Evaluation of the genetic variability of Ophrys insectifera L. populations growing in Belarus using molecular iPBS markers

2021 ◽  
Vol 66 (2) ◽  
pp. 223-231
Author(s):  
N. V. Samokhvalova ◽  
A. V. Kruchonok ◽  
B. Yu. Anoshenko ◽  
V. V. Titok
Keyword(s):  
Genetic Heterogeneity ◽  
Population Genetic ◽  
Natural Populations ◽  
Biosphere Reserve ◽  
Major Fraction ◽  
Principal Coordinates Analysis ◽  
Molecular Variance ◽  
Intrapopulation Variation ◽  
Principal Coordinates ◽  
Two Populations

An analysis of genetic heterogeneity was performed for two populations of Ophrys insectifera L. located in the Berezinsky Biosphere Reserve and the Verkudy village. The species are critically endangered (CR). The analysis of data obtained using iPBS markers detected the higher risk of extinction of the population in the Berezinsky Biosphere Reserve than the population from the Verkudy village, since the level of population genetic heterogeneity from the Verkudy is higher compared to the Berezinsky Biosphere Reserve. Molecular variance analysis (AMOVA) and other parameters of genetic variation showed the major fraction of intrapopulation variation (64 %, Gst = 0.26). Principal Coordinates Analysis (PCoA) revealed two groups that coincided with natural populations, and confirmed a larger genetic heterogeneity in the population from the Verkudy.

Isolation and characterisation of 16 novel polymorphic microsatellite loci for the Eurasian coot (Fulica atra)

2016 ◽  
Vol 64 (6) ◽  
pp. 430
Author(s):  
Tianshu Lv ◽  
Wanchao Zhu ◽  
Shuyu Xue ◽  
Huanxin Zhang ◽  
Xiaodong Gao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Genomic Library ◽  
Enriched Genomic Library ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Fulica Atra ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Microsatellite ◽  
Two Populations

To study the genetic diversity of the Eurasian coot (Fulica atra), 16 novel microsatellites were isolated and characterised using a (AC)12-enriched genomic library. Polymorphism of each locus was detected in 19 individuals from Weishan Lake and Zhaoyang Lake, both located in Shandong Province, China. These microsatellite loci revealed 3–12 alleles in two populations. One locus (Fa6) showed significant deviations from Hardy–Weinberg equilibrium in the Zhaoyang Lake population. By means of Principal Coordinates Analysis, 19 individuals were divided into two groups, which verified they were from two populations. These novel microsatellites will be useful for further studies and genetic analyses of the Eurasian coot.

scholarly journals A comparative analysis of mathematical methods for homogeneity estimation of the Lithuanian population

2020 ◽  
Vol 26 (4) ◽  
pp. 211-216
Author(s):  
Alma Molytė ◽  
Alina Urnikytė ◽  
Vaidutis Kučinskas
Keyword(s):  
Comparative Analysis ◽  
Genetic Structure ◽  
Multidimensional Scaling ◽  
Population Genetic ◽  
Venous Blood ◽  
Principal Component ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Background Population ◽  
Principal Coordinates

Background. Population genetic structure is one of the most important population genetic parameters revealing its demographic features. The aim of this study was to evaluate the homogeneity of the Lithuanian population on the basis of the genome-wide genotyping data. The comparative analysis of three methods – multidimensional scaling, principal components, and principal coordinates analysis – to visualize multidimensional genetics data was performed. The results of visualization (mapping images) are also presented. Materials and methods. The data set consisted of 425 samples from six ethnolinguistic groups of the Lithuanian population. Genomic DNA was extracted from whole venous blood using either the phenol-chloroform extraction method or the automated DNA extraction platform TECAN Freedom EVO. Genotyping was performed at the Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Lithuania, with the Illumina HumanOmniExpress-12 v1.1 and the Infinium OmniExpress-24. For the estimation of homogeneity of the Lithuanian population, PLINK data file was obtained using PLINK v1.07 program. The Past3 software was used to visualize the genotype data with multidimensional scaling and principal coordinates methods. The SmartPCA from EIGENSOFT 7.2.1 program was used in the principal component analysis to determine the population structure. Conclusions. Methods of multidimensional scaling, principal coordinate, and principal component for the genetic structure of the Lithuanian population were investigated and compared. The principal coordinate and principal component methods can be used for genotyping data visualization, since any essential differences in the results obtained were not observed and compared to multidimensional scaling. The Lithuanian population is homogenous whereas the points are strongly close when we use the principal coordinates or principal component methods.

scholarly journals Evolutionary dynamics of spore killers.

Genetics ◽  
1993 ◽  
Vol 135 (3) ◽  
pp. 923-930 ◽  
Author(s):  
M J Nauta ◽  
R F Hoekstra
Keyword(s):  
Life Cycle ◽  
Segregation Distortion ◽  
Population Genetic ◽  
Field Data ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Additional Advantage ◽  
Genetic Modeling ◽  
Spore Killing ◽  
Ascospore Formation

Abstract Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of "heterozygous" advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing.

scholarly journals Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1803
Author(s):  
Valentino Palombo ◽  
Elena De Zio ◽  
Giovanna Salvatore ◽  
Stefano Esposito ◽  
Nicolaia Iaffaldano ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Fishery Management ◽  
Snp Array ◽  
Fine Scale ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Management Actions ◽  
Principal Coordinates ◽  
Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

scholarly journals Tree Species Diversity and Composition of Miombo Woodlands in South-Central Angola: A Chronosequence of Forest Recovery after Shifting Cultivation

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Francisco M. P. Gonçalves ◽  
Rasmus Revermann ◽  
Amândio L. Gomes ◽  
Marcos P. M. Aidar ◽  
Manfred Finckh ◽  
...  
Keyword(s):  
Shifting Cultivation ◽  
Stand Structure ◽  
Woody Species ◽  
Distinct Group ◽  
Forest Recovery ◽  
Miombo Woodlands ◽  
Principal Coordinates Analysis ◽  
South Central ◽  
Principal Coordinates ◽  
Management Plans

The study was carried out in the Cusseque area of the Municipality of Chitembo in south-central Angola. Our objectives were to assess the floristic diversity, the species composition, and stand structure of Miombo woodlands during regeneration after shifting cultivation. A total of 40 plots of 1000 m2were surveyed and analyzed, corresponding to mature forests/woodlands and three fallow types of different age. The analyses were based on plot inventories of all trees with DBH ≥ 5 cm. A total of 51 woody species, 38 genera, and 19 families were recorded. The dominant family was Fabaceae, with subfamily Caesalpinioideae being very abundant. Shannon Diversity and Evenness were highest in mature forests and young fallows, while the mature forest stands showed the highest species richness. A Principal Coordinates Analysis (PCoA) showed many species shared between the intermediate fallow types, but only few species were shared with young fallows. Mature forests formed a clearly distinct group. This study shows potential pathways of forest recovery in terms of faster regeneration after agricultural abandonment and, thus, the results presented here can be used in future conservation and management plans in order to reduce the pressure on mature forests.

scholarly journals Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Runzhi Zhang ◽  
Alejandro R. Walker ◽  
Susmita Datta
Keyword(s):  
Machine Learning ◽  
Error Rates ◽  
Average Error ◽  
Importance Score ◽  
Learning Methods ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Total Variability ◽  
The Common ◽  
Feature Selecting

Abstract Background Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets. Results Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively. Conclusions The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.

Population genetic structure and dispersal of Pinus occidentalis in the Dominican Republic by chloroplastic SSR with implications for its conservation, management, and reforestation

2021 ◽  
Author(s):  
Luis E. Rodríguez de Francisco ◽  
Rosanna Carreras-De León ◽  
Rafael M. Navarro Cerrillo ◽  
Liz A. Paulino-Gervacio ◽  
María-Dolores Rey ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Dominican Republic ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Conservation Management ◽  
Natural Populations ◽  
Limited Information ◽  
High Genetic Diversity ◽  
The Impact ◽  
Pinus Occidentalis

<i>Pinus occidentalis</i> is the dominant species of forest ecosystems in the Dominican Republic, located between 200 and 3000 meters above sea level, with extensive and overexploited natural populations. However, over the years, various restoration plans have been performed, which could affect the genetic structure of <i>P. occidentalis</i>. Despite being the species with the highest occurrence in the Dominican forests, there is no existing information on genetic structure and molecular characterization among natural populations with limited information on both phenological and productive characterization. In this study, the genetic structure, diversity, and gene flow of the five <i>P. occidentalis</i> natural populations of the Dominican Republic were determined using microsatellite markers. A total of 145 individuals were genotyped with eight polymorphic chloroplastic microsatellites, producing an average of 41 haplotypes with high genetic diversity across populations (H<sub>E</sub> = 0.90). Significant population genetic structure was found between populations (F<sub>ST</sub> = 0.123). These results reflect the impact of reforestation programs on natural populations and diluting the natural genetic signature. Analysis of population genetic data is, therefore, crucial for the breeding and conservation programs of <i>P. occidentalis</i> in the country.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

2014 ◽  
Vol 92 (2) ◽  
pp. 149-162 ◽  
Author(s):  
Christina M. Davy ◽  
Robert W. Murphy
Keyword(s):  
Population Genetics ◽  
Freshwater Turtles ◽  
Population Declines ◽  
Isolated Populations ◽  
Principal Coordinates Analysis ◽  
Turtle Species ◽  
Principal Coordinates ◽  
Clemmys Guttata ◽  
Spotted Turtle ◽  
Cast Doubt

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.

Use of multivariate methods in forest research site selection

1991 ◽  
Vol 21 (11) ◽  
pp. 1573-1580 ◽  
Author(s):  
Andrew J. Burton ◽  
Carl W. Ramm ◽  
Kurt S. Pregitzer ◽  
David D. Reed
Keyword(s):  
Site Selection ◽  
Large Scale ◽  
Multivariate Methods ◽  
Data Bases ◽  
Principal Coordinates Analysis ◽  
Research Site ◽  
Principal Coordinates ◽  
Alternative Sites ◽  
Existing Data ◽  
Selection Of

In large-scale gradient studies, selection of the best research sites is critical but time-consuming and costly. Multivariate methods can be used to quickly identify suitable sites from existing data bases. Based on a study of acid deposition in the Great Lakes region (the Michigan Gradient Study), we illustrate the use of multivariate methods in screening potential research sites for similarity. Sites were examined using cluster analysis, principal coordinates analysis, and correspondence analysis. The graphical displays generated by the multivariate methods were used to identify similar sites across the gradient. A list of 31 potential sites was reduced to 5 similar research sites and several alternative sites. The results of the multivariate methods compared well with more traditional methods of research site selection but allowed for multiple comparisons of many potential sites using a variety of data from existing data bases. By eliminating sites that are unacceptable with respect to available data, the multivariate methods reduce the number of sites that require field visitation prior to final site verification. This process represents a substantial savings in time and effort when dealing with a long list of potential research sites.

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