Feature Papers in Population and Evolutionary Genetics and Genomics 2023

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 October 2023) | Viewed by 17584

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Guest Editor Assistant
Department of Biochemistry and Biotechnology, University of Thessaly, 41221 Larissa, Greece
Interests: male infertility; animal genomics; evolution; genetics; non-coding RNAs

Special Issue Information

Dear Colleagues,

This Special Issue, “Feature Papers in Population and Evolutionary Genetics and Genomics 2023”, aims to collect high-quality research articles, review articles, and communications on advances in the research area of population and evolutionary genetics and genomics. Since the aim of this topical collection is to illustrate, through selected works, frontier research in the field of population and evolutionary genetics and genomics, we encourage Editorial Board Members of the Section “Population and Evolutionary Genetics and Genomics” to contribute feature papers reflecting the latest progress in their research field, or to invite relevant senior experts and colleagues to make contributions to this Special Issue. We aim to represent our Section as an attractive open-access publishing platform for population genetics research. Topics include but are not limited to:

  • Genetic polymorphism;
  • Geographic variation;
  • Gene flow and introgression;
  • Selection in natural populations;
  • Phylogenetics;
  • Metagenomics;
  • Ancient DNA.

Prof. Dr. Zissis Mamuris
Guest Editor

Maria-Anna Kyrgiafini
Guest Editor Assistant

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.

Published Papers (9 papers)

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Editorial

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4 pages, 160 KiB  
Editorial
Feature Papers in Population and Evolutionary Genetics and Genomics 2023: Unraveling Population Dynamics, Diversity, and Evolutionary Paths
by Maria-Anna Kyrgiafini and Zissis Mamuris
Genes 2024, 15(4), 446; https://doi.org/10.3390/genes15040446 - 1 Apr 2024
Viewed by 1024
Abstract
The dialogue between population genetics and evolutionary biology, which historically followed separate paths, has now developed into a complex and interdisciplinary field of study [...] Full article

Research

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15 pages, 2737 KiB  
Article
Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia
by Rute R. da Fonseca, Paula F. Campos, Alba Rey-Iglesia, Gustavo V. Barroso, Lucie A. Bergeron, Manuel Nande, Fernando Tuya, Sami Abidli, Montse Pérez, Isabel Riveiro, Pablo Carrera, Alba Jurado-Ruzafa, M. Teresa G. Santamaría, Rui Faria, André M. Machado, Miguel M. Fonseca, Elsa Froufe and L. Filipe C. Castro
Genes 2024, 15(2), 170; https://doi.org/10.3390/genes15020170 - 27 Jan 2024
Cited by 1 | Viewed by 1288
Abstract
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that [...] Read more.
The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species’ distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria–Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries. Full article
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14 pages, 321 KiB  
Article
Assessment of the Genetic Characteristics of a Generation Born during a Long-Term Socioeconomic Crisis
by Svetlana V. Mikhailova, Dinara E. Ivanoshchuk, Pavel S. Orlov, Ahmad Bairqdar, Maksim S. Anisimenko and Diana V. Denisova
Genes 2023, 14(11), 2064; https://doi.org/10.3390/genes14112064 - 11 Nov 2023
Cited by 1 | Viewed by 1861
Abstract
Background: A socioeconomic crisis in Russia lasted from 1991 to 1998 and was accompanied by a sharp drop in the birth rate. The main factor that influenced the refusal to have children during this period is thought to be prolonged social stress. Methods: [...] Read more.
Background: A socioeconomic crisis in Russia lasted from 1991 to 1998 and was accompanied by a sharp drop in the birth rate. The main factor that influenced the refusal to have children during this period is thought to be prolonged social stress. Methods: comparing frequencies of common gene variants associated with stress-induced diseases among generations born before, after, and during this crisis may show which genes may be preferred under the pressure of natural selection during periods of increased social stress in urban populations. Results: In the “crisis” group, a statistically significant difference from the other two groups was found in rs6557168 frequency (p = 0.001); rs4522666 was not in the Hardy–Weinberg equilibrium in this group, although its frequency did not show a significant difference from the other groups (p = 0.118). Frequencies of VNTRs in SLC6A3 and MAOA as well as common variants rs17689918 in CRHR1, rs1360780 in FKBP5, rs53576 in OXTR, rs12720071 and rs806377 in CNR1, rs4311 in ACE, rs1800497 in ANKK1, and rs7412 and rs429358 in APOE did not differ among the groups. Conclusions: a generation born during a period of prolonged destructive events may differ from the rest of the gene pool of the population in some variants associated with personality traits or stress-related disorders. Full article
11 pages, 1582 KiB  
Article
Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China
by Jiewen Fu, Binghui Song, Jie Qian, Ting He, Hanchun Chen, Jingliang Cheng and Junjiang Fu
Genes 2023, 14(10), 1904; https://doi.org/10.3390/genes14101904 - 2 Oct 2023
Cited by 2 | Viewed by 1295
Abstract
Han is the largest of China’s 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short [...] Read more.
Han is the largest of China’s 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research. Full article
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15 pages, 3105 KiB  
Article
Karyotype and Phylogenetic Relationship Analysis of Five Varieties and Cultivars of Zanthoxylum armatum Based on Oligo-FISH
by Zhoujian He, Yuting Lei, Wei Gong, Meng Ye and Xiaomei Luo
Genes 2023, 14(7), 1459; https://doi.org/10.3390/genes14071459 - 17 Jul 2023
Cited by 2 | Viewed by 1139
Abstract
Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we [...] Read more.
Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we utilized oligo-FISH to distinguish five varieties and cultivars of Z. armatum on the basis of three oligonucleotide probes of 5S rDNA, (AG3T3)3, and (GAA)6. Karyotype analysis of the five varieties and cultivars of Z. armatum showed that the Z. armatum ‘Tengjiao’ karyotype formula was 2n = 2x = 98m with karyotype type 1C and an arm ratio of 4.3237, including two pairs of 5S rDNA signals and five pairs of (GAA)6 signals. The karyotype formula of Z. armatum ‘Youkangtengjiao’ was 2n = 2x = 128m + 8sm with karyotype type 2B and an arm ratio of 3.5336, including three pairs of 5S rDNA signals and 17 pairs of (GAA)6 signals. The karyotype formula of Z. armatum var. novemfolius was 2n = 2x = 134m + 2sm with karyotype type 1C and an arm ratio of 5.5224, including two pairs of 5S rDNA signals and eight pairs of (GAA)6 signals. The karyotype formula of Z. armatum ‘YT-03’ was 2n = 2x = 2M + 128m + 4sm + 2st with karyotype type 2C and an arm ratio of 4.1829, including three pairs of 5S rDNA signals and nine pairs of (GAA)6 signals. The karyotype formula of Z. armatum ‘YT-06’ was 2n = 2x = 126m + 10sm with cytotype 2B and an arm ratio of 3.3011, including three pairs of 5S rDNA signals and two pairs of (GAA)6 signals. The five varieties and cultivars of Z. armatum had (AG3T3)3 signals on all chromosomes. The chromosomal symmetry of Z. armatum ‘Tengjiao’ was high, whereas the chromosomal symmetry of Z. armatum 'YT-03' was low, with the karyotypes of the five materials showing a trend toward polyploid evolution. The phylogenetic relationship between Z. armatum ‘Tengjiao’ and Z. armatum var. novemfolius was the closest, while that between Z. armatum ‘YT-03’ and Z. armatum ‘YT-06’ was closer than with Z. armatum ‘Youkangtengjiao’ according to oligo-FISH. The results provided a karyotype profile and a physical map that contributes to the distinction of varieties and cultivars of Z. armatum and provides strategies for distinguishing other cultivated species. Full article
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24 pages, 8130 KiB  
Article
Effects of Forest Fragmentation on Connectivity and Genetic Diversity in an Endemic and an Invasive Rodent in Northwestern Madagascar
by Malcolm S. Ramsay, Gabriele M. Sgarlata, Christopher D. Barratt, Jordi Salmona, Bertrand Andriatsitohaina, Frederik Kiene, Sophie Manzi, Miarisoa L. Ramilison, Romule Rakotondravony, Lounès Chikhi, Shawn M. Lehman and Ute Radespiel
Genes 2023, 14(7), 1451; https://doi.org/10.3390/genes14071451 - 15 Jul 2023
Cited by 1 | Viewed by 1340
Abstract
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. [...] Read more.
Habitat loss and fragmentation are of concern to conservation biologists worldwide. However, not all organisms are affected equally by these processes; thus, it is important to study the effects of living in fragmented habitats on species that differ in lifestyle and habitat requirements. In this study, we examined the dispersal and connectivity patterns of rodents, one endemic (Eliurus myoxinus) and one invasive (Rattus rattus), in two landscapes containing forest fragments and adjacent continuous forest patches in northwestern Madagascar. We generated genetic (RADseq) data for 66 E. myoxinus and 81 R. rattus individuals to evaluate differences in genetic diversity as well as inbreeding and connectivity in two landscapes. We found higher levels of inbreeding and lower levels of genetic diversity in E. myoxinus compared with R. rattus. We observed related dyads both within and between habitat patches and positive spatial autocorrelation at lower distance classes for both species, with a stronger pattern of spatial autocorrelation in R. rattus. Across each site, we identified contrasting migration rates for each species, but these did not correspond to habitat–matrix dichotomies. The relatively low genetic diversity in the endemic E. myoxinus suggests ecological constraints that require further investigation. Full article
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10 pages, 3674 KiB  
Article
Mosquito (MS), a DD37E Family of Tc1/Mariner, Displaying a Distinct Evolution Profile from DD37E/TRT and DD37E/L18
by Kuilin Xiang, Mikhail Puzakov, Shasha Shi, Mohamed Diaby, Numan Ullah, Bo Gao and Chengyi Song
Genes 2023, 14(7), 1379; https://doi.org/10.3390/genes14071379 - 29 Jun 2023
Cited by 1 | Viewed by 882
Abstract
Diverse Tc1/mariner elements with the DD37E signature have been detected. However, their evolutionary relationship and profiles are largely unknown. Using bioinformatics methods, we defined the evolution profile of a Tc1/Mariner family, which harbors the catalytic domain with the DD37E signature, and renamed it [...] Read more.
Diverse Tc1/mariner elements with the DD37E signature have been detected. However, their evolutionary relationship and profiles are largely unknown. Using bioinformatics methods, we defined the evolution profile of a Tc1/Mariner family, which harbors the catalytic domain with the DD37E signature, and renamed it DD37E/Mosquito (MS). MS transposons form a separate monophyletic clade in the phylogenetic tree, distinct from the other two groups of elements with the DD37E signature, DD37E/L18 and DD37E/TRT (transposon related to Tc1), and represent a very different taxonomic distribution from that of DD37E/TRT. MS is only detected in invertebrate and is mostly present in Arthropoda, as well as in Cnidaria, Ctenophora, Mollusca, Nematoda, and Platyhelminthes, with a total length of about 1.3 kb, containing an open reading frame (ORF) encoding about 340 amino acids transposases, with a conserved DD37E catalytic domain. The terminal inverted repeat (TIR) lengths range from 19 bp to 203 bp, and the target site duplication (TSD) is TA. We also identified few occurrences of MS horizontal transfers (HT) across lineages of diptera. In this paper, the distribution characteristics, structural characteristics, phylogenetic evolution, and horizontal transfer of the MS family are fully analyzed, which is conducive to supplementing and improving the Tc1/Mariner superfamily and excavating active transposons. Full article
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14 pages, 1928 KiB  
Article
Opening the Black Box of Imputation Software to Study the Impact of Reference Panel Composition on Performance
by Thibault Dekeyser, Emmanuelle Génin and Anthony F. Herzig
Genes 2023, 14(2), 410; https://doi.org/10.3390/genes14020410 - 4 Feb 2023
Cited by 3 | Viewed by 1716
Abstract
Genotype imputation is widely used to enrich genetic datasets. The operation relies on panels of known reference haplotypes, typically with whole-genome sequencing data. How to choose a reference panel has been widely studied and it is essential to have a panel that is [...] Read more.
Genotype imputation is widely used to enrich genetic datasets. The operation relies on panels of known reference haplotypes, typically with whole-genome sequencing data. How to choose a reference panel has been widely studied and it is essential to have a panel that is well matched to the individuals who require missing genotype imputation. However, it is broadly accepted that such an imputation panel will have an enhanced performance with the inclusion of diversity (haplotypes from many different populations). We investigate this observation by examining, in fine detail, exactly which reference haplotypes are contributing at different regions of the genome. This is achieved using a novel method of inserting synthetic genetic variation into the reference panel in order to track the performance of leading imputation algorithms. We show that while diversity may globally improve imputation accuracy, there can be occasions where incorrect genotypes are imputed following the inclusion of more diverse haplotypes in the reference panel. We, however, demonstrate a technique for retaining and benefitting from the diversity in the reference panel whilst avoiding the occasional adverse effects on imputation accuracy. What is more, our results more clearly elucidate the role of diversity in a reference panel than has been shown in previous studies. Full article
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Review

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10 pages, 1643 KiB  
Review
Integrating Linguistic, Archaeological and Genetic Perspectives Unfold the Origin of Ugrians
by Tibor Török
Genes 2023, 14(7), 1345; https://doi.org/10.3390/genes14071345 - 26 Jun 2023
Cited by 2 | Viewed by 6279
Abstract
In the last year two publications shed new light on the linguistic and genomic history of ancient Uralic speakers. Here I show that these novel genetic and linguistic data are compatible with each-other and with the archaeological inferences, allowing us to formulate a [...] Read more.
In the last year two publications shed new light on the linguistic and genomic history of ancient Uralic speakers. Here I show that these novel genetic and linguistic data are compatible with each-other and with the archaeological inferences, allowing us to formulate a very plausible hypothesis about the prehistory of Ugric speakers. Both genetic and archaeological data indicate the admixture of the Mezhovskaya population with northern forest hunters in the late Bronze Age, which gave rise to a “proto-Ugric” community. This finding is consistent with the linguistic reconstruction of the proto-Ugric language. Genetic data indicate an admixture of proto-Hungarians with early Sarmatians and early Huns, and I show that the first admixture can be reconciled with the formation of the Gorokhovo culture and its integration into the early Sarmatian Prokhorovka culture, while the second admixture corresponds to the transformation of the Sargat and Sarmatian cultures due to Xiongnu invasions. Full article
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