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Biology
Special Issues
Genetic Variability within and between Populations
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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 2025 | Viewed by 4862

Special Issue Editor

Dr. Sankar Subramanian

E-Mail Website
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 (6 papers)

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Research

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
Viewed by 114
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 469
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 507
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 795
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
Viewed by 1115
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 1042
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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