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Genetic Structure of Human Populations
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Genetic Structure of Human Populations

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (5 November 2022) | Viewed by 11984

Special Issue Editors

Prof. Dr. Chuan-Chao Wang

E-Mail Website
Guest Editor
School of Life Sciences, Xiamen University, Xiamen, China
Interests: ancient DNA; genome-wide variations; whole-genome sequence; admixture and adaptation history; molecular anthropology
Prof. Dr. Guanglin He

E-Mail Website
Guest Editor
1. Department of Anthropology and Ethnology, School of Life Sciences, Xiamen University, Xiamen 361005, China
2. School of Humanities, Nanyang Technological University, Nanyang 639798, Singapore
Interests: genome-wide SNPs; forensic and population genetics; genetic admixture and introgression; biological adaptation

Special Issue Information

Dear Colleagues,

Anatomically modern humans migrated out of Africa around 50,000 years ago. In the subsequent peopling of Eurasia, Oceania, and America, human populations underwent complex evolutionary events, mainly including population bottleneck, mutation, initial genetic isolation and the resulting admixture with incoming populations, and the adaptation of extreme environment introgressed with archaic hominins. This complex migration and admixture history contributed to the formation of the genetic structure of ethnolinguistically diverse populations. With the advent of an array of genotyping and next-generation sequencing, genetic studies have provided the basal framework of the genetic landscape of worldwide populations from different perspectives in the past three decades. The population genetic structure correlates well with geography and language, radically changing our understanding of human population history and cultural interactions. The genetic variations within and between populations are also widely used in the eras of human evolution, precision medicine, and forensic identification. As large-scale genomic data become more routine, we move towards an integrated comprehensive understanding of human populations.

We propose this Special Issue to highlight research on the "Genetic Structure of Human Populations". We call for high-quality review articles, original papers, and short communications with a focus on the fine-scale reconstruction of population genetic structure via mitochondrial DNA, Y-chromosome, and autosomal variations of both modern and ancient humans.

Prof. Dr. Chuan-Chao Wang
Prof. Dr. Guanglin He
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genome-wide variations (SNPs, STRs, InDels and CNVs)
  • ancient DNA and computation techniques
  • population admixture and biological adaptation
  • fine-scale population structure reconstruction
  • uniparentally inherited genetic markers (Y-chromosomes and Mitochondrial DNA)
  • patterns of sharing alleles and haplotypes

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Published Papers (4 papers)

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Research

8 pages, 602 KiB  
Article
Population Genetic Data of 30 Insertion-Deletion Markers in the Polish Population
by Monica Abreu-Glowacka, Witold Pepinski, Eliza Michalak, Magdalena Konarzewska, Krzysztof Zak, Malgorzata Skawronska, Anna Niemcunowicz-Janica, Ireneusz Soltyszewski, Pawel Krajewski and Czeslaw Zaba
Genes 2022, 13(10), 1683; https://doi.org/10.3390/genes13101683 - 20 Sep 2022
Viewed by 1906
Abstract
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included [...] Read more.
(1) Background: Insertion-deletion (InDel) markers show the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) and are considered alternative markers in forensic genetics. (2) Methods: Allelic frequencies and corresponding forensic efficiency parameters of 30 autosomal polymorphic InDel loci included in the Investigator DIPplex kit (Qiagen) were obtained in a sample of 631 unrelated Polish individuals. Allelic frequency data were compared with those reported for selected populations (3) Results: All the loci conformed with Hardy-Weinberg equilibrium after applying a Bonferroni correction and no pair-wise significant linkage disequilibrium was detected. (4) Conclusions: DIPplex Kit differences were high among populations worldwide. The InDel markers are highly discriminating for human identification purposes in the Polish population. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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15 pages, 11643 KiB  
Article
Forensic Analysis and Genetic Structure Construction of Chinese Chongming Island Han Based on Y Chromosome STRs and SNPs
by Xiao Zhang, Zhen Tang, Bin Wang, Xindao Zhou, Limin Zhou, Gongying Zhang, Junzhe Tian, Yiqi Zhao, Zhiqing Yao, Lu Tian, Suhua Zhang, Hao Xia, Li Jin, Chengtao Li and Shilin Li
Genes 2022, 13(8), 1363; https://doi.org/10.3390/genes13081363 - 29 Jul 2022
Cited by 2 | Viewed by 2989
Abstract
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of [...] Read more.
Y-chromosome short tandem repeat (Y-STR) and Y-chromosome single nucleotide polymorphism (Y-SNP) are genetic markers on the male Y chromosome for individual identification, forensic applications, and paternal genetic history analysis. In this study we successfully genotyped 38 Y-STR loci and 24 Y-SNP loci of Pudong Han (n = 689) and Chongming Han (n = 530) in Shanghai. The haplotype diversity of the Y filer platinum genotyping system was the highest in the Han population in the Pudong area of Shanghai (0.99996) and Chongming Island (0.99997). The proportion of unique haplotypes was 97.10% (Pudong) and 98.49% (Chongming), respectively. The multidimensional scaling analysis and phylogenetic analysis were performed according to the genetic distance Rst, which was calculated based on the Y-STR gene frequency data. Moreover, we made a comparison on the frequency distribution analysis and principal component analysis of haplogroups in both populations. As a result, Shanghai Pudong Han, Chongming Island Han, and Jiangsu Han were determined to have a strong genetic affinity. The haplogroup distribution characteristics of the Pudong Han and Chongming Han populations were similar to those of the southern Han population. The results of haplotype network analysis showed that Jiangsu Wujiang Han and Jiangsu Changshu Han had more paternal genetic contributions to the formation of Shanghai Pudong Han and Chongming Island Han. Through the joint analysis of SNPs and STRs, this study deeply analyzed the paternal genetic structure of the Pudong Han and Chongming Han populations. The addition of Y-SNP haplogroups to forensic applications can provide information for pedigree investigation. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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16 pages, 2777 KiB  
Article
A New Computational Deconvolution Algorithm for the Analysis of Forensic DNA Mixtures with SNP Markers
by Yu Yin, Peng Zhang and Yu Xing
Genes 2022, 13(5), 884; https://doi.org/10.3390/genes13050884 - 15 May 2022
Cited by 2 | Viewed by 2993
Abstract
Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To [...] Read more.
Single nucleotide polymorphisms (SNPs) support robust analysis on degraded DNA samples. However, the development of a systematic method to interpret the profiles derived from the mixtures is less studied, and it remains a challenge due to the bi-allelic nature of SNP markers. To improve the discriminating power of SNPs, this study explored bioinformatic strategies to analyze mixtures. Then, computer-generated mixtures were produced using real-world massively parallel sequencing (MPS) data from the single samples processed with the Precision ID Identity Panel. Moreover, the values of the frequency of major allele reads (FMAR) were calculated and applied as key parameters to deconvolve the two-person mixtures and estimate mixture ratios. Four custom R language scripts (three for autosomes and one for Y chromosome) were designed with the K-means clustering method as a core algorithm. Finally, the method was validated with real-world mixtures. The results indicated that the deconvolution accuracy for evenly balanced mixtures was 100% or close to 100%, which was the same as the deconvolution accuracy of inferring the genotypes of the major contributor of unevenly balanced mixtures. Meanwhile, the accuracy of inferring the genotypes of the minor contributor decreased as its proportion in the mixture decreased. Moreover, the estimated mixture ratio was almost equal to the actual ratio between 1:1 and 1:6. The method proposed in this study provides a new paradigm for mixture interpretation, especially for inferring contributor profiles of evenly balanced mixtures and the major contributor profile of unevenly balanced mixtures. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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18 pages, 9698 KiB  
Article
Molecular Evolutionary Rate Predicts Intraspecific Genetic Polymorphism and Species-Specific Selection
by Jiaqi Wu, Takahiro Yonezawa and Hirohisa Kishino
Genes 2022, 13(4), 708; https://doi.org/10.3390/genes13040708 - 17 Apr 2022
Viewed by 2884
Abstract
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, [...] Read more.
It is unknown what determines genetic diversity and how genetic diversity is associated with various biological traits. In this work, we provide insight into these issues. By comparing genetic variation of 14,671 mammalian gene trees with thousands of individual human, chimpanzee, gorilla, mouse, and dog/wolf genomes, we found that intraspecific genetic diversity can be predicted by long-term molecular evolutionary rates rather than de novo mutation rates. This relationship was established during the early stage of mammalian evolution. Moreover, we developed a method to detect fluctuations of species-specific selection on genes based on the deviations of intraspecific genetic diversity predicted from long-term rates. We showed that the evolution of epithelial cells, rather than connective tissue, mainly contributed to morphological evolution of different species. For humans, evolution of the immune system and selective sweeps caused by infectious diseases are the most representative examples of adaptive evolution. Full article
(This article belongs to the Special Issue Genetic Structure of Human Populations)
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