Carina Schlebusch

• BSc, BSc (hons), MSc (Cancer Genetics), PhD (Human Evolutionary Genetics)
• Professor at Uppsala University

The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million single-nucleotide polymorphisms in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but population structure within the Khoe-San dated back to about 35,000 years ago. G...

Adaptation drives genomic changes; however, evidence of specific adaptations in humans remains limited. We found that inhabitants of the northern Argentinean Andes, an arid region where elevated arsenic concentrations in available drinking water is common, have unique arsenic metabolism, with efficient methylation and excretion of the major metabol...

Ancient DNA pushes human emergence back Anatomically modern humans evolved in Africa, but pinpointing when has been difficult. Schlebusch et al. sequenced three ancient African genomes from the Stone Age, about 2000 years old, and four from the Iron Age, 300 to 500 years old. One of the oldest samples, sequenced to 13× coverage, appears most closel...

In the last three decades, genetic studies have played an increasingly important role in exploring human history. They have helped to conclusively establish that anatomically modern humans first appeared in Africa roughly 250,000-350,000 years before present and subsequently migrated to other parts of the world. The history of humans in Africa is c...

The spread of farming practices in various parts of the world had a marked influence on how humans live today and how we are distributed around the globe. Warmer conditions during the Holocene led to population increases, coinciding with the invention of farming in several places around the world. Archaeological evidence attests to the spread of th...

The migration of Austronesian-speaking populations through Oceania has intrigued researchers for decades. The Kiribati islands, situated along the boundaries of Micronesia and Polynesia, provide a crucial link in this migration. We analyzed the genome-wide data of the Kiritimati population of Kiribati to uncover their genetic origins and connection...

Sub-equatorial Africa is today inhabited predominantly by Bantu-speaking groups of Western African descent who brought agriculture to the Luangwa valley in eastern Zambia ~2000 years ago. Before their arrival the area was inhabited by hunter-gatherers, who in many cases were subsequently replaced, displaced or assimilated. In Zambia, we know little...

The deep history of humans in Africa and the complex divergences and migrations among ancient human genetic lineages remain poorly understood and are the subject of ongoing debate. We produced 73 high-quality whole genome sequences from 14 Central and Southern African populations with diverse, well-documented, languages, subsistence strategies, and...

The Fulani people, one of the most important pastoralist groups in sub-Saharan Africa, are still largely underrepresented in population genomic research. They speak a Niger-Congo language called Fulfulde or Pulaar and live in scattered locations across the Sahel/Savannah Belt, from the Atlantic Ocean to Lake Chad. According to historical records, t...

The South African Coloured (SAC) population, a prominent admixed population in South Africa, reflects centuries of migration, admixture, and historical segregation. Descendants of local Khoe-San and Bantu-speaking populations, European settlers, and enslaved individuals from Africa and Asia, SAC individuals embody diverse ancestries. This study inv...

The expansion of people speaking Bantu languages is the most dramatic demographic event in Late Holocene Africa and fundamentally reshaped the linguistic, cultural and biological landscape of the continent1–7. With a comprehensive genomic dataset, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Afri...

Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern popul...

Ancient DNA (aDNA) has added a wealth of information about our species’ history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underex...

Society of Africanist Archaeologists, 2023 Houston, Texas Niger-Congo (NC) is one of the world's largest language phyla-incorporating more than 1500 languages spoken across all except Northern Africa. Although the earliest stages of NC's development are not well understood, its purported origins lay between ~20-12 kya within West Africa. This timef...

Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studi...

With the largest genomic dataset to date of Bantu-speaking populations, including newly generated data of modern-day and ancient DNA from previously unsampled regions in Africa, we shed fresh light on the expansion of peoples speaking Bantu languages that started ∼4000 years ago in western Africa. We have genotyped 1,740 participants, including 1,4...

The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inad...

In this article, we reassess the human remains from the Mumbwa Caves housed in the Raymond A. Dart Archaeological Human Remains Collection at the University of the Witwatersrand, South Africa. Based on new radiocarbon dates from human bone collagen and stable isotope analysis, our results revealed that the poorly preserved remains, comprising mostl...

Only 400 km off the coast of East Africa, the island of Madagascar is one of the last large land masses to have been colonized by humans. While many questions surround the human occupation of Madagascar, recent studies raise the question of human impact on endemic biodiversity and landscape transformation. Previous genetic and linguistic analyses h...

The Sahel/Savannah belt harbors diverse populations with different demographic histories and different subsistence patterns. However, populations from this large African region are notably under-represented in genomic research. To investigate the population structure and adaptation history of populations from the Sahel/Savannah space, we generated...

Recent studies have identified Northeast Africa as an important area for human movements during the Holocene. Eurasian populations have moved back into Northeastern Africa and contributed to the genetic composition of its people. By gathering the largest reference dataset to date of Northeast, North, and East African as well as Middle Eastern popul...

Humans living in the Andes Mountains have been historically exposed to arsenic from natural sources, including drinking water. Enzymatic methylation of arsenic allows it to be excreted more efficiently by the human body. Adaptation to high-arsenic environments via enhanced methylation and excretion of arsenic was first reported in indigenous women...

Resurrecting extinct species through de-extinction by genome editing requires full and unbiased information from the extinct species’ genome. A new study establishes a framework to assess how much of an extinct species genome can be recovered by ancient DNA sequencing and which factors influence recovery.

Background Hunter-gatherer lifestyles dominated the southern African landscape up to ~ 2000 years ago, when herding and farming groups started to arrive in the area. First, herding and livestock, likely of East African origin, appeared in southern Africa, preceding the arrival of the large-scale Bantu-speaking agro-pastoralist expansion that introd...

Background Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays. Results We show that...

This book explores important chapters of past and recent African history from a multidisciplinary perspective. It covers an extensive time range from the evolution of early humans to the complex cultural and genetic diversity of modern-day populations in Africa. Through a comprehensive list of chapters, the book focuses on different time-periods, g...

Africa is the continent of our species’ origin and the deep history of humans is represented by African genetic variation. Through genetic studies, it has become evident that deep African population history is captured by relationships among African hunter-gatherers and that the world’s deepest population divergences occur among these groups. In th...

Background Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools and the available genomes are increasing in number. Studies have evaluated and compared some of these technologies and tools, such a...

Various skeletons from the uThukela region of the uKhahlamba-Drakensberg Mountains of South Africa were excavated from rock shelters there during the early part of the twentieth century, with limited accompanying data or analysis. This paper analyses and reports on nine such graves (eight of which contained human remains), excavated during 1931 nea...

Multiple lines of evidence show that modern humans interbred with archaic Denisovans. Here, we report an account of shared demographic history between Australasians and Denisovans distinctively in Island Southeast Asia. Our analyses are based on ∼2.3 million genotypes from 118 ethnic groups of the Philippines, including 25 diverse self-identified N...

Attempts to identify a ‘homeland’ for our species from genetic data are widespread in the academic literature. However, even when putting aside the question of whether a ‘homeland’ is a useful concept, there are a number of inferential pitfalls in attempting to identify the geographic origin of a species from contemporary patterns of genetic variat...

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...

Island Southeast Asia has recently produced several surprises regarding human history, but the region’s complex demography remains poorly understood. Here, we report ∼2.3 million genotypes from 1,028 individuals representing 115 indigenous Philippine populations and genome-sequence data from two ∼8,000-y-old individuals from Liangdao in the Taiwan...

Significance A key link to understand human history in Island Southeast Asia is the Philippine archipelago and its poorly investigated genetic diversity. We analyzed the most comprehensive set of population-genomic data for the Philippines: 1,028 individuals covering 115 indigenous communities. We demonstrate that the Philippines were populated by...

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture co-evolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various ext...

For humans, like any sexually reproducing diploid organism, mating may be random in the sense that individuals are equally likely to mate and produce offspring. Such a view of a population has been important in population genetics as a basis for modeling and analysis. Population structure denotes deviation from this panmixia, regardless of the caus...

Previous studies show that the indigenous people of the southern Cape of South Africa were dramatically impacted by the arrival of European colonists starting ~400 years ago and their descendants are today mixed with Europeans and Asians. To gain insight on the occupants of the Vaalkrans Shelter located at the southernmost tip of Africa, we investi...

The present-day distribution of Bantu languages is commonly thought to reflect the early stages of the Bantu Expansion, the greatest migration event in African prehistory. Using 1149 radiocarbon dates linked to 115 pottery styles recovered from 726 sites throughout the Congo rainforest and adjacent areas, we show that this is not the case. Two peri...

The presence of Early and Middle Stone Age human remains and associated archaeological artefacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of...

Despite Africa’s central role in the origin of our species, our knowledge of the genomic diversity in Africa is remarkably sparse. A recent publication by Choudhury et al. underscores the scientific imperative for a broader characterisation of African genomic diversity to better understand demographic history and improve global human health.

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...

Objectives Archeological evidence shows that first nomadic pastoralists came to the African Sahel from northeastern Sahara, where milking is reported by ~7.5 ka. A second wave of pastoralists arrived with the expansion of Arabic tribes in 7th–14th century CE. All Sahelian pastoralists depend on milk production but genetic diversity underlying their...

Although the human Y chromosome has effectively shown utility in uncovering facets of human evolution and population histories, the ascertainment bias present in early Y-chromosome variant data sets limited the accuracy of diversity and TMRCA estimates obtained from them. The advent of next-generation sequencing, however, has removed this bias and...

The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, there is insufficient evidence for ancient human-pathogen interactions in the region...

The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group ha...

The history of human populations in Africa is complex and includes various demographic events that influenced patterns of genetic variation across the continent. Through genetic studies of modern-day, and most recently, ancient African genetic variation, it became evident that deep African history is captured by the relationships among hunter-gathe...

Lactase persistence (LP) is a well-studied example of a Mendelian trait under selection in some human groups due to gene-culture co-evolution. We investigated the frequencies of genetic variants linked to LP in Sudanese and South Sudanese populations. These populations have diverse subsistence patterns, and some are dependent on milk to various ext...

Background: The Afrikaner population of South Africa is the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the Coloured...

Each region of the world, and the human groups living in them, have unique histories of migration, genetic mixing (admixture) and adaptation that have shaped their past. While archaeology has been of extreme value in elucidating this complex, multifaceted past, the genesis of DNA studies has enriched their story, and now ancient DNA (aDNA) has help...

South Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong ev...

Background: Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral populatio...

Chan and colleagues in their paper titled “Human origins in a southern African palaeo-wetland and first migrations” (https://www.nature.com/articles/s41586-019-1714-1) report 198 novel whole mitochondrial DNA (mtDNA) sequences and infer that ‘anatomically modern humans’ originated in the Makgadikgadi–Okavango palaeo-wetland of southern Africa aroun...

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory r...

Southern African indigenous groups, traditionally hunter-gatherers (San) and herders (Khoekhoe), are commonly referred to as "Khoe-San" populations and have a long history in southern Africa. Their ancestors were largely isolated up until ∼2,000 years ago before the arrival of pastoralists and farmers in southern Africa. Assessing relationships amo...

The Bantu expansion, which started in West Central Africa around 5,000 BP, constitutes a major migratory movement involving the joint spread of peoples and languages across sub-Saharan Africa. Despite the rich linguistic and archaeological evidence available, the genetic relationships between different Bantu-speaking populations and the migratory r...

Human population history in the Holocene was profoundly impacted by changes in lifestyle following the invention and adoption of food-production practices. These changes triggered significant increases in population sizes and expansions over large distances. Here we investigate the population history of the Fulani, a pastoral population extending t...

We have sampled five out of the eleven previously identified human specimens and some faunal remains from the Plovers Lake site in the Cradle of Humankind, South Africa, for ancient DNA. We were successful in obtaining positive results for three of the human individuals and three 'buffalo' teeth. Based on ages obtained for flowstone and one bovid t...

We have sampled five out of the eleven previously identified human specimens and some faunal remains from the Plovers Lake site in the Cradle of Humankind, South Africa, for ancient DNA. We were successful in obtaining positive results for three of the human individuals and three ‘buffalo’ teeth. Based on ages obtained for flowstone and one bovid t...

We report further details on four partial human skeletons from KwaZulu-Natal previously selected for genetic analysis. Dating and genetic results indicate that they derived from agriculturist communities of the mid-second millennium AD. Morphological and genetic analysis shows that three individuals were female; identification of the fourth as fema...

The Afrikaner population of South Africa are the descendants of European colonists who started to colonize the Cape of Good Hope in the 1600’s. In the early days of the colony, mixed unions between European males and non-European females gave rise to admixed children who later became incorporated into either the Afrikaner or the “Coloured” populati...

Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the ass...

Northeast Africa has a long history of human habitation, with fossil-finds from the earliest anatomically modern humans, and housing ancient civilizations. The region is also the gate-way out of Africa, as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula. We investigate the population history of...

Detailed methods and additional results. (PDF)

Inferred admixture fractions using ADMIXTURE [51] for dat3h for the clusters 2–20. The cluster number can be found on the left along with the amount of iterations that support this cluster out of 50 (CLUMPP) [52, 53]. (PDF)

Inferred admixture fractions using ADMIXTURE [51] for diploid dat1 for the clusters 2–7. The cluster number can be found on the left along with the amount of iterations that support this cluster out of 50 (CLUMPP) [52, 53]. (PDF)

Inferred admixture fractions using ADMIXTURE [51] for diploid dat3 for the clusters 2–20. The cluster number can be found on the left along with the amount of iterations that support this cluster out of 50 (CLUMPP) [52, 53]. (PDF)

D-Statistic results. (A) Results for D(Ju|’hoansi, LBK; Mota, X) to account for non-African admixture in population X, where X is the population on the y-axis. (B) Results for D(Ju|’hoansi, X; Egypt, Copt) to investigate whether Egyptians or Copts received more admixture of source X, where X is the population on the y-axis. (PDF)

f4 ratios. (A) shows the Mota-like proportion in the populations on the Y axis. Horizontal bars display 2SE. (B) shows the Neanderthal-like proportion in the populations on the Y axis. Horizontal bars display 2SE. (C) Correlation of the Neanderthal and European proportions (r = 0.925). The European proportion was calculated as 1- Mota-like proporti...

Principal component analysis for PC1 –PC4 in dat1. (A) No outlier removal. (B) Five outliers removed. (PDF)

Principal component analysis for PC1 –PC4 in dat1h. (PDF)

Principal component analysis for PC1 –PC4 in dat2. No outlier removal. (A) Diploid dataset. (B) Haploid dataset. (PDF)

Inferred admixture fractions using ADMIXTURE [51] for dat1h for the clusters 2–7. The cluster number can be found on the left along with the amount of iterations that support this cluster out of 50 (CLUMPP) [52, 53]. (PDF)

Fst. (A) Weir and Cockerhams estimator of FST. (B) Wrights FST for pseudo-unadmixed allele frequencies. (PDF)

Comparison of heterozygosity between datasets of different amount of SNPs to see the effect of ascertainment bias. Average value of heterozygosity per population after removal of one outlier in the Nzime in dat1. (PDF)

Distribution of runs of homozygosity for the Sudanese populations of the unmerged phased dataset. The average total length of the genome in runs of homozygosity in a number of length categories is plotted for each Sudanese population. Error bars represent one standard deviation. (A) Runs of homozygosity for the diploid dataset. (B) Runs of homozygo...