Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians

Ding, Qiliang; Hu, Ya; Xu, Shuhua; Wang, Jiucun; Li, Jin

doi:10.1093/molbev/mst260

Cited by 73 publications

(71 citation statements)

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“…W 2013 r. Ding i wsp. [10] odkryli u mieszkańców Azji Wschodniej wysoką częstość neandertalskiego introgresywnego haplotypu o długości ok. 200 tys. par zasad (pz) na chromosomie 3p21.31.…”

Section: Wstępunclassified

“…Region ten obejmował loci 18 genów, w tym loci genów: HYAL1, HYAL2 i HYAL3 kodujących odpowiednio: typ 1, typ 2 i typ 3 enzymu hialuronoglukozoaminidaza (hialuronidaza, EC 3.2.1.35), który depolimeryzuje kwas hialuronowy. Według tych autorów bardzo ścisłe sprzężenie swoistej dla neandertalskiego haplotypu w Eurazji transwersji g.50318299T>G (rs35455589) genu HYAL2 (c.1252A>C, p.Ile418Leu) z polimorfizmem rs11130248 (g.50314769A>G) predysponującym do bliznowca u Japończyków [11] sugeruje jej związek z ryzykiem bliznowca również w populacji kontynentalnej Azji Wschodniej [10].…”

Section: Wstępunclassified

“…Odkryta w 2013 r. neandertalska introgresja na chromosomie 3p21.31 występuje z częstością 49,4-66,5% wśród mieszkańców Azji Wschodniej i jest obecna, ale znacznie rzadziej (< 5%), w niektórych społecznościach europejskich [10]. Ding i wsp.…”

Section: Dyskusjaunclassified

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Brak związku pomiędzy pochodzącą od człowieka neandertalskiego transwersją g.50318299T>G genu HYAL2 a predyspozycją do bliznowca

Dmytrzak¹,

Małyszek

Łoniewska

et al. 2017

Pomeranian J Life Sci

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26Brak związku pomiędzy pochodzącą od człowieka neandertalskiego transwersją g.50318299T>G genu HYAL2 a predyspozycją do bliznowca ABSTRACT Introduction: Homo neanderthalensis-derived DNA accounts for an estimated 1-4% of the genome in contemporary Eurasian populations. The g.50318299T>G (c.1252A>C, rs35455589) transversion of the HYAL2 gene, encoding type 2 hyaluronidase, is in East Asians a highly prevalent marker for the Neanderthal-introgressed haplotype at chromosome 3p21.31. The HYAL2 transversion is in strong linkage disequilibrium with rs11130248 (g.50314769A>G), which predisposes to keloid scarring in the Japanese population. This therefore raises the questions of whether the g.50318299T>G HYAL2 transversion is present in contemporary Poles and whether it predisposes to keloids in our population. Materials and methods: The g.50318299T>G HYAL2 transversion was identified by sequencing genomic DNA samples isolated from the umbilical blood of 200 full-term, healthy newborns and from the peripheral blood of 62 adults with keloids. Results: There were 2 TG heterozygotes (1%) and 198 wild-type TT homozygotes (99%) in the newborn group. Only TT homozygotes were found in the adult group with keloids. The HYAL2 genotype distribution conformed to the expected Hardy-Weinberg equilibrium. Conclusions: Neanderthal-derived g.50318299T>G HYAL2 transversion rarely presents in the genome of contemporary Poles and is not associated with the predisposition to keloids in this population.

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Brak związku pomiędzy pochodzącą od człowieka neandertalskiego transwersją g.50318299T>G genu HYAL2 a predyspozycją do bliznowca

Dmytrzak¹,

Małyszek

Łoniewska

et al. 2017

Pomeranian J Life Sci

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“…For example, genes involved in functions related to keratin filaments, sugar metabolism, muscle contraction, body fat distribution, enamel thickness and oocyte meiosis have been targeted by adaptive introgression from Neanderthals Racimo et al, 2017;Zanolli et al, 2017). Genes involved in the variation of skin pigmentation and hair morphology (BNC2, MC1R) also show the signature of positive selection as the result of adaptation to diverse habitats with different degree of insolation (Dannemann & Kelso, 2017;Ding et al, 2014;Frost et al, 2017). Advantageous immune variants introduced into the modern human population from archaic genomes have substantially contributed in the present-day diversity of immune genes (Mendez et al, 2012;Mendez et al, 2013;Nédélec et al, 2016;Quach et al, 2016;Racimo et al, 2015).…”

Section: Genomic Signatures Of Adaptive Introgression From Archaic Tomentioning

confidence: 99%

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Dolgova

Lao

2018

Preprint

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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.Keywords: archaic introgression, fitness, natural selection, Neanderthal, Denisova, anatomically modern humans. Peer-reviewed version available at Genes 2018, 9, 358; doi:10.3390/genes9070358 2 Widespread interbreeding between homininsThe demographic history of anatomically modern humans (AMH) is complex, and involves a large number of migrations, genetic admixtures and introgressions, population extinctions and genetic adaptations, which overlap both in time and in space (see Figure 1). Due to this complexity, the evolutionary history of humankind is still far from being fully understood (Nielsen et al., 2017). During the last 30 years, the most accepted demographic scenario for explaining recent evolution of AMH has been the Out of Africa model (OOA). According to this model, AMH evolved in Africa around 100-200 thousands years ago (kya) in East Africa and migrated to the rest of the world. Classical "pure" OOA assumes that admixture with other archaic populations such as Neanderthals or Denisovans, present at the time of the rise of AMH, either did not occur or was negligible (Lalueza-Fox & Gilbert, 2011). Figure 1. Family tree of the four groups of early humans living in Eurasia 50,000 years ago and the inferred gene flow between the groups due to interbreeding (based on Prüfer et al., 2014;Mondal et al., 2016;Hsieh et al., 2016; Medina-Gomez et al., 2017). The direction and estimated magnitude of inferred gene flow events are shown. Branch lengths and timing of gene flows are not scaled. The dashed line indicates that it is uncertain whether Denisovan gene flow into modern humans in mainland Asia occurred directly or via Oceania. Light violet color indicates introgression events from unknown archaic populations (Ghost).However, genomic studies of ancient DNA have revealed that AMH interbred with other hominid lineages, such as Neanderthals and Denisovans, present in Eurasia up to ∼30,000-50,000 years ago Quach & Quintana-Murci, 2017;Vattathil & Akey, 2015 New studies based on current genetic diversity are suggesting that the events of archaic introgression in AMH did occur out of Africa with other hidden "ghost" archaic populations (Mondal et al., 2016). Furthermore, there i...

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“…Many studies have found evidence for "adaptive archaic introgression" [87][88][89][90][91][92]. Since the advent of whole genome sequencing, evidence has emerged that there was admixture between humans and two archaic hominids, Neanderthals [33,93,94] and Denisovans [95,96].…”

Section: Analysis Of Archaic Introgressionmentioning

confidence: 99%

Models, methods and tools for ancestry inference and admixture analysis

Yuan

Zhou

et al. 2017

Quant. Biol.

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Background: Genetic admixture refers to the process or consequence of interbreeding between two or more previously isolated populations within a species. Compared to many other evolutionary driving forces such as mutations, genetic drift, and natural selection, genetic admixture is a quick mechanism for shaping population genomic diversity. In particular, admixture results in "recombination" of genetic variants that have been fixed in different populations, which has many evolutionary and medical implications. Results: However, it is challenging to accurately reconstruct population admixture history and to understand of population admixture dynamics. In this review, we provide an overview of models, methods, and tools for ancestry inference and admixture analysis. Conclusions: Many methods and tools used for admixture analysis were originally developed to analyze human data, but these methods can also be directly applied and/or slightly modified to study non-human species as well.

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Neanderthal Introgression at Chromosome 3p21.31 Was Under Positive Natural Selection in East Asians

Cited by 73 publications

References 43 publications

Brak związku pomiędzy pochodzącą od człowieka neandertalskiego transwersją g.50318299T>G genu HYAL2 a predyspozycją do bliznowca

Brak związku pomiędzy pochodzącą od człowieka neandertalskiego transwersją g.50318299T>G genu HYAL2 a predyspozycją do bliznowca

Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Models, methods and tools for ancestry inference and admixture analysis

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