Evolutionary Genetics and Admixture in African Populations

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Evolutionary Genetics and Admixture in African Populations

2023-05-01 16:24| 来源: 网络整理| 查看: 265

Abstract

As the ancestral homeland of our species, Africa contains elevated levels of genetic diversity and substantial population structure. Importantly, African genomes are heterogeneous: They contain mixtures of multiple ancestries, each of which have experienced different evolutionary histories. In this review, we view population genetics through the lens of admixture, highlighting how multiple demographic events have shaped African genomes. Each of these historical vignettes paints a recurring picture of population divergence followed by secondary contact. First, we give a brief overview of genetic variation in Africa and examine deep population structure within Africa, including the evidence of ancient introgression from archaic “ghost” populations. Second, we describe the genetic legacies of admixture events that have occurred during the past 10,000 years. This includes gene flow between different click-speaking Khoe-San populations, the stepwise spread of pastoralism from eastern to southern Africa, multiple migrations of Bantu speakers across the continent, as well as admixture from the Middle East and Europe into the Sahel region and North Africa. Furthermore, the genomic signatures of more recent admixture can be found in the Cape Peninsula and throughout the African diaspora. Third, we highlight how natural selection has shaped patterns of genetic variation across the continent, noting that gene flow provides a potent source of adaptive variation and that selective pressures vary across Africa. Finally, we explore the biomedical implications of population structure in Africa on health and disease and call for more ethically conducted studies of genetic variation in Africa.

admixture, africa, demographic history, evolutionary genetics, population genetics, population structureSignificance

Despite recent progress, African populations are still dramatically underrepresented in genetic studies, and more studies of African genetic variation and population structure are needed. Such studies may not only hold new insights about human origins but are also crucial for equitable biomedical research, with implications that possibly extend beyond Africa. In this review, we provide an overview of our current understanding of how admixture—mostly during the last 10,000 years—has shaped present-day population structure in Africa and how recent genetic studies complement linguistics and archeology in reconstructing the history of African populations.

Glossary

Linkage disequilibrium (LD)—The nonrandom association of two alleles at different loci.

Effective population size (Ne)—The number of breeding individuals in an idealized randomly mating population. Ne determines the strength of genetic drift acting on a population.

Population structure—Systematic differences in allele frequencies between subpopulations.

Admixture—The interbreeding of individuals from two or more subpopulations that were isolated for a relatively short evolutionary time.

Out-of-Africa (OOA) model —Hypothesis that anatomically modern humans evolved in Africa and subsequently peopled the rest of the world.

Serial founder effect—The successive loss of genetic variation when populations are sequentially founded by a small number of individuals.

Haplotype—A set of linked genetic variants that are coinherited.

Population bottleneck—An event that drastically reduces the effective size of a population, leading to increased genetic drift.

Genetic cline—A gradual change of allele frequencies over a specified geographic area.

Genetic ancestry—The genealogical paths through which an individual inherits DNA from specific ancestors in a reference population. Individuals with shared genetic ancestry tend to be more genetically similar.

Principal components—A set of uncorrelated variables derived from the original data set through linear transformations, which maximize the variance between samples and reduce the dimensionality of the data while preserving the most important information.

Gene flow—The movement of individuals and their genetic material from one population to another population.

Introgression—The interbreeding of individuals from two or more populations that were isolated for a long evolutionary time but are not yet reproductively isolated.

Holocene—The current geological epoch that started after the Last Glacial Maximum ∼12 kya.

Iron Age—The period of time during human prehistory when people began making tools from iron and steel, extending from ∼4 to 1.5 kya in Africa.

Neolithic (New Stone Age)—The period of time when people began using more sophisticated stone tools, leading to the emergence of farming and herding, extending from ∼12 kya to 6.5 kya in Africa.

Paleolithic (Old Stone Age)—The period of time in human evolution when people initially started using stone tools, extending from ∼3.3 million years ago (Mya) to 12 kya.

Uniparental markers—Mitochondrial DNA and Y chromosomes, which are transmitted exclusively maternally or paternally without recombination.

Fine-mapping—The processes of refining the location of trait-associated variants in the genomic region of interest to identify likely causal variants based on association statistics and linkage disequilibrium patterns.

Isolation-by-distance model—A theoretical framework explaining how genetic differentiation between populations increases with geographic distance due to spatially limited gene flow, that is, decreasing migration rate with increasing distance.

FST (Fixation index)—The extent of genetic differentiation of two populations. Higher values of FST are indicative of greater population structure.

Introduction

Africa exhibits vast cultural and linguistic diversity, including a wide range of subsistence strategies and ∼2,000 spoken languages. In addition, African populations harbor the greatest genetic diversity, exhibit the lowest levels of linkage disequilibrium (LD), have the largest long-term effective population sizes (Ne), and show the deepest split times of all human lineages (Tishkoff et al. 2009; Auton et al. 2015; Mallick et al. 2016; Bergström et al. 2020). For these reasons, Africa is commonly accepted as the cradle of humankind (Henn et al. 2018), and African population history is of exceptional interest to human evolution.

Most of our knowledge about African population history is derived from archeological and linguistic studies, as Africa has long been neglected in genetic studies (Popejoy and Fullerton 2016; Martin et al. 2018; Sirugo et al. 2019; Fatumo et al. 2022). However, archeological and linguistic studies are largely unable to disentangle cultural diffusion from demic diffusion, that is, movements of people (Robertson and Bradley 2000; Diamond and Bellwood 2003). By contrast, genetic studies are uniquely equipped to identify large-scale demic movements (e.g., Tishkoff et al. 2009). In the last decade, the importance of studying genetic variation in Africa has become more appreciated, and a heap of genetic studies of contemporary and ancient individuals has revealed complex population structure and history in Africa, complementing archeological and linguistic studies (e.g., Tishkoff et al. 2009; Schlebusch et al. 2012; Choudhury et al. 2020; Lipson et al. 2022).

In this review, we focus on genetic studies that uncovered extensive archaic, prehistoric, and recent gene flow that has occurred in Africa. We start by putting genetic variation in Africa into a global context and giving a brief overview of population structure in Africa inferred from ancient and extant genomes, focusing on hunter–gatherer groups and deep population structure in the continent. We then discuss how this population structure was shaped by archaic and recent admixture, moving from the deeper past to more recent times. Given the scope of this review paper, we cannot comprehensively review the evolutionary history of every population. Instead, we focus on representative examples of major migratory and admixture events. Finally, we briefly review the evidence for local adaption and discuss the biomedical implication of population structure in Africa. In light of this, we call for more (responsibly conducted) studies of genetic variation in Africa and research capacity building on the African continent. Note that we tried to refer to populations according to current naming conventions, and when we refer to admixture between specific populations, this does not necessarily imply the mixing of these exact populations, but rather the mixing of genetically similar populations.

Patterns of Genetic Variation in Africa

Compared with the rest of the world, each African genome harbors ∼25% more polymorphisms than each non-African genome (Auton et al. 2015; Mallick et al. 2016; Bergström et al. 2020). Furthermore, variants that are rare on a global level ( 10 kya) (Goudie 2003). An additional central Khoe-San–related ancestry component has been identified in more recent studies that leveraged bigger and more diverse data sets (Uren et al. 2016; Montinaro et al. 2017; Vicente, Jakobsson, et al. 2019). Notably, these three ancestry components correlate with geography but not linguistics or present-day subsistence strategy. The Kx`a-speaking Ju|’Hoan and !Xun and the Khoekhoe-speaking Hai||om are representative of the North Khoe-San ancestry component, the Khoekhoe-speaking Nama and Tuu-speaking ‡Khomani and Karretije are representative of the South Khoe-San ancestry component, and all remaining Khoe-San population are representative of the central Khoe-San ancestry component (Montinaro et al. 2017; Vicente, Jakobsson et al. 2019). Interestingly, the pairwise genetic divergences of these three components were found to be similar (i.e., similar fixation index [FST] values), and the divergence time was estimated to be ∼25 kya (95% CI: 18–32 kya) (Montinaro et al. 2017).

Although most of the genetic variation among Khoe-San populations is explained under an isolation-by-distance model (Montinaro et al. 2017; Vicente, Jakobsson, et al. 2019), there is evidence of modest admixture between the three Khoe-San–related ancestry components. In formal admixture tests (f3-analysis), the ‡Khomani (southern component) showed significant evidence of admixture with Taa populations (central), and the Ju|’Hoan (northern) showed significant signs of admixture with the !Xun (northern) and the Naro (central). Additionally, the Naro (central) showed evidence of admixture with the Ju|’Hoan (northern) and another population characterized by the Central Khoe-San component (e.g., Taa or |Gui). However, none of the populations characterized by the central Khoe-San component showed significant evidence of being a mixture between northern and southern Khoe-San groups (Montinaro et al. 2017). Using SpaceMix analyses, Vicente, Jakobsson et al. (2019) found additional evidence for gene flow from the Ju|’Hoan (northern) into the ‡Hoan (central), from the |Gui/Xade San (central) into the Naro (central), and from an undefined Khoe-San population into the Nama (southern). Note that these tests do not definitively establish admixture between specific populations—the actual historical gene flow may have involved other related populations. It has been argued that this gene flow must have occurred within the last 10 ky after the prehistoric lake Makgadikgadi dried up (Barbieri et al. 2014). However, more studies of whole genome sequences are needed for exact dating. For further review of the history of Khoe-San populations, see Pakendorf and Stoneking (2021).

Complex Spread of Pastoralism in Eastern and Southern Africa

Recent genetic studies paint a complex picture of population continuity and admixture in eastern Africa since the introduction of pastoralism in northeastern Africa some 8 kya (e.g., Haber et al. 2016; Skoglund et al. 2017; Prendergast et al. 2019; Naidoo et al. 2020; Wang et al. 2020a). Using DNA from ancient individuals from Kenya and Tanzania, it has been proposed that herding and farming spread in multiple steps into eastern Africa (Prendergast et al. 2019). First, in northeastern Africa, admixture between a population related to contemporary Nilo-Saharan speakers (e.g., the Dinka or Nuer) and a population related to modern groups from northern Africa or the Levant created a group of “early northeastern pastoralists.” This group then migrated to eastern Africa and admixed with local foragers ∼4 kya, receiving ∼20% ancestry from a group related to a 4,500-year-old ancient individual from the Mota cave in Ethiopia that is genetically similar to the isolated, Afro-Asiatic–speaking Aari (Gallego Llorente et al. 2015) and present-day Afro-Asiatic speakers (fig. 4A). Given the high genetic affinity of a pastoralist individual who lived 4000 years ago in northern Sudan with ancient individuals from Kenya and Tanzania, it has been argued that this initial dispersal of northeastern pastoralists into East Africa occurred rapidly (Wang et al. 2022). Lastly, this group received another pulse of gene flow from a population related to Nilo-Saharan–speaking Dinka in Sudan ∼2.2 kya, that is, during the Iron Age (fig. 4A; Prendergast et al. 2019; Fan et al. 2019). Based on varying amounts of Mota-related and Dinka-related ancestry in ancient individuals from the Democratic Republic of Congo, Uganda, and Botswana, it has been argued that a model with repeated, unidirectional gene flow from east African forager groups and Nilo-Saharan–speaking groups into the “early northeastern pastoralist” group provides a better fit (Wang et al. 2020a). However, with the currently available data, it is impossible to distinguish between multiple waves of migration and complex population structure.

Fig. 4.Visual summary of key admixture events in Africa. (A) The stepwise spread of lactose persistence from northeastern Africa into eastern Africa and subsequently into southern Africa. (B) Southward migration of Bantu-speaking people through the rainforest to modern-day Angola (ANG) and Zambia (ZMB) before splitting into eBSPs and seBSPs, in concordance with the late-split hypothesis. (C) Extensive admixture between Sahelian populations with European groups in the West and Middle Eastern groups in the East, but only limited gene flow among Sahelian populations. (D) Repetitive gene flow from the Middle East/Europe and sub-Saharan Africa into Northern African populations.Open in new tabDownload slide

Visual summary of key admixture events in Africa. (A) The stepwise spread of lactose persistence from northeastern Africa into eastern Africa and subsequently into southern Africa. (B) Southward migration of Bantu-speaking people through the rainforest to modern-day Angola (ANG) and Zambia (ZMB) before splitting into eBSPs and seBSPs, in concordance with the late-split hypothesis. (C) Extensive admixture between Sahelian populations with European groups in the West and Middle Eastern groups in the East, but only limited gene flow among Sahelian populations. (D) Repetitive gene flow from the Middle East/Europe and sub-Saharan Africa into Northern African populations.

In line with archeological studies, genetic studies of Khoe-San confirmed that pastoralism spread from East Africa to southern Africa by demic diffusion (Breton et al. 2014; Macholdt et al. 2014; Ranciaro et al. 2014; Schlebusch et al. 2017; Skoglund et al. 2017). Khoekhoe-speaking populations (e.g., the Nama), who currently practice a pastoralist lifestyle, have a high-frequency lactase persistence (LP) allele that is also found in East African populations (Schlebusch et al. 2012; Breton et al. 2014; Macholdt et al. 2014). This “East African” LP single nucleotide polymorphism (SNP) (14010G > C) is distinct from the “European” LP SNP (1391 °C > T) and is rare in southern African Bantu-speaking groups (Breton et al. 2014; Macholdt et al. 2014). Among Khoe-San groups, this “East African” LP SNP is found at the highest frequency in the Nama with a frequency of ∼35%, which is much higher than expected given the ∼13% East African admixture fraction in the Nama, suggesting positive selection (Breton et al. 2014; Macholdt et al. 2014). Interestingly, Prendergast et al. found that the “East African” LP allele is largely absent from ancient pastoralist individuals from Kenya and Tanzania, indicating that east African pastoralists were lactose intolerant as recently as 3–1 kya (Prendergast et al. 2019). However, it is also possible that this allele has not been detected in ancient samples due to a limited number of surveyed individuals.

A direct link between Afro-Asiatic–speaking eastern African (i.e., Amhara- or Oromo-related ancestry) and southern African pastoralists has been established by showing that a 1,200-year-old individual from southern Africa, who has genetic similarities with modern Khoekhoe-speaking pastoralist groups (e.g., the Nama), traces ∼40% of their ancestry to a Eurasian admixed group related to a 3,100-year-old pastoralist individual from Luxmanda, Tanzania (Skoglund et al. 2017). Thus, this study indicates that admixture of Khoe-San groups with eastern African pastoralists occurred at least ∼1.2 kya (fig. 4A). Concordantly, another study estimated that all modern Khoe-San populations received 9–30% gene flow from an admixed East African/Eurasian pastoralist group 1.5–1.3 kya (Schlebusch et al. 2017). Furthermore, east African pastoralist contributions to Khoe-San groups are lower on X chromosomes than autosomes (Vicente et al. 2021), indicating that male-biased admixture occurred. Overall, these results suggest that eastern African pastoralists reached southern Africa prior to and independently of Bantu-speaking groups. For a detailed review of the spread of lactase persistence in Africa, see Campbell and Ranciaro (2021).

Multiple Migration Waves of Bantu Speakers

Genetic studies showed that the spread of Bantu languages, agricultural practices, and iron use 5–3 kya was accompanied by multiple migration waves of Bantu speakers from western Africa (i.e., current eastern Nigeria and western Cameroon) to other regions in sub-Saharan Africa (Tishkoff et al. 2009; Schlebusch et al. 2012; Li et al. 2014). Consequently, the Bantu expansion extensively contributed to population structure due to differential levels of admixture with and replacement of local hunter–gatherer groups over the past 3,500 years (Skoglund et al. 2017; Sengupta et al. 2021; González-Santos et al. 2022).

Two major migratory routes of Bantu-speaking populations (BSPs) have been hypothesized. The early-split hypothesis suggests that BSPs split at an early stage north of the rainforest, with one group then moving directly South through the rainforest, whereas the other migrated East, north of the rainforest, toward the Great African Lakes. In contrast, the late-split hypothesis states that BSPs first migrated South through the rainforest before splitting into two groups, with one moving further South and the other one migrating East toward the Great African Lakes. Similarly to phylolinguistics (e.g., Rexová et al. 2006), genetics are in favor of the late-split hypothesis, as eastern BSPs (eBSPs) and south-eastern BSPs (seBSPs) are genetically closer to western BSPs (wBSPs) south of the rainforest (i.e., Angola) than to wBSPs north of the rainforest (Patin et al. 2017). A subsequent study using samples from wider geographic and ethnolinguistic groups showed that eBSPs, seBSPs, and southwestern BSPs (swBSPs) are genetically closest to Bantu speakers from Zambia (Choudhury et al. 2020). Together, these findings suggest that Bantu speakers first migrated South through the rainforest to Angola and subsequently to Zambia before splitting into two groups (fig. 4B).

In western Africa, wBSPs asymmetrically mixed with resident RHG groups, with RHG groups receiving higher amounts of gene flow from wBSPs (Jarvis et al. 2012; Hsieh, Veeramah, et al. 2016; Patin et al. 2017; Lopez et al. 2018). wBSPs in Angola have small amounts of RHG-related ancestry from an admixture event that occurred after the split of BSPs ∼800 ya (Patin et al. 2017), although a recent study inferred a more ancient admixture date of ∼1.9 kya for Bantu speakers in Cabinda, Angola (Tallman et al. 2022). The amount of gene flow from wBSPs into individual RHG groups varied. Whereas the Mbuti and the Biaka have 350 ya (de Wit et al. 2010; Petersen et al. 2013; Choudhury et al. 2017). The SAC population represents >49% of the estimated 7 million inhabitants in this province, with the vast majority being historically Afrikaans speakers (a unique South African language ancestrally linked to Dutch), although this is more recently changing (Patterson et al. 2010; Republic of South Africa 2021). Their complex origin of admixture is attributed to significant historical events that occurred within the last few millennia, starting ∼1.7 kya with the arrival of Bantu-speaking agro-pastoralists in South Africa (Sengupta et al. 2021). During the last few centuries, European colonization of the Cape by the Dutch, Germans, and French, later followed by British seizure and rule, contributed to the complex admixture patterns at the Western Cape. During this time, slaves were trade by the Dutch East India Company from East Africa, Madagascar and surrounding islands, India, and Indonesia, leading to settler–slave admixture, including indigenous Khoe-San people (de Wit et al. 2010; Patterson et al. 2010; Montinaro and Capelli 2018). Genomic studies of the SAC population revealed that these historic events correlate with the complex five-way admixture observed in this population, with ancestral contributions occurring predominantly from the indigenous Khoe-San, the Bantu-speaking Africans, European-descent groups, and Southeast Asian and South Asian populations (de Wit et al. 2010; Daya et al. 2013; Petersen et al. 2013; Chimusa et al. 2014; Choudhury et al. 2017; Swart et al. 2020). In addition, cultural and religious practices contributed to the high degree of heterogeneity in ancestral contributions among SAC individuals sampled from different regions of South Africa (de Wit et al. 2010; Daya et al. 2014; Choudhury et al. 2017).

Several studies have revealed a sex-biased gene flow in SAC that supports the historical records indicating that almost all mixed marriages were between a male settler and either a free Black female (where the man bought the slave their freedom) or an indigenous Khoe-San female (Patterson et al. 2010; Petersen et al. 2013; Choudhury et al. 2017). Petersen et al. (2013) used uniparental markers to ascertain likely ancestral contributions using unique population-specific mtDNA and Y chromosomal haplogroup identifiers. Khoe-San derived maternal lineage L0d had a 68% representation in the SAC group studied, while the M/N Eurasian mtDNA lineages were only represented at low frequencies. In contrast, there was a significant Eurasian paternal contribution (71.4%) defined by haplogroups R/I/G/N/O/J in the same group, and the Western European R1b haplogroup was prevalent at 44.4%. Similar distributions of mtDNA and Y haplogroups were observed from whole genome sequencing data of a small group of SAC males from the Western Cape region (Choudhury et al. 2017). Overall, these findings demonstrate that recent admixture involved sex-biased gene flow.

Admixture in the African Diaspora following the Transatlantic Slave Trade

As a consequence of the transatlantic slave trade, >12.5 million people were forcefully displaced from Africa to the Americas between the sixteenth and nineteenth centuries, creating the largest present-day African diaspora (Eltis 2007). Subsequent admixture with European-like ancestry and Native American-like ancestry populations was spatially and temporally complex, leading to varying amounts of recent African-like ancestry in admixed populations in the Americas (Bryc et al. 2010; Ongaro et al. 2019; Gouveia et al. 2020; Micheletti et al. 2020). African-related ancestry is the highest in the British Caribbean (∼75%) and the United States (∼71%) and the lowest in South America (∼11–12%) and Central America (∼8%, including Mexico) (Micheletti et al. 2020). The remaining ancestry can be predominantly assigned as European-like, with minor contributions from Native American groups in some populations (Micheletti et al. 2020). Additionally, despite more males being deported to the Americas, it has been shown that African contributions to gene pools in the Americas were likely female-biased, whereas European contributions were likely male-biased (Mathias et al. 2016; Ongaro et al. 2019; Micheletti et al. 2020). However, the magnitude of the sex bias is difficult to pinpoint from X chromosomal and autosomal ancestry proportions due to potential confounding from complex demographic histories, among others (Pfennig and Lachance 2023).

Broadly in agreement with historical records of the transatlantic slave trade, genetic studies of admixed populations from the Americas showed that most of the African ancestry can be traced to West–Central Africa, for example, similar to the Yoruba or Esan from Nigeria, with a smaller fraction being similar to south-eastern African ancestry, for example, Mbukushu-like from Botswana and/or Luhya-like from Kenya (Patin et al. 2014; Gouveia et al. 2020; Micheletti et al. 2020). However, the distribution of these African ancestries varies between different populations in the Americas, with western/central African-related ancestry being more common in the northern parts, for example, the United States, and south-eastern African-related ancestry being more common in the southern parts, for example, Brazil (Gouveia et al. 2020). The different sources of African-like ancestry and the different timing of admixture for different African source populations in the Americas may be attributed to geography and changing geopolitics at the time, influencing the voyage routes (Ongaro et al. 2019; Gouveia et al. 2020). Interestingly, there is less differentiation between the African ancestries found in admixed genomes in the Americas (as quantified by FST statistics) compared with what is seen between each of the contributing ancestries in Africa (Gouveia et al. 2020). For a more granular review of the demographic histories in light of the transatlantic slave trade of admixed population in the Americas, see Fortes-Lima and Verdu (2021).

Evidence of Local Adaptation in African Genomes

Environmental conditions vary over time and space. Because of this, African populations have experienced a heterogeneous mix of selection pressures. Nonetheless, African populations are connected via gene flow, which can serve as a potent source of adaptive variation. Although the specific genes implicated in African scans of selection vary by the method used and population studied, some common themes arise. Regulatory DNA appears to be a frequent target of adaptation in African genomes (Quiver and Lachance 2022). Furthermore, many noteworthy instances of selection in Africa are associated with physiology, diet, or pathogen pressure.

One key evolutionary challenge involves physiological responses to extreme conditions, including high-altitude desert environments. In Africa, the Ethiopian Highlands are 1,500 meters above sea level, with summits as high as 4,550 meters above sea level. For example, the Amahara people have adapted to low barometric pressure and hypoxia in the Ethiopian Highlands over the past 5,000 years. Interestingly, the specific adaptive mutations seen in the Ethiopian Highlands differ from what has been observed in the Tibetan Plateau and the Andean Altiplano. Selection scans comparing Amhara individuals living at high altitude to individuals living in lowland areas have implicated a number of adaptive loci, including rs10803083, a SNP that is associated with hemoglobin levels (Alkorta-Aranburu et al. 2012); BHLHE41, a gene that is involved in hypoxia response and circadian rhythm (Huerta-Sánchez et al. 2013); and EGNL1, a gene that plays a central role in mammalian oxygen homeostasis (Scheinfeldt et al. 2012). Intriguingly, EGLN1 has also been implicated in selection scans of the click-speaking Sandawe people, who are traditional foragers from Tanzania (Lachance et al. 2012). This suggests that the benefits of adaptive EGLN1 haplotypes may extend beyond high-altitude conditions.

Arid desert environments also present an evolutionary challenge in Africa. For instance, despite frequent droughts, the ‡Khomani San have lived in the Kalahari Desert for thousands of years. Using SWIF(r), an approach that combines multiple statistics to generate posterior probabilities of sweeps, researchers have identified multiple genes associated with adiponectin, body mass index (BMI), and metabolism as potential targets of selection in the ‡Khomani San (Sugden et al. 2018).

Another example of adaptation to extreme conditions are RHG groups, who evolved a short stature (mean adult height 0.05) but rare outside of Africa (i.e., frequency

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Ansari-Pour N, Plaster CA, Bradman N.

2013. Evidence from Y-chromosome analysis for a late exclusively eastern expansion of the Bantu-speaking people. Eur J Hum Genet. 21:423–429.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Arauna LR, et al. 

2017. Recent historical migrations have shaped the gene pool of Arabs and Berbers in North Africa. Mol Biol Evol. 34:318–329.

Google Scholar

PubMedOpenURL Placeholder Text

WorldCat

 

Auton A, et al. 

2015. A global reference for human genetic variation. Nature 526:68–74.

Google Scholar

PubMedOpenURL Placeholder Text

WorldCat

 

Bajić V, et al. 

2018. Genetic structure and sex-biased gene flow in the history of southern African populations. Am J Phys Anthropol. 167:656–671.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Barbieri C, et al. 

2014. Unraveling the complex maternal history of Southern African Khoisan populations. Am J Phys Anthropol. 153:435–448.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Batai K, Hooker S, Kittles RA.

2021. Leveraging genetic ancestry to study health disparities. Am J Phys Anthropol. 175:363–375.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Bergström A, et al. 

2020. Insights into human genetic variation and population history from 929 diverse genomes. Science 367:eaay5012.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Bower J.

1991. The pastoral Neolithic of East Africa. J World Prehistory 5:49–82.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Bress A, et al. 

2012. Effect of NQO1 and CYP4F2 genotypes on warfarin dose requirements in Hispanic–Americans and African–Americans. Pharmacogenomics 13:1925–1935.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Breton G, et al. 

2014. Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists. Curr Biol. 24:852–858.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Bryc K, et al. 

2010. Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci. 107:786–791.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Busby GB, et al. 

2016. Admixture into and within sub-Saharan Africa Pickrell, JK, editor. eLife 5:e15266.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Campbell MC, Ranciaro A.

2021. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet. 30:R98–R109.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Cavalli-Sforza LL, Piazza A.

1993. Human genomic diversity in Europe: a summary of human genomic diversity in Europe: a summary of recent research and prospects for the future. Eur J Hum Genet. 1:3–18.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Černý V, Fortes-Lima C, Tříska P.

2021. Demographic history and admixture dynamics in African Sahelian populations. Hum Mol Genet. 30:R29–R36.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Chaichoompu K, et al. 

2020. A different view on fine-scale population structure in Western African populations. Hum Genet. 139:45–59.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Chen L, Wolf AB, Fu W, Li L, Akey JM.

2020. Identifying and interpreting apparent neanderthal ancestry in African individuals. Cell 180:677–687.e16.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Chimusa ER, et al. 

2013. Determining ancestry proportions in complex admixture scenarios in South Africa using a novel proxy ancestry selection method. PLoS One 8:e73971.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Chimusa ER, et al. 

2014. Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. Hum Mol Genet. 23:796–809.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Choudhury A, et al. 

2017. Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nat Commun. 8:2062.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Choudhury A, et al. 

2020. High-depth African genomes inform human migration and health. Nature 586:741–748.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Choudhury A, Sengupta D, Ramsay M, Schlebusch C.

2021. Bantu-speaker migration and admixture in Southern Africa. Hum Mol Genet. 30:R56–R63.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Čížková M, et al. 

2017. Genetic structure of the western and Eastern African Sahel/Savannah belt and the role of nomadic pastoralists as inferred from the variation of D-loop mitochondrial DNA sequences. Hum Biol. 89:281–302.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Coelho M, Sequeira F, Luiselli D, Beleza S, Rocha J.

2009. On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol Biol. 9:80.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Crawford NG, et al. 

2017. Loci associated with skin pigmentation identified in African populations. Science 358:eaan8433.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Dandara C, et al. 

2011. Genetic variants in CYP (-1A2, -2C9, -2C19, -3A4 and -3A5), VKORC1 and ABCB1 genes in a black South African population: a window into diversity. Pharmacogenomics 12:1663–1670.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

D’Atanasio E, et al. 

2018. The peopling of the last Green Sahara revealed by high-coverage resequencing of trans-Saharan patrilineages. Genome Biol. 19:20.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Daya M, et al. 

2013. A panel of ancestry informative markers for the complex five-way admixed South African Coloured population. PLoS One 8:e82224.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Daya M, et al. 

2014. Using multi-way admixture mapping to elucidate TB susceptibility in the South African Coloured population. BMC Genomics 15:1021.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

de Wit E, et al. 

2010. Genome-wide analysis of the structure of the South African Coloured population in the Western Cape. Hum Genet. 128:145–153.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Diallo MY, et al. 

2022. Circum-Saharan prehistory through the lens of mtDNA diversity. Genes (Basel). 13:533.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Diamond J, Bellwood P.

2003. Farmers and their languages: the first expansions. Science 300:597–603.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Durvasula A, Sankararaman S.

2020. Recovering signals of ghost archaic introgression in African populations. Sci Adv. 6:eaax5097.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Eltis D.

2007. A brief overview of the trans-atlantic slave trade,’ slave voyages: the Trans-Atlantic Slave Trade Database. https://www.slavevoyages.org/ (Accessed July 6, 2021).

Fadhlaoui-Zid K, et al. 

2011. Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. Am J Phys Anthropol. 145:107–117.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Fadhlaoui-Zid K, et al. 

2013. Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa. PLoS One 8:e80293.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Fan S, et al. 

2019. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 20:1–14.

Google Scholar

PubMedOpenURL Placeholder Text

WorldCat

 

Fan S, et al. 

2023. Whole-genome sequencing reveals a complex African population demographic history and signatures of local adaptation. Cell 186:923–939.e14.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Fatumo S, et al. 

2022. A roadmap to increase diversity in genomic studies. Nat Med. 28:243–250.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Fortes-Lima C, et al. 

2022. Demographic and selection histories of populations across the Sahel/Savannah belt. Mol Biol Evol. 39:msac209.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Fortes-Lima C, Verdu P.

2021. Anthropological genetics perspectives on the transatlantic slave trade. Hum Mol Genet. 30:R79–R87.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Fregel R, et al. 

2018. Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe. Proc Natl Acad Sci. 115:6774–6779.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Gallego Llorente M, et al. 

2015. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350:820–822.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Gibbon VE.

2020. African ancient DNA research requires robust ethics and permission protocols. Nat Rev Genet. 21:645–647.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

González-Santos M, et al. 

2022. Exploring the relationships between genetic, linguistic and geographic distances in Bantu-speaking populations. Am J Biol Anthropol. 179:104–117.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Gopalan S, et al. 

2022. Hunter–gatherer genomes reveal diverse demographic trajectories during the rise of farming in Eastern Africa. Curr Biol. 32:1852–1860.e5.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Goudie AS.

2003. Great warm deserts of the world: landscapes and evolution. Oxford, New York: Oxford University Press.

Google Scholar

Google Preview

OpenURL Placeholder Text

WorldCat

COPAC 

Gouveia MH, et al. 

2020. Origins, admixture dynamics, and homogenization of the African gene pool in the Americas. Mol Biol Evol. 37:1647–1656.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Green RE, et al. 

2010. A draft sequence of the neandertal genome. Science 328:710–722.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Gurdasani D, et al. 

2015. The African Genome Variation Project shapes medical genetics in Africa. Nature 517:327–332.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Haak W, et al. 

2010. Ancient DNA from European Early Neolithic farmers reveals their Near Eastern affinities. PLOS Biol. 8:e1000536.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Haber M, et al. 

2016. Chad genetic diversity reveals an African history marked by multiple Holocene Eurasian migrations. Am J Hum Genet. 99:1316–1324.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hamid I, Korunes KL, Beleza S, Goldberg A.

2021. Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde przeworski, M, kana, BD, racimo, F, & busby, G, editors. eLife 10:e63177.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Hammer MF, Woerner AE, Mendez FL, Watkins JC, Wall JD.

2011. Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci. 108:15123–15128.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Harvati K, et al. 

2011. The later stone age Calvaria from Iwo Eleru, Nigeria: morphology and chronology. PLoS One 6:e24024.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Henn BM, et al. 

2011. Hunter–gatherer genomic diversity suggests a Southern African origin for modern humans. Proc Natl Acad Sci. 108:5154–5162.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Henn BM, et al. 

2012. Genomic ancestry of North Africans supports back-to-Africa migrations. PLOS Genet. 8:e1002397.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Henn BM, Steele TE, Weaver TD.

2018. Clarifying distinct models of modern human origins in Africa. Curr Opin Genet Dev. 53:148–156.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hervella M, et al. 

2016. The mitogenome of a 35,000-year-old homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Sci Rep. 6:25501.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hey J, et al. 

2018. Phylogeny estimation by integration over isolation with migration models. Mol Biol Evol. 35:2805–2818.

Google Scholar

PubMedOpenURL Placeholder Text

WorldCat

 

Hindorff LA, et al. 

2018. Prioritizing diversity in human genomics research. Nat Rev Genet. 19:175–185.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hollfelder N, et al. 

2017. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLOS Genet. 13:e1006976.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Hollfelder N, Breton G, Sjödin P, Jakobsson M.

2021. The deep population history in Africa. Hum Mol Genet. 30:R2–R10.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hsieh P, Veeramah KR, et al. 

2016. Whole-genome sequence analyses of Western Central African pygmy hunter–gatherers reveal a complex demographic history and identify candidate genes under positive natural selection. Genome Res. 26:279–290.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Hsieh P, Woerner AE, et al. 

2016. Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African pygmies. Genome Res 26(3):291–300.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Huerta-Sánchez E, et al. 

2013. Genetic signatures reveal high-altitude adaptation in a set of Ethiopian populations. Mol Biol Evol. 30:1877–1888.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Jallow M, et al. 

2009. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet. 41:657–665.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Jarvis JP, et al. 

2012. Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies. PLOS Genet. 8:e1002641.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Johnson J, et al. 

2017. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for pharmacogenetics-guided warfarin dosing: 2017 update. Clin Pharmacol Ther. 102:397–404.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Kariuki SN, Williams TN.

2020. Human genetics and malaria resistance. Hum Genet. 139:801–811.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Karlsson EK, Kwiatkowski DP, Sabeti PC.

2014. Natural selection and infectious disease in human populations. Nat Rev Genet. 15:379–393.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Kim HL, et al. 

2014. Khoisan hunter–gatherers have been the largest population throughout most of modern-human demographic history. Nat Commun. 5:5692.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lachance J, et al. 

2012. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter–gatherers. Cell 150:457–469.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lazaridis I, et al. 

2016. Genomic insights into the origin of farming in the ancient near east. Nature 536:419–424.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lemke AA, et al. 

2022. Addressing underrepresentation in genomics research through community engagement. Am J Hum Genet. 109:1563–1571.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Li S, Schlebusch C, Jakobsson M.

2014. Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proc R Soc B Biol Sci. 281:20141448.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Lipson M, et al. 

2020. Ancient West African foragers in the context of African population history. Nature 577:665–670.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lipson M, et al. 

2022. Ancient DNA and deep population structure in sub-Saharan African foragers. Nat 2022:1–7.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Lokki AI, et al. 

2011. Lactase persistence genotypes and malaria susceptibility in Fulani of Mali. Malar J. 10:9.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lopez M, et al. 

2018. The demographic history and mutational load of African hunter–gatherers and farmers. Nat Ecol Evol. 2:721–730.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lorente-Galdos B, et al. 

2019. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations. Genome Biol. 20:77.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lucas-Sánchez M, Font-Porterias N, Calafell F, Fadhlaoui-Zid K, Comas D.

2021. Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. Sci Rep. 11:21125.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Lucas-Sánchez M, Serradell JM, Comas D.

2021. Population history of North Africa based on modern and ancient genomes. Hum Mol Genet. 30:R17–R23.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Macholdt E, et al. 

2014. Tracing pastoralist migrations to Southern Africa with lactase persistence alleles. Curr Biol. 24:875–879.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Majara L, et al. 

2023. Low and differential polygenic score generalizability among African populations due largely to genetic diversity. Hum Genet Genomics Adv. 4:100184.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Mallick S, et al. 

2016. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538:201–206.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Manning K, Timpson A.

2014. The demographic response to Holocene climate change in the Sahara. Quat Sci Rev. 101:28–35.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Marcus J, Ha W, Barber RF, Novembre J.

2021. Fast and flexible estimation of effective migration surfaces perry, GH, alves, I, & tansey, W, editors. eLife 10:e61927.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Marshall F, Hildebrand E.

2002. Cattle before crops: the beginnings of food production in Africa. J World Prehistory 16:99–143.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Martin AR, Teferra S, Möller M, Hoal EG, Daly MJ.

2018. The critical needs and challenges for genetic architecture studies in Africa. Curr Opin Genet Dev. 53:113–120.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Mathias RA, et al. 

2016. A continuum of admixture in the western hemisphere revealed by the African diaspora genome. Nat Commun. 7:12522.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Matjuda EN, Engwa GA, Anye SNC, Nkeh-Chungag BN, Goswami N.

2021. Cardiovascular risk factors and their relationship with vascular dysfunction in South African children of African ancestry. J Clin Med. 10:354.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Meyer M, et al. 

2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–226.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Micheletti SJ, et al. 

2020. Genetic consequences of the transatlantic slave trade in the Americas. Am J Hum Genet. 107:265–277.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Mölder F, et al. 

2021. Sustainable data analysis with Snakemake. F1000Res 10:33.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Montinaro F, et al. 

2017. Complex ancient genetic structure and cultural transitions in Southern African populations. Genetics 205:303–316.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Montinaro F, Capelli C.

2018. The evolutionary history of Southern Africa. Curr Opin Genet Dev. 53:157–164.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Naidoo T, et al. 

2020. Y-chromosome variation in Southern African Khoe-San populations based on whole-genome sequences. Genome Biol Evol. 12:1031–1039.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Ndadza A, et al. 

2021. Profiling of warfarin pharmacokinetics-associated genetic variants: Black Africans portray unique genetic markers important for an African specific warfarin pharmacogenetics-dosing algorithm. J Thromb Haemost. 19:2957–2973.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Newman J.

1995. The peopling of Africa: a geographic interpretation. New Haven: Yale University Press.

Google Scholar

Google Preview

OpenURL Placeholder Text

WorldCat

COPAC 

Norris ET, et al. 

2020. Admixture-enabled selection for rapid adaptive evolution in the Americas. Genome Biol. 21:29.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Nováčková J, et al. 

2020. Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel. Am J Phys Anthropol. 171:496–508.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Ongaro L, et al. 

2019. The genomic impact of European colonization of the Americas. Curr Biol. 29:3974–3986.e4.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pagani L, et al. 

2012. Ethiopian genetic diversity reveals linguistic stratification and complex influences on the Ethiopian gene pool. Am J Hum Genet. 91:83–96.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pagani L, et al. 

2015. Tracing the route of modern humans out of Africa by using 225 human genome sequences from Ethiopians and Egyptians. Am J Hum Genet. 96:986–991.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pakendorf B, Stoneking M.

2021. The genomic prehistory of peoples speaking Khoisan languages. Hum Mol Genet. 30:R49–R55.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Patin E, et al. 

2014. The impact of agricultural emergence on the genetic history of African rainforest hunter–gatherers and agriculturalists. Nat Commun. 5:3163.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Patin E, et al. 

2017. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America. Science 356:543 LP–543546.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Patin E, Quintana-Murci L.

2018. The demographic and adaptive history of Central African hunter–gatherers and farmers. Curr Opin Genet Dev. 53:90–97.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Patterson N, et al. 

2010. Genetic structure of a unique admixed population: implications for medical research. Hum Mol Genet. 19:411–419.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pennarun E, et al. 

2012. Divorcing the Late Upper Palaeolithic demographic histories of mtDNA haplogroups M1 and U6 in Africa. BMC Evol Biol. 12:234.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pereira L, et al. 

2010. Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel. Eur J Hum Genet. 18:915–923.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pereira L, Mutesa L, Tindana P, Ramsay M.

2021. African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet. 22:284–306.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Perera MA, et al. 

2013. Genetic variants associated with warfarin dose in African–American individuals: a genome-wide association study. Lancet. 382:790–796.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Perry GH, et al. 

2007. Diet and the evolution of human amylase gene copy number variation. Nat Genet. 39:1256–1260.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Petersen DC, et al. 

2013. Complex patterns of genomic admixture within Southern Africa. PLOS Genet. 9:e1003309.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Pfennig A, Lachance J.

2023. Challenges of accurately estimating sex-biased admixture from X chromosomal and autosomal ancestry proportions. Am J Hum Genet. 110:359–367.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Pickrell JK, et al. 

2012. The genetic prehistory of Southern Africa. Nat Commun. 3:1143.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Plagnol V, Wall JD.

2006. Possible ancestral structure in human populations. PLOS Genet. 2:e105.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Popejoy AB, Fullerton SM.

2016. Genomics is failing on diversity. Nat 5387624 538:161–164.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Prendergast ME, et al. 

2019. Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa. Science 365:eaaw6275.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Prendergast ME.

2020. The history of Eastern African foragers. Oxf Res Encycl Afr Hist. https://doi.org/10.1093/acrefore/9780190277734.013.405

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Prendergast ME, Sawchuk EA, Sirak KA.

2022. Genetics and the African past. Oxf Res Encycl Afr Hist. https://doi.org/10.1093/acrefore/9780190277734.013.143

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Priehodová E, et al. 

2017. The historical spread of Arabian pastoralists to the Eastern African Sahel evidenced by the lactase persistence −13,915*G allele and mitochondrial DNA. Am J Hum Biol. 29:e22950.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Priehodová E, et al. 

2020. Sahelian pastoralism from the perspective of variants associated with lactase persistence. Am J Phys Anthropol. 173:423–436.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Privé F, et al. 

2022. Portability of 245 polygenic scores when derived from the UK Biobank and applied to 9 ancestry groups from the same cohort. Am J Hum Genet. 109:12–23.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Quiver MH, Lachance J.

2022. Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. Hum Genet Genomics Adv. 3:100083.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Ragsdale AP et al. 

2022. A weakly structured stem for human origins in Africa. bioRxiv. https://doi.org/10.1101/2022.03.23.485528

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Ranciaro A, et al. 

2014. Genetic origins of lactase persistence and the spread of pastoralism in Africa. Am J Hum Genet. 94:496–510.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Rasmussen M, et al. 

2011. An aboriginal Australian genome reveals separate human dispersals into Asia. Science 334:94–98.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Rees JS, Castellano S, Andrés AM.

2020. The genomics of human local adaptation. Trends Genet. 36:415–428.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Republic of South Africa SD.

2021. Statistical release (P0302): mid-year population estimates 2021. http://www.statssa.gov.za/publications/P0302/P03022021.pdf

Rexová K, Bastin Y, Frynta D.

2006. Cladistic analysis of Bantu languages: a new tree based on combined lexical and grammatical data. Naturwissenschaften 93:189–194.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Robertson JH, Bradley R.

2000. A new paradigm: the African early iron age without Bantu migrations. Hist Afr. 27:287–323.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Rotimi CN, Jorde LB.

2010. Ancestry and disease in the age of genomic medicine. N Engl J Med. 363:1551–1558.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schaefer NK, Shapiro B, Green RE.

2021. An ancestral recombination graph of human, neanderthal, and Denisovan genomes. Sci Adv. 7:1–17.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Scheinfeldt LB, et al. 

2012. Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biol. 13:R1.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Scheinfeldt LB, et al. 

2019. Genomic evidence for shared common ancestry of East African hunting–gathering populations and insights into local adaptation. Proc Natl Acad Sci. 116:4166–4175.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schlebusch CM, et al. 

2012. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338:374–379.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schlebusch CM, et al. 

2017. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358:652–655.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schlebusch CM, et al. 

2020. Khoe-San genomes reveal unique variation and confirm the deepest population divergence in homo sapiens. Mol Biol Evol. 37:2944–2954.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schlebusch CM, Jakobsson M.

2018. Tales of human migration, admixture, and selection in Africa. Annu Rev Genomics Hum Genet. 19:405–428.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Schlebusch CM, Sjödin P, Skoglund P, Jakobsson M.

2013. Stronger signal of recent selection for lactase persistence in Maasai than in Europeans. Eur J Hum Genet. 21:550–553.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Segurel L, Bon C.

2017. On the evolution of lactase persistence in humans. Annu Rev Genomics Hum Genet. 18:297–319.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Semo A, et al. 

2020. Along the Indian ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion. Mol Biol Evol. 37:406–416.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Sengupta D, et al. 

2021. Genetic substructure and complex demographic history of South African Bantu speakers. Nat Commun. 121 12:1–13.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Serra-Vidal G, et al. 

2019. Heterogeneity in Palaeolithic population continuity and Neolithic expansion in North Africa. Curr Bioldm 29:3953–3959.e4.

Google Scholar

CrossrefSearch ADS

WorldCat

 

Shriner D, Rotimi CN.

2018a. Genetic history of Chad. Am J Phys Anthropol. 167:804–812.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Shriner D, Rotimi CN.

2018b. Whole-genome-sequence-based haplotypes reveal single origin of the sickle allele during the Holocene wet phase. Am J Hum Genet. 102:547–556.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Sirugo G, Williams SM, Tishkoff SA.

2019. The missing diversity in human genetic studies. Cell 177:1080.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Sjöstrand AE, et al. 

2021. Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians. Eur J Hum Genet. 29:325–337.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Skoglund P, et al. 

2017. Reconstructing prehistoric African population structure. Cell 171:59–71.e21.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Solé-Morata N, et al. 

2017. Whole Y-chromosome sequences reveal an extremely recent origin of the most common North African paternal lineage E-M183 (M81). Sci Rep. 7:15941.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Sugden LA, et al. 

2018. Localization of adaptive variants in human genomes using averaged one-dependence estimation. Nat Commun. 9:703.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Swart Y, Uren C, van Helden PD, Hoal EG, Möller M.

2021. Local ancestry adjusted allelic association analysis robustly captures tuberculosis susceptibility loci. Front Genet. 12:716558.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Swart Y, van Eeden G, Sparks A, Uren C, Möller M.

2020. Prospective avenues for human population genomics and disease mapping in Southern Africa. Mol Genet Genomics 295:1079–1089.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Tallman S, Sungo M das D, Saranga S, Beleza S.

2022. Whole-genome sequencing of Bantu-speakers from Angola and Mozambique reveals complex dispersal patterns and interactions throughout sub-Saharan Africa. bioRxiv. https://doi.org/10.1101/2022.02.07.478793

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Tishkoff SA, et al. 

2009. The genetic structure and history of Africans and African Americans. Science 324:1035–1044.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Triska P, et al. 

2015. Extensive admixture and selective pressure across the Sahel belt. Genome Biol Evol. 7:3484–3495.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Uren C, et al. 

2016. Fine-scale human population structure in Southern Africa reflects ecogeographic boundaries. Genetics 204:303–314.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Vai S, et al. 

2019. Ancestral mitochondrial N lineage from the Neolithic ‘green’ Sahara. Sci Rep. 9:3530.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Van De Loosdrecht M, et al. 

2018. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 360:548–552.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Verdu P, et al. 

2013. Sociocultural behavior, sex-biased admixture, and effective population sizes in Central African pygmies and non-pygmies. Mol Biol Evol. 30:918–937.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Vicente M, et al. 

2021. Male-biased migration from East Africa introduced pastoralism into Southern Africa. BMC Biol. 19:259.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM.

2019. Genetic affinities among Southern Africa hunter–gatherers and the impact of admixing farmer and herder populations. Mol Biol Evol. 36:1849–1861.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Vicente M, Priehodová E, et al. 

2019. Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait. BMC Genomics 20:915.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Wall JD, et al. 

2019. Identification of African-specific admixture between modern and archaic humans. Am J Hum Genet. 105:1254–1261.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Wang K, et al. 

2020a. Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa. Sci Adv. 6:eaaz0183.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Wang K, et al. 

2022. 4000-Year-old hair from the Middle Nile highlights unusual ancient DNA degradation pattern and a potential source of early Eastern Africa pastoralists. Sci Rep. 12:20939.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Wang K, Mathieson I, O’Connell J, Schiffels S.

2020. Tracking human population structure through time from whole genome sequences. PLOS Genet. 16:e1008552.

Google Scholar

OpenURL Placeholder Text

WorldCat

 

Wohlers I, et al. 

2020. An integrated personal and population-based Egyptian genome reference. Nat Commun. 11:4719.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

World Health Organization.

2021. World malaria report 2021. Geneva.

Xu D, et al. 

2017. Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation. Mol Biol Evol. 34:2704–2715.

Google Scholar

CrossrefSearch ADS PubMed

WorldCat

 

Zhou Q, Zhao L, Guan Y.

2016. Strong selection at MHC in Mexicans since admixture. PLOS Genet. 12:e1005847.

Google Scholar

OpenURL Placeholder Text

WorldCat

  © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected]


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