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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 "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (25 August 2022) | Viewed by 12468

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 Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

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

The genetic diversification of human populations is a wide topic about the origin and genetic structure of populations both historically and in the present day, as well as the adaptation, selection, phenomic association, and other relevant aspects. The field began very early in the middle of the last century, represented by the works of Luca Cavalisforza etc., and soon revealed the genetic diversity of the classical markers among world populations. In 1987, the discovery of mitochondrial Eva initiated the phylogeny research of human genetic markers. The most outstanding findings about population history and relationship were contributed by Y-chromosome phylogenetic studies, which have strong expressions of the long history of patriarchy. After the Human Genomic Project, more papers on whole genomes have told us many stories under the horizon of our history records. Furthermore, in the last two decades, developments in ancient DNA analyses provided an increasingly clear view of human evolution. Linking the diversities in human genomes and phenomes is ongoing, allowing us to continue further in this direction.

This Special Issue will collect reviews and original contributions regarding 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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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

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

Published Papers (3 papers)

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Research

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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://0-doi-org.brum.beds.ac.uk/10.3390/genes13122251 - 30 Nov 2022
Viewed by 1937
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://0-doi-org.brum.beds.ac.uk/10.3390/genes13101776 - 01 Oct 2022
Viewed by 7263
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://0-doi-org.brum.beds.ac.uk/10.3390/genes13050890 - 17 May 2022
Cited by 3 | Viewed by 2235
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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