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The Genetic Diversification of Human Populations

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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 27395

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Prof. Dr. Hui Li

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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 (8 papers)

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Research

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10 pages, 728 KiB

Open AccessArticle

Genetic Diversity and Forensic Parameters of 27 Y-STRs in Two Mestizo Populations from Western Mexico

by Astrid Desireé Sánchez-Méndez, Silvia Elena Narvaez-Rivera, Héctor Rangel-Villalobos, Jorge Hernández-Bello, Andrés López-Quintero, José Miguel Moreno-Ortíz, Benito Ramos-González and José Alonso Aguilar-Velázquez

Genes 2025, 16(3), 352; https://doi.org/10.3390/genes16030352 - 19 Mar 2025

Viewed by 641

Abstract

Background: Analyzing Y-chromosome short tandem repeats (Y-STRs) is essential in forensic genetics and population studies. The Yfiler™ Plus kit, which includes 27 Y-STR markers, enhances the discrimination power for forensic and kinship applications. However, this genetic system has not been analyzed in Mexican populations, which limits its application and representativeness in international databases. Objectives: We wished to examine the genetic diversity and forensic parameters of the 27 Y-STRs included in the YFiler™ Plus kit in two populations from Western Mexico (Jalisco and Michoacán). Methods: Male DNA samples were amplified using the Yfiler™ Plus kit, followed by a fragment analysis via capillary electrophoresis (CE). The haplotype frequencies and forensic parameters were calculated. The haplogroups of all samples were predicted, and the distribution and percentages of ancestries were determined. The Rst genetic distances, including reference populations, were calculated and graphically represented in a multidimensional scaling (MDS) plot. Results: A total of 224 haplotypes were identified in all of the samples, of which 98.66% corresponded to unique haplotypes. Bi- and tri-allelic patterns were observed in both populations. The observed discriminatory capacity was 98.4% for Jalisco and 98.9% for Michoacán, while the haplotype diversity values were 0.9998 and 0.9997, respectively. The most frequent haplogroup was R1b, followed by Q, representing the European and Native American ancestries, in both populations. Conclusions: This study is the first to report the haplotype diversity and forensic parameters of the 27 Y-STRs included in the Yfiler™ Plus kit in Mexican populations. These findings confirm the forensic utility of these markers for human identification, biological relationship testing, and criminal investigations, reinforcing their applicability in forensic casework. Full article

(This article belongs to the Special Issue The Genetic Diversification of Human Populations)

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22 pages, 14926 KiB

Open AccessArticle

Origin and Genealogy of Rare mtDNA Haplotypes Detected in the Serbian Population

by Slobodan Davidović, Jelena M. Aleksić, Marija Tanasković, Pavle Erić, Milena Stevanović and Nataša Kovačević-Grujičić

Genes 2025, 16(1), 106; https://doi.org/10.3390/genes16010106 - 20 Jan 2025

Viewed by 1240

Abstract

Background: The Balkan Peninsula has served as an important migration corridor between Asia Minor and Europe throughout humankind’s history and a refugium during the Last Glacial Maximum. Past migrations such as the Neolithic expansion, Bronze Age migrations, and the settlement of Slavic tribes in the Early Middle Ages, are well known for their impact on shaping the genetic pool of contemporary Balkan populations. They have contributed to the high genetic diversity of the region, especially in mitochondrial DNA (mtDNA) lineages. Serbia, located in the heart of the Balkans, reflects this complex history in a broad spectrum of mtDNA subhaplogroups. Methods: To explore genetic diversity in Serbia and the wider Balkan region, we analyzed rare mtDNA subclades—R0a, N1a, N1b, I5, W, and X2—using publicly available data. Our dataset included already published sequences from 3499 HVS-I/HVS-II and 1426 complete mitogenomes belonging to West Eurasian and African populations, containing both contemporary and archaeological samples. We assessed the parameters of genetic diversity found in different subclades across the studied regions and constructed detailed phylogeographic trees and haplotype networks to determine phylogenetic relationships. Results: Our analyses revealed the observable geographic structure and identified novel mtDNA subclades, some of which may have originated in the Balkan Peninsula (e.g., R0a1a5, I5a1, W1c2, W3b2, and X2n). Conclusions: The geographic distribution of rare subclades often reveals patterns of past population movements, routes, and gene flows. By tracing the origin and diversity of these subclades, our study provided new insights into the impact of historical migrations on the maternal gene pool of Serbia and the wider Balkan region, contributing to our understanding of the complex genetic history of this important European crossroads. Full article

(This article belongs to the Special Issue The Genetic Diversification of Human Populations)

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13 pages, 3101 KiB

Open AccessArticle

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 4165

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 1989

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 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

Open AccessArticle

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 Orozco Show full author list Hide full author list

Genes 2022, 13(12), 2251; https://doi.org/10.3390/genes13122251 - 30 Nov 2022

Cited by 4 | Viewed by 3939

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 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

Open AccessArticle

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 7 | Viewed by 10596

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 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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21 pages, 4375 KiB

Open AccessReview

Haplotype-Based Approach Represents Locus Specificity in the Genomic Diversification Process in Humans (Homo sapiens)

by Makoto K. Shimada and Tsunetoshi Nishida

Genes 2024, 15(12), 1554; https://doi.org/10.3390/genes15121554 - 29 Nov 2024

Viewed by 731

Abstract

Background/Objectives: Recent progress in evolutionary genomics on human (Homo sapiens) populations has revealed complex demographic events and genomic changes. These include population expansion with complicated migration, substantial population structure, and ancient introgression from other hominins, as well as human characteristics selections. Nevertheless, the genomic regions in which such evolutionary events took place have remained unclear. Methods: Here, we focused on eight loci containing the haplotypes that were previously presented as atypical for the mutation pattern in sequence and/or geographic distribution pattern with the model of recent African origin, which constitute two major clusters: African only, and global. This was the consensus model before information regarding introgression from Neanderthal (Homo neanderthalensis) was available. We compared diversity in identical datasets of the modern human population genome, with the 1000 Genomes project among them. Results/Conclusions: This study identified representative genomic regions that show traces of various demographic events and genomic changes that modern humans have undergone by categorizing the relationships in sequence similarity and in worldwide geographic distribution among haplotypes. Full article

(This article belongs to the Special Issue The Genetic Diversification of Human Populations)

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15 pages, 2501 KiB

Open AccessReview

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 5 | Viewed by 3272

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, 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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