauna characteristic of the south-western Cape, South Africa, and is the only galaxiid found in continental Africa. A 284-bp fragment of the cytochrome b region of the mtDNA was sequenced from 48 individual galaxiids, representing 10 populations from the Cape Peninsula. Five sequences, for four additional populations sampled at the extremes of the species range, were obtained from the literature. Analysis of cyt b mtDNA from these 14 populations of G. zebratus revealed five distinct and highly divergent lineages with low levels of intra-population mtDNA haplotype diversity. A new and distinct genetic lineage is described from the southern part of the Cape Peninsula. Estimates of genetic divergence between populations ranged from <1% to >17%. The observed level of sequence divergence represents the largest yet reported for any single fish species. The distribution of these lineages and their degree of sequence divergence refutes a model of isolation by distance. Results suggest that periods of low sea level may have been important in creating opportunities and alternative routes for dispersal and migration for Cape Peninsula populations.     

Pinnacle Point Cave 13B (Western Cape Province, South Africa) in context: The Cape Floral kingdom, shellfish, and modern human origins

Genetic and anatomical evidence suggests that Homo sapiens arose in Africa between 200 and 100ka, and recent evidence suggests that complex cognition may have appeared between ~164 and 75ka. This evidence directs our focus to Marine Isotope Stage (MIS) 6, when from 195-123ka the world was in a fluctuating but predominantly glacial stage, when much of Africa was cooler and drier, and when dated archaeological sites are rare. Previously we have shown that humans had expanded their diet to include marine resources by ~164ka (±12ka) at Pinnacle Point Cave 13B (PP13B) on the south coast of South Africa, perhaps as a response to these harsh environmental conditions. The associated material culture documents an early use and modification of pigment, likely for symbolic behavior, as well as the production of bladelet stone tool technology, and there is now intriguing evidence for heat treatment of lithics. PP13B also includes a later sequence of MIS 5 occupations that document an adaptation that increasingly focuses on coastal resources. A model is developed that suggests that the combined richness of the Cape Floral Region on the south coast of Africa, with its high diversity and density of geophyte plants and the rich coastal ecosystems of the associated Agulhas Current, combined to provide a stable set of carbohydrate and protein resources for early modern humans along the southern coast of South Africa during this crucial but environmentally harsh phase in the evolution of modern humans. Humans structured their mobility around the use of coastal resources and geophyte abundance and focused their occupation at the intersection of the geophyte rich Cape flora and coastline. The evidence for human occupation relative to the distance to the coastline over time at PP13B is consistent with this model.     

Genomewide analysis of admixture and adaptation in the Africanized honeybee

Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole‐genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene‐rich 1.4‐Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0 years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.     

Coetzee on South Africa's Past: Remembering in the Time of Forgetting

As an intellectual figure in South Africa, J. M. Coetzee has consistently engaged with the politics of the past, particularly the contemporary ethical ramifications of the colonial past, alongside the more recent and bitter history of oppression under apartheid. As archaeologists, we aim to excavate these engagements through his novels and essays, particularly his long-standing concerns with the Khoekhoe communities of the Cape. In South Africa today, the tensions between remembering and forgetting are palpable and, in the aftermath of the Truth and Reconciliation Commission (TRC), we suggest that not all forgetting can be cast as therapeutic. Throughout his complex relationships with the nation's history, Coetzee foregrounds the colonial past and reiterates the ethical responsibilities of remembering so that the patterns of the past are not repeated.     

The Admixture Structure and Genetic Variation of the Archipelago of Cape Verde and Its Implications for Admixture Mapping Studies

Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.     

Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus

The Cape hake species, Merluccius capensis and Merluccius paradoxus are the most important resource of the South African and Namibian demersal fishery, but it is unclear whether there is a single population of each shared by both countries. We analysed the population structure and evolutionary history of these two species using the variable 5' region of the mtDNA control region for 311 specimens of M. capensis and 333 specimens of M. paradoxus sampled between Lüderitz (southern Namibia) to south of Cape Point (South Africa). 107 haplotypes for M. capensis and eight haplotypes for M. paradoxus were recovered. AMOVA and pairwise Phi(st) analyses revealed no structure in M. capensis, however significant genetic differentiation between Namibian and South African 'populations' was detected for M. paradoxus. This was only restricted to mature fish older than 3 and 4 years and not for juvenile fish younger than 3 years. Analyses reveal that M. capensis has undergone population expansion (Fu's Fs=-26.65, P<0.001), possibly within the last 4500-23,000 years, whereas M. paradoxus has not. Our study highlights the utility of genetic markers to unravel the evolutionary history of sympatric species, as well as addressing management issues within regions where commercially valuable fish stocks are shared between nations.     

A Panel of Ancestry Informative Markers for the Complex Five-Way Admixed South African Coloured Population

Admixture is a well known confounder in genetic association studies. If genome-wide data is not available, as would be the case for candidate gene studies, ancestry informative markers (AIMs) are required in order to adjust for admixture. The predominant population group in the Western Cape, South Africa, is the admixed group known as the South African Coloured (SAC). A small set of AIMs that is optimized to distinguish between the five source populations of this population (African San, African non-San, European, South Asian, and East Asian) will enable researchers to cost-effectively reduce false-positive findings resulting from ignoring admixture in genetic association studies of the population. Using genome-wide data to find SNPs with large allele frequency differences between the source populations of the SAC, as quantified by Rosenberg et. al''s -statistic, we developed a panel of AIMs by experimenting with various selection strategies. Subsets of different sizes were evaluated by measuring the correlation between ancestry proportions estimated by each AIM subset with ancestry proportions estimated using genome-wide data. We show that a panel of 96 AIMs can be used to assess ancestry proportions and to adjust for the confounding effect of the complex five-way admixture that occurred in the South African Coloured population.     

The Kalash Genetic Isolate: Ancient Divergence,Drift, and Selection

The Kalash represent an enigmatic isolated population of Indo-European speakers who have been living for centuries in the Hindu Kush mountain ranges of present-day Pakistan. Previous Y chromosome and mitochondrial DNA markers provided no support for their claimed Greek descent following Alexander III of Macedon''s invasion of this region, and analysis of autosomal loci provided evidence of a strong genetic bottleneck. To understand their origins and demography further, we genotyped 23 unrelated Kalash samples on the Illumina HumanOmni2.5M-8 BeadChip and sequenced one male individual at high coverage on an Illumina HiSeq 2000. Comparison with published data from ancient hunter-gatherers and European farmers showed that the Kalash share genetic drift with the Paleolithic Siberian hunter-gatherers and might represent an extremely drifted ancient northern Eurasian population that also contributed to European and Near Eastern ancestry. Since the split from other South Asian populations, the Kalash have maintained a low long-term effective population size (2,319–2,603) and experienced no detectable gene flow from their geographic neighbors in Pakistan or from other extant Eurasian populations. The mean time of divergence between the Kalash and other populations currently residing in this region was estimated to be 11,800 (95% confidence interval = 10,600−12,600) years ago, and thus they represent present-day descendants of some of the earliest migrants into the Indian sub-continent from West Asia.