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Diversity
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Population Genetics of Animals and Plants
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Population Genetics of Animals and Plants

A special issue of Diversity (ISSN 1424-2818). This special issue belongs to the section "Biodiversity Conservation".

Deadline for manuscript submissions: closed (31 March 2024) | Viewed by 16222

Special Issue Editor

Dr. Petras Prakas

E-Mail Website
Guest Editor
Nature Research Centre, Akademijos Str. 2, 08412 Vilnius, Lithuania
Interests: parasitology; population genetics; taxonomy; phylogeny; conservation genetics; molecular ecology; molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Population genetics is closely related to genetics, ecology, and evolution. The main evolutionary factors changing allele and genotype frequencies in current natural populations are gene drift, gene flow, mutation, and natural selection. This branch of modern biology aims to identify intra-population and inter-population genetic variability. The genetic diversity of natural populations expressed in heterozygosity, allelic richness or nucleotide diversity is essential for long-term population survival and adaptation to constantly changing environmental conditions. Genetic variability between subpopulations of a metapopulation can lead to genetic differentiation between these subpopulations. The most important tools of population genetics are genetic markers (such as SNP, microsatellites, AFLP, and others) and the DNA sequencing of a certain highly polymorphic locus. With the help of these molecular tools, the frequencies of genotypes and alleles and the heterozygosity of populations are determined, and the main evolutionary factors influencing the genetic diversity, structure and adaptation of populations are examined.

Recent advances in molecular biology, genomics, and bioinformatics, as well as advances in statistical tests and packages analysing genetic polymorphism data led to the rapid development of population genetics and the accumulation of large amounts of empirical data in wildlife populations of animals and plants. Due to direct and indirect human activities, biodiversity is decreasing on our planet. Many species have already become extinct, while others have experienced a decline in their population size. Therefore, one of the main directions of current population genetics is conservation. In a changing world, population genetics does not only deal with theoretical research, but also with population fragmentation, small population sizes and inbreeding depression, anthropogenic hybridisation, phylogeography, invasive species, determination of population boundaries, and management of exploited populations.

We invite submissions of a manuscripts that focus on various theoretical and practical topics of population genetics, and we are looking forward to studies that have been conducted in any geographical region examining wildlife animals and plants. If you are interested in this opportunity or have any queries, please do not hesitate to contact us.

Dr. Petras Prakas
Guest Editor

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. Diversity 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 2100 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.

Keywords

  • genetic variability
  • genetic structure
  • conservation
  • fragmentation
  • hybridization
  • phylogeography
  • migration
  • population demography
  • invasive species
  • exploited populations

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Related Special Issue

Published Papers (8 papers)

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Research

13 pages, 3111 KiB  
Article
Joint Identification and Application of Microsatellite Markers in Genetic Diversity Study of Closely Related Species Teucrium montanum, T. capitatum and Their Natural Hybrid
by Filip Varga, Zlatko Liber, Ante Turudić, Jernej Jakše, Lea Juzbašić, Nina Jeran, Martina Grdiša, Miloš Zbiljić and Zlatko Šatović
Diversity 2024, 16(4), 206; https://doi.org/10.3390/d16040206 - 28 Mar 2024
Cited by 2 | Viewed by 1884
Abstract
Teucrium montanum L. and T. capitatum L. are two plant species with overlapping distribution in the Balkan Peninsula, especially in Croatia, where several occurrences of their putative hybrid species T. × rohlenae have been recorded. Next-generation sequencing of both species and de novo [...] Read more.
Teucrium montanum L. and T. capitatum L. are two plant species with overlapping distribution in the Balkan Peninsula, especially in Croatia, where several occurrences of their putative hybrid species T. × rohlenae have been recorded. Next-generation sequencing of both species and de novo assembly was carried out resulting in 120 contigs for T. montanum and 1685 contigs for T. capitatum assembled. The Dig-up primers pipeline was used for SSR mining of both assemblies, applying different criteria that resulted in 112 SSR candidates for testing. A subset of 41 SSRs was selected and after two rounds of testing, twelve SSRs were developed and characterized. A total of 232 alleles were detected with 5 to 29 alleles per locus, based on the test sample. The genetic diversity analysis of three Teucrium taxa from a single location revealed a higher level of diversity in T. montanum than in T. capitatum with intermediate values for the hybrid species. The NeighborNet diagram and genetic structure analysis grouped the taxa into two separate clusters, the first of which consisted exclusively of T. montanum, while the other was composed of intermixed T. capitatum and T. × rohlenae individuals. The availability of SSR markers for two Teucrium taxa will allow in-depth analysis of genetic diversity and structure, as well as molecular identification of their putative hybrids in the future. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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18 pages, 2343 KiB  
Article
Genetic Variation among Aeluropus lagopoides Populations Growing in Different Saline Regions
by Basharat A. Dar, Abdullah A. Al-Doss, Abdulaziz M. Assaeed, Muhammad M. Javed, Abdelhalim I. Ghazy, Saud L. Al-Rowaily and Ahmed M. Abd-ElGawad
Diversity 2024, 16(1), 59; https://doi.org/10.3390/d16010059 - 16 Jan 2024
Cited by 2 | Viewed by 1744
Abstract
Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of [...] Read more.
Aeluropus lagopoides is a halophytic grass growing in different sabkhas of Saudi Arabia. In this study, 14 inter-simple sequence repeat (ISSR) and 15 sequence-related amplified polymorphism (SRAP) molecular markers were selected to investigate the genetic diversity within and among five natural populations of A. Lagopiodes. The genetic diversity varied within and among populations. ISSR markers were slightly more efficient than SRAP markers in evaluating genetic diversity. Average polymorphism information content, effective number of alleles, Nei’s genetic diversity, and Shannon’s information index values of ISSR markers were higher than SRAP. Analysis of molecular variance revealed about 40% genetic variation among the population and 60% within the population. Overall, the genetic diversity was lowest in Jouf (40%), while the Qaseem populations were the highest (60%). Jizan populations were highly dissimilar to other regions. A Mantel test indicated a positive correlation between geographic and genetic distance. The cluster analysis showed three groups; the first group comprises Jouf and Salwa populations, the second group comprises Qareenah and Qaseem, and the third group comprises the Jizan population. This observation matched the geographic distribution of the species. These findings can help in the conservation of a diverse population of A. lagopoides in saline regions as well as rehabilitation of these degraded unique habitats. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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15 pages, 2399 KiB  
Article
Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites
by Aija Brakovska and Nataļja Škute
Diversity 2023, 15(11), 1128; https://doi.org/10.3390/d15111128 - 31 Oct 2023
Viewed by 1661
Abstract
We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most [...] Read more.
We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (Hobs) and the expected heterozygosity (Hexp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (Na), the average effective number of alleles at the locus (Ne), the FST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ2-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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16 pages, 2808 KiB  
Article
Assessment of Anthropogenic Impacts on the Genetic Diversity of Phragmites australis in Small-River Habitats
by Jolanta Patamsytė, Carla Lambertini, Jurgita Butkuvienė, Donatas Naugžemys and Donatas Žvingila
Diversity 2023, 15(11), 1116; https://doi.org/10.3390/d15111116 - 26 Oct 2023
Cited by 2 | Viewed by 1682
Abstract
Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study [...] Read more.
Common reed is often used as a model plant to study the anthropogenic impacts on ecosystems at local and global scales. As a community-forming species, it is directly exposed to the impacts of human activities on the ecosystem. The aim of our study was to evaluate the patterns of genetic diversity in common reed stands located in habitats that are differently affected by anthropogenic factors. We studied whether riverbed modifications, land cover in the neighborhood of the stand and the chemical and physical parameters of the river water affect the genetic diversity of P. australis at the studied sites. Using DNA fingerprinting, we genotyped 747 plants from 42 sites located in 16 small Lithuanian rivers. Bayesian clustering and principal coordinate analysis revealed two main gene pools at the population (river) level. At the site level (i.e., considering all sites independently of their rivers), polymorphism was high even between sites in the same river. Our study revealed a negative relationship between the concentration of nitrogen compounds and the genotypic richness of P. australis populations. We did not find any correlations between the other chemical parameters of the water and the parameters of the genetic diversity. Additionally, there were no genetic differences between sites in modified and unmodified river sections or between sites that differed in land cover type in the neighborhood of the stand. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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13 pages, 1681 KiB  
Article
Temporal Variation of Genetic Diversity in Rutilus rutilus Populations from Lithuania Using mtDNA Markers in the Context of Anthropogenic Activities
by Dalius Butkauskas, Ieva Ignatavičienė, Adomas Ragauskas and Vytautas Rakauskas
Diversity 2023, 15(11), 1113; https://doi.org/10.3390/d15111113 - 26 Oct 2023
Cited by 1 | Viewed by 1530
Abstract
One of the most abundant fish species, Rutilus rutilus, is widely distributed in Lithuania and its potential to adapt to environmental changes attracted our interest. Unfortunately, it is not properly understood how anthropogenic activities can affect the genetic diversity within this species. [...] Read more.
One of the most abundant fish species, Rutilus rutilus, is widely distributed in Lithuania and its potential to adapt to environmental changes attracted our interest. Unfortunately, it is not properly understood how anthropogenic activities can affect the genetic diversity within this species. We studied three populations of roaches (samples collected in the Neris and Žeimena rivers, and Lake Drūkšiai) over a period of five years (from 2017 to 2022) to determine genetic diversity using mtDNA D-loop and ATP6 genetic markers. Genetic diversity parameters, AMOVA analysis, haplotype network, and PCoA analysis revealed a greater genetic variability in roach samples collected in 2017, and the greatest differences were noticed in the population inhabiting Lake Drūkšiai, as compared with other samples studied over a five-year period. Differences in genetic diversity detected after a five-year period led us to the assumption that roach populations may be related to the effects of natural (changing climatic conditions) and anthropogenic (operating nuclear power plant) origin. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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14 pages, 4228 KiB  
Article
Development of Polymorphic Microsatellite Markers and Identification of Applications for Wild Walnut (Juglans regia L.) in Middle Asia
by Xuerong Li, Xiyong Wang, Zhijun Cui, Wei Shi, Junhua Huang and Jiancheng Wang
Diversity 2023, 15(10), 1073; https://doi.org/10.3390/d15101073 - 10 Oct 2023
Cited by 6 | Viewed by 1902
Abstract
The common walnut (Juglans regia L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this [...] Read more.
The common walnut (Juglans regia L.), a species of significant economic and ecological importance, along with its variant, holds developmental value. Simple sequence repeat (SSR) markers are used as an effective method for material identification due to their co-dominant inheritance. In this work, a total of 357629 SSR loci were searched based on previously published walnut genome sequences, with a density of 662.28 (SSRs/Mb). The majority of all these loci were found to be single nucleotide A/T (58.49%), followed by the dinucleotide AT (19.48%). Based on the results of genome-wide SSR site design, 22 effective primer pairs were designed and screened to analyze the genetic diversity of 48 wild walnut samples from three countries. Each locus had an average of 5.17 effective alleles (Ne), with an average polymorphism information content (PIC) of 0.71, average heterozygosity (He) of 0.52, and average genetic differentiation index (Fst) of 0.09. The analysis of 48 wild walnut samples from three countries (Kyrgyzstan, Tajikistan, and China) using the unweighted pairwise clustering method and arithmetic mean (UPGMA) along with principal coordinate analysis revealed the division of all samples into three groups. In summary, these novel SSR markers serve as a reference for the identification of wild walnut germplasm in Central Asia and for the development and utilization of wild walnut seed resources. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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17 pages, 3209 KiB  
Article
Population Structure and Genetic Diversity of the Spotted Sleeper Odontobutis interrupta (Odontobutidae), a Fish Endemic to Korea
by Kang-Rae Kim, Hee-kyu Choi, Taek Won Lee, Hyuk Je Lee and Jeong-Nam Yu
Diversity 2023, 15(8), 913; https://doi.org/10.3390/d15080913 - 7 Aug 2023
Cited by 6 | Viewed by 2539
Abstract
The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. [...] Read more.
The spotted sleeper, Odontobutis interrupta, is a fish species endemic to Korea and shows potential as an aquaculture species. Nevertheless, the population size of this species has declined significantly in recent years. To characterize the population structure and genetic diversity of O. interrupta in Korea, we analyzed four microsatellite loci in twelve populations from four major river systems. The provenance of the population was investigated to discern the origin of the translocated populations. The genetic diversity of the microsatellite ranged from 0.440 to 0.756, showing a high level of diversity similar to that of other freshwater fishes. However, mitochondrial DNA analysis exhibited low genetic diversity (Hd: 0.000–0.674, π: 0.00000–0.00159). The FST values of microsatellites and mitochondrial DNA ranged from 0.096 to 0.498 and −0.046 to 0.951, suggesting genetic admixture among populations. All populations exhibited an effective population size of <100; therefore, preservation efforts to prevent inbreeding depression would be required. The genetic structure could be divided into unique genotypes from the Seomjingang and Geumgang Rivers. However, genetic admixture was observed in all populations, rendering it impossible to distinguish them. Our findings provide fundamental but significant genetic insights pursuant to devising conservation strategies for O. interrupta. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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14 pages, 3620 KiB  
Article
Genetic Variation and Evolutionary History of the Threatened Dipterocarpus turbinatus C.F.Gaertn. Detected Using Microsatellites
by Nguyen Minh Duc, Nguyen Huy Hoang, Tran Thi Huong Giang, Nguyen Thi Thuy Huong, Vu Dinh Duy, Nguyen Phan Lan Hong, Truong Ngoc Minh and Nguyen Minh Tam
Diversity 2023, 15(8), 894; https://doi.org/10.3390/d15080894 - 28 Jul 2023
Cited by 2 | Viewed by 1731
Abstract
Dipterocarpus turbinatus C.F.Gaertn. is a valuable timber tree indigenous to the lowland tropical forests of southern and central Vietnam. It is in danger of extinction due to fragmented habitats and overexploitation. Therefore, assessing the genetic diversity and demographic history of this species is [...] Read more.
Dipterocarpus turbinatus C.F.Gaertn. is a valuable timber tree indigenous to the lowland tropical forests of southern and central Vietnam. It is in danger of extinction due to fragmented habitats and overexploitation. Therefore, assessing the genetic diversity and demographic history of this species is essential to providing a platform for conservation activities. Herein, we analyzed 281 D. turbinatus trees from 10 populations representing their natural distribution range in Vietnam using nine polymorphic microsatellites to provide valuable information for conservation activities. We detected genetic diversity within these populations (0.285 and 0.328 for observed and expected heterozygosity, respectively), as well as population genetic differentiation (a Wei and Cockerham value of 0.202 and a Hedrick value of 0.32). Clustering analysis based on different approaches revealed three genetic clusters which were significantly correlated to gene flow across the geographic distribution range of D. turbinatus in tropical evergreen forests. Approximate Bayesian computation suggested that the D. turbinatus populations had an evolutionary history consistent with divergence during the last glacial maximum. Based on our results, we recommend the in situ conservation of several populations with high genetic diversity, high allelic richness, or private alleles, and the gathering of the seeds of the remaining populations for ex situ conservation. Full article
(This article belongs to the Special Issue Population Genetics of Animals and Plants)
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