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 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 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 Blockwise Site Frequency Spectra for Inferring Complex Population Histories and Recombination

2016 ◽  
Author(s):  
Champak R. Beeravolu ◽  
Michael J. Hickerson ◽  
Laurent A.F. Frantz ◽  
Konrad Lohse
Keyword(s):  
Demographic History ◽  
Composite Likelihood ◽  
Model Organisms ◽  
Secondary Contact ◽  
Parameter Estimates ◽  
Genome Sequences ◽  
Frequency Spectra ◽  
Genome Wide ◽  
Complex Population ◽  
History Of

AbstractWe introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (∼300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.

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 Ancient Hybridization and Adaptive Introgression of an Invadolysin Gene in Schistosome Parasites

2019 ◽  
Vol 36 (10) ◽  
pp. 2127-2142 ◽  
Author(s):  
Roy N Platt ◽  
Marina McDew-White ◽  
Winka Le Clec’h ◽  
Frédéric D Chevalier ◽  
Fiona Allan ◽  
...  
Keyword(s):  
High Frequency ◽  
Parasite Species ◽  
Single Gene ◽  
Sub Saharan Africa ◽  
Species Boundaries ◽  
Urogenital Schistosomiasis ◽  
Adaptive Introgression ◽  
Introgression Event ◽  
Sub Saharan ◽  
Ancient Hybridization

Abstract Introgression among parasite species has the potential to transfer traits of biomedical importance across species boundaries. The parasitic blood fluke Schistosoma haematobium causes urogenital schistosomiasis in humans across sub-Saharan Africa. Hybridization with other schistosome species is assumed to occur commonly, because genetic crosses between S. haematobium and livestock schistosomes, including S. bovis, can be staged in the laboratory, and sequencing of mtDNA and rDNA amplified from microscopic miracidia larvae frequently reveals markers from different species. However, the frequency, direction, age, and genomic consequences of hybridization are unknown. We hatched miracidia from eggs and sequenced the exomes from 96 individual S. haematobium miracidia from infected patients from Niger and the Zanzibar archipelago. These data revealed no evidence for contemporary hybridization between S. bovis and S. haematobium in our samples. However, all Nigerien S. haematobium genomes sampled show hybrid ancestry, with 3.3–8.2% of their nuclear genomes derived from S. bovis, providing evidence of an ancient introgression event that occurred at least 108–613 generations ago. Some S. bovis-derived alleles have spread to high frequency or reached fixation and show strong signatures of directional selection; the strongest signal spans a single gene in the invadolysin gene family (Chr. 4). Our results suggest that S. bovis/S. haematobium hybridization occurs rarely but demonstrate profound consequences of ancient introgression from a livestock parasite into the genome of S. haematobium, the most prevalent schistosome species infecting humans.

scholarly journals Natural selection for the Duffy-null allele in the recently admixed people of Madagascar

2014 ◽  
Vol 281 (1789) ◽  
pp. 20140930 ◽  
Author(s):  
Jason A. Hodgson ◽  
Joseph K. Pickrell ◽  
Laurel N. Pearson ◽  
Ellen E. Quillen ◽  
António Prista ◽  
...  
Keyword(s):  
Natural Selection ◽  
High Frequency ◽  
Vivax Malaria ◽  
Null Allele ◽  
Sub Saharan Africa ◽  
Adaptive Genetic Variation ◽  
Genome Wide ◽  
Admixed Population ◽  
Selection For ◽  
Sub Saharan

While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan 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.

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