Post by djoser-xyyman on Jul 11, 2018 8:13:20 GMT -5
Henn and the - 2018 SMBE Symposium
Reconstructing the human population history of Africa
Brenna M Henn1
1UC Davis (United States)
Over twenty-five years ago, geneticists sequenced mitochondrial DNA from a diverse sample of human populations and hypothesized that all humans have a common origin in Africa 200,000 years ago.The broad outlines of this hypothesis remain remarkably unaltered, but many details of our African origin continue to be elusive. After decades of advances in human genetics, we are no longer data limited (either in terms of samples or genomic loci) but there is little consensus on most key issues. I will outline the models underlying the origin of modern humans. For example, was there a single ancestral population or multiple ancestral populations? Additionally, is there a discordance between anatomically modern humans and behaviorally modern humans? I will explore patterns of genetic diversity across Africa, and specifically focus on the complex history of southern African KhoeSan groups and adaptations to African environments. I will highlight our recent research on the evolution of skin pigmentation, malarial resistance, and infectious disease. We demonstrate that Africa continues to be an evolutionarily dynamic, heterogenous continent for human populations.
ANCESTRAL AND ADMIXTURE HISTORIES IN THE INDIAN SUBCONTINENT
Partha P Majumder1
1National Institute of Biomedical Genomics (India)
Based on the analyses of genome-scale SNP data and whole-genome sequence data from individuals drawn from a large number of extant ethnic groups, we have estimated archaic admixture contributions of Neanderthal and Denisovan genomes to extant ethnic groups in the Indian sub-continent. We have found a high level of Denisovan admixture among the Negrito tribals of Andaman and Nicobar Islands. Comparison with similar data from other Asian populations has provided clues to areas of interaction of modern humans and Denisovans. Some populations from South and Southeast Asia harbour a small proportion of ancestry from an unknown extinct hominin; this ancestry is absent from Europeans and East Asians. Our results show that that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. Systematic analysis of genome-wide data, using multiple robust statistical methods, from individuals drawn from populations selected to represent geographic, linguistic, and ethnic diversities have revealed four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be co-ancestral to Oceanic populations. Prior to the establishment of the socially-stratified caste system in India that imposed strict rules of endogamy, there was wide admixture across tribal and caste groups which came to an abrupt end 1,900 to 4,200 years before present.
Genome wide analysis of negrito groups in Southeast Asia
Timothy Jinam1, Naruya Saitou1
1National Institute of Genetics (Japan)
The term "negrito" refers to indigenous groups in the Philippines, Malaysia and Andaman Islands who share some physical characteristics such as short stature, frizzy hair and darker skin. Genome-wide SNP analysis showed the negrito groups are phylogenetically basal to other Southeast and East Asians, but negritos also experienced substantial gene flow from these populations. SNP loci which have low Fst among all negrito groups but highly differentiated with East Asians may be associated with height, skin pigmentation and malarial resistance. We also found relatively high traces of Denisovan introgression in the Philippine Negritos, particularly in the Aeta. We will present preliminary results of whole genome sequencing analysis of 10 Philippine negritos.
Xyyman comment – if these genomes become downloaded-able….GREAT!!!!! We can do our own analysis
Human prehistoric demography revealed by polymorphic pattern of CpG transitions
Xiaoming Liu1
1School of Public Health, The University of Texas Health Science Center at Houston (United States)
Prehistoric demography of human populations is one essential piece of information to illustrate our own evolution. Despite its importance our knowledge is very limited, even for the relatively recent population dynamics during and around the Holocene. Here we inferred demographic histories from 1 to 40 thousand years ago (kya) for 24 population samples, using a newly developed model-flexible method with 36 million non-coding CpG sites genome-wide. Our results show many population growth events likely due to the Neolithic Revolution (i.e. shifting from hunting and gathering to agriculture and settlement): Han Chinese experienced a dramatic ~10 fold population growth around 8 kya to 12 kya; some South European and South Asian populations also began their long-term population growth around 10 kya but in a more gradual fashion; and British and Western European populations began their takeoff around 6-7 kya. The potential agriculture-associated population growth of Luhya in Webuye, Kenya (LWK) came relatively late (no earlier than 3 kya) compared to other African populations, in **CONTRAST TO THE ASSUMPTION **that they are the direct descendants of Bantu-speaking immigrants from West Africa. We also observed several population growth events dated before the introduction of agriculture. Our results help to paint a clearer picture of human's prehistoric demography, confirming the significant impact of agriculture to population expansion, and provide new hypotheses and directions for future research.
Xyyman comment – so another debunking of the supposed Bantu expansion. No mention of Agriculture in the rest of Africa except Kenya…which was late …they say.
Population Genomic Inference from Palaeo-Neutralomes of Mediaeval Germans
Joachim Burger1, Michaela Harbeck2, Krishna R. Veeramah3
1Institute of Organismic and Molecular Evolution, Mainz University (Germany), 2SNSB Munich (Germany), 3Stony Brook University (United States)
Many modern European states trace their roots back to the Early Medieval period. To genetically better characterize this formative phase of Central European population history we have conducted a population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Germany mostly dating to around 500 AD. We developed a novel capture array that generated high coverage (mean 72x) sequence data in all individuals from neutral regions spanning a total of 5Mb, as well as 486 functional polymorphic sites. Examination of the panel of functional loci revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ~1,500 years ago. Analysis of the neutralome indicates that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from West Europe to East Asia. The inferred female-biased migration indicates complex demographic processes during the Early Medieval Period may have contributed in an unexpected way to the making of the modern European genetic landscape. Lastly, we used the Medieval neutralome data to generate the allele frequency spectrum (AFS) and estimate the start and rate of recent European population growth.
Xyyman comment – no Africans in Europe??!!
Distinction between ancient introgression and incomplete lineage sorting in modern human genomes
Makoto Shimada1
1Institute for Comprehensive Medical Science, Fujita Health University (Japan)
Recent advancements of massive individual human genome and high-quality ancient genomes of other hominins have provided the evidences of diverse population structure in ancestral modern human **before** out-of-Africa, as well as ancient hybridization between modern human and archaic hominins such as Neanderthals. This brings a difficulty to distinguish current haplotype origins between ancient introgression from archaic hominins and incomplete lineage sorting **before** out-of-Africa. To clarify origin of diversified haplotypes in modern human, I focused on eight loci (23 kb - 550 kb in length) containing diversified haplotypes that have been discussed whether these are exceptions of out-of-Africa model or not. As many modern human haplotypes obtained from the 1000 genomes project as possible were used for comparison in topology between phylogenetic tree and network to understand actual picture of reticulation for each locus. Using S* and EHH (Extended Haplotype Homozygosity) analyses, we examined patterns of linkage disequilibrium (LD) of haplotypes to distinguished haplotypes origins between ancient introgression and ancestral polymorphism followed by incomplete lineage sorting. These examination on LD analyses with gene genealogy showed actual state of complexity of human genome diversity and difference in origin of the diversified haplotypes among introgressed from archaic hominins whose genome sequences are available such as Neanderthal and Denisova, that from unknown other extinct hominins, and derived from ancient polymorphism **without** introgression.
Xyyman comments – so it looks like they are sort out Neanderthal and AMH doing the nasty vs sub-structure.
No Evidence for Protracted Selection Against Neandertal Alleles in Humans
Benjamin Vernot1, Martin Petr1, Svante Paabo1, Janet Kelso1
1Max-Planck-Institute for Evolutionary Anthropology (Germany)
Approximately 2% of the genomes of present-day non-Africans descends from Neandertal ancestors as a result of interbreeding between Neandertals and modern humans approximately 55,000 years ago. Negative selection against Neandertal alleles in the modern human population has been the subject of many studies. When the proportion of Neandertal DNA has been estimated in ancient modern human specimens that range in age from 45,000 years to present-day, an apparent monotonic decline over time has been observed, and interpreted to be the result of negative selection against Neandertal alleles [Yang & Fu, 2018]. Here, we use a recently sequenced Neandertal genome from Croatia [Pruefer et al 2017] to better estimate Neandertal ancestry in ancient modern human genomes. In contrast to previous results, we observe no long-term decline of Neandertal ancestry. We show that the previous observation is likely an artifact produced by migration between Europe and Africa that altered relationships between European and African populations in a time-dependent manner. With simulations using realistic recombination maps and selection coefficients, we show that selection against Neandertal alleles is likely to have occurred within the first 500 generations after introgression, i.e. prior to the age of most ancient human specimens analyzed to date. We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles, e.g. a relative depletion of Neandertal alleles around coding sequence and the presence of "deserts" of Neandertal sequence of size 10-15Mb.
Xyyman comment: - So Paabo is at it again. And again makes a stupid comment like “We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles’ But careful now. The title used “Protracted”. Also agreeing with Lazaridis ..Basal Eurasian diluted “Neanderthal” DNA in Europeans.
Insights into the population history of the "Hidden Ones": From oral history to genome-wide analysis
Hiba Babiker1, Abbie Hantgan1, Johann-Mattis List1, Jeffrey Heath2, Russell Gray1
1Max Planck Institute for the Science of Human History (Germany), 2University of Michigan (United States)
Africa contains nearly one-third of the world's languages, and its populations have the highest genetic diversity. The depiction of genetic diversity in Africa is critical for reconstructing modern human origins and demographic history. Exploring the linguistic diversity in Africa is reframing current classification system regarding language families and isolates. The sub-Saharan fringe in Western Africa is becoming ripe for extensive research in linguistics, genetics, archaeology and cultural evolution. However, some populations are under-represented in multifaceted studies. Our research focuses on the Dogon and Bangande populations of the Bandiagara Escarpment in Central Eastern Mali who claim a "Mande" origin and a collective Dogon ethnicity. We used genome-wide data to understand the genetic structure of these populations and the evolutionary forces that shaped their genomes. We also leveraged lexical data representing the languages spoken by these populations to document historical contacts. We used state of the art analyses in population genetics and computational linguistics as well as simulation modelling. My talk will explore recent findings and will discuss the impact of cultural and geographical barriers on gene flow and population admixture. These findings shed light on the co-evolution of languages and genes. The results highlight the importance of interdisciplinary research in depicting the complex linguistic and genetic histories, hence, decoding unanswered questions in the human history.
Xyyman comment: - Computational linguistics is new. They are finally getting around to West Africans diversity
New Insights into the Genetic Basis and Evolutionary History of Lactase Persistence in Africa
Alessia Ranciaro1, Michael C. Campbell2, Elizabeth Eyerman1, Simon Thompson1, William Beggs1, Sununguko Wata Mpoloka3, Gaonyadiwe George Mokone4, Thomas Nyambo5, Dawit Wolde Meskel6, Gurja Belay6, Meredith Yeager7, Stephen Chanock8, Sarah A Tishkoff1, 9
1University of Pennsylvania (United States), 2Howard University (United States), 3University of Botswana (Botswana), 4University of Botswana School of Medicine (Botswana), 5Muhimbili University of Health and Allied Sciences (Tanzania), 6Addis Ababa University (Ethiopia), 7 National Cancer Institute (United States), 8Leidos Biomedical Research Inc (United States), 9University of Pennsylvania (United States)
Lactase persistence (LP) is a recent adaptive trait in humans that evolved mainly in populations practicing milk production.Prior studies of African populations have identified **novel **common variants in intron 13 of the MCM6 gene (a known candidate enhancer region for LCT) associated with LP primarily in pastoralists. While these variants account for a large proportion of the phenotypic variance, there may be additional polymorphisms that contribute to the LP trait. To test this hypothesis, we resequenced 555 bp of intron 13 of MCM6 in 1588 African individuals from diverse populations in Ethiopia, Tanzania and Botswana. We also genotyped these same individuals using the Illumina Omni 5M SNP array, and integrated our sequencing data with the 5M genotype data to detect signatures of selection. In addition, we performed the lactose tolerance test for a subset of 457 individuals. Based on our analyses, we identified for the** first time** the presence of the C-14010 and G-13915 variants in the Hadza hunter-gatherers from Tanzania. We also observed the G-13915 variant in the Burunge and Maasai populations from Tanzania, which has never previously been reported. Furthermore, we confirmed the presence of the G-13907 and the G-13915 alleles in Ethiopia. In addition, we detected a strong association between LP and genomic regions on several chromosomes in the Maasai pastoralists based on Fisher's Exact Test, suggesting candidate regions that might contribute to LP in this population. Overall, this genome-wide study offers new insights into the genetic basis and evolutionary history of LP in Africa.
Xyyman comment: - More and more is being revealed about LCT in Africa and it’s immense diversity
Reconstructing the human population history of Africa
Brenna M Henn1
1UC Davis (United States)
Over twenty-five years ago, geneticists sequenced mitochondrial DNA from a diverse sample of human populations and hypothesized that all humans have a common origin in Africa 200,000 years ago.The broad outlines of this hypothesis remain remarkably unaltered, but many details of our African origin continue to be elusive. After decades of advances in human genetics, we are no longer data limited (either in terms of samples or genomic loci) but there is little consensus on most key issues. I will outline the models underlying the origin of modern humans. For example, was there a single ancestral population or multiple ancestral populations? Additionally, is there a discordance between anatomically modern humans and behaviorally modern humans? I will explore patterns of genetic diversity across Africa, and specifically focus on the complex history of southern African KhoeSan groups and adaptations to African environments. I will highlight our recent research on the evolution of skin pigmentation, malarial resistance, and infectious disease. We demonstrate that Africa continues to be an evolutionarily dynamic, heterogenous continent for human populations.
ANCESTRAL AND ADMIXTURE HISTORIES IN THE INDIAN SUBCONTINENT
Partha P Majumder1
1National Institute of Biomedical Genomics (India)
Based on the analyses of genome-scale SNP data and whole-genome sequence data from individuals drawn from a large number of extant ethnic groups, we have estimated archaic admixture contributions of Neanderthal and Denisovan genomes to extant ethnic groups in the Indian sub-continent. We have found a high level of Denisovan admixture among the Negrito tribals of Andaman and Nicobar Islands. Comparison with similar data from other Asian populations has provided clues to areas of interaction of modern humans and Denisovans. Some populations from South and Southeast Asia harbour a small proportion of ancestry from an unknown extinct hominin; this ancestry is absent from Europeans and East Asians. Our results show that that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration. Systematic analysis of genome-wide data, using multiple robust statistical methods, from individuals drawn from populations selected to represent geographic, linguistic, and ethnic diversities have revealed four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be co-ancestral to Oceanic populations. Prior to the establishment of the socially-stratified caste system in India that imposed strict rules of endogamy, there was wide admixture across tribal and caste groups which came to an abrupt end 1,900 to 4,200 years before present.
Genome wide analysis of negrito groups in Southeast Asia
Timothy Jinam1, Naruya Saitou1
1National Institute of Genetics (Japan)
The term "negrito" refers to indigenous groups in the Philippines, Malaysia and Andaman Islands who share some physical characteristics such as short stature, frizzy hair and darker skin. Genome-wide SNP analysis showed the negrito groups are phylogenetically basal to other Southeast and East Asians, but negritos also experienced substantial gene flow from these populations. SNP loci which have low Fst among all negrito groups but highly differentiated with East Asians may be associated with height, skin pigmentation and malarial resistance. We also found relatively high traces of Denisovan introgression in the Philippine Negritos, particularly in the Aeta. We will present preliminary results of whole genome sequencing analysis of 10 Philippine negritos.
Xyyman comment – if these genomes become downloaded-able….GREAT!!!!! We can do our own analysis
Human prehistoric demography revealed by polymorphic pattern of CpG transitions
Xiaoming Liu1
1School of Public Health, The University of Texas Health Science Center at Houston (United States)
Prehistoric demography of human populations is one essential piece of information to illustrate our own evolution. Despite its importance our knowledge is very limited, even for the relatively recent population dynamics during and around the Holocene. Here we inferred demographic histories from 1 to 40 thousand years ago (kya) for 24 population samples, using a newly developed model-flexible method with 36 million non-coding CpG sites genome-wide. Our results show many population growth events likely due to the Neolithic Revolution (i.e. shifting from hunting and gathering to agriculture and settlement): Han Chinese experienced a dramatic ~10 fold population growth around 8 kya to 12 kya; some South European and South Asian populations also began their long-term population growth around 10 kya but in a more gradual fashion; and British and Western European populations began their takeoff around 6-7 kya. The potential agriculture-associated population growth of Luhya in Webuye, Kenya (LWK) came relatively late (no earlier than 3 kya) compared to other African populations, in **CONTRAST TO THE ASSUMPTION **that they are the direct descendants of Bantu-speaking immigrants from West Africa. We also observed several population growth events dated before the introduction of agriculture. Our results help to paint a clearer picture of human's prehistoric demography, confirming the significant impact of agriculture to population expansion, and provide new hypotheses and directions for future research.
Xyyman comment – so another debunking of the supposed Bantu expansion. No mention of Agriculture in the rest of Africa except Kenya…which was late …they say.
Population Genomic Inference from Palaeo-Neutralomes of Mediaeval Germans
Joachim Burger1, Michaela Harbeck2, Krishna R. Veeramah3
1Institute of Organismic and Molecular Evolution, Mainz University (Germany), 2SNSB Munich (Germany), 3Stony Brook University (United States)
Many modern European states trace their roots back to the Early Medieval period. To genetically better characterize this formative phase of Central European population history we have conducted a population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Germany mostly dating to around 500 AD. We developed a novel capture array that generated high coverage (mean 72x) sequence data in all individuals from neutral regions spanning a total of 5Mb, as well as 486 functional polymorphic sites. Examination of the panel of functional loci revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ~1,500 years ago. Analysis of the neutralome indicates that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from West Europe to East Asia. The inferred female-biased migration indicates complex demographic processes during the Early Medieval Period may have contributed in an unexpected way to the making of the modern European genetic landscape. Lastly, we used the Medieval neutralome data to generate the allele frequency spectrum (AFS) and estimate the start and rate of recent European population growth.
Xyyman comment – no Africans in Europe??!!
Distinction between ancient introgression and incomplete lineage sorting in modern human genomes
Makoto Shimada1
1Institute for Comprehensive Medical Science, Fujita Health University (Japan)
Recent advancements of massive individual human genome and high-quality ancient genomes of other hominins have provided the evidences of diverse population structure in ancestral modern human **before** out-of-Africa, as well as ancient hybridization between modern human and archaic hominins such as Neanderthals. This brings a difficulty to distinguish current haplotype origins between ancient introgression from archaic hominins and incomplete lineage sorting **before** out-of-Africa. To clarify origin of diversified haplotypes in modern human, I focused on eight loci (23 kb - 550 kb in length) containing diversified haplotypes that have been discussed whether these are exceptions of out-of-Africa model or not. As many modern human haplotypes obtained from the 1000 genomes project as possible were used for comparison in topology between phylogenetic tree and network to understand actual picture of reticulation for each locus. Using S* and EHH (Extended Haplotype Homozygosity) analyses, we examined patterns of linkage disequilibrium (LD) of haplotypes to distinguished haplotypes origins between ancient introgression and ancestral polymorphism followed by incomplete lineage sorting. These examination on LD analyses with gene genealogy showed actual state of complexity of human genome diversity and difference in origin of the diversified haplotypes among introgressed from archaic hominins whose genome sequences are available such as Neanderthal and Denisova, that from unknown other extinct hominins, and derived from ancient polymorphism **without** introgression.
Xyyman comments – so it looks like they are sort out Neanderthal and AMH doing the nasty vs sub-structure.
No Evidence for Protracted Selection Against Neandertal Alleles in Humans
Benjamin Vernot1, Martin Petr1, Svante Paabo1, Janet Kelso1
1Max-Planck-Institute for Evolutionary Anthropology (Germany)
Approximately 2% of the genomes of present-day non-Africans descends from Neandertal ancestors as a result of interbreeding between Neandertals and modern humans approximately 55,000 years ago. Negative selection against Neandertal alleles in the modern human population has been the subject of many studies. When the proportion of Neandertal DNA has been estimated in ancient modern human specimens that range in age from 45,000 years to present-day, an apparent monotonic decline over time has been observed, and interpreted to be the result of negative selection against Neandertal alleles [Yang & Fu, 2018]. Here, we use a recently sequenced Neandertal genome from Croatia [Pruefer et al 2017] to better estimate Neandertal ancestry in ancient modern human genomes. In contrast to previous results, we observe no long-term decline of Neandertal ancestry. We show that the previous observation is likely an artifact produced by migration between Europe and Africa that altered relationships between European and African populations in a time-dependent manner. With simulations using realistic recombination maps and selection coefficients, we show that selection against Neandertal alleles is likely to have occurred within the first 500 generations after introgression, i.e. prior to the age of most ancient human specimens analyzed to date. We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles, e.g. a relative depletion of Neandertal alleles around coding sequence and the presence of "deserts" of Neandertal sequence of size 10-15Mb.
Xyyman comment: - So Paabo is at it again. And again makes a stupid comment like “We note that our simulations **agree with other observations **supporting negative selection against Neandertal alleles’ But careful now. The title used “Protracted”. Also agreeing with Lazaridis ..Basal Eurasian diluted “Neanderthal” DNA in Europeans.
Insights into the population history of the "Hidden Ones": From oral history to genome-wide analysis
Hiba Babiker1, Abbie Hantgan1, Johann-Mattis List1, Jeffrey Heath2, Russell Gray1
1Max Planck Institute for the Science of Human History (Germany), 2University of Michigan (United States)
Africa contains nearly one-third of the world's languages, and its populations have the highest genetic diversity. The depiction of genetic diversity in Africa is critical for reconstructing modern human origins and demographic history. Exploring the linguistic diversity in Africa is reframing current classification system regarding language families and isolates. The sub-Saharan fringe in Western Africa is becoming ripe for extensive research in linguistics, genetics, archaeology and cultural evolution. However, some populations are under-represented in multifaceted studies. Our research focuses on the Dogon and Bangande populations of the Bandiagara Escarpment in Central Eastern Mali who claim a "Mande" origin and a collective Dogon ethnicity. We used genome-wide data to understand the genetic structure of these populations and the evolutionary forces that shaped their genomes. We also leveraged lexical data representing the languages spoken by these populations to document historical contacts. We used state of the art analyses in population genetics and computational linguistics as well as simulation modelling. My talk will explore recent findings and will discuss the impact of cultural and geographical barriers on gene flow and population admixture. These findings shed light on the co-evolution of languages and genes. The results highlight the importance of interdisciplinary research in depicting the complex linguistic and genetic histories, hence, decoding unanswered questions in the human history.
Xyyman comment: - Computational linguistics is new. They are finally getting around to West Africans diversity
New Insights into the Genetic Basis and Evolutionary History of Lactase Persistence in Africa
Alessia Ranciaro1, Michael C. Campbell2, Elizabeth Eyerman1, Simon Thompson1, William Beggs1, Sununguko Wata Mpoloka3, Gaonyadiwe George Mokone4, Thomas Nyambo5, Dawit Wolde Meskel6, Gurja Belay6, Meredith Yeager7, Stephen Chanock8, Sarah A Tishkoff1, 9
1University of Pennsylvania (United States), 2Howard University (United States), 3University of Botswana (Botswana), 4University of Botswana School of Medicine (Botswana), 5Muhimbili University of Health and Allied Sciences (Tanzania), 6Addis Ababa University (Ethiopia), 7 National Cancer Institute (United States), 8Leidos Biomedical Research Inc (United States), 9University of Pennsylvania (United States)
Lactase persistence (LP) is a recent adaptive trait in humans that evolved mainly in populations practicing milk production.Prior studies of African populations have identified **novel **common variants in intron 13 of the MCM6 gene (a known candidate enhancer region for LCT) associated with LP primarily in pastoralists. While these variants account for a large proportion of the phenotypic variance, there may be additional polymorphisms that contribute to the LP trait. To test this hypothesis, we resequenced 555 bp of intron 13 of MCM6 in 1588 African individuals from diverse populations in Ethiopia, Tanzania and Botswana. We also genotyped these same individuals using the Illumina Omni 5M SNP array, and integrated our sequencing data with the 5M genotype data to detect signatures of selection. In addition, we performed the lactose tolerance test for a subset of 457 individuals. Based on our analyses, we identified for the** first time** the presence of the C-14010 and G-13915 variants in the Hadza hunter-gatherers from Tanzania. We also observed the G-13915 variant in the Burunge and Maasai populations from Tanzania, which has never previously been reported. Furthermore, we confirmed the presence of the G-13907 and the G-13915 alleles in Ethiopia. In addition, we detected a strong association between LP and genomic regions on several chromosomes in the Maasai pastoralists based on Fisher's Exact Test, suggesting candidate regions that might contribute to LP in this population. Overall, this genome-wide study offers new insights into the genetic basis and evolutionary history of LP in Africa.
Xyyman comment: - More and more is being revealed about LCT in Africa and it’s immense diversity