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 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 Genomic epidemiology ofMycobacterium bovisinfection in sympatric badger and cattle populations in Northern Ireland

2021 ◽  
Author(s):  
Assel Akhmetova ◽  
Jimena Guerrero ◽  
Paul McAdam ◽  
Liliana C.M. Salvador ◽  
Joseph Crispell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Spatial Distribution ◽  
Genetic Structure ◽  
Northern Ireland ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Transmission Dynamics ◽  
Data Set ◽  
Hair Samples ◽  
Disease Persistence

AbstractBackgroundBovine tuberculosis (bTB) is a costly epidemiologically complex, multi-host, endemic disease. Lack of understanding of transmission dynamics may undermine eradication efforts. Pathogen whole genome sequencing improves epidemiological inferences, providing a means to determine the relative importance of inter- and intra- species host transmission for disease persistence. We sequenced an exceptional data set of 619Mycobacterium bovisisolates from badgers and cattle in a 100km2bTB ‘hotspot’ in Northern Ireland. Historical molecular subtyping data permitted the targeting of an endemic pathogen lineage, whose long-term persistence provided a unique opportunity to study disease transmission dynamics in unparalleled detail. Additionally, to assess whether badger population genetic structure was associated with the spatial distribution of pathogen genetic diversity, we microsatellite genotyped hair samples from 769 badgers trapped in this area.ResultsGraph transmission tree methods and structured coalescent analyses indicated the majority of bacterial diversity was found in the local cattle population. Results pointed to transmission from cattle to badger being more common than badger to cattle. Furthermore, the presence of significant badger population genetic structure in the landscape was not associated with the spatial distribution ofM. bovisgenetic diversity, suggesting that badger-to-badger transmission may not be a key determinant of disease persistence.SignificanceOur data were consistent with badgers playing a smaller role in the maintenance ofM. bovisinfection in this study site, compared to cattle. Comparison to other areas suggests thatM. bovistransmission dynamics are likely to be context dependent, and the role of wildlife difficult to generalise.

scholarly journals Morphological and genetic diversity of Senecio vulgaris L. (Asteraceae) in Iran

2021 ◽  
Vol 80 (2) ◽  
Author(s):  
Mostafa Ebadi ◽  
Rosa Eftekharian
Keyword(s):  
Genetic Diversity ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Morphological Data ◽  
Principal Coordinates Analysis ◽  
Cauline Leaf ◽  
Senecio Vulgaris ◽  
Molecular Features ◽  
Principal Coordinates

Senecio vulgaris L., an annual herb belonging to the Asteraceae, is widely distributed in different regions of the world. There is no information on the intraspecific variations of the morphological and molecular features of this species. In the present investigation, we studied the morphological and genetic diversity of 81 accessions of S. vulgaris collected from 10 geographical populations. Eleven inter simple sequence repeat (ISSR) primers were used for the examination of genetic variations among the populations. Analysis of molecular variance (AMOVA) and GST analyses revealed significant differences among the investigated populations. A significant correlation between genetic distance and geographical distance was revealed by the Mantel test. However, reticulation analysis indicated the occurrence of gene flow among most of the populations studied. Principal component analysis (PCA) plot showed that the number of capitula, length of the cauline leaf and plant height were the most variable morphological characters. Principal coordinates analysis (PCoA) plot revealed two groups of populations, according to molecular and morphological data. The results suggested the existence of possible intraspecific taxonomic ranks within this species.

scholarly journals High-Throughput Genotype, Morphology, and Quality Traits Evaluation for the Assessment of Genetic Diversity of Wheat Landraces from Sicily

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 116 ◽  
Author(s):  
Fiore ◽  
Mercati ◽  
Spina ◽  
Blangiforti ◽  
Venora ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Durum Wheat ◽  
Extreme Environments ◽  
Principal Component ◽  
Detailed Knowledge ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Wide Range ◽  
Wheat Landraces ◽  
Durum Wheat Landraces

During the XX Century, the widespread use of modern wheat cultivars drastically reduced the cultivation of ancient landraces, which nowadays are confined to niche cultivation areas. Several durum wheat landraces adapted to the extreme environments of the Mediterranean region, are still being cultivated in Sicily, Italy. Detailed knowledge of the genetic diversity of this germplasm could lay the basis for their efficient management in breeding programs, for a wide-range range of traits. The aim of the present study was to characterize a collection of durum wheat landraces from Sicily, using single nucleotide polymorphisms (SNP) markers, together with agro-morphological, phenological and quality-related traits. Two modern cv. Simeto, Claudio, and the hexaploid landrace, Cuccitta, were used as outgroups. Cluster analysis and Principal Coordinates Analysis (PCoA) allowed us to identify four main clusters across the analyzed germplasm, among which a cluster included only historical and modern varieties. Likewise, structure analysis was able to distinguish the ancient varieties from the others, grouping the entries in seven cryptic genetic clusters. Furthermore, a Principal Component Analysis (PCA) was able to separate the modern testers from the ancient germplasm. This approach was useful to classify and evaluate Sicilian ancient wheat germplasm, supporting their safeguard and providing a genetic fingerprint that is necessary for avoiding commercial frauds to sustaining the economic profits of farmers resorting to landraces cultivation.

scholarly journals A comparative analysis of proximity measures to determine the Lithuanian population structure

2021 ◽  
Vol 62 ◽  
pp. 86-93
Author(s):  
Alma Molytė ◽  
Alina Urnikytė
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Comparative Analysis ◽  
Multidimensional Scaling ◽  
Principal Component ◽  
Genetic Data ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Proximity Measures

In this paper the multidimensional scaling, the principal coordinate and principal component methods for the Lithuanian population structure have investigated, taken that the proximity measures are Euclid, Gower, Bray-Curtis, Kulczynski, Jaccard and Morisita. The genome-wide single nucleotide polymorphism genetic data analyzed. A comparative analysis of proximity measures performed. The results of visualization are also presented.

scholarly journals Evaluating the Predictive Power of Ordination Methods in Ecological Context

Mathematics ◽  
2018 ◽  
Vol 6 (12) ◽  
pp. 295 ◽  
Author(s):  
Otto Wildi
Keyword(s):  
Goodness Of Fit ◽  
Optimal Choice ◽  
Alternative Methods ◽  
Site Factors ◽  
Real World Data ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Ordination Methods ◽  
Principal Coordinates ◽  
Almost All

When striving for the ordination methods best predicting independently measured site factors, the following questions arise: does the optimal choice depend on the kind of biological community analysed? Are there different ordination methods needed to address different site factors? Simultaneously, I explore alternative similarity approaches of entire ordinations, as well as the role of the transformations applied to the scale used in measuring species performance. The combination of methods and data transformations results in 96 alternative solutions for any one data set. These are compared by a graphical display, that is, an ordination of ordinations. The goodness-of-fit of independently measured site factors is assessed by two alternative methods. The resulting 96 performance values serve as independent variables in trend surfaces overlaid to the ordination of ordinations. The results from two real-world data sets indicate that some ordination methods greatly vary with data transformation. Scores close to a binary scale perform best in almost all ordination methods. Methods that intrinsically constrain the range of species scores, such as principal components analysis based on correlation, correspondence analysis (including its detrended version), nonmetric multidimensional scaling, as well as principal coordinates analysis based on the Bray-Curtis distance, always figure among the most successful methods, irrespective of data used.

Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Zhao-Wei Liu ◽  
Robert L. Jarret ◽  
Ronny R. Duncan ◽  
Stephen Kresovich
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Seashore Paspalum ◽  
Principal Coordinates ◽  
Paspalum Vaginatum ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

scholarly journals Comparative Analysis of Gut Microbiota in Captive and Wild Oriental White Storks: Implications for Conservation Biology

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Wu ◽  
Fang-Ting Wu ◽  
Qi-Hai Zhou ◽  
Da-Peng Zhao
Keyword(s):  
Community Structure ◽  
Comparative Analysis ◽  
Gut Microbiota ◽  
Species Composition ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Α Diversity ◽  
White Storks

The oriental white stork (Ciconia boyciana) is considered an endangered species based on the International Union for Conservation of Nature (IUCN) Red List. This study presents the first evidence on comparative analysis of gut microbial diversity of C. boyciana from various breeding conditions. To determine the species composition and community structure of the gut microbiota, 24 fecal samples from Tianjin Zoo and Tianjin Qilihai Wetland were characterized by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Firmicutes was found to be the predominant phylum. Analysis of community structure revealed significant differences in the species diversity and richness between the populations of the two breeding conditions. The greatest α-diversity was found in wild C. boyciana, while artificial breeding storks from Tianjin Zoo had the least α-diversity. Principal coordinates analysis showed that the microbial communities were different between the two studied groups. In conclusion, this study reveals the species composition and structure of the gut microbiota of oriental white storks under two breeding conditions, and our findings could contribute to the integrative conservation of this endangered bird.

scholarly journals Taxonomic revision of Ceropegia sec. Huernia (Asclepiadoideae – Apocynaceae) in Saudi Arabia with four new combinations

2020 ◽  
Author(s):  
Samah Alharbi ◽  
Rahmah Al Qthanin
Keyword(s):  
Saudi Arabia ◽  
Principal Component ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
New Combinations ◽  
Principal Coordinates Analysis ◽  
Distribution Maps ◽  
Principal Coordinates ◽  
Conservation Assessments ◽  
Iucn Criteria

This study provides a taxonomic revision for Ceropegia sec. Huernia in the flora of Saudi Arabia. Forty-eight quantitative and qualitative morphological characters were analysed using principal component analysis (PCA), principal coordinates analysis (PCoA) and the unweighted pairs group using mean average (UPGMA) to separate and help delimit taxa. We proposed to reduce the number of names reported in Saudi Arabia from 11 to four species: C. arabica comb. nov.,C. Khalidbinsultanii comb. nov., C. laevis and C. lodarensis. This study also suggested reducing two of Plowes’ new names to a variety level under C. lodarensis (var. foetida comb. nov. and var. rubrosticta comb. nov.). A key to the species, detailed morphological descriptions, illustrations, distribution maps, ecology, etymology and preliminarily conservation assessments following IUCN criteria are provided.

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