Genetic Variability within and between Populations

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Evolutionary Biology".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 10323

Special Issue Editor


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Guest Editor
Centre for Bioinnovation, School of Science, Technology, and Engineering, The University of the Sunshine Coast, 1 Moreton Parade, Petrie, Moreton Bay, QLD 4502, Australia
Interests: genetic drift; population bottleneck; mutation; effective population size; population structure; population phylogeny; divergence time; neutral theory

Special Issue Information

Dear Colleagues,

The difference in the genetic variation within and between populations is an important measure that is routinely used in population genetics, ecology, and evolutionary biology. A number of methods have been developed to capture this difference, which is called the fixation index or FST. This reveals the level of genetic structure and gene flow between populations. Traditionally, allele frequencies were used to calculate FST. With the advent of DNA sequencing technologies, population structure or differentiation was estimated using microsatellites and single nucleotide variations (SNVs).  Recent developments in sequencing technologies have resulted in a drastic reduction in the cost of sequencing whole genomes, which has enabled researchers to decipher the sequences of whole genomes of populations. Using the large volume of genome data, it is now possible to measure the amounts of genetic variations within and among populations with high precision. Importantly, whole genome- or SNP array-based estimates are able to detect the fine-scale population structure in many species that were not recognized before. These results have provided detailed insights and revised our understanding of the demography of populations and the signatures of natural selection that shaped the evolution of various species. Therefore, a comprehensive issue of Biology comprising articles highlighting the above will be useful for researchers in the fields of genetics, ecology, and evolutionary biology.

This Special Issue of Biology aims to publish research focused on the demography of populations, including genetic structure, migration, gene flow, introgression, inbreeding, and population divergence. Population genetics studies addressing questions in the applied fields such as medicine, agriculture, veterinary, fisheries, and conservation are also welcome. We consider original research articles, short communications, methods, reviews, and opinions. The deadline is only for submission, and articles will be published immediately after acceptance.

Dr. Sankar Subramanian
Guest Editor

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Keywords

  • genetic structure
  • population differentiation
  • FST or fixation index
  • migration
  • gene flow
  • admixture
  • heterozygosity
  • inbreeding
  • coalescence time
  • allele frequency
  • random mating

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Published Papers (12 papers)

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Research

15 pages, 9995 KiB  
Article
Unveiling Genetic Variation in the Seed Bug Spilostethus pandurus (Scopoli, 1763) (Hemiptera: Lygaeidae) in Thailand Using Mitochondrial CO1 Sequence
by Warayutt Pilap, Nakorn Pradit, Chavanut Jaroenchaiwattanachote, Jatupon Saijuntha, Watee Kongbuntad, Wittaya Tawong, Chairat Tantrawatpan and Weerachai Saijuntha
Biology 2025, 14(8), 1022; https://doi.org/10.3390/biology14081022 - 8 Aug 2025
Viewed by 304
Abstract
Spilostethus pandurus is a phytophagous insect widely distributed across Asia, Europe, and Africa, yet its genetic variation remains poorly understood. This study presents the first comprehensive analysis of the genetic diversity and structure of S. pandurus in Thailand using mitochondrial cytochrome c oxidase [...] Read more.
Spilostethus pandurus is a phytophagous insect widely distributed across Asia, Europe, and Africa, yet its genetic variation remains poorly understood. This study presents the first comprehensive analysis of the genetic diversity and structure of S. pandurus in Thailand using mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences from 202 individuals across 27 localities. A total of 58 haplotypes were identified, with high haplotype and nucleotide diversity observed, suggesting substantial genetic variation. The haplotype network revealed a star-like topology, indicating recent population expansion or ongoing gene flow. Neutrality tests and mismatch distribution analyses showed no strong signal of recent demographic expansion. Phylogenetic analysis confirmed that all Thai specimens clustered within a well-supported S. pandurus clade along with sequences from India, Namibia, and Europe. Analysis of Molecular Variance (AMOVA) revealed significant genetic differentiation among four continental groups, indicating that geographic isolation and restricted gene flow have shaped genetic divergence at a broad biogeographic scale. Further research using highly polymorphic nuclear markers is recommended to better resolve the population structure and evolutionary history of S. pandurus in Thailand and beyond. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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14 pages, 1840 KiB  
Article
Population Genetics of the Asian Buffalo Leech (Hirudinaria manillensis) in Southern China Based on Mitochondrial Protein-Coding Genes
by Gonghua Lin, Jingjing Yin, Wenting Zhang, Zuhao Huang, Zichao Liu, Huanhuan Chen, Lizhou Tang and Fang Zhao
Biology 2025, 14(8), 926; https://doi.org/10.3390/biology14080926 - 23 Jul 2025
Viewed by 300
Abstract
Leeches hold significant medical and pharmaceutical value for antithrombotic treatments, yet their genetic diversity patterns remain poorly understood. We performed population genetic analyses on seven Hirudinaria manillensis populations from southern China using mitochondrial protein-coding genes (MitPCGs). Complete sequences of all 13 MitPCGs were [...] Read more.
Leeches hold significant medical and pharmaceutical value for antithrombotic treatments, yet their genetic diversity patterns remain poorly understood. We performed population genetic analyses on seven Hirudinaria manillensis populations from southern China using mitochondrial protein-coding genes (MitPCGs). Complete sequences of all 13 MitPCGs were obtained from 74 individuals. Haplotype diversity exhibited a logarithmic relationship with the gene length (R2 = 0.858, p < 0.001), while nucleotide diversity showed a near-perfect alternating low-high pattern (Z = 2.938, p = 0.003). Concatenated sequence analyses indicated high haplotype diversity (>0.5) and low nucleotide diversity (<0.005) across all populations, suggesting a historical bottleneck followed by rapid expansion and mutation accumulation. The haplotype network, haplotype phylogenetics, and genetic structure analyses revealed moderate genetic differentiation across populations, dividing them into three clades: a basal Yunnan population (YNHH), sub-basal Guangxi populations (GXGG, GXLZ, and GXYL), and distal Guangdong/Hainan populations (GDMM, GDZJ, and HNDA). Analysis of historical population demography revealed five phases from ancient to recent times (P1–5): growth, prolonged stability, rapid decline, rapid growth, and secondary decline. These phases correlate strongly with past climatic events, demonstrating that glacial–interglacial cycles profoundly impacted the leech’s effective population size. This study provides a key scientific basis for H. manillensis resource conservation and utilization. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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13 pages, 1649 KiB  
Article
Assessing the Population Demographic History of the Tsushima Leopard Cat and Its Genetic Divergence Time from Continental Populations
by Hideyuki Ito, Nobuyoshi Nakajima, Manabu Onuma, Takushi Kishida and Miho Inoue-Murayama
Biology 2025, 14(7), 880; https://doi.org/10.3390/biology14070880 - 18 Jul 2025
Viewed by 359
Abstract
The Tsushima leopard cat (Prionailurus bengalensis euptilurus), an endangered feline endemic to Tsushima Island, Japan, faces critical threats due to its small and isolated population. Understanding its demographic history and genetic differentiation from continental populations is essential for conservation planning. In [...] Read more.
The Tsushima leopard cat (Prionailurus bengalensis euptilurus), an endangered feline endemic to Tsushima Island, Japan, faces critical threats due to its small and isolated population. Understanding its demographic history and genetic differentiation from continental populations is essential for conservation planning. In this study, we performed whole-genome sequencing of four Tsushima individuals and applied demographic inference methods, including pairwise sequentially Markovian coalescent (PSMC) and Sequentially Markovian Coalescent (SMC++), to reconstruct the historical effective population size (Ne) and estimate divergence times. PSMC revealed a population expansion between 200,000 and 100,000 years ago, followed by a long-term decline. SMC++ inferred a continuous decline and estimated that the divergence from the Korean leopard cat population occurred approximately 30,000–20,000 years ago. Genetic diversity analysis showed that the Tsushima population has significantly lower heterozygosity and higher inbreeding levels than continental populations. Genetic clustering based on genome-wide SNPs indicated that the Tsushima population is genetically closest to the Korean population, forming a northern cluster distinct from southern populations, such as Borneo and the Malay Peninsula. These findings provide valuable insights into the evolutionary history and genetic status of the Tsushima leopard cat and contribute critical data for the design of future conservation strategies targeting this unique insular lineage. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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22 pages, 2749 KiB  
Article
Genetic Diversity, Population Structure, and Historical Gene Flow Patterns of Nine Indigenous Greek Sheep Breeds
by Sofia Michailidou, Maria Kyritsi, Eleftherios Pavlou, Antiopi Tsoureki and Anagnostis Argiriou
Biology 2025, 14(7), 845; https://doi.org/10.3390/biology14070845 - 10 Jul 2025
Viewed by 567
Abstract
Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the F [...] Read more.
Ιn this study, we evaluated the genetic resources of nine Greek sheep breeds. The genotyping data of 292 animals were acquired from Illumina’s OvineSNP50 Genotyping BeadChip. The genetic diversity and inbreeding levels were evaluated using the observed and expected heterozygosity indices, the FIS inbreeding coefficient, and runs of homozygosity (ROH). The genetic differentiation of breeds was assessed using the FST index, whereas their population structure was analyzed using admixture and principal components analysis (PCA). Historical recombination patterns and genetic drift were evaluated based on linkage disequilibrium, effective population sizes, and gene flow analysis to reveal migration patterns. PCA revealed distinct clusters mostly separating mountainous, insular, and lowland breeds. The FST value was the lowest between Serres and Karagouniko breeds (0.050). Admixture analysis revealed a genetic substructure for Serres and Kalarritiko breeds, while Chios, followed by Katsika, demonstrated the highest within-breed genetic uniformity. ROH analysis revealed low levels of inbreeding for all breeds. Genetic introgression from both Anatolia and Eastern Europe has been evidenced for Greek sheep breeds. The results also revealed that Greek sheep breeds maintain adequate levels of genetic diversity, without signs of excessive inbreeding, and can serve as valuable resources for the conservation of local biodiversity. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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17 pages, 7493 KiB  
Article
Profiling Genetic Variation: Divergence Patterns and Population Structure of Thailand’s Endangered Celastrus paniculatus Willd
by Kornchanok Kaenkham, Warayutt Pilap, Weerachai Saijuntha and Sudarat Thanonkeo
Biology 2025, 14(6), 725; https://doi.org/10.3390/biology14060725 - 19 Jun 2025
Viewed by 666
Abstract
This study examined genetic diversity in the endangered medicinal plant Celastrus paniculatus using 62 individual samples from seven natural populations in northern and northeastern Thailand to inform conservation strategies. The analysis of the nuclear internal transcribed spacer (ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [...] Read more.
This study examined genetic diversity in the endangered medicinal plant Celastrus paniculatus using 62 individual samples from seven natural populations in northern and northeastern Thailand to inform conservation strategies. The analysis of the nuclear internal transcribed spacer (ITS) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) markers revealed 17 haplotypes (CpI1–CpI17) across these populations, with 15 being population-specific. The genetic diversity varied significantly among populations: CMI showed the highest diversity (Hd = 0.944 ± 0.070), while LEI and LPN displayed complete homogeneity. The haplotype network identified a central shared haplotype (CpI4), suggesting a common ancestry, with the PLK population showing a distinct genetic divergence through unique haplotypes separated by multiple mutation steps. Genetic distance calculations revealed close relationships between LEI and NPM populations (distance = 0.0004), with greater differentiation between PLK and other populations (distances > 0.005). Phylogenetic analyses confirmed the species integrity while highlighting population clusters, especially PLK in ITS analyses and LPN in rbcL analyses. This genetic structure information provides a foundation for targeted conservation planning. Results suggest that conservation efforts should prioritize both genetically diverse populations (like CMI and MKM) and genetically distinct ones (like PLK) to preserve the maximum evolutionary potential. This study delivers crucial molecular data for developing evidence-based conservation strategies to protect this valuable medicinal species from further decline. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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15 pages, 597 KiB  
Article
Halfway Through Ex Situ Population Genetic Lifespan: The Case of Cochlearia polonica
by Anna Rucińska, Katarzyna Joanna Chwedorzewska, Piotr Tomasz Bednarek, Maja Boczkowska, Jerzy Puchalski, Piotr Androsiuk and Ewa Czaplicka
Biology 2025, 14(6), 681; https://doi.org/10.3390/biology14060681 - 11 Jun 2025
Viewed by 997
Abstract
Although the usage of genetic data for the conservation management of threatened species is growing rapidly, the assessment of the trajectory and persistence of ex situ and in situ populations suffers from a lack of monitoring of genetic indicators. To fill this gap, [...] Read more.
Although the usage of genetic data for the conservation management of threatened species is growing rapidly, the assessment of the trajectory and persistence of ex situ and in situ populations suffers from a lack of monitoring of genetic indicators. To fill this gap, we conducted a comparative analysis of the genetic structure ex situ and its source population of Cochlearia polonica to improve conservation outcomes for this species. C. polonica, as a range-restricted endemic species in Poland, exists in the wild in a single reintroduced population, which was the source for establishing an ex situ population in the botanical garden, and both populations have been well studied in abundance time series until the extinction of artificial populations due to genetic constraints. We collected AFLP data from individuals sampled after the peak recovery phase following the founder effect in the ex situ population, as well as from the source population, to assess the genetic consequences of long-term cultivation. The genetic profile of both populations suggested their strong differentiation. The genetic variation in the ex situ population expressed by Shannon’s Information Index and expected heterozygosity (He) was approximately half that of the source population. While ex situ population growth was high, the gene pool was homogenised, and genetic diversity waned, leading to its extinction across merely 5–6 generations. Thus, the only reintroduced population of C. polonica left in the wild is more threatened with extinction than previously thought, and conservation action should be taken immediately. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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11 pages, 1547 KiB  
Article
Temporal and Spatial Population Genetic Variation in Chilean Jack Mackerel (Trachurus murphyi)
by Cristian B. Canales-Aguirre, Sandra Ferrada Fuentes and Ricardo Galleguillos
Biology 2025, 14(5), 510; https://doi.org/10.3390/biology14050510 - 7 May 2025
Cited by 1 | Viewed by 516
Abstract
Trachurus murphyi have been studied for population genetic structures for decades, identifying only one large population across the South Pacific Ocean. Although all of these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of [...] Read more.
Trachurus murphyi have been studied for population genetic structures for decades, identifying only one large population across the South Pacific Ocean. Although all of these studies have extensively examined the spatial genetic pattern, there remains a gap in understanding the potential role of temporality. Our study aims to elucidate spatial and temporal genetic patterns in T. murphyi populations in the South Pacific Ocean, examining genetic composition across seasons, including feeding and spawning seasons, where the latter was not previously investigated. Using 10 microsatellite loci, our study confirms an overall consistent and stable population genetic pattern in T. murphyi across its geographic distribution observed over multiple years and seasons. The only exception was found for New Zealand in the spring–summer season. Furthermore, we identify potential genetic markers for monitoring variability in the species. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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12 pages, 2110 KiB  
Article
Genetic Diversity and Structure of Korean Pacific Oyster (Crassostrea gigas) for Determining Selective Breeding Groups
by Kang-Rae Kim, Dain Lee, Kyung-Hee Kim, Hyun Chul Kim, So Hee Kim, Su Jin Park and Deok-Chan Lee
Biology 2025, 14(4), 449; https://doi.org/10.3390/biology14040449 - 21 Apr 2025
Viewed by 873
Abstract
This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas [...] Read more.
This study investigated the genetic diversity and structure of thirteen wild populations of Crassostrea gigas in Korea. The purpose of this investigation was to provide foundational data for selecting reference populations to enhance genetic diversity. Overall, the genetic diversity of Korean C. gigas was relatively low. Analysis using AMOVA, genetic differentiation, and DAPC revealed a genetic structure that was consistent with one group. This study identified reference populations to be used for selective breeding to increase the genetic diversity of Korean C. gigas and provided essential data on genetic diversity and structure for future selective breeding efforts in C. gigas. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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15 pages, 716 KiB  
Article
Assessment of Germplasm Improvement in Three Farmed Grass Carp Populations Based on Genetic Variability
by Zhongyuan Shen, Liming Shao, Xixi Liu, Haiqi Li, Haipeng Guo, Lang Qin, Kaikun Luo, Wuhui Li, Jing Wang, Shengnan Li, Qianhong Gu, Liang Guo, Xu Huang, Qinbo Qin and Shaojun Liu
Biology 2025, 14(3), 230; https://doi.org/10.3390/biology14030230 - 25 Feb 2025
Viewed by 829
Abstract
The assessment of genetic improvement was comprehensively analyzed using the mtDNA Cyt b gene and SSR markers among three farmed grass carp populations caught in May 2024. The results of an mtDNA Cyt b gene analysis in 198 individuals showed that the haplotype [...] Read more.
The assessment of genetic improvement was comprehensively analyzed using the mtDNA Cyt b gene and SSR markers among three farmed grass carp populations caught in May 2024. The results of an mtDNA Cyt b gene analysis in 198 individuals showed that the haplotype diversity index (Hi) and nucleotide diversity index (Pi) were 0.555 and 0.00058, respectively. The results of the analysis of SSR marker data in 196 individuals indicated that the unequal dosage amplification at the same locus was found in the CC population. Moreover, the total number of alleles (A: 338), number of alleles per locus (Na: 15.36), observed heterozygosity (Ho: 0.8391), expected heterozygosity (He: 0.8380), and polymorphic information content (PIC: 0.8191) in the KC population was relatively higher than that in the CC (A: 129; Na: 5.86; Ho: 0.0025; He: 0.6191; PIC: 0.5747) and CY (A: 293; Na: 8.77; Ho: 0.821; He: 0.7483; and PIC: 0.5747) populations. The FST and AMOVA analysis showed the existence of a significant differentiation (p < 0.001), with a high genetic differentiation between the CC and CY populations. In summary, a high genetic variability exists in the KC population, while the father (CY) and mother (CC) populations have relatively low genetic variability. This study reveals evidence of the existence of a “micro-hybrid”. Moreover, the results demonstrated that combining both gynogenesis and backcross breeding technology is vital for the genetic improvement of grass carp. Moreover, continuous research into the genetic health of these populations is required as well as support for the protection of germplasm resources and artificial breeding. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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23 pages, 4681 KiB  
Article
Ammopiptanthus nanus Population Dynamics: Bridging the Gap Between Genetic Variation and Ecological Distribution Patterns
by Jingdian Liu, Mengmeng Wei, Jiayi Lu, Shiqing Liu, Xuerong Li, Xiyong Wang, Jiancheng Wang, Daoyuan Zhang, Ting Lu and Wei Shi
Biology 2025, 14(2), 105; https://doi.org/10.3390/biology14020105 - 21 Jan 2025
Viewed by 1099
Abstract
Ammopiptanthus nanus, a Tertiary-era endangered plant, is of great scientific value. In this research, we focus on A. nanus population dynamics in an effort to bridge the divide between micro genetic variation and a macroscopic ecological pattern of distribution. The population structure [...] Read more.
Ammopiptanthus nanus, a Tertiary-era endangered plant, is of great scientific value. In this research, we focus on A. nanus population dynamics in an effort to bridge the divide between micro genetic variation and a macroscopic ecological pattern of distribution. The population structure of 129 wild specimens of A. nanus from eight populations was analyzed using EST-SSR molecular markers in this research. The Mantel test and RDA analysis have been used in this research to investigate the factors that influence the genetic diversity of A. nanus. Using 15 pairs of SSR primers, a total of 227 alleles were detected in 129 samples from 8 populations. The mean number of alleles was 17, and the average expected heterozygosity was 0.405. It is shown that wild A. nanus is divided into six individual populations. A. nanus are significantly affected by wind speed in terms of the variation of genetics. It is suggested that a nature conservation area for A. nanus be established as soon as possible, based on our results and the current natural distribution of the species. It is necessary to focus on the issue of pests and diseases while simultaneously preventing the continuation of anthropogenic woodcutting and disaster. Manual seedling collection should be employed in regions where the environment permits. Through making use of manual breeding techniques, this will contribute to the growth of the natural population of A. nanus. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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17 pages, 2585 KiB  
Article
Population Genetic Characteristics of Siberian Roe Deer in the Cold Temperate Forest Ecosystem of the Greater Khingan Mountains, Northeast China
by Xinxin Liu, Yang Hong, Jinhao Guo, Ning Zhang, Shaochun Zhou, Lu Jin, Xiaoqian Ma, Ziao Yuan, Hairong Du, Minghai Zhang and Jialong Wang
Biology 2024, 13(11), 935; https://doi.org/10.3390/biology13110935 - 16 Nov 2024
Cited by 1 | Viewed by 1380
Abstract
This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance [...] Read more.
This study focuses on the Siberian roe deer population in the Greater Khingan Mountains, Northeast China. The cold temperate forest ecosystem in this area is distinctive. The Siberian roe deer is a crucial ecological indicator species, and its living conditions hold significant importance for ecological balance. From the winter of 2019 to 2022, 269 fecal samples of Siberian roe deer were collected from four protected areas in the northern part of the Greater Khingan Mountains, Heilongjiang Province. These samples were comprehensively analyzed using mitochondrial DNA and microsatellite markers, combined with conservation genetics evaluation methods. The results revealed that 244 individuals were identified in the fecal samples. The results of a Cyt b genetic analysis of the samples indicated that the haplotype and nucleotide diversity were 88.1% and 20.3%, respectively. The evaluation of 14 pairs of microsatellite loci showed that the average number of alleles was 11.2, and the average expected and observed heterozygosity were 0.672 and 0.506, respectively. Therefore, the overall genetic diversity level is high, but some populations of Siberian roe deer are at risk. AMOVA analysis and STRUCTURE Bayesian clustering confirmed the existence of obvious genetic differentiation among the populations. Historical studies have shown that the HZ and SH populations underwent the earliest diffusion events, and the BJC and SL populations also exhibited related signs (HZ: Huzhong Nature Reserve in the Greater Khingan Mountains; SH: Shuanghe National Nature Reserve in Heilongjiang Province; BJC: Heilongjiang Beijicun National Nature Reserve; SL: Songling District in Heilongjiang Province). Mismatch distribution and neutral tests indicated no expansion events or bottleneck effects in the population, and the inbreeding coefficient was positive, suggesting the possibility of inbreeding. The development potential of the population in the future varies among the various local populations. This study supports the biodiversity of Siberian roe deer at the genetic level to save the population and provides important scientific basis and reference for the protection and management of Siberian roe deer. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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12 pages, 930 KiB  
Article
Purifying Selection Influences the Comparison of Heterozygosities between Populations
by Sankar Subramanian
Biology 2024, 13(10), 810; https://doi.org/10.3390/biology13100810 - 10 Oct 2024
Viewed by 1279
Abstract
Heterozygosity is a fundamental measure routinely used to compare between populations to infer the level of genetic variation and their relative effective population sizes. However, such comparison is highly influenced by the magnitude of selection pressure on the genomic regions used. Using over [...] Read more.
Heterozygosity is a fundamental measure routinely used to compare between populations to infer the level of genetic variation and their relative effective population sizes. However, such comparison is highly influenced by the magnitude of selection pressure on the genomic regions used. Using over 2 million Single Nucleotide Variants (SNVs) from chimpanzee and mouse populations, this study shows that the heterozygosities estimated using neutrally evolving sites of large populations were two times higher than those of small populations. However, this difference was only ~1.6 times for the heterozygosities estimated using nonsynonymous sites. This suggests an excess in the nonsynonymous heterozygosities due to the segregation of deleterious variants in small populations. This excess in the nonsynonymous heterozygosities of the small populations was estimated to be 23–31%. Further analysis revealed that the magnitude of the excess is modulated by effective population size (Ne) and selection intensity (s). Using chimpanzee populations, this investigation found that the excess in nonsynonymous diversity in the small population was little (6%) when the difference between the Ne values of large and small populations was small (2.4 times). Conversely, this was high (23%) when the difference in Ne was large (5.9 times). Analysis using mouse populations showed that the excess in the nonsynonymous diversity of highly constrained genes of the small population was much higher (38%) than that observed for the genes under relaxed selective constraints (21%). Similar results were observed when the expression levels of genes were used as a proxy for selection intensity. These results emphasize the use of neutral regions, less constrained genes, or lowly expressed genes when comparing the heterozygosities between populations. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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