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The Genetic Diversification of Human Populations
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The Genetic Diversification of Human Populations

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: 5 May 2025 | Viewed by 17224

Special Issue Editor

Prof. Dr. Hui Li

E-Mail Website
Guest Editor
School of Life Sciences, Fudan University, Shanghai, China
Interests: human genetic diversification; gene environment disease coevolution; gene association of human phenotype

Special Issue Information

Dear Colleagues,

In the last 70,000 years, modern humans have dispersed to most regions of the world. Along with this dispersal, their genomes have diversified under various mechanisms, which warrants further investigation and analysis in order to reveal the history of human evolution as well as future developments.

The genetic diversification of human populations is an extensive topic addressing the origin and genetic structure of populations both historically and in the present day, as well adaptation, selection, phenomic association, and other relevant aspects. Interest in this topic began in the mid-1900s, and was represented by the works of Luca Cavalisforza, etc. Research soon revealed the genetic diversity of the classical markers that exist among world populations. In 1987, the discovery of mitochondrial Eva initiated the phylogeny research of human genetic markers. The most outstanding findings regarding population history and relationships were contributed by Y-chromosome phylogenetic studies, which are strongly related to the long history of patriarchy. After the Human Genomic Project, additional studies on whole genomes have revealed much information that was previously overlooked by our history records. Furthermore, in the last two decades, developments in ancient DNA analyses have provided an increasingly clear view of human evolution. The evaluation of the diversities in human genomes and phenomes is ongoing, and it is allowing us to continue research in this direction.

This Special Issue will collect reviews and original contributions regarding the whole-genome diversity of the world population, Y chromosome resequencing and high-resolution phylogeny, ancient DNA studies, phenomic-related genetic diversity, and other studies about the genetic diversity of human populations.

Prof. Dr. Hui Li
Guest Editor

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Keywords

  • human populations
  • genome diversity
  • ancient DNA
  • genetic diversity
  • Y chromosome resequencing
  • high-resolution phylogeny

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Published Papers (5 papers)

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Research

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13 pages, 3101 KiB  
Article
Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan
by Maxat Zhabagin, Assel Tashkarayeva, Alizhan Bukayev, Aigul Zhunussova, Georgy Ponomarev, Saltanat Tayshanova, Albina Maxutova, Dmitry Adamov, Elena Balanovska and Zhaxylyk Sabitov
Genes 2024, 15(12), 1501; https://doi.org/10.3390/genes15121501 - 22 Nov 2024
Viewed by 851
Abstract
This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis [...] Read more.
This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating. Subhaplogroups Q1a and Q1b identified in Turkmenistan trace back to ancient Y-chromosome lineages from the Bronze Age. Comparative analyses, including genetic distance (RST), median-joining network, and multidimensional scaling (MDS), highlight the genetic proximity of the Turkmen in Turkmenistan to those in Afghanistan and Iran, while Iraqi Turkmen display unique characteristics, aligning with Near Eastern populations. This study underscores the Central Asian genetic affinity across most Turkmen populations. It demonstrates the value of deep-sequencing Y-chromosome data in tracing the patrilineal history of Central Asia for future studies. These findings contribute to a more comprehensive understanding of Turkmen genetic ancestry and add new data to the ongoing study of Central Asian population genetics. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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14 pages, 4217 KiB  
Article
Local Ancestry Inference Based on Population-Specific Single-Nucleotide Polymorphisms—A Study of Admixed Populations in the 1000 Genomes Project
by Haoyue Fu and Gang Shi
Genes 2024, 15(8), 1099; https://doi.org/10.3390/genes15081099 - 21 Aug 2024
Viewed by 1116
Abstract
Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we [...] Read more.
Human populations have interacted throughout history, and a considerable portion of modern human populations show evidence of admixture. Local ancestry inference (LAI) is focused on detecting the genetic ancestry of chromosomal segments in admixed individuals and has wide applications. In this work, we proposed a new LAI method based on population-specific single-nucleotide polymorphisms (SNPs) and applied it in the analysis of admixed populations in the 1000 Genomes Project (1KGP). Based on population-specific SNPs in a sliding window, we computed local ancestry information vectors, which are moment estimators of local ancestral proportions, for two haplotypes of an admixed individual and inferred the local ancestral origins. Then we used African (AFR), East Asian (EAS), European (EUR) and South Asian (SAS) populations from the 1KGP and indigenous American (AMR) populations from the Human Genome Diversity Project (HGDP) as reference populations and conducted the proposed LAI analysis on African American populations and American populations in the 1KGP. The results were compared with those obtained by RFMix, G-Nomix and FLARE. We demonstrated that the existence of alleles in a chromosomal region that are specific to a particular reference population and the absence of alleles specific to the other reference populations provide reasonable evidence for determining the ancestral origin of the region. Contemporary AFR, AMR and EUR populations approximate ancestral populations of the admixed populations well, and the results from RFMix, G-Nomix and FLARE largely agree with those from the Ancestral Spectrum Analyzer (ASA), in which the proposed method was implemented. When admixtures are ancient and contemporary reference populations do not satisfactorily approximate ancestral populations, the performances of RFMix, G-Nomix and FLARE deteriorate with increased error rates and fragmented chromosomal segments. In contrast, our method provides fair results. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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10 pages, 31874 KiB  
Article
Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico
by Humberto García-Ortiz, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Austin W. Reynolds, Marlen Flores-Huacuja, Meradeth Snow, Jazmín Ramos-Madrigal, Elvia Mendoza-Caamal, Paulina Baca, Tomás A. López-Escobar, Deborah A. Bolnick, Silvia Esperanza Flores-Martínez, Rocio Ortiz-Lopez, Aleksandar David Kostic, José Rafael Villafan-Bernal, Carlos Galaviz-Hernández, Federico Centeno-Cruz, Alejandra Guadalupe García-Zapién, Tulia Monge-Cázares, Blanca Patricia Lazalde-Ramos, Francisco Loeza-Becerra, María del Carmen Abrahantes-Pérez, Héctor Rangel-Villalobos, Martha Sosa-Macías, Augusto Rojas-Martínez, Angélica Martínez-Hernández and Lorena Orozcoadd Show full author list remove Hide full author list
Genes 2022, 13(12), 2251; https://doi.org/10.3390/genes13122251 - 30 Nov 2022
Cited by 3 | Viewed by 2647
Abstract
Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and [...] Read more.
Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and population branch statistics, in 325 Mexican Indigenous individuals with at least 99% Native American ancestry from five previously defined geographical regions. Although each region exhibited its own local adaptation profile, only PPARG and AJAP1, both negative regulators of the Wnt/β catenin signaling pathway, showed significant adaptation signals in all the tested regions. Several signals were found, mainly in the genes related to the metabolic processes and immune response. A pathway enrichment analysis revealed the overrepresentation of selected genes related to several biological phenotypes/conditions, such as the immune response and metabolic pathways, in agreement with previous studies, suggesting that immunological and metabolic pressures are major drivers of human adaptation. Genes related to the gut microbiome measurements were overrepresented in all the regions, highlighting the importance of studying how humans have coevolved with the microbial communities that colonize them. Our results provide a further explanation of the human evolutionary history in response to environmental pressures in this region. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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11 pages, 2106 KiB  
Article
Ancient Components and Recent Expansion in the Eurasian Heartland: Insights into the Revised Phylogeny of Y-Chromosomes from Central Asia
by Maxat Zhabagin, Lan-Hai Wei, Zhaxylyk Sabitov, Peng-Cheng Ma, Jin Sun, Zhanargul Dyussenova, Elena Balanovska, Hui Li and Yerlan Ramankulov
Genes 2022, 13(10), 1776; https://doi.org/10.3390/genes13101776 - 1 Oct 2022
Cited by 5 | Viewed by 9217
Abstract
In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic [...] Read more.
In the past two decades, studies of Y chromosomal single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) have shed light on the demographic history of Central Asia, the heartland of Eurasia. However, complex patterns of migration and admixture have complicated population genetic studies in Central Asia. Here, we sequenced and analyzed the Y-chromosomes of 187 male individuals from Kazakh, Kyrgyz, Uzbek, Karakalpak, Hazara, Karluk, Tajik, Uyghur, Dungan, and Turkmen populations. High diversity and admixture from peripheral areas of Eurasia were observed among the paternal gene pool of these populations. This general pattern can be largely attributed to the activities of ancient people in four periods, including the Neolithic farmers, Indo-Europeans, Turks, and Mongols. Most importantly, we detected the consistent expansion of many minor lineages over the past thousand years, which may correspond directly to the formation of modern populations in these regions. The newly discovered sub-lineages and variants provide a basis for further studies of the contributions of minor lineages to the formation of modern populations in Central Asia. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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Review

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15 pages, 2501 KiB  
Review
An Update on the Evolutionary History of Bregs
by Michel-Edwar Mickael, Irmina Bieńkowska and Mariusz Sacharczuk
Genes 2022, 13(5), 890; https://doi.org/10.3390/genes13050890 - 17 May 2022
Cited by 3 | Viewed by 2847
Abstract
The relationship between the evolutionary history and the differentiation of Bregs is still not clear. Bregs were demonstrated to possess a regulatory effect on B cells. Various subsets of Bregs have been identified including T2-MZP, MZ, B10, IL10-producing plasma cells, IL10 producing plasmablasts, [...] Read more.
The relationship between the evolutionary history and the differentiation of Bregs is still not clear. Bregs were demonstrated to possess a regulatory effect on B cells. Various subsets of Bregs have been identified including T2-MZP, MZ, B10, IL10-producing plasma cells, IL10 producing plasmablasts, immature IL10 producing B cells, TIM1, and Br1. It is known that B cells have evolved during fish emergence. However, the origin of Bregs is still not known. Three main models have been previously proposed to describe the origin of Bregs, the first known as single–single (SS) suggests that each type of Bregs subpopulation has emerged from a single pre-Breg type. The second model (single–multi) (SM) assumes that a single Bregs gave rise to multiple types of Bregs that in turn differentiated to other Breg subpopulations. In the third model (multi–multi) (MM), it is hypothesized that Bregs arise from the nearest B cell phenotype. The link between the differentiation of cells and the evolution of novel types of cells is known to follow one of three evolutionary patterns (i.e., homology, convergence, or concerted evolution). Another aspect that controls differentiation and evolution processes is the principle of optimization of energy, which suggests that an organism will always use the choice that requires less energy expenditure for survival. In this review, we investigate the evolution of Breg subsets. We studied the feasibility of Breg origination models based on evolution and energy constraints. In conclusion, our review indicates that Bregs are likely to have evolved under a combination of SM–MM models. This combination ensured successful survival in harsh conditions by following the least costly differentiation pathway, as well as adapting to changing environmental conditions. Full article
(This article belongs to the Special Issue The Genetic Diversification of Human Populations)
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