scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 358 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

2018 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH introgressed with archaic hominins once they left the African continent. Current out of African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

scholarly journals Novel insights on demographic history of tribal and caste groups from West Maharashtra (India) using genome-wide data

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guilherme Debortoli ◽  
Cristina Abbatangelo ◽  
Francisco Ceballos ◽  
Cesar Fortes-Lima ◽  
Heather L. Norton ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
Caste Groups

scholarly journals The timing of human adaptation from Neanderthal introgression

2020 ◽  
Author(s):  
Sivan Yair ◽  
Kristin M. Lee ◽  
Graham Coop
Keyword(s):  
Demographic History ◽  
Low Frequency ◽  
Modern Human ◽  
Allele Frequencies ◽  
Population Divergence ◽  
Human Populations ◽  
Human Adaptation ◽  
Adaptive Introgression ◽  
History Of ◽  
Spatio Temporal

AbstractAdmixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of Neanderthal adaptive introgression. From these, we identify cases in which Neanderthal introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation, contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples, and identifies cases of temporally varying selection that are sometimes shared across large geographic distances.

scholarly journals Demographic History of Oceania Inferred from Genome-wide Data

2010 ◽  
Vol 20 (22) ◽  
pp. 1983-1992 ◽  
Author(s):  
Andreas Wollstein ◽  
Oscar Lao ◽  
Christian Becker ◽  
Silke Brauer ◽  
Ronald J. Trent ◽  
...  
Keyword(s):  
Demographic History ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of

scholarly journals The timing of human adaptation from Neanderthal introgression

Genetics ◽  
2021 ◽  
Author(s):  
Sivan Yair ◽  
Kristin M Lee ◽  
Graham Coop
Keyword(s):  
Demographic History ◽  
Low Frequency ◽  
Modern Human ◽  
Allele Frequencies ◽  
Population Divergence ◽  
Human Populations ◽  
Human Adaptation ◽  
Adaptive Introgression ◽  
History Of ◽  
Spatio Temporal

Abstract Admixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of Neanderthal adaptive introgression. From these, we identify cases in which Neanderthal introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation and contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples.

scholarly journals Signatures of long-term balancing selection in human genomes

2017 ◽  
Author(s):  
Bárbara Domingues Bitarello ◽  
Cesare de Filippo ◽  
João Carlos Teixeira ◽  
Joshua M. Schmidt ◽  
Philip Kleinert ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Theoretical Perspective ◽  
Human Populations ◽  
Protein Coding ◽  
Human Genomes ◽  
Genome Wide ◽  
Higher Power ◽  
Genome Wide Data ◽  
Immune Related Genes

AbstractBalancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe the Non-Central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p < 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

scholarly journals SRGAP2 and the gradual evolution of the modern human language faculty

2017 ◽  
Author(s):  
Pedro Tiago Martins ◽  
Maties Marí ◽  
Cedric Boeckx
Keyword(s):  
Axon Guidance ◽  
Evolutionary History ◽  
Vocal Learning ◽  
Modern Human ◽  
Language Faculty ◽  
Molecular Pathway ◽  
Human Genomes ◽  
Gradual Evolution ◽  
Anatomically Modern Humans ◽  
History Of

AbstractIn this paper we examine a new source of evidence that draws on data from archaic human genomes to support the hypothesis that vocal learning in Homo preceded the emergence of Anatomically Modern Humans. We build our claim on the evolutionary history of the SLITROBO GTPase 2 gene (SRGAP2). The SLIT-ROBO molecular pathway has been shown to have an important role in the context of vocal learning. Though the relevance of the SRGAP2 gene duplication in the emergence of some aspect of language has not gone completely unnoticed, recent results now allow us to articulate a mechanistic hypothesis of its role in the context of axon guidance. Specifically, SRGAP2C, a duplication of SRGAP2 crucially also found in Neanderthals and Denisovans, but not in extant mammals, inhibits the ancestral SRGAP2A, which in turn modulates the axon guidance function of the SLIT-ROBO molecular pathway. This, we claim, could have contributed to the establishment of the critical cortico-laryngeal connection of the vocal learning circuit. Our conclusions support the idea that complex vocal learning could already have been part of the arsenal of some of our extinct ancestors.

scholarly journals Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia

2020 ◽  
Author(s):  
João C. Teixeira ◽  
Guy S. Jacobs ◽  
Chris Stringer ◽  
Jonathan Tuke ◽  
Georgi Hudjashov ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Fossil Record ◽  
Modern Human ◽  
Human Populations ◽  
Island Southeast Asia ◽  
Human Genomes ◽  
Anatomically Modern Humans ◽  
Archaic Admixture ◽  
Comprehensive Search ◽  
Archaic Introgression

AbstractThe hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species – Homo luzonensis and H. floresiensis – were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

scholarly journals Population-specific sequence and expression differentiation in Europeans

2019 ◽  
Author(s):  
Xueyuan Jiang ◽  
Raquel Assis
Keyword(s):  
Target Genes ◽  
Demographic History ◽  
Copy Number Variations ◽  
Human Populations ◽  
Rna Seq ◽  
Nucleotide Polymorphism ◽  
Specific Sequence ◽  
Single Nucleotide ◽  
Genome Wide ◽  
History Of

AbstractMuch of the enormous phenotypic variation observed across human populations is thought to have arisen from events experienced as our ancestors peopled different regions of the world. However, little is known about the genes involved in these population-specific adaptations. Here we explore this problem by simultaneously examining population-specific sequence and expression differentiation in four human populations. In particular, we design a branch-based statistic to estimate population-specific differentiation in four populations, and apply this statistic to single nucleotide polymorphism (SNP) and RNA-seq data from Italian, British, Finish, and Yoruban populations. As expected, genome-wide estimates of sequence and expression differentiation each independently recapitulate the known demographic history of these four human populations, highlighting the utility of our statistic for identifying genic targets of population-specific adaptations. Application of our statistic reveals that genes containing large copy number variations (CNVs) have elevated levels of population-specific sequence and expression differentiation, consistent with the hypothesis that gene turnover is a key reservoir of adaptive variation. Further, European genes displaying population-specific sequence and expression differentiation are enriched for functions related to epigenetic regulation, immunity, and reproduction. Together, our findings illustrate that population-specific sequence and expression differentiation in humans may preferentially target genes with CNVs and play important roles in a diversity of adaptive and disease-related phenotypes.

scholarly journals Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians

2021 ◽  
Vol 7 (13) ◽  
pp. eabe4414
Author(s):  
Guido Alberto Gnecchi-Ruscone ◽  
Elmira Khussainova ◽  
Nurzhibek Kahbatkyzy ◽  
Lyazzat Musralina ◽  
Maria A. Spyrou ◽  
...  
Keyword(s):  
Bronze Age ◽  
Iron Age ◽  
Gene Pools ◽  
Social Rules ◽  
Eurasian Steppe ◽  
Central Asian ◽  
Genome Wide ◽  
Genome Wide Data ◽  
History Of ◽  
First Millennium

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE. Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures. To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe. We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively. Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE. Compared to the high genetic heterogeneity of the past, the homogenization of the present-day Kazakhs gene pool is notable, likely a result of 400 years of strict exogamous social rules.

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