Adaptation of human skin color in various populations

Deng, Lian; Xu, Shuhua

doi:10.1186/s41065-017-0036-2

Cited by 84 publications

(85 citation statements)

References 123 publications

(142 reference statements)

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“…In support of this, skin reflectance values vary closely according to the UV exposure of a population’s environment [25] . A large number of mutations have contributed to the lightening of human skin, and these have evolved independently in separate human lineages [31–33] . Variants in the skin pigment genes SLC45A2, SLC24A5 are nearly fixed in Europeans but exhibit low allele frequencies in Africans and East Asians, whereas separate variants are present in MC1R, TYRP1, and OCA2 for European and East Asian populations.…”

Section: Loss Of Body Hair and Evolution Of Skin Pigmentationmentioning

confidence: 99%

Recent evolution of the human skin barrier

Brettmann

Strong

2018

Experimental Dermatology

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The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here, we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations.

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Section: Loss Of Body Hair and Evolution Of Skin Pigmentationmentioning

confidence: 99%

Recent evolution of the human skin barrier

Brettmann

Strong

2018

Experimental Dermatology

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“…In human, the SLC24A5 gene, a major driver of variation in skin pigmentation, has been shown to be under positive selection in European population (36, 41, 42). The causal mutation for the light skin phenotype was not present in HGDP data (SNP rs1426654, position: 15_46213776), but the SNPs we used (i.e.…”

Section: Discussionmentioning

confidence: 99%

A fast linkage disequilibrium-based statistical test for Genome-Wide Epistatic Selection Scans in structured populations

Boyrie

Moreau

Frugier

et al. 2020

Preprint

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22The quest for genome-wide signatures of selection in populations using SNP data has 23 proven efficient to uncover genes involved in conserved or adaptive molecular functions, but 24 none of the statistical methods were designed to identify interacting genes as targets of 25 selective processes. Here, we propose a straightforward statistical test aimed at detecting 26 epistatic selection, based on a linkage disequilibrium (LD) measure accounting for population 27 structure and heterogeneous relatedness between individuals. SNP-based ( ) and window-28 based ( 1 ) statistics fit a Student distribution, allowing to easily and quickly test the 29 significance of correlation coefficients in the frame of Genome-Wide Epistatic Selection 30 Scans (GWESS) using candidate genes as baits. As a proof of concept, use of SNP data from 31 the Medicago truncatula symbiotic legume plant uncovered a previously unknown gene 32 coadaptation between the MtSUNN (Super Numeric Nodule) receptor and the MtCLE02 33 (CLAVATA3-Like) signalling peptide, and experimental evidence accordingly supported a 34 MtSUNN-dependent negative role of MtCLE02 in symbiotic root nodulation. Using human 35 HGDP-CEPH SNP data, our new statistical test uncovered strong LD between SLC24A5 and 36 EDAR worldwide, which persists after correction for population structure and relatedness in 37 Central South Asian populations. This result suggests adaptive genetic interaction or 38 coselection between skin pigmentation and the ectodysplasin pathway involved in the 39 development of ectodermal organs (hairs, teeth, sweat glands), in some human populations. 40 Applying this approach to genome-wide SNP data will foster the identification of 41 evolutionary coadapted gene networks. 42 43 Author summary 46 Population genomic methods have allowed to identify many genes associated with 47 adaptive processes in populations with complex histories. However, they are not designed to 48 identify gene coadaptation between genes through epistatic selection, in structured 49 populations. To tackle this problem, we developed a straightforward LD-based statistical test 50 accounting for population structure and heterogeneous relatedness between individuals, using 51 SNP-based ( ) or windows-based ( 1 ) statistics. This allows easily and quickly testing 52 for significance of correlation coefficients between polymorphic loci in the frame of Genome 53 Wide Epistatic Selection Scans (GWESS). Following detection of gene coadaptation using 54 SNP data from human and the model plant Medicago truncatula, we report experimental 55 evidence of genetic interaction between two receptors involved in the regulation of root 56 nodule symbiosis in Medicago truncatula. This test opens new avenues for exploring the 57 evolution of genes as interacting units and thus paves the way to infer new networks based on 58 evolutionary coadaptation between genes. 59 60 65 selection against deleterious mutations (1-3). Identifying genes showing such selection 66 signatures has been a major goal of population...

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“…Skin color is a biologically important trait, which is a fascinating research topic and has great implications on biological adaption, commercial value, and skin health[22, 23]. In our study, most genes involved in pigmentation development, regulation and synthesis can be found in our assembled genome.…”

Section: Discussmentioning

confidence: 96%

The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

Sun

Wang

et al. 2019

Preprint

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17Mekong tiger perch (Datnioides undecimradiatus) is one ornamental fish and a 18 vulnerable species, which belongs to order Lobotiformes. Here, we report a ~595 Mb 19 D. undecimradiatus genome, which is the first whole genome sequence in the order 20 Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that 21 Lobotiformes and Sciaenidae are closer than Tetraodontiformes, resolving a long-time 22 dispute. We depicted the pigment synthesis pathway in Mekong tiger perch and result 23 confirmed that this pathway had evolved from the shared whole genome duplication. 24 We also estimated the demographic history of Mekong tiger perch, showing the 25 effective population size suffered a continuous reduction possibly related to the 26 contraction of immune-related genes. Our study provided a reference genome 27 resource for the Lobotiformes, as well as insights into the phylogeny of Eupercaria 28 and biological conservation. 29 30 Instruction 31 Mekong tiger perch (Datnioides undecimradiatus) [1] is one tropical freshwater fish, 32belonging to the order Lobotiformes under series Eupercaria. It is native to Mekong 33 river and usually found in the main waterway and large tributaries of the Mekong 34 river basins, feeding on small fishes and shrimps [2]. It is also one ornamental fish, 35 which is kept for its vertical yellow and black stripes running its body. 36 37 Eupercaria is by far the largest series of percomorphs with more than 6,600 species 38 arranged in 161 families and at least 16 orders. The phylogenetic relationship of the 39 order Lobotiformes, Tetraodontiformes, and the family Sciaenidae is in conflict. 40 Mirande reported Sciaedidae as the sister clade of Tetraodontiformes, and then 41 followed by Lobotiformes based on 44 DNA makers from uncompleted nuclear and 42 mitochondrial sequences combined with morphological characters [3]. Compared to it, 43 Betancur-R et al. reported Lobotiformes was more closely related to 44 Tetraodontiformes than Sciaedidae using molecular and genomic data, which was also 45 not complete or whole-genome sequenced for most of species. [4], agreed with this 46 phylogeny by investigating. However, more recently Lobotiformes was reported to be 47 more closely related to Sciaenidae than Tetraodontiformes based on complete 48 mitochondrial genome [5]using and transcriptomic data [6]. Furthermore, fourteen 49 families of Eupercaria included in order-level incertae sedis, which are called "new 50 bush at the top", were not arranged to explicit orders and interrelationships among 51 them was a long-term issue [7]. Therefore, the whole-genome containing 52 comprehensive evolutionary information is called for resolving the long-time dispute 53 on the phylogenetic relationships of the huge number of species in Eupercaria, 54 especially for the problem of "new bush at the top". 55 56 In addition to its evolutionary importance, Mekong tiger perch has a body color 57 pattern with vertical yellow and black stripes. Body color diversity in a...

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Adaptation of human skin color in various populations

Cited by 84 publications

References 123 publications

Recent evolution of the human skin barrier

Recent evolution of the human skin barrier

A fast linkage disequilibrium-based statistical test for Genome-Wide Epistatic Selection Scans in structured populations

The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenic position of Lobotiformes and biological conservation

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