Feature Papers in Population and Evolutionary Genetics and Genomics

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 September 2022) | Viewed by 31032

Special Issue Editors


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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”, 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 “Population and Evolutionary Genetics and Genomics Section” 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 (11 papers)

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Editorial

Jump to: Research, Review

4 pages, 194 KiB  
Editorial
Special Issue “Feature Papers in Population and Evolutionary Genetics and Genomics”
by Maria-Anna Kyrgiafini and Zissis Mamuris
Genes 2023, 14(1), 38; https://doi.org/10.3390/genes14010038 - 23 Dec 2022
Viewed by 944
Abstract
Theodosius Dobzhansky famously wrote in 1973 that “nothing in biology makes sense except in the light of evolution” [...] Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)

Research

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14 pages, 1090 KiB  
Article
Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides
by Larisa Fedorova, Oleh A. Mulyar, Jan Lim and Alexei Fedorov
Genes 2022, 13(11), 2053; https://doi.org/10.3390/genes13112053 - 7 Nov 2022
Cited by 3 | Viewed by 1721
Abstract
The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over [...] Read more.
The public UCNEbase database, comprising 4273 human ultra-conserved noncoding elements (UCNEs), was thoroughly investigated with the aim to find any nucleotide signals or motifs that have made these DNA sequences practically unchanged over three hundred million years of evolution. Each UCNE comprises over 200 nucleotides and has at least 95% identity between humans and chickens. A total of 31,046 SNPs were found within the UCNE database. We demonstrated that every human has over 300 mutations within 4273 UCNEs. No association of UCNEs with non-coding RNAs, nor preference of a particular meiotic recombination rate within them were found. No sequence motifs associated with UCNEs nor their flanking regions have been found. However, we demonstrated that UCNEs have strong nucleotide and dinucleotide sequence abnormalities compared to genome averages. Specifically, UCNEs are depleted for CC and GG dinucleotides, while GC dinucleotides are in excess of 28%. Importantly, GC dinucleotides have extraordinarily strong stacking free-energy inside the DNA helix and unique resistance to dissociation. Based on the adjacent nucleotide stacking abnormalities within UCNEs, we conjecture that peculiarities in dinucleotide distribution within UCNEs may create unique 3D conformation and specificity to bind proteins. We also discuss the strange dynamics of multiple SNPs inside UCNEs and reasons why these sequences are extraordinarily conserved. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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17 pages, 2004 KiB  
Article
Analysis of Common SNPs across Continents Reveals Major Genomic Differences between Human Populations
by Larisa Fedorova, Andrey Khrunin, Gennady Khvorykh, Jan Lim, Nicholas Thornton, Oleh A. Mulyar, Svetlana Limborska and Alexei Fedorov
Genes 2022, 13(8), 1472; https://doi.org/10.3390/genes13081472 - 18 Aug 2022
Cited by 6 | Viewed by 3978
Abstract
Common alleles tend to be more ancient than rare alleles. These common SNPs appeared thousands of years ago and reflect intricate human evolution including various adaptations, admixtures, and migration events. Eighty-four thousand abundant region-specific alleles (ARSAs) that are common in one continent but [...] Read more.
Common alleles tend to be more ancient than rare alleles. These common SNPs appeared thousands of years ago and reflect intricate human evolution including various adaptations, admixtures, and migration events. Eighty-four thousand abundant region-specific alleles (ARSAs) that are common in one continent but absent in the rest of the world have been characterized by processing 3100 genomes from 230 populations. Also computed were 17,446 polymorphic sites with regional absence of common alleles (RACAs), which are widespread globally but absent in one region. A majority of these region-specific SNPs were found in Africa. America has the second greatest number of ARSAs (3348) and is even ahead of Europe (1911). Surprisingly, East Asia has the highest number of RACAs (10,524) and the lowest number of ARSAs (362). ARSAs and RACAs have distinct compositions of ancestral versus derived alleles in different geographical regions, reflecting their unique evolution. Genes associated with ARSA and RACA SNPs were identified and their functions were analyzed. The core 100 genes shared by multiple populations and associated with region-specific natural selection were examined. The largest part of them (42%) are related to the nervous system. ARSA and RACA SNPs are important for both association and human evolution studies. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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11 pages, 535 KiB  
Article
NUMTs Can Imitate Biparental Transmission of mtDNA—A Case in Drosophila melanogaster
by Maria-Eleni Parakatselaki, Chen-Tseh Zhu, David Rand and Emmanuel D. Ladoukakis
Genes 2022, 13(6), 1023; https://doi.org/10.3390/genes13061023 - 6 Jun 2022
Cited by 3 | Viewed by 1977
Abstract
mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression [...] Read more.
mtDNA sequences can be incorporated into the nuclear genome and produce nuclear mitochondrial fragments (NUMTs), which resemble mtDNA in their sequence but are transmitted biparentally, like the nuclear genome. NUMTs can be mistaken as real mtDNA and may lead to the erroneous impression that mtDNA is biparentally transmitted. Here, we report a case of mtDNA heteroplasmy in a Drosophila melanogaster DGRP line, in which the one haplotype was biparentally transmitted in an autosomal manner. Given the sequence identity of this haplotype with the mtDNA, the crossing experiments led to uncertainty about whether heteroplasmy was real or an artifact due to a NUMT. More specific experiments revealed that there is a large NUMT insertion in the X chromosome of a specific DGRP line, imitating biparental inheritance of mtDNA. Our result suggests that studies on mtDNA heteroplasmy and on mtDNA inheritance should first exclude the possibility of NUMT interference in their data. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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26 pages, 2816 KiB  
Article
Inter-Specific Genetic Exchange Despite Strong Divergence in Deep-Sea Hydrothermal Vent Gastropods of the Genus Alviniconcha
by Jade Castel, Stéphane Hourdez, Florence Pradillon, Claire Daguin-Thiébaut, Marion Ballenghien, Stéphanie Ruault, Erwan Corre, Adrien Tran Lu Y, Jean Mary, Pierre-Alexandre Gagnaire, François Bonhomme, Corinna Breusing, Thomas Broquet and Didier Jollivet
Genes 2022, 13(6), 985; https://doi.org/10.3390/genes13060985 - 31 May 2022
Cited by 6 | Viewed by 2417
Abstract
Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more [...] Read more.
Deep hydrothermal vents are highly fragmented and unstable habitats at all temporal and spatial scales. Such environmental dynamics likely play a non-negligible role in speciation. Little is, however, known about the evolutionary processes that drive population-level differentiation and vent species isolation and, more specifically, how geography and habitat specialisation interplay in the species history of divergence. In this study, the species range and divergence of Alviniconcha snails that occupy active Western Pacific vent fields was assessed by using sequence variation data of the mitochondrial Cox1 gene, RNAseq, and ddRAD-seq. Combining morphological description and sequence datasets of the three species across five basins, we confirmed that A. kojimai, A. boucheti, and A. strummeri, while partially overlapping over their range, display high levels of divergence in the three genomic compartments analysed that usually encompass values retrieved for reproductively isolated species with divergences rang from 9% to 12.5% (mtDNA) and from 2% to 3.1% (nuDNA). Moreover, the three species can be distinguished on the basis of their external morphology by observing the distribution of bristles and the shape of the columella. According to this sampling, A. boucheti and A. kojimai form an east-to-west species abundance gradient, whereas A. strummeri is restricted to the Futuna Arc/Lau and North Fiji Basins. Surprisingly, population models with both gene flow and population size heterogeneities among genomes indicated that these three species are still able to exchange genes due to secondary contacts at some localities after a long period of isolation. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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0 pages, 3244 KiB  
Article
RETRACTED: RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar
by Helena Teixeira, Tobias van Elst, Malcolm S. Ramsay, Romule Rakotondravony, Jordi Salmona, Anne D. Yoder and Ute Radespiel
Genes 2022, 13(5), 913; https://doi.org/10.3390/genes13050913 - 19 May 2022
Cited by 1 | Viewed by 2344 | Retraction
Abstract
The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited [...] Read more.
The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited opportunity for natural hybridization. This study examines RADseq data from 480 individuals to investigate whether the recent expansion of Microcebus murinus towards the northwest and subsequent secondary contact with Microcebus ravelobensis has resulted in the occurrence of hybridization between the two species. Admixture analysis identified one individual with 26% of nuclear admixture, which may correspond to an F2- or F3-hybrid. A composite-likelihood approach was subsequently used to test the fit of alternative phylogeographic scenarios to the genomic data and to date introgression. The simulations yielded support for low levels of gene flow (2Nm0 = 0.063) between the two species starting before the Last Glacial Maximum (between 54 and 142 kyr). Since M. murinus most likely colonized northwestern Madagascar during the Late Pleistocene, the rather recent secondary contact with M. ravelobensis has likely created the opportunity for occasional hybridization. Although reproductive isolation between these distantly related congeners is not complete, it is effective in maintaining species boundaries. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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12 pages, 2001 KiB  
Article
The Difference in the Proportions of Deleterious Variations within and between Populations Influences the Estimation of FST
by Sankar Subramanian
Genes 2022, 13(2), 194; https://doi.org/10.3390/genes13020194 - 22 Jan 2022
Cited by 4 | Viewed by 2397
Abstract
Estimating the extent of genetic differentiation between populations is an important measure in population genetics, ecology and evolutionary biology. The fixation index, or FST, is an important measure, which is routinely used to quantify this. Previous studies have shown that the FST estimated [...] Read more.
Estimating the extent of genetic differentiation between populations is an important measure in population genetics, ecology and evolutionary biology. The fixation index, or FST, is an important measure, which is routinely used to quantify this. Previous studies have shown that the FST estimated for selectively constrained regions was significantly lower than that estimated for neutral regions. By deriving the theoretical relationship between FST at neutral and constrained sites, we show that excess in the fraction of deleterious variations segregating within populations compared to those segregating between populations is the cause for the reduction in FST estimated at constrained sites. Using whole-genome data, our results revealed that the magnitude of reduction in FST estimates obtained for selectively constrained regions was much higher for distantly related populations compared to those estimated for closely related pairs. For example, the reduction was 47% for comparison between Europeans and Africans, 30% for the European and Asian comparison, 16% for the Northern and Southern European pair, and only 4% for the comparison involving two Southern European (Italian and Spanish) populations. Since deleterious variants are purged over time due to purifying selection, their contribution to the among-population diversity at constrained sites decreases with the increase in the divergence between populations. However, within-population diversities remain the same for all pairs compared; therefore, the FST estimated at constrained sites for distantly related populations are much smaller than those estimated for closely related populations. We obtained similar results when only the SNPs with similar allele frequencies at neutral and constrained sites were used. Our results suggest that the level of population divergence should be considered when comparing constrained site FST estimates from different pairs of populations. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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18 pages, 2701 KiB  
Article
Analysis of the Batch Effect Due to Sequencing Center in Population Statistics Quantifying Rare Events in the 1000 Genomes Project
by Iago Maceda and Oscar Lao
Genes 2022, 13(1), 44; https://doi.org/10.3390/genes13010044 - 24 Dec 2021
Cited by 1 | Viewed by 2606
Abstract
The 1000 Genomes Project (1000G) is one of the most popular whole genome sequencing datasets used in different genomics fields and has boosting our knowledge in medical and population genomics, among other fields. Recent studies have reported the presence of ghost mutation signals [...] Read more.
The 1000 Genomes Project (1000G) is one of the most popular whole genome sequencing datasets used in different genomics fields and has boosting our knowledge in medical and population genomics, among other fields. Recent studies have reported the presence of ghost mutation signals in the 1000G. Furthermore, studies have shown that these mutations can influence the outcomes of follow-up studies based on the genetic variation of 1000G, such as single nucleotide variants (SNV) imputation. While the overall effect of these ghost mutations can be considered negligible for common genetic variants in many populations, the potential bias remains unclear when studying low frequency genetic variants in the population. In this study, we analyze the effect of the sequencing center in predicted loss of function (LoF) alleles, the number of singletons, and the patterns of archaic introgression in the 1000G. Our results support previous studies showing that the sequencing center is associated with LoF and singletons independent of the population that is considered. Furthermore, we observed that patterns of archaic introgression were distorted for some populations depending on the sequencing center. When analyzing the frequency of SNPs showing extreme patterns of genotype differentiation among centers for CEU, YRI, CHB, and JPT, we observed that the magnitude of the sequencing batch effect was stronger at MAF < 0.2 and showed different profiles between CHB and the other populations. All these results suggest that data from 1000G must be interpreted with caution when considering statistics using variants at low frequency. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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19 pages, 2474 KiB  
Article
Comparative Phylogeography and Phylogeny of Pennah Croakers (Teleostei: Sciaenidae) in Southeast Asian Waters
by Hong-Chiun Lim, Ahasan Habib and Wei-Jen Chen
Genes 2021, 12(12), 1926; https://doi.org/10.3390/genes12121926 - 29 Nov 2021
Cited by 3 | Viewed by 2665
Abstract
A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals [...] Read more.
A broad-scale comparative phylogeographic and phylogenetic study of pennah croakers, mainly Pennahia anea, P. macrocephalus, and P. ovata was conducted to elucidate the mechanisms that may have driven the diversification of marine organisms in Southeast Asian waters. A total of 316 individuals from the three species, and an additional eight and six individuals of P. argentata and P. pawak were employed in this study. Two genetically divergent lineages each of P. argentata and P. anea (lineages L1 and L2) were respectively detected from the analyses based on mitochondrial cytochrome b gene data. Historical biogeography analysis with a multi-gene dataset revealed that Pennahia species most likely originated in the South China Sea and expanded into the eastern Indian Ocean, East China Sea, and northwestern Pacific Ocean through three separate range expansions. The main diversifications of Pennahia species occurred during Miocene and Pliocene periods, and the occurrences of lineage divergences within P. anea and P. argentata were during the Pleistocene, likely as a consequence of cyclical glaciations. The population expansions that occurred after the sea level rise might be the reason for the population homogeneity observed in P. macrocephalus and most P. anea L2 South China Sea populations. The structure observed between the two populations of P. ovata, and the restricted distributions of P. anea lineage L1 and P. ovata in the eastern Indian Ocean, might have been hampered by the northward flowing ocean current at the Malacca Strait and by the distribution of coral reefs or rocky bottoms. While our results support S. Ekman’s center-of-origin hypothesis taking place in the South China Sea, the Malacca Strait serving as the center of overlap is a supplementary postulation for explaining the present-day high diversity of pennah croakers centered in these waters. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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12 pages, 1268 KiB  
Article
Genome-Wide Landscape of North-Eastern European Populations: A View from Lithuania
by Alina Urnikyte, Alma Molyte and Vaidutis Kučinskas
Genes 2021, 12(11), 1730; https://doi.org/10.3390/genes12111730 - 28 Oct 2021
Cited by 3 | Viewed by 6054
Abstract
There are still several unanswered questions regarding about ancient events in the Lithuanian population. The Lithuanians, as the subject of this study, are of great interest as they represent a partially isolated population maintaining an ancient genetic composition and show genetic uniqueness in [...] Read more.
There are still several unanswered questions regarding about ancient events in the Lithuanian population. The Lithuanians, as the subject of this study, are of great interest as they represent a partially isolated population maintaining an ancient genetic composition and show genetic uniqueness in European comparisons. To elucidate the genetic relationships between the Lithuania and North-Eastern European and West Siberian populations, we analyzed the population structure, effective population size, and recent positive selection from genome-wide single nucleotide polymorphism (SNP) data. We identified the close genetic proximity of Lithuanians to neighboring populations (Latvians, Estonians, Belarusians) and in part with West and South Slavs (Poles, Slovaks, and Slovenians), however, with particular genetic distinctiveness. The estimated long-term Ne values ranged from ~5900 in the Estonian population to ~2400 in the South Russian population. The divergence times between the Lithuanian and study populations ranged from 240 to 12,871 YBP. We also found evidence of selection in 24 regions, 21 of which have not been discovered in previous analyses of selection. Undoubtedly, the genetic diversity analysis of geographically specific regions may provide new insights into microevolutionary processes affecting local human populations. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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Review

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24 pages, 1110 KiB  
Review
Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother’s Curse
by Maria-Anna Kyrgiafini, Themistoklis Giannoulis, Katerina A. Moutou and Zissis Mamuris
Genes 2022, 13(11), 2151; https://doi.org/10.3390/genes13112151 - 18 Nov 2022
Cited by 3 | Viewed by 2651
Abstract
The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the [...] Read more.
The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother’s Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother’s Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother’s Curse. Full article
(This article belongs to the Special Issue Feature Papers in Population and Evolutionary Genetics and Genomics)
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