Genetic diversity and its conservation implications of Vitex rotundifolia (Lamiaceae) populations in East Asia

Vitex rotundifolia is an important coastal and medicinal plant, and is recorded in the List of the Important Wild Plants for Conservation in China and Japan. However, an effective conservation strategy is lacking. In the present study, the genetic diversity and population structure were analyzed using phylogeographical methods based on the trnH-psbA and trnG-trnS intergenic spacers of the chloroplast DNA (cpDNA) sequences from 157 individuals from 25 sampling sites for V. rotundifolia and V. trifolia plus the internal transcribed spacer (ITS) of the nuclear ribosomal DNA (nrDNA) sequences of 177 individuals from 27 sampling sites. The results showed that V. rotundifolia and V. trifolia had eight cpDNA and two nrDNA haplotypes, respectively, and the V. rotundifolia has a low level of genetic diversity (haplotype diversity hd,cp = 0.360, hd,nr = 0.440), a more pronounced genetic differentiation among populations (population differentiation at the species level (GST) = 0.201, population differentiation at the allele level (NST) = 0.462), and an insignificantly different phylogeographical structure (NST > GST, P > 0.05). In addition, haplotype network analyses indicated that V. rotundifolia and V. trifolia have distinct haplotypes. Divergence dating based on BEAST software analyses showed that most cpDNA clades diverged in the late Pleistocene era. Demographic analysis indicated that V. rotundifolia underwent a rapid demographic expansion. Some scientific strategies are suggested for resource conservation of V. rotundifolia based on its genetic diversity and population structure.

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High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Forests ◽

10.3390/f11040469 ◽

2020 ◽

Vol 11 (4) ◽

pp. 469 ◽

Cited By ~ 1

Author(s):

Yanwen Deng ◽

Tingting Liu ◽

Yuqing Xie ◽

Yaqing Wei ◽

Zicai Xie ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variation ◽

Human Disturbance ◽

Haplotype Diversity ◽

Conservation Strategy ◽

Ex Situ ◽

Conservation Strategies ◽

High Genetic Diversity ◽

Cpdna Markers

Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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Genetic diversity and variation of seven Chinese grass shrimp (Palaemonetes sinensis) populations based on the mitochondrial COI gene

BMC Ecology and Evolution ◽

10.1186/s12862-021-01893-8 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Yingying Zhao ◽

Xiaochen Zhu ◽

Ye Jiang ◽

Zhi Li ◽

Xin Li ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Haplotype Diversity ◽

Grass Shrimp ◽

Haplotype Network ◽

Coi Gene ◽

Wild Populations ◽

Important Species ◽

Network Analyses ◽

Maximum Variation

Abstract Background Chinese grass shrimp (Palaemonetes sinensis) is an important species widely distributed throughout China, which is ecologically relevant and possesses ornamental and economic value. These organisms have experienced a sharp decline in population due to overfishing. Therefore interest in P. sinensis aquaculture has risen in an effort to alleviate fishing pressure on wild populations. Therefore, we investigated the genetic diversity and variation of P. sinensis to verify the accuracy of previous research results, as well as to assess the risk of diversity decline in wild populations and provide data for artificial breeding. Methods Palaemonetes sinensis specimens from seven locations were collected and their genetic variability was assessed based on mitochondrial COI gene segments. DNA sequence polymorphisms for each population were estimated using DNASP 6.12. The demographic history and genetic variation were evaluated using Arlequin 3.11. At last, the pairwise genetic distance (Ds) values and dendrograms were constructed with the MEGA 11 software package. Results Our study obtained sequences from 325 individuals, and 41 haplotypes were identified among the populations. The haplotype diversity (Hd) and nucleotide diversity (π) indices ranged from 0.244 ± 0.083 to 0.790 ± 0.048 and from 0.0004 ± 0.0001 to 0.0028 ± 0.0006, respectively. Haplotype network analyses identified haplotype Hap_1 as a potential maternal ancestral haplotype for the studied populations. AMOVA results indicated that genetic variations mainly occurred within populations (73.07%). Moreover, according to the maximum variation among groups (FCT), analysis of molecular variance using the optimal two-group scheme indicated that the maximum variation occurred among groups (53.36%). Neutrality and mismatch distribution tests suggested that P. sinensis underwent a recent population expansion. Consistent with the SAMOVA analysis and haplotype network analyses, the Ds and FST between the population pairs indicated that the JN population was distinctive from the others. Conclusions Our study conducted a comprehensive characterization of seven wild P. sinensis populations, and our findings elucidated highly significant differences within populations. The JN population was differentiated from the other six populations, as a result of long-term geographical separation. Overall, the present study provided a valuable basis for the management of genetic resources and a better understanding of the ecology and evolution of this species.

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Genome-wide genetic diversity, population structure and admixture analysis in Eritrean Indigenous Cattle

South African Journal of Animal Science ◽

10.4314/sajas.v49i6.12 ◽

2020 ◽

Vol 49 (6) ◽

pp. 1083-1092

Author(s):

S Goitom ◽

M.G. Gicheha ◽

F.K. Njonge ◽

N Kiplangat

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Population Differentiation ◽

Principal Component ◽

Vital Role ◽

Group Method ◽

Indigenous Cattle ◽

Ecological Zones ◽

Genome Wide

Indigenous cattle play a vital role in subsistence and livelihood of pastoral producers in Eritrea. In order to optimally utilize and conserve these valuable indigenous cattle genetic resources, the need to carry out an inventory of their genetic diversity was recognized. This study assessed the genetic variability, population structure and admixture of the indigenous cattle populations (ICPs) of Eritrea using a genotype by sequencing (GBS) approach. The authors genotyped 188 animals, which were sampled from 27 cattle populations in three diverse agro-ecological zones (western lowlands, highlands and eastern lowlands). The genome-wide analysis results from this study revealed genetic diversity, population structure and admixture among the ICPs. Averages of the minor allele frequency (AF), observed heterozygosity (HO), expected heterozygosity (HE), and inbreeding coefficient (FIS) were 0.157, 0.255, 0.218, and -0.089, respectively. Nei’s genetic distance (Ds) between populations ranged from 0.24 to 0.27. Mean population differentiation (FST) ranged from 0.01 to 0.30. Analysis of molecular variance revealed high genetic variation between the populations. Principal component analysis and the distance-based unweighted pair group method and arithmetic mean analyses revealed weak substructure among the populations, separating them into three genetic clusters. However, multi-locus clustering had the lowest cross-validation error when two genetically distinct groups were modelled. This information about genetic diversity and population structure of Eritrean ICPs provided a basis for establishing their conservation and genetic improvement programmes. Keywords: genetic variability, molecular characterization, population differentiation

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Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

Archives of Polish Fisheries ◽

10.1515/aopf-2016-0010 ◽

2016 ◽

Vol 24 (2) ◽

pp. 85-97 ◽

Cited By ~ 2

Author(s):

Sylvanus A. Nwafili ◽

Tian-Xiang Gao

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Control Region ◽

Haplotype Diversity ◽

Population Expansion ◽

Mitochondrial Control Region ◽

Recent Population Expansion ◽

Base Pair Fragment ◽

Population Structures ◽

High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

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Genetic diversity and population structure of Hemibagrus guttatus (Bagridae, Siluriformes) in the larger subtropical Pearl River based on COI and Cyt b genes analysis

Annales de Limnologie - International Journal of Limnology ◽

10.1051/limn/2021005 ◽

2021 ◽

Vol 57 ◽

pp. 7

Author(s):

Tianxu Kuang ◽

Fangmin Shuai ◽

Xinhui Li ◽

Weitao Chen ◽

Sovan Lek

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Sustainable Use ◽

Haplotype Diversity ◽

Pearl River ◽

Germplasm Resources ◽

Geographical Populations ◽

Commercially Important ◽

The Pearl River ◽

F Statistics

Understanding the genetic diversity and population structure of fish species is crucial for the sustainable use and protection of fish germplasm resources. Hemibagrus guttatus (Bagridae, Siluriformes) is widely distributed in the large subtropical Pearl River (China) and is commercially important. It's population have been declining. The genetic diversity of wild H. guttatus is not clear, despite its important ecological significance. In this paper, genes mitochondrial cytochrome c oxidase subunit I (COI) and cytochrome b (Cyt b) were used to analyze the genetic structure of H. guttatus population collected from six geographical populations in the main streams of the Pearl River. The results showed that the nucleotide diversity (π) and haplotype diversity (Hd) of wild H. guttatus was low (π < 0.005; Hd < 0.5). In addition, H. guttatus haplotypes did not cluster into clades according to geographical distribution, as revealed by neighbor-joining tree analysis. Analysis of molecular variance analysis (AMOVA) and F-statistics (Fst) values showed high homogeneity among wild H. guttatus populations. Our results suggest that there is degradation in germplasm resources of H. guttatus that could destabilize the sustainable use of this species and there was an urgent need for conservation of this species in South China.

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Study of genetic differences among Slovak Tsigai populations using microsatellite markers

Czech Journal of Animal Science ◽

10.17221/1670-cjas ◽

2009 ◽

Vol 54 (No. 10) ◽

pp. 468-474 ◽

Cited By ~ 3

Author(s):

S. Kusza ◽

E. Gyarmathy ◽

J. Dubravska ◽

I. Nagy ◽

A. Jávor ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Distance ◽

Microsatellite Markers ◽

Mating System ◽

Population Differentiation ◽

Genetic Relationships ◽

The Other ◽

Potential Risks ◽

Substantial Degree

In this study genetic diversity, population structure and genetic relationships of Tsigai populations in Slovakia were investigated using microsatellite markers. Altogether 195 animals from 12 populations were genotyped for 16 microsatellites. 212 alleles were detected on the loci. The number of identified alleles per locus ranged from 11 to 35. In the majority of the populations heterozygosity deficiency and potential risks of inbreeding could be determined. High values of <I>F</I><sub>ST</sub> (0.133) across all the loci revealed a substantial degree of population differentiation. The estimation of genetic distance value showed that the Slovak Vojin population was the most different from the other populations. The 12 examined populations were able to group into 4 clusters. With this result our aim is to help the Slovak sheep breeders to establish their own mating system, to avoid genetic loss and to prevent diversity of Tsigai breed in Slovakia.

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Insights into the Migration Routes and Historical Dispersion of Species Surviving the Messinian Crisis: The Case of Patella ulyssiponensis and Epizoic Rhodolith Lithophyllum hibernicum

Hydrobiology ◽

10.3390/hydrobiology1010003 ◽

2021 ◽

Vol 1 (1) ◽

pp. 10-38

Author(s):

Nuno Gomes ◽

Carlos Antunes ◽

Dimítri de Araújo Costa

Keyword(s):

Haplotype Diversity ◽

Haplotype Network ◽

Coralline Algae ◽

Migration Routes ◽

Separate Species ◽

Northeast Atlantic ◽

Network Analyses ◽

The Mediterranean ◽

And Migration ◽

Patella Ulyssiponensis

The genus Patella (Patellogastropoda, Mollusca) is represented by a group of species exclusive to the Northeast Atlantic Ocean (including Macaronesian archipelagos) and Mediterranean Sea. The species Patella ulyssiponensis and Patella aspera are common in European waters, with the first inhabiting continental coast, and the second endemic to Macaronesian archipelagos. However, the acceptance of these two lineages as separate species is still highly debated. The red coralline species algae Lithophyllum hibernicum, distributed from Northeast Atlantic to the Mediterranean, is usually found as epilithic crusts or unattached forms (named rhodolith beds), although it also forms epizoic crusts on other organisms, e.g., shell surfaces. In order to study the historic dispersal and migration routes of the Patella ulyssiponensis-aspera complex, taxonomic, genetic and biogeographic approaches were employed based on haplotype network analyses and estimations for the most common recent ancestor (TMRCA), using Cytochrome Oxydase I. A synonymy for these two species is proposed, with the presence of a shared haplotype between the continental (P. ulyssiponensis) and insular (P. aspera) lineages, and with basis of morphological and nomenclatural data. We propose an evolutionary scenario for its dispersal based on a high haplotype diversity for the Mediterranean regions, indicating its possible survival during the Messinian Salinity Crisis (6–5.3 Mya), followed by a colonization of the Proto-Macaronesian archipelagos. The epizoic association of L. hibernicum on P. ulyssiponensis shell adult surface is recorded in this study, likewise the promotion of settlement conditions provided by these coralline algae to P. ulyssiponensis larvae, may explain the reach of P. ulyssiponensis distribution through rhodolith transportation.

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Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers

PLoS ONE ◽

10.1371/journal.pone.0253600 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0253600

Author(s):

Charles U. Uba ◽

Happiness O. Oselebe ◽

Abush A. Tesfaye ◽

Wosene G. Abtew

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

West Africa ◽

East Africa ◽

Unknown Origin ◽

Snp Markers ◽

Bambara Groundnut ◽

Conservation Strategy ◽

Population Structure Analysis ◽

Geographical Regions

Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.

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Two partial mitochondrial gene sequences (COI and 12S-rRNA) suggested that Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) (Asteroidea: Goniasteridae) from the Japanese waters are probably of the same species

Zoosymposia ◽

10.11646/zoosymposia.15.1.15 ◽

2019 ◽

Vol 15 (1) ◽

pp. 129-140

Author(s):

DAVIN H.E. SETIAMARGA ◽

RENA SHIBA ◽

YUKI KAMITO ◽

MASAKI YAMAMOTO ◽

NAZIFA NAZIHA BT. RAZALI ◽

...

Keyword(s):

Mitochondrial Dna ◽

Population Structure ◽

Mitochondrial Gene ◽

Haplotype Network ◽

12S Rrna ◽

National Museum ◽

Network Analyses ◽

Morphological Studies ◽

The Pacific ◽

Japanese Waters

Our recent morphological studies on the echinoderm collection of the National Museum of Nature and Science, Tokyo (NMST), indicated that the goniasterid starfishes Ceramaster japonicus (Sladen, 1889) and Ceramaster patagonicus (Sladen, 1889) are distributed in the Pacific Oceanside of Japan. In this study, we studied the NMST samples of C. japonicus and C. patagonicus from Japan, by using two mitochondrial DNA genes, the COI and 12S-rRNA, as markers to test relationships between these species in Japan. C. patagonicus sequences from GenBank were mined and included in the analyses. Results of phylogenetic and haplotype network analyses of both genes (final sequence lengths: COI = 317 bp, 12S = 477 bp) suggested that "Ceramaster patagonicus" and "Ceramaster japonicus" from Japanese waters are almost certainly synonymous without any population structure inside Japan.

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Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

Turkish Journal of Fisheries and Aquatic Sciences ◽

10.4194/1303-2712-v20_10_06 ◽

2020 ◽

Vol 20 (10) ◽

pp. 767-776

Author(s):

Yusuf Bektas ◽

Ismail Aksu ◽

Gokhan Kalayci ◽

Davut Turan

Keyword(s):

Genetic Diversity ◽

Control Region ◽

Mismatch Distribution ◽

Phylogenetic Trees ◽

Goodness Of Fit ◽

Haplotype Diversity ◽

Mitochondrial Control Region ◽

Haplotype Network ◽

Silurus Glanis ◽

Low Genetic Diversity

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

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