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Population Structure and Human Genetic Diversity
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Population Structure and Human Genetic Diversity

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 (15 January 2024) | Viewed by 5969

Special Issue Editor

Prof. Juan Carlos Fernández-López

E-Mail Website
Guest Editor
Computational Genomics Department, National Institute of Genomic Medicine, Mexico City 14610, Mexico
Interests: medical and population genetics; complex traits; human genetics; computational genomics and genome wide association studies

Special Issue Information

Dear Colleagues,

For the past 15 years, studies on human genetics have revealed amazing discoveries in genomic medicine and have described the genomic diversity of human structure for many populations. In the field of complex diseases and traits, the NHGRI-EBI catalog of human genome-wide association studies has cataloged over 421,000 genomic positions associated with the main ancestries across the world populations in more than 5,900 scientific publications. This genomics approach provides a powerful and extraordinary tool that is set to examine large sets of genetic variations using low-cost and high-accuracy DNA sequencing and genotyping technologies. Most studies have occurred in European and East Asian populations, contributing to the genetic basis of many diseases and complex traits, such as type 2 diabetes, neurodegenerative diseases, and various types of cancer. However, the latest studies in population genetics applied to health have shown the usefulness of generating studies in multiple ethnicities to reveal new genetic targets positions associated with all these traits in populations worldwide.

In this Special Issue, we encourage researchers from institutions and universities across the world focused especially, but not limited to, in European and non-European populations or multi-ethnic genomic studies to understand the structural diversity of the unrepresented human populations and studies about common and rare traits. We would greatly appreciate your contributions to this Special Issue.

Prof. Juan Carlos Fernández-López
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

  • medical and populations genetics
  • statistical genetics and genomics
  • genome wide association studies (GWAS)
  • human population structure
  • complex traits
  • human genomics diversity

Published Papers (4 papers)

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Research

16 pages, 328 KiB  
Article
Genomic Signatures of Positive Selection in Human Populations of the OXT, OXTR, AVP, AVPR1A and AVR1B Gene Variants Related to the Regulation of Psychoemotional Response
by Siroj Yu. Bakoev, Anna V. Korobeinikova, Arina I. Mishina, Shuanat Sh. Kabieva, Sergey I. Mitrofanov, Alexey A. Ivashechkin, Alexsandra I. Akinshina, Ekaterina A. Snigir, Sergey M. Yudin, Vladimir S. Yudin, Lyubov V. Getmantseva and Elmira A. Anderzhanova
Genes 2023, 14(11), 2053; https://doi.org/10.3390/genes14112053 - 08 Nov 2023
Viewed by 1043
Abstract
The neurobiological systems of maintenance and control of behavioral responses result from natural selection. We have analyzed the selection signatures for single nucleotide variants (SNV) of the genes of oxytocin (OXT, OXTR) and vasopressin (AVP, AVPR1A, AVPR1B [...] Read more.
The neurobiological systems of maintenance and control of behavioral responses result from natural selection. We have analyzed the selection signatures for single nucleotide variants (SNV) of the genes of oxytocin (OXT, OXTR) and vasopressin (AVP, AVPR1A, AVPR1B) systems, which are associated with the regulation of social and emotional behavior in distinct populations. The analysis was performed using original WGS (whole genome sequencing) data on Eastern Slavs (SlEast), as well as publicly available data from the 1000 Genomes Project on GBR, FIN, IBR, PUR, BEB, CHB, and ACB populations (the latter were taken as reference). To identify selection signatures, we rated the integrated haplotype scores (iHS), the numbers of segregating sites by length (nSl), and the integrated haplotype homozygosity pooled (iHH12) measures; the fixation index Fst was implemented to assess genetic differentiation between populations. We revealed that the strongest genetic differentiation of populations was found with respect to the AVPR1B gene, with the greatest differentiation observed in GRB (Fst = 0.316) and CHB (Fst = 0.325) in comparison to ACB. Also, high Fst values were found for SNVs of the AVPR1B gene rs28499431, rs33940624, rs28477649, rs3883899, and rs28452187 in most of the populations. Selection signatures have also been identified in the AVP, AVPR1A, OXT, and OXTR genes. Our analysis shows that the OXT, OXTR, AVP, AVPR1A, and AVPR1B genes were subject to positive selection in a population-specific process, which was likely contributing to the diversity of adaptive emotional response types and social function realizations. Full article
(This article belongs to the Special Issue Population Structure and Human Genetic Diversity)
23 pages, 2015 KiB  
Article
Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley
by Daniel Uricoechea Patiño, Andrew Collins, Oscar Julián Romero García, Gustavo Santos Vecino, Pablo Aristizábal Espinosa, Jaime Eduardo Bernal Villegas, Escilda Benavides Benitez, Saray Vergara Muñoz and Ignacio Briceño Balcázar
Genes 2023, 14(11), 2036; https://doi.org/10.3390/genes14112036 - 02 Nov 2023
Cited by 1 | Viewed by 1802
Abstract
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The [...] Read more.
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal lineages using DNA samples obtained from skeletal remains. The results illuminate a remarkable degree of biological diversity within these populations and provide insights into their genetic connections with other ancient and indigenous groups across the American continent. The findings strongly support the widely accepted hypothesis that the migration of the first American settlers occurred through Beringia, a land bridge connecting Siberia to North America during the last Ice Age. Subsequently, these early settlers journeyed southward, crossing the North American ice cap. Of particular note, the study unveils the presence of ancestral lineages from Asian populations, which played a pivotal role in populating the Americas. The implications of these results extend beyond delineating migratory routes and settlement patterns of ancient populations. They also enrich our understanding of the genetic diversity inherent in indigenous populations of the region. By revealing the genetic heritage of pre-Hispanic individuals from the Aburrá Valley, this study offers valuable insights into the history of human migration and settlement in the Americas. Furthermore, it enhances our comprehension of the intricate genetic tapestry that characterizes indigenous communities in the area. Full article
(This article belongs to the Special Issue Population Structure and Human Genetic Diversity)
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13 pages, 1080 KiB  
Article
High Mitochondrial Haplotype Diversity Found in Three Pre-Hispanic Groups from Colombia
by Daniel Uricoechea Patiño, Andrew Collins, Oscar Julián Romero García, Gustavo Santos Vecino, José Vicente Rodríguez Cuenca, Jaime E. Bernal, Escilda Benavides Benítez, Saray Vergara Muñoz and Ignacio Briceño Balcázar
Genes 2023, 14(10), 1853; https://doi.org/10.3390/genes14101853 - 23 Sep 2023
Cited by 1 | Viewed by 1166
Abstract
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has [...] Read more.
The analysis of mitochondrial DNA (mtDNA) hypervariable region (HVR) sequence data from ancient human remains provides valuable insights into the genetic structure and population dynamics of ancient populations. mtDNA is particularly useful in studying ancient populations, because it is maternally inherited and has a higher mutation rate compared to nuclear DNA. To determine the genetic structure of three Colombian pre-Hispanic populations and compare them with current populations, we determined the haplotypes from human bone remains by sequencing several mitochondrial DNA segments. A wide variety of mitochondrial polymorphisms were obtained from 33 samples. Our results support a high population heterogeneity among pre-Hispanic populations in Colombia. Full article
(This article belongs to the Special Issue Population Structure and Human Genetic Diversity)
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12 pages, 290 KiB  
Article
Allele Frequencies and Forensic Data of 25 STR Markers for Individuals in Northeast Brazil
by Natalia Bahia Pinheiro dos Santos, Márcio Fabrício Falcão de Paula Filho, Abigail Marcelino dos Santos Silva, Enio Paulo Teló, José Bandeira do Nascimento Junior, Valdir de Queiroz Balbino, Iukary Oliveira Takenami and Isaac Farias Cansanção
Genes 2023, 14(6), 1185; https://doi.org/10.3390/genes14061185 - 29 May 2023
Viewed by 1418
Abstract
Identifying DNA markers such as Short Tandem Repeats (STR) can be used to investigate genetic diversity based on levels of heterozygosity within and between populations. Allele frequencies and forensic data for STRs were obtained from a sample of 384 unrelated individuals living in [...] Read more.
Identifying DNA markers such as Short Tandem Repeats (STR) can be used to investigate genetic diversity based on levels of heterozygosity within and between populations. Allele frequencies and forensic data for STRs were obtained from a sample of 384 unrelated individuals living in Bahia, Northeastern Brazil. Thus, the present study aimed to identify the allele frequency distribution, in addition to the forensic and genetic data, of 25 STR loci in the population of Bahia. Buccal swabs or fingertip punctures were utilized to amplify and detect 25 DNA markers. The most polymorphic loci were SE33 (43), D21S11, and FGA (21). The least polymorphic were TH01 (6), TPOX, and D3S1358 (7). Forensic and statistical data were obtained through data analysis, which revealed a large genetic diversity, with an average value of 0.813 for the analyzed population. The present study was more robust than previous STR marker studies and will contribute to future research on population genetics in Brazil and worldwide. The results of this study allowed the establishment of haplotypes found in the forensic samples of Bahia State to serve as a reference in the elucidation of criminal cases and paternity tests, as well as population and evolutionary investigations. Full article
(This article belongs to the Special Issue Population Structure and Human Genetic Diversity)
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