Identifying genes underlying skin pigmentation differences among human populations

Myles, Sean
Somel, Mehmet
Tang, Kun
Kelso, Janet
Stoneking, Mark
Skin pigmentation is a human phenotype that varies greatly among human populations and it has long been speculated that this variation is adaptive. We therefore expect the genes that contribute to these large differences in phenotype to show large allele frequency differences among populations and to possibly harbor signatures of positive selection. To identify the loci that likely contribute to among-population human skin pigmentation differences, we measured allele frequency differentiation among Europeans, Chinese and Africans for 24 human pigmentation genes from 2 publicly available, large scale SNP data sets. Several skin pigmentation genes show unusually large allele frequency differences among these populations. To determine whether these allele frequency differences might be due to selection, we employed a within-population test based on long-range haplotype structure and identified several outliers that have not been previously identified as putatively adaptive. Most notably, we identify the DCT gene as a candidate for recent positive selection in the Chinese. Moreover, our analyses suggest that it is likely that different genes are responsible for the lighter skin pigmentation found in different non-African populations.


Identification and analysis of genomic regions with large between-population differentiation in humans
Myles, S.; Tang, K.; Somel, Mehmet; Green, R. E.; Kelso, J.; Stoneking, M. (Wiley, 2008-01-01)
The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that...
Selection of representative SNP sets for genome-wide association studies: a metaheuristic approach
Ustunkar, Gurkan; AKYÜZ, SÜREYYA; Weber, Gerhard W.; Friedrich, Christoph M.; Aydın Son, Yeşim (2012-08-01)
After the completion of Human Genome Project in 2003, it is now possible to associate genetic variations in the human genome with common and complex diseases. The current challenge now is to utilize the genomic data efficiently and to develop tools to improve our understanding of etiology of complex diseases. Many of the algorithms needed to deal with this task were originally developed in management science and operations research (OR). One application is to select a subset of the Single Nucleotide Polymor...
HENDEN, Şevki Onur; Can, Tolga; Department of Computer Engineering (2021-9-9)
Characterizing the human genome's molecular functions and their variations across people is vital for understanding the cellular processes behind human genetic characteristics and diseases. With the advent of single-cell RNA sequencing (scRNA-seq), it is now possible to investigate gene expression in individual cells. Although a number of scRNA-seq bioinformatics tools are now available, many of them focus on overall gene expression levels and, as a result, often ignore heterogeneity caused by individual tr...
The Effects of plant originated bioactive compounds on melanogenesis and tyrosinase
Şahin, Şule; Çoruh, Nursen; Adalı, Orhan; Department of Biochemistry (2016)
Melanin is a dark pigment, found in skin, hair and eye. Its main function is to protect skin from the damaging ultraviolet rays of the sun. The skin color irregularity is caused by abnormalities in melanocytes, where the melanin synthesis is catalyzed by tyrosinase enzyme responsible for the pigmentation. Against these skin imperfections, unfortunately, an effective medication has not been available, yet. Nevertheless, in folk medicine, plants have been used effectively for the treatment of many skin diseas...
Widespread splicing changes in human brain development and aging
Mazin, Pavel; Xiong, Jieyi; Liu, Xiling; Yan, Zheng; Zhang, Xiaoyu; Li, Mingshuang; He, Liu; Somel, Mehmet; Yuan, Yuan; Chen, Yi-Ping Phoebe; Li, Na; Hu, Yuhui; Fu, Ning; Ning, Zhibin; Zeng, Rong; Yang, Hongyi; Chen, Wei; Gelfand, Mikhail; Khaitovich, Philipp (EMBO, 2013-01-01)
While splicing differences between tissues, sexes and species are well documented, little is known about the extent and the nature of splicing changes that take place during human or mammalian development and aging. Here, using high-throughput transcriptome sequencing, we have characterized splicing changes that take place during whole human lifespan in two brain regions: prefrontal cortex and cerebellum. Identified changes were confirmed using independent human and rhesus macaque RNA-seq data sets, exon ar...
Citation Formats
S. Myles, M. Somel, K. Tang, J. Kelso, and M. Stoneking, “Identifying genes underlying skin pigmentation differences among human populations,” HUMAN GENETICS, pp. 613–621, 2007, Accessed: 00, 2020. [Online]. Available: