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Trends in Population Genetics and Identification—Impact on Anthropology

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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 (10 November 2022) | Viewed by 39819

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Special Issue Editors

Prof. Dr. Antonio Amorim

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Guest Editor

i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
Interests: population genetics; forensic genetics; evolution

Dr. Veronica Gomes

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Co-Guest Editor

1. Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
2. Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
Interests: population genetics; genetic diversity; human evolution; human population history; human migrations and admixtures; genetics of disease; uniparental lineages; Y chromosome

Dr. Luisa Azevedo

E-Mail Website
Co-Guest Editor

i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
Interests: population genetics; medical genetics; human evolution

Special Issue Information

Dear Colleagues，

The recent advances in genotyping technologies and data analyses have brought significant advances in our understanding of human origins and evolution and provided extremely powerful approaches in the forensic and medical fields, reshaping entirely our anthropological perspectives.

Although these advances are still far from being fully exploited, we feel it is nevertheless timely and useful to organize a Special Issue on this topic, allowing the scientific community to review, reflect and problematize the related questions – those that are already on sight as well as those we might envisage to be faced with in the future.

We expect to receive contributions on – but not limited to - the topics of (1) evolution, (2) intra and interpopulation human genetic diversity in health and disease, (3) individual identification and population assignment, (4) genome and phenome, and, of course, (5) ethical and legal implications.

We do hope that this Special Issue will provide a space for reviews and original contributions on this exciting, revived interface between genetics and anthropology which will attract the interest of research community and the readers of this journal.

Prof. Dr. Antonio Amorim
Dr. Veronica Gomes
Dr. Luisa Azevedo
Guest Editors

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Keywords

population genetics
identification
anthropology
genetic diversity
mutation
evolution
genome
phenome
ethics
forensics

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Published Papers (10 papers)

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Editorial

Jump to: Research, Review, Other

3 pages, 165 KiB

Open AccessEditorial

Editorial for the Special Issue: Trends in Population Genetics and Identification—Impact on Anthropology

by Verónica Gomes, Luísa Azevedo and Antonio Amorim

Genes 2024, 15(11), 1387; https://doi.org/10.3390/genes15111387 - 29 Oct 2024

Viewed by 442

Abstract

Technological advances in genetics have revealed many aspects of human ancestry as well as how our genome was shaped by new environments encountered during ancient migrations [...] Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

Research

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20 pages, 3082 KiB

Open AccessArticle

Tierra Del Fuego: What Is Left from the Precolonial Male Lineages?

by Pedro Rodrigues, Irina Florencia Velázquez, Julyana Ribeiro, Filipa Simão, António Amorim, Elizeu F. Carvalho, Claudio Marcelo Bravi, Néstor Guillermo Basso, Luciano Esteban Real, Claudio Galli, Andrea del Carmen González, Ariana Gamulin, Romina Saldutti, Maria Laura Parolin, Verónica Gomes and Leonor Gusmão

Genes 2022, 13(10), 1712; https://doi.org/10.3390/genes13101712 - 23 Sep 2022

Cited by 4 | Viewed by 4463

Abstract

Similar to other South American regions, Tierra del Fuego has an admixed population characterized by distinct ancestors: Native Americans who first occupied the continent, European settlers who arrived from the late 15th century onwards, and Sub-Saharan Africans who were brought to the Americas for slave labor. To disclose the paternal lineages in the current population from Tierra del Fuego, 196 unrelated males were genotyped for 23 Y-STRs and 52 Y-SNPs. Haplotype and haplogroup diversities were high, indicating the absence of strong founder or drift events. A high frequency of Eurasian haplogroups was detected (94.4%), followed by Native American (5.1%) and African (0.5%) ones. The haplogroup R was the most abundant (48.5%), with the sub-haplogroup R-S116* taking up a quarter of the total dataset. Comparative analyses with other Latin American populations showed similarities with other admixed populations from Argentina. Regarding Eurasian populations, Tierra del Fuego presented similarities with Italian and Iberian populations. In an in-depth analysis of the haplogroup R-M269 and its subtypes, Tierra del Fuego displayed a close proximity to the Iberian Peninsula. The results from this study are in line with the historical records and reflect the severe demographic change led mainly by male newcomers with paternal European origin. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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10 pages, 296 KiB

Open AccessArticle

Mutation Rate Analysis of RM Y-STRs in Deep-Rooted Multi-Generational Punjabi Pedigrees from Pakistan

by Shahid Nazir, Atif Adnan, Rahat Abdul Rehman, Wedad Saeed Al-Qahtani, Abrar B. Alsaleh, Hussam S. Al-Harthi, Fatmah Ahmed Safhi, Reem Almheiri, Reem Lootah, Afra Alreyami, Imran Almarri, Chuan-Chao Wang, Allah Rakha and Sibte Hadi

Genes 2022, 13(8), 1403; https://doi.org/10.3390/genes13081403 - 7 Aug 2022

Cited by 7 | Viewed by 2304

Abstract

Y chromosome short tandem repeat polymorphisms (Y-STRs) are important in many areas of human genetics. Y chromosomal STRs, being normally utilized in the field of forensics, exhibit low haplotype diversity in consanguineous populations and fail to discriminate among male relatives from the same pedigree. Rapidly mutating Y-STRs (RM Y-STRs) have received much attention in the past decade. These 13 RM Y-STRs have high mutation rates (>10⁻²) and have considerably higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, showing remarkable power when it comes to differentiation in paternal lineages in endogamous populations. Previously, we analyzed two to four generations of 99 pedigrees with 1568 pairs of men covering one to six meioses from all over Pakistan and 216 male relatives from 18 deep-rooted endogamous Sindhi pedigrees covering one to seven meioses. Here, we present 861 pairs of men from 62 endogamous pedigrees covering one to six meioses from the Punjabi population of Punjab, Pakistan. Mutations were frequently observed at DYF399 and DYF403, while no mutation was observed at DYS526a/b. The rate of differentiation ranged from 29.70% (first meiosis) to 80.95% (fifth meiosis), while overall (first to sixth meiosis) differentiation was 59.46%. Combining previously published data with newly generated data, the overall differentiation rate was 38.79% based on 5176 pairs of men related by 1–20 meioses, while Yfiler differentiation was 9.24% based on 3864 pairs. Using father–son pair data from the present and previous studies, we also provide updated RM Y-STR mutation rates. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

11 pages, 1804 KiB

Open AccessFeature PaperArticle

Estimations of Mutation Rates Depend on Population Allele Frequency Distribution: The Case of Autosomal Microsatellites

by Sofia Antão-Sousa, Eduardo Conde-Sousa, Leonor Gusmão, António Amorim and Nádia Pinto

Genes 2022, 13(7), 1248; https://doi.org/10.3390/genes13071248 - 14 Jul 2022

Cited by 5 | Viewed by 2307

Abstract

Microsatellites (or short-tandem repeats (STRs)) are widely used in anthropology and evolutionary studies. Their extensive polymorphism and rapid evolution make them the ideal genetic marker for dating events, such as the age of a gene or a population. This usage requires the estimation of mutation rates, which are usually estimated by counting the observed Mendelian incompatibilities in one-generation familial configurations (typically parent(s)–child duos or trios). Underestimations are inevitable when using this approach, due to the occurrence of mutational events that do not lead to incompatibilities with the parental genotypes (‘hidden’ or ‘covert’ mutations). It is known that the likelihood that one mutation event leads to a Mendelian incompatibility depends on the mode of genetic transmission considered, the type of familial configuration (duos or trios) considered, and the genotype(s) of the progenitor(s). In this work, we show how the magnitude of the underestimation of autosomal microsatellite mutation rates varies with the populations’ allele frequency distribution spectrum. The Mendelian incompatibilities approach (MIA) was applied to simulated parent(s)/offspring duos and trios in different populational scenarios. The results showed that the magnitude and type of biases depend on the population allele frequency distribution, whatever the type of familial data considered, and are greater when duos, instead of trios, are used to obtain the estimates. The implications for molecular anthropology are discussed and a simple framework is presented to correct the naïf estimates, along with an informatics tool for the correction of incompatibility rates obtained through the MIA. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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16 pages, 1752 KiB

Open AccessArticle

Identification and Characterization of Variants in Intron 6 of the LPL Gene Locus among a Sample of the Kuwaiti Population

by Reem T. Al-Shammari, Ahmad E. Al-Serri, Sahar A. Barhoush and Suzanne A. Al-Bustan

Genes 2022, 13(4), 664; https://doi.org/10.3390/genes13040664 - 9 Apr 2022

Cited by 4 | Viewed by 2345

Abstract

Lipoprotein lipase (LPL) is responsible for the hydrolysis of lipoproteins; hence defective LPL is associated with metabolic disorders. Here, we identify certain intronic insertions and deletions (InDels) and single nucleotide polymorphisms (SNPs) in intron 6 of the LPL gene and investigate their associations with different phenotypic characteristics in a cohort of the general Kuwaiti population. Two specific regions of intron 6 of the LPL gene, which contain InDels, were amplified via Sanger sequencing in 729 subjects. Genotypic and allelic frequencies were estimated, and genetic modeling was used to investigate genetic associations of the identified variants with lipid profile, body mass index (BMI), and risk of coronary heart disease (CHD). A total of 16 variants were identified, including 2 InDels, 2 novel SNPs, and 12 known SNPs. The most common variants observed among the population were rs293, rs274, rs295, and rs294. The rs293 “A” insertion showed a significant positive correlation with elevated LDL levels, while rs295 was significantly associated with increased BMI. The rs274 and rs294 variants showed a protective effect of the minor allele with decreased CHD prevalence. These findings shed light on the possible role of LPL intronic variants on metabolic disorders. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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11 pages, 781 KiB

Open AccessEditor’s ChoiceArticle

Are Roma People Descended from the Punjab Region of Pakistan: A Y-Chromosomal Perspective

by Atif Adnan, Allah Rakha, Hayder Lazim, Shahid Nazir, Wedad Saeed Al-Qahtani, Maha Abdullah Alwaili, Sibte Hadi and Chuan-Chao Wang

Genes 2022, 13(3), 532; https://doi.org/10.3390/genes13030532 - 17 Mar 2022

Cited by 4 | Viewed by 6897

Abstract

Gypsies are a separate ethnic group living in Pakistan and some other countries as well. They are mostly known as ‘Roma’ and ‘untouchables’. They have different types of lifestyles as compared to other common people, as they always keep migrating from one place to another. They do not have proper houses; they live in tent houses and most probably work on daily wages to earn their living. Gypsies cannot be specified according to the place of residence and can only be classified according to their migration route. Previous historical and linguistic research showed the north Indian origin of Roma people. The present study collected 285 unrelated Roma individuals living in Punjab and typed with the Goldeneye Y20 system. Allelic frequencies ranged between 0.0035 and 0.5266, with haplotype diversity (HD) of 0.9999 and discrimination capacity (DC) of 0.8790. Gene diversity (GD) ranged from 0.6489 (DYS391) to 0.9764 (DYS391) (DY385ab). A total of 223 unique alleles were observed. Interestingly, the haplogroup R accounted for 40.56% and J for 22.06%. In MDS analysis, Pakistani Roma formed a close cluster with Roma from Constanta, Romania. The migration pattern of the Roma population from Pakistan, India and Europe was inferred using coalescence theory in the Migrate-n program. Overlapping Y-STR data were used to test different migration models. These migration models showed us the dominant gene flow from Pakistan to India and Europe to Pakistan. The results of our study showed that Y STRs provided substantially stronger discriminatory power in the Pakistani Roma population. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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12 pages, 1328 KiB

Open AccessArticle

Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians

by Catarina Branco, Marina Kanellou, Antonio González-Martín and Miguel Arenas

Genes 2022, 13(2), 384; https://doi.org/10.3390/genes13020384 - 21 Feb 2022

Cited by 3 | Viewed by 3386

Abstract

The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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Review

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14 pages, 1186 KiB

Open AccessFeature PaperReview

Population Genetics of the European Roma—A Review

by Giacomo Francesco Ena, Julen Aizpurua-Iraola, Neus Font-Porterias, Francesc Calafell and David Comas

Genes 2022, 13(11), 2068; https://doi.org/10.3390/genes13112068 - 8 Nov 2022

Cited by 4 | Viewed by 7485

Abstract

The Roma are a group of populations with a common origin that share the Romani identity and cultural heritage. Their genetic history has been inferred through multiple studies based on uniparental and autosomal markers, and current genomic data have provided novel insights into their genetic background. This review was prompted by two factors: (i) new developments to estimate the genetic structure of the Roma at a fine-scale resolution have precisely identified the ancestral components and traced migrations that were previously documented only in historical sources, clarifying and solving debates on the origins and the diaspora of the Roma; (ii) while there has been an effort to review the health determinants of the Roma, the increasing literature on their population genetics has not been subjected to a dedicated review in the last two decades. We believe that a summary on the state of the art will benefit both the public and scholars that are approaching the subject. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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Other

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11 pages, 1064 KiB

Open AccessSystematic Review

Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects

by Leonard Taufik, João C. Teixeira, Bastien Llamas, Herawati Sudoyo, Raymond Tobler and Gludhug A. Purnomo

Genes 2022, 13(12), 2373; https://doi.org/10.3390/genes13122373 - 16 Dec 2022

Cited by 1 | Viewed by 4206

Abstract

Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace’s and Lydekker’s Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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9 pages, 1051 KiB

Open AccessBrief Report

Genetic Polymorphism of 27 Y-STR Loci in the Western Kazakh Tribes from Kazakhstan and Karakalpakstan, Uzbekistan

by Yeldar Ashirbekov, Zhaxylyk Sabitov, Baglan Aidarov, Arman Abaildayev, Zukhra Junissova, Alena Cherusheva, Viktoriya V. Saidamarova, Kamalidin Sharipov, Yerlan Ramankulov and Maxat Zhabagin

Genes 2022, 13(10), 1826; https://doi.org/10.3390/genes13101826 - 9 Oct 2022

Cited by 6 | Viewed by 3540

Abstract

Data on the genetic polymorphism of 27 Y-STR in Kazakhs of the Junior Zhuz has been presented and analyzed in relation to forensic features. A total of 464 representatives of the Western Kazakh tribes of Kazakhstan (Western Kazakhs, n = 405) and Uzbekistan (Karakalpakstan Kazakhs, n = 59) were examined by the Yfiler Plus set. The data are available in the YHRD under accession numbers YA006010 and YA006009. Genetic analysis (AMOVA and MDS) did not show significant differences between the two groups (Kazakhstan and Karakalpakstan Kazakhs) in terms of Y-chromosome diversity. Both groups are characterized by haplogroup C2a1a2 as a founder effect, which dominated two of the three tribes: Alimuly (67%), Baiuly (74.6%), and Zhetiru (25.8%). At the same time, the phylogenetic network for each tribe found its own clusters within C2a1a2. Western Kazakhs and Karakalpakstan Kazakhs present high values of unique haplotypes (84.44% and 96.61%), discrimination capacity (90.37% and 98.30%), and haplotype diversity (0.9991 and 0.9994). A set of 27 Y-STR loci distinguishes closely related individuals within the Western Kazakh tribes quite well. It is suitable for forensic application, and is also optimal for population genetics studies. Full article

(This article belongs to the Special Issue Trends in Population Genetics and Identification—Impact on Anthropology)

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