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Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men

Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men

Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men

Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men

Africa is the birthplace of the human species and home to great linguistic, cultural, and genetic diversity. Despite this, the genetics of the peoples of the continent remains understudied. In this thesis, I apply population genetic approaches, to contribute to the knowledge of human demographic history in Africa. Specifically, I investigated three events that have had major impacts on human population genetics in Africa. Paper I, investigated Eurasian back migrations into Northeast Africa and what genetic patterns this has left in the current-day populations of the area. I identified complex demography and linguistic stratification of Eurasian admixture in the region. These genetic patterns coincide in time with historical events such as the spread of Islam, the fall of the Kingdom of Aksum, and trade routes across the Red Sea. Paper II focused on the Bantu expansion, the different migratory routes of Bantu-speakers out of West Africa, and how they shaped the genetic makeup of the peoples of sub-equatorial Africa. We compiled the most comprehensive geographically distributed genetic dataset of Bantu-speaking individuals to date. I investigated the spatial patterns of migrations and the decline of genetic diversity from their homeland. I find evidence for serial founder events and migrations across Zambia and the Congo basin to the rest of sub-equatorial Africa. Paper III and IV involved South Africa and the effects that European colonialism and 20:th century policies have had on the country's genetic landscape. Paper III focuses on the Afrikaner population of South Africa, descendants of the first European settlers of the Cape colony, I describe the extent of African and Asian admixture in this population and investigate evidence of selection and adaptive admixture. Paper IV focuses on the Coloured population of South Africa, an emergent cultural identity. The Coloured population traces their origin primarily to Khoe-San women, manumitted slaves, and European men

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-lik

Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-lik

Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-lik

Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-lik

Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV

Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming. I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution. I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-lik

Africa is the continent where modern humans originated and yet, African demographic history remains largely unknown. Through analyzing the genetic composition of extant and extinct individuals, it is possible to reveal signals of past demographic history and adaptation. In this thesis, I applied population genetic methods to investigate both deep African history and demographic changes associated with the migrations of farmers in Africa. While Paper I and II assess the genomic landscape before the arrival farming groups, Paper III, IV and V focus on the demographic patterns associated with the emergence of various African agro-pastoral societies and how shifts in ways of subsistence resulted in different selective pressures on the genomic level. The genomes from Southern African San hunter-gatherers harbor the earliest diverging lineages and represent the first population divergence event within the modern human phylogeny. However, gene-flow from farming groups has complicated the investigation of genetic relationships between different San groups. In Paper I, I established that Southern African hunter-gatherer genetic diversity fitted an isolation-by-distance model when genomic segments that trace their ancestry to farming groups were excluded. Paper II confirmed that all extant Southern African hunter-gatherers received admixture from farming groups, through comparison with ancient DNA data from three 2,000-year-old southern African Stone Age individuals. New date estimates for the first population divergence event in the modern human phylogeny, based on the Stone Age individuals, coincided with a period in the fossil record associated with transition between archaic humans into anatomically modern humans. Paper III assesses the genetic variation of four ancient Iron Age women from current-day South Africa. I was able to further refine their genetic profiles, which were closest related to southeast Bantu-speaking farmers from current-day South Africa. In Paper IV

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa. Both of these regions are population melting-pots, with many historically known major migrations. In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper. I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations. The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population. Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy. This thesis contributes to a deeper understanding of African demographic history in general and of some

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa. Both of these regions are population melting-pots, with many historically known major migrations. In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper. I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations. The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population. Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy. This thesis contributes to a deeper understanding of African demographic history in general and of some

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa. Both of these regions are population melting-pots, with many historically known major migrations. In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper. I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations. The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population. Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy. This thesis contributes to a deeper understanding of African demographic history in general and of some

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa. Both of these regions are population melting-pots, with many historically known major migrations. In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper. I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations. The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population. Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy. This thesis contributes to a deeper understanding of African demographic history in general and of some

The origin of humans lies in Africa, as has been shown by archaeology, paleontology and genetics. Here, we can find the largest genetic diversity and the deepest split among human populations. African genetic diversity has been shaped by a long and complex history. In this thesis, I applied population genomic methods to investigate different aspects of the demographic history of Africa, specifically northeast and southern Africa. Both of these regions are population melting-pots, with many historically known major migrations. In northeast African populations, Eurasian admixture in central, northern, and eastern Sudanese populations was identified to be of Middle Eastern origin and the admixture time coincides with the Arab expansion. In northeast Africa I also studied alleles associated with lactase persistence, the ability to digest milk at an adult age. A wide diversity of these alleles was detected in Sudan, most commonly among pastoralists. The presence of a Middle Eastern LP-allele and absence of a European LP-allele is consistent with the admixture pattern observed in the first paper. I deciphered the patterns of genetic admixture in the Afrikaner population of South Africa and compared admixture patterns of the X-chromosome and autosomes to disentangle sex-biased admixture in southern African populations. The Afrikaner were shown to carry on average 5% non-European admixture, mostly from Khoe-San, East and South Asian sources. The admixture was sex-biased, with larger contributions from European males and admixture with Africans can be dated to 9-10 generations ago – fitting previous genealogical estimates of the age and the history of the population. Bantu-speaker/Khoe-San contact shows a pattern of female Bantu-speaker bias, which is conflicting with previous mtDNA and Y-chromosome studies. A change in mate-choice over time could explain this discrepancy. This thesis contributes to a deeper understanding of African demographic history in general and of some

The site frequency spectrum characterizes the variation found within different studied populations, providing insight on past demographic history. Here, I describe two methods of studying demographic history that condition or transform the site frequency spectrum to provide greater understanding of demographic history. The doubly conditioned site frequency spectrum helps to highlight differences between admixture and ancient structure models, helping to confirm that Neanderthals did admix with the ancestors of non-African humans. Projection analysis compares a single test genome to a reference population and provides insight on the demographic relationship between the reference and test populations analyzed. This method has been applied in humans to better articulate human demographic history and demonstrate the utility of the method. It has also been applied to genomic data from ancient and modern horses, highlighting admixture between the Przewalski’s horse and domestic horses, as well as the relationship of several ancient horse genomes to present day horse populations.

BACKGROUND: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. METHODS: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. RESULTS: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. CONCLUSIONS: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.

BACKGROUND: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. METHODS: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. RESULTS: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. CONCLUSIONS: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.

The site frequency spectrum characterizes the variation found within different studied populations, providing insight on past demographic history. Here, I describe two methods of studying demographic history that condition or transform the site frequency spectrum to provide greater understanding of demographic history. The doubly conditioned site frequency spectrum helps to highlight differences between admixture and ancient structure models, helping to confirm that Neanderthals did admix with the ancestors of non-African humans. Projection analysis compares a single test genome to a reference population and provides insight on the demographic relationship between the reference and test populations analyzed. This method has been applied in humans to better articulate human demographic history and demonstrate the utility of the method. It has also been applied to genomic data from ancient and modern horses, highlighting admixture between the Przewalski’s horse and domestic horses, as well as the relationship of several ancient horse genomes to present day horse populations.

BACKGROUND: Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions. METHODS: DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software. RESULTS: From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region. CONCLUSIONS: The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.