scholarly journals Recovering signals of ghost archaic introgression in African populations

2020 ◽  
Vol 6 (7) ◽  
pp. eaax5097 ◽  
Author(s):  
Arun Durvasula ◽  
Sriram Sankararaman
Keyword(s):  
High Frequency ◽  
West African ◽  
Substantial Contribution ◽  
Modern Humans ◽  
Frequency Spectra ◽  
Adaptive Introgression ◽  
Genome Wide ◽  
African Populations ◽  
Archaic Introgression ◽  
Lines Of Evidence

While introgression from Neanderthals and Denisovans has been documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. We provide complementary lines of evidence for archaic introgression into four West African populations. Our analyses of site frequency spectra indicate that these populations derive 2 to 19% of their genetic ancestry from an archaic population that diverged before the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day West African populations.

scholarly journals Recovering signals of ghost archaic introgression in African populations

2018 ◽  
Author(s):  
Arun Durvasula ◽  
Sriram Sankararaman
Keyword(s):  
High Frequency ◽  
Substantial Contribution ◽  
Genome Sequences ◽  
Modern Humans ◽  
Frequency Spectra ◽  
Adaptive Introgression ◽  
Genome Wide ◽  
African Populations ◽  
Archaic Introgression ◽  
Sub Saharan

AbstractWhile introgression from Neanderthals and Denisovans has been well-documented in modern humans outside Africa, the contribution of archaic hominins to the genetic variation of present-day Africans remains poorly understood. Using 405 whole-genome sequences from four sub-Saharan African populations, we provide complementary lines of evidence for archaic introgression into these populations. Our analyses of site frequency spectra indicate that these populations derive 2-19% of their genetic ancestry from an archaic population that diverged prior to the split of Neanderthals and modern humans. Using a method that can identify segments of archaic ancestry without the need for reference archaic genomes, we built genome-wide maps of archaic ancestry in the Yoruba and the Mende populations that recover about 482 and 502 megabases of archaic sequence, respectively. Analyses of these maps reveal segments of archaic ancestry at high frequency in these populations that represent potential targets of adaptive introgression. Our results reveal the substantial contribution of archaic ancestry in shaping the gene pool of present-day African populations.One sentence summaryMultiple present-day African populations inherited genes from an unknown archaic population that diverged before modern humans and Neanderthals split.

scholarly journals Unexpected high frequency of P46L TNFRSF1A allele in sub-Saharan West African populations

2004 ◽  
Vol 13 (4) ◽  
pp. 513-515 ◽  
Author(s):  
Dimitri Tchernitchko ◽  
Mihelaiti Chiminqgi ◽  
Frédéric Galactéros ◽  
Claude Préhu ◽  
Yvon Segbena ◽  
...  
Keyword(s):  
High Frequency ◽  
West African ◽  
African Populations ◽  
Sub Saharan

scholarly journals Genome-wide scans provide evidence for positive selection of genes implicated in Lassa fever

2012 ◽  
Vol 367 (1590) ◽  
pp. 868-877 ◽  
Author(s):  
Kristian G. Andersen ◽  
Ilya Shylakhter ◽  
Shervin Tabrizi ◽  
Sharon R. Grossman ◽  
Christian T. Happi ◽  
...  
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Lassa Fever ◽  
West African ◽  
Lassa Virus ◽  
Genome Wide ◽  
African Populations ◽  
Genome Wide Data ◽  
Differential Gene ◽  
Selection Of

Rapidly evolving viruses and other pathogens can have an immense impact on human evolution as natural selection acts to increase the prevalence of genetic variants providing resistance to disease. With the emergence of large datasets of human genetic variation, we can search for signatures of natural selection in the human genome driven by such disease-causing microorganisms. Based on this approach, we have previously hypothesized that Lassa virus (LASV) may have been a driver of natural selection in West African populations where Lassa haemorrhagic fever is endemic. In this study, we provide further evidence for this notion. By applying tests for selection to genome-wide data from the International Haplotype Map Consortium and the 1000 Genomes Consortium, we demonstrate evidence for positive selection in LARGE and interleukin 21 ( IL21 ), two genes implicated in LASV infectivity and immunity. We further localized the signals of selection, using the recently developed composite of multiple signals method, to introns and putative regulatory regions of those genes. Our results suggest that natural selection may have targeted variants giving rise to alternative splicing or differential gene expression of LARGE and IL21 . Overall, our study supports the hypothesis that selective pressures imposed by LASV may have led to the emergence of particular alleles conferring resistance to Lassa fever, and opens up new avenues of research pursuit.

scholarly journals Archaic introgression and variation in pharmacogenes and implications for local adaptation

2021 ◽  
Author(s):  
Tadeusz H Wroblewski ◽  
Kelsey E Witt ◽  
Seung-been Lee ◽  
Ripan S Malhi ◽  
Emilia Huerta-Sanchez ◽  
...  
Keyword(s):  
Gene Evolution ◽  
Modern Human ◽  
Small Subset ◽  
Human Populations ◽  
Modern Humans ◽  
Environmental Pressures ◽  
African Populations ◽  
Archaic Admixture ◽  
Archaic Introgression ◽  
Altered Metabolism

Modern humans carry Neanderthal and Denisovan (archaic) genome elements which may have been a result of environmental adaptation. These effects may be particularly evident in pharmacogenes - genes responsible for the processing of exogenous substances such as food, pollutants, and medications. However, the health implications and contribution of archaic ancestry in pharmacogenes of modern humans remains understudied. We characterize eleven key cytochrome P450 (CYP450) genes involved in drug metabolizing reactions in three Neanderthal and one Denisovan individuals and examine archaic introgression in modern human populations. We infer the metabolizing efficiency of these eleven genes in archaic individuals and show important genetic differences relative to modern human variants. We identify archaic-specific SNVs in each CYP450 gene, including some that are potentially damaging, which may result in altered metabolism in modern human people carrying these variants. We highlight four genes which display interesting patterns of archaic variation: CYP2B6 - we find a large number of unique variants in the Vindija Neanderthal, some of which are shared with a small subset of African modern humans; CYP2C9 - containing multiple variants that are shared between Europeans and Neanderthals; CYP2A6*12 - a variant defined by a hybridization event that was found in humans and Neanderthals, suggesting the recombination event predates both species; and CYP2J2 - in which we hypothesize a Neanderthal variant was re-introduced in non-African populations by archaic admixture. The genetic variation identified in archaic individuals imply environmental pressures that may have driven CYP450 gene evolution.

scholarly journals Polygenic patterns of adaptive introgression in modern humans are mainly shaped by response to pathogens

2019 ◽  
Author(s):  
Alexandre Gouy ◽  
Laurent Excoffier
Keyword(s):  
Functional Enrichment ◽  
Modern Humans ◽  
Adaptive Introgression ◽  
Metabolic Functions ◽  
Gene Sets ◽  
Sequential Selection ◽  
Anatomically Modern Humans ◽  
Polygenic Adaptation ◽  
The Subject ◽  
Archaic Introgression

AbstractAnatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (sub-networks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity-related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.

scholarly journals Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens

2020 ◽  
Vol 37 (5) ◽  
pp. 1420-1433 ◽  
Author(s):  
Alexandre Gouy ◽  
Laurent Excoffier
Keyword(s):  
Functional Enrichment ◽  
Modern Humans ◽  
Adaptive Introgression ◽  
Metabolic Functions ◽  
Gene Sets ◽  
Sequential Selection ◽  
Anatomically Modern Humans ◽  
Polygenic Adaptation ◽  
The Subject ◽  
Archaic Introgression

Abstract Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet. In this study, we analyze archaic introgression maps with refined functional enrichment methods to find signals of polygenic adaptation of introgressed variants. We first apply a method to detect sets of connected genes (subnetworks) within biological pathways that present higher-than-expected levels of archaic introgression. We then introduce and apply a new statistical test to distinguish between epistatic and independent selection in gene sets of present-day humans. We identify several known targets of adaptive introgression, and we show that they belong to larger networks of introgressed genes. After correction for genetic linkage, we find that signals of polygenic adaptation are mostly explained by independent and potentially sequential selection episodes. However, we also find some gene sets where introgressed variants present significant signals of epistatic selection. Our results confirm that archaic introgression has facilitated local adaptation, especially in immunity related and metabolic functions and highlight its involvement in a coordinated response to pathogens out of Africa.

scholarly journals Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Nature ◽  
2021 ◽  
Vol 592 (7853) ◽  
pp. 253-257 ◽  
Author(s):  
Mateja Hajdinjak ◽  
Fabrizio Mafessoni ◽  
Laurits Skov ◽  
Benjamin Vernot ◽  
Alexander Hübner ◽  
...  
Keyword(s):  
Family History ◽  
East Asia ◽  
Late Pleistocene ◽  
Modern Human ◽  
Human Migration ◽  
Upper Palaeolithic ◽  
Modern Humans ◽  
Genome Wide ◽  
Genome Wide Data

AbstractModern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

scholarly journals Inverse Associations of Human Leukocyte Antigen and Malaria Parasite Types in Two West African Populations

2005 ◽  
Vol 73 (2) ◽  
pp. 953-955 ◽  
Author(s):  
Karen Young ◽  
Angela Frodsham ◽  
Ogobara K. Doumbo ◽  
Sunetra Gupta ◽  
Amagana Dolo ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Malaria Parasite ◽  
Human Leukocyte ◽  
West African ◽  
Allelic Association ◽  
Surprising Result ◽  
Biological Mechanism ◽  
Leukocyte Antigen ◽  
African Populations ◽  
Polygenic Diseases

ABSTRACT Differences in allelic associations between populations continue to cause difficulties in the mapping and identification of susceptibility genes for complex polygenic diseases. Although well recognized, the basis of such interpopulation differences is poorly understood. We present an example of an inverse allelic association of an immune response genotype to an infectious disease in two neighboring West African populations. In this case, both the key environmental contributor, i.e., the malaria parasite, and a major biological mechanism are well defined. We show that this surprising result fits well with the predictions of a mathematical model describing the population genetics and dynamics of this interaction.

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