Morphological evaluation of common bean diversity in Bosnia and Herzegovina using the discriminant analysis of principal components (DAPC) multivariate method

In order to analyze morphological characteristics of locally cultivated common bean landraces from Bosnia and Herzegovina (B&H), thirteen quantitative and qualitative traits of 40 P. vulgaris accessions, collected from four geographical regions (Northwest B&H, Northeast B&H, Central B&H and Sarajevo) and maintained at the Gene bank of the Faculty of Agriculture and Food Sciences in Sarajevo, were examined. Principal component analysis (PCA) showed that the proportion of variance retained in the first two principal components was 54.35%. The first principal component had high contributing factor loadings from seed width, seed height and seed weight, whilst the second principal component had high contributing factor loadings from the analyzed traits seed per pod and pod length. PCA plot, based on the first two principal components, displayed a high level of variability among the analyzed material. The discriminant analysis of principal components (DAPC) created 3 discriminant functions (DF), whereby the first two discriminant functions accounted for 90.4% of the variance retained. Based on the retained DFs, DAPC provided group membership probabilities which showed that 70% of the accessions examined were correctly classified between the geographically defined groups. Based on the taxonomic distance, 40 common bean accessions analyzed in this study formed two major clusters, whereas two accessions Acc304 and Acc307 didn?t group in any of those. Acc360 and Acc362, as well as Acc324 and Acc371 displayed a high level of similarity and are probably the same landrace. The present diversity of Bosnia and Herzegovina?s common been landraces could be useful in future breeding programs.

Download Full-text

Comparison of Principal Component Solutions in Two Populations

Methodology ◽

10.1027/1614-2241/a000099 ◽

2016 ◽

Vol 12 (1) ◽

pp. 11-20 ◽

Cited By ~ 1

Author(s):

Gregor Sočan

Keyword(s):

Simulation Study ◽

Principal Components ◽

Common Factor ◽

Principal Component ◽

Component Model ◽

Bootstrap Procedure ◽

Factor Loadings ◽

Component Loadings ◽

Principal Component Model ◽

Two Populations

Abstract. When principal component solutions are compared across two groups, a question arises whether the extracted components have the same interpretation in both populations. The problem can be approached by testing null hypotheses stating that the congruence coefficients between pairs of vectors of component loadings are equal to 1. Chan, Leung, Chan, Ho, and Yung (1999) proposed a bootstrap procedure for testing the hypothesis of perfect congruence between vectors of common factor loadings. We demonstrate that the procedure by Chan et al. is both theoretically and empirically inadequate for the application on principal components. We propose a modification of their procedure, which constructs the resampling space according to the characteristics of the principal component model. The results of a simulation study show satisfactory empirical properties of the modified procedure.

Download Full-text

Morphometrics and paleoecology of Catenipora (Tabulata) from the Xiazhen Formation (Upper Ordovician), Zhuzhai, South China

Journal of Paleontology ◽

10.1017/jpa.2016.60 ◽

2016 ◽

Vol 90 (6) ◽

pp. 1027-1048 ◽

Cited By ~ 7

Author(s):

Kun Liang ◽

Robert J. Elias ◽

Suk-Joo Choh ◽

Dong-Chan Lee ◽

Dong-Jin Lee

Keyword(s):

Discriminant Analysis ◽

Geometric Morphometrics ◽

South China ◽

Morphological Characteristics ◽

Principal Component ◽

Morphological Characters ◽

Depositional Environments ◽

Heterogeneous Environments ◽

Upper Ordovician ◽

Species Specific

AbstractCatenipora is one of the most common tabulate coral genera occurring in various lithofacies in the Upper Ordovician Xiazhen Formation at Zhuzhai in South China. A combination of traditional multivariate analysis and geometric morphometrics is applied to a large number of specimens to distinguish and identify species. Based on three major principal components extracted from 11 morphological characters, three major groups as determined by the cluster-analysis dendrogram are considered to be morphospecies. Their validity and distinctiveness are confirmed by discriminant analysis, descriptive statistics, and bivariate plots. Tabularium area and common wall thickness are the most meaningful characters to distinguish the three morphospecies. Geometric morphometrics is adopted to compare the morphospecies with types and/or figured specimens of species previously reported from the vicinity of Zhuzhai. Despite discrepancies in corallite size, principal component analysis and discriminant analysis, as well as consideration of overall morphological characteristics, indicate that the morphospecies represent C. zhejiangensis Yu in Yu et al., 1963, C. shiyangensis Lin and Chow, 1977, and C. dianbiancunensis Lin and Chow, 1977.Catenipora occurs in seven stratigraphic intervals in the Xiazhen Formation at Zhuzhai, representing a variety of heterogeneous environments. The coralla preservation is variable due to differential compaction; coralla preserved in limestones are commonly intact and in growth position, whereas those in shales are mostly crushed or fragmentary. The size and shape of corallites are considered primarily to be species-specific characters, but are also related to the depositional environments. In all species, morphological characters, including corallite size, septal development, and shape and size of lacunae, show high variability in accordance with lithofacies and stratigraphic position. The intraspecific differences in corallite size at various localities in the Zhuzhai area may indicate responses to local environmental factors, but may also reflect genetic differences if there was limited connection among populations.

Download Full-text

Using the Method of Principal Components and Discriminant Analysis with Aim of Simplifying the Selection of Analogue Object for New Area

Oil and Gas technologies ◽

10.32935/1815-2600-2021-133-2-42-46 ◽

2021 ◽

Vol 133 (2) ◽

pp. 42-46

Author(s):

R. I. Bulatov ◽

Keyword(s):

Discriminant Analysis ◽

Discriminant Function ◽

Principal Components ◽

Principal Component ◽

Physical Parameters ◽

Principal Component Method ◽

Component Method ◽

Method Of Principal Components ◽

New Development ◽

Selection Of

The article discusses the main geo-physical parameters from 66 development objects. This data is analyzed using component and discriminant analysis methods. Using the principal component method, relatively homogeneous analog groups are distinguished, and discriminant analysis is used to derive the discriminant function and its constants. Based on the values of this function and constants, the new development object is assigned to the analog group.

Download Full-text

MORPHOMETRIC CHARACTER AND MORPHOLOGY OF ABALONE Haliotis squamata REEVE 1864 IN COASTAL SOUTHERN JAVA AND BALI

Jurnal Ilmu dan Teknologi Kelautan Tropis ◽

10.29244/jitkt.v11i2.24672 ◽

2019 ◽

Vol 11 (2) ◽

pp. 273-284

Author(s):

Syamsul Bachry ◽

Dedy Duryadi Solihin ◽

Rudhy Gustiano ◽

Kadarwan Soewardi ◽

Nurlisa A. Butet

Keyword(s):

Discriminant Analysis ◽

Sampling Method ◽

Morphological Characteristics ◽

Principal Component ◽

Canonical Discriminant Analysis ◽

Shell Morphology ◽

Morphometric Character ◽

Color Patterns ◽

And Cluster Analysis ◽

Key Characters

The standard of measurement of abalone is very important because it can help to identify accurately abalone shellfish based on shell morphology. This research was aimed to examine the truss morphometric and morphologycal characters of Haliotis squamata intraspecies in the southern coastal Java and Bali. The research was conducted from December 2014 to August 2016. Abalone was collected based on the purposive sampling method, it was then identified. The shellfish of abalone was measured and analyzed by using principal component analysis (PCA), canonical discriminant analysis and cluster analysis. The results showed that PCA was able to separate Haliotis squamata populations from Java and Bali using combination of PCIII and PCIV based on the factor coefficient values. The key characters that separated Haliotis squamata from the population of Java and Bali were the combination of characters BF (0.535) for PCIII and characters CH (0.522) for PCIV. Canonical discriminant analysis showed that Bali was the highest sharing component value (100%) of intra population and also the lowest sharing component of inter population (0%). The highest percentage of similarity was 99.91% that indicated the population of Binuangeun and Pangandaran, while the lowest was 99.31% for the population of Banyuwangi and Bali. The morphological characteristics of Haliotis squamata species in several locations showed specific characters such as color patterns, textures and shapes.

Download Full-text

Classification of cannabis strains in the Canadian market with discriminant analysis of principal components using genome-wide single nucleotide polymorphisms

PLoS ONE ◽

10.1371/journal.pone.0253387 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0253387

Author(s):

Dan Jin ◽

Philippe Henry ◽

Jacqueline Shan ◽

Jie Chen

Keyword(s):

Discriminant Analysis ◽

Single Nucleotide Polymorphisms ◽

Principal Components ◽

Large Scale ◽

Therapeutic Potential ◽

Morphological Characteristics ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide

The cannabis community typically uses the terms “Sativa” and “Indica” to characterize drug strains with high tetrahydrocannabinol (THC) levels. Due to large scale, extensive, and unrecorded hybridization in the past 40 years, this vernacular naming convention has become unreliable and inadequate for identifying or selecting strains for clinical research and medicinal production. Additionally, cannabidiol (CBD) dominant strains and balanced strains (or intermediate strains, which have intermediate levels of THC and CBD), are not included in the current classification studies despite the increasing research interest in the therapeutic potential of CBD. This paper is the first in a series of studies proposing that a new classification system be established based on genome-wide variation and supplemented by data on secondary metabolites and morphological characteristics. This study performed a whole-genome sequencing of 23 cannabis strains marketed in Canada, aligned sequences to a reference genome, and, after filtering for minor allele frequency of 10%, identified 137,858 single nucleotide polymorphisms (SNPs). Discriminant analysis of principal components (DAPC) was applied to these SNPs and further identified 344 structural SNPs, which classified individual strains into five chemotype-aligned groups: one CBD dominant, one balanced, and three THC dominant clusters. These structural SNPs were all multiallelic and were predominantly tri-allelic (339/344). The largest portion of these SNPs (37%) occurred on the same chromosome containing genes for CBD acid synthases (CBDAS) and THC acid synthases (THCAS). The remainder (63%) were located on the other nine chromosomes. These results showed that the genetic differences between modern cannabis strains were at a whole-genome level and not limited to THC or CBD production. These SNPs contained enough genetic variation for classifying individual strains into corresponding chemotypes. In an effort to elucidate the confused genetic backgrounds of commercially available cannabis strains, this classification attempt investigated the utility of DAPC for classifying modern cannabis strains and for identifying structural SNPs.

Download Full-text

DIVERGÊNCIA GENÉTICA ENTRE GENÓTIPOS DE Mauritia flexuosa L. f. POR MEIO DE MORFOMETRIA DE FRUTOS E SEMENTES

Nativa ◽

10.31413/nativa.v8i4.8622 ◽

2020 ◽

Vol 8 (4) ◽

pp. 585-590

Author(s):

Rosimeire Barboza Bispo ◽

Juliana de Freitas Encinas Dardengo ◽

Rosimara Barboza Bispo ◽

Rosieli Barboza Bispo ◽

Ana Aparecida Bandini Rossi

Keyword(s):

Principal Component Analysis ◽

Genetic Variability ◽

Principal Components ◽

Morphological Characteristics ◽

Principal Component ◽

Optimization Method ◽

Mato Grosso ◽

Upgma Dendrogram ◽

Mauritia Flexuosa ◽

Formation Of Groups

O objetivo do estudo foi caracterizar a variabilidade genética entre vinte genótipos de butiris (M. flexuosa L.f.) em vegetação natural nos municípios de Alta Floresta e Carlinda, MT, com base nas características morfológicas dos frutos e sementes, com o método de Otimização de Tocher, UPGMA e Análise de Componentes Principais. Foram amostrados 20 genótipos e avaliadas 8 caracteres morfológicos dos frutos e sementes. Os resultados foram obtidos através de medidas de Dissimilaridade, com o uso do programa GENES. O método de Tocher formou dois grupos, assim como o agrupamento UPGMA com corte a 80%. Com os Componentes Principais houve a formação de três grupos. As três metodologias utilizadas revelaram que existe divergência genética entre os vinte genótipos de buritis avaliados. A divergência evidenciada neste trabalho permite inferir que para melhor representar a diversidade encontrada em M. flexuosa deve-se amostrar indivíduos pertencentes aos três grupos formados pela dispersão gráfica dos componentes principais, já que o dendrograma UPGMA também evidencia essa classificação, assim, pode-se indicar essas árvores para futuras pesquisas de melhoramento e conservação da espécie. Palavras-chave: buriti; marcadores morfológicos; variabilidade genética. GENETIC DIVERGENCE AMONG Mauritia flexuosa L. f. GENOTYPES BASED ON SEED AND FRUIT MORPHOMETRY ABSTRACT: The objective of the study was to characterize the genetic variability among twenty genotypes of M. flexuosa L. f. in natural vegetation in the municipalities of Alta Floresta and Carlinda, Mato Grosso state, Brazil, based on the morphological characteristics of the fruits and seeds, with the Tocher Optimization method, UPGMA and Principal Component Analysis. Twenty genotypes were sampled and eight morphological characteristics of fruits and seeds were evaluated. The results were based on the Dissimilarities Measures methodology, using the GENES program. The Tocher method formed two groups, as well as the UPGMA cluster with 80% cut. The Principal Components formed three groups. All methods used showed agreement on the formation of groups. The divergence presented in this research allows us to infer that in order to better represent the diversity found in M. flexuosa, individuals belonging to the three groups formed by the graphic dispersion of the principal components must be sampled, since the UPGMA dendrogram also shows this classification, so we indicate these trees for future breeding and conservation researches. Keywords: buriti; morphological characteristics; genetic variability.

Download Full-text

PATTERN OF VARIATIONS AMONGST SWEET CORN GENOTYPES GROWN UNDER ORGANIC ENVIRONMENT

10.31219/osf.io/qch2w ◽

2017 ◽

Author(s):

Mohammad Chozin ◽

Sigit Sudjatmiko ◽

Zainal Muktamar ◽

Nanik Setyowati

Keyword(s):

Principal Components ◽

Sweet Corn ◽

Morphological Characteristics ◽

Principal Component ◽

Farming Systems ◽

Farming System ◽

Organic Production ◽

Growth And Yield ◽

Marketable Yield ◽

Eigen Values

Status: PostprintCurrently, organic sweet corn growers depend on varieties bred for intensive farming systems. The present study was addressed to elucidate the pattern of variations among 20 sweet corn genotypes under organic farming system and to classify them into distinct groups on the basis of their agro-morphological characteristics. Data were collected from two growing seasons for growth and yield characteristic and subjected to univariate and multivariate analyses. Combined analysis of variance across two seasons revealed that tasseling date, harvesting date, kernel row number, and marketable yield exhibited significant season x genotype interaction effect, while the rest of the observed characters showed significant both season and genotype effects. Principal component analysis showed that first season data had first three principal components with Eigen values > 1 accounted 82% of the total variation, while second season data had first two principal components with Eigen values > 1 accounted for 79%. In both seasons, ear length, ear diameter, ear weight, and marketable yield were the most important characters in first principal component. Based on cluster analysis, the genotypes could be classified into 5 clusters for both seasons. These results can be used by the growers in deciding the most suitable sweet corn variety for organic production.

Download Full-text

Taxonomic studies on the Chara section Hartmania in Poland based on morphological and molecular data

PhytoKeys ◽

10.3897/phytokeys.135.36714 ◽

2019 ◽

Vol 135 ◽

pp. 71-90

Author(s):

Jacek Urbaniak ◽

Paweł Kwiatkowski

Keyword(s):

Discriminant Analysis ◽

Morphological Characteristics ◽

Principal Component ◽

Taxonomic Status ◽

Component Analysis ◽

Molecular Data ◽

Morphological Features ◽

Green Macroalgae ◽

Molecular Group ◽

Water Ecosystems

Charophytes are aquatic green macroalgae, which inhabit fresh and brackish water ecosystems. In this study, four species belonging to the genus Chara were examined to determine their taxonomic status. Morphological characteristics of the plant bodies as well as plastid psaB barcoding genes were applied to test the relations among Chara species. Plants were initially classified using morphological features into four species: C. baltica, C. hispida, C. polyacantha and C. rudis, and twelve quantitative characters were used in a principal component analysis and discriminant analysis to determine groupings among the species and to determine the morphological features that best separated the groups. In the component analysis and discriminant analysis, results showed that only C. polyacantha and partly C. baltica formed separate groups. The other species C. hispida and C. rudis were only partially distinguishable. All species from one molecular group, and no differentiation in the psaB variability between them has been found.

Download Full-text

Use of morphological differences for the identification of two picarel species Spicara flexuosa and Spicara maena (Pisces: Centracanthidae)

Mediterranean Marine Science ◽

10.12681/mms.423 ◽

2013 ◽

Vol 14 (3) ◽

pp. 26 ◽

Cited By ~ 1

Author(s):

G. MINOS ◽

A. IMSIRIDOU ◽

G. KATSELIS

Keyword(s):

Principal Component Analysis ◽

Discriminant Analysis ◽

Principal Component ◽

The Body ◽

Head Length ◽

Maturity Stage ◽

Morphometric Features ◽

Morphological Differences ◽

Head Height ◽

High Level

The recognition and identification of the two species of Spicara genus (Spicara flexuosa, picarel and Spicara maena, blotched picarel) is difficult, due to a systematic confusion until now. In the present work a number of external morphometric features (ten body ratios) are evaluated for their diagnostic possibilities. According to Principal Component Analysis results, the body ratios head length to standard length, head height to head length and the ratios of two body heights, indicated that these characters were not related to the maturity stage of the species. The discriminant analysis based on the above body ratios, indicated rather high level of discrimination (83.2%) of the examined samples in two species. The results are discussed, and possibilities of improvement in the identification methodology for the two species are proposed.

Download Full-text

Structuring Assessments of Psychopathology

Journal of Individual Differences ◽

10.1027/1614-0001.27.2.87 ◽

2006 ◽

Vol 27 (2) ◽

pp. 87-92 ◽

Cited By ~ 2

Author(s):

Willem K.B. Hofstee ◽

Dick P.H. Barelds ◽

Jos M.F. Ten Berge

Keyword(s):

Principal Components ◽

Personality Assessment ◽

Clinical Sample ◽

Principal Component ◽

Normal Sample ◽

Normative Sample ◽

Assessment Data ◽

Obsessive Compulsive ◽

Oblique Rotation ◽

Two Samples

Hofstee and Ten Berge (2004a) have proposed a new look at personality assessment data, based on a bipolar proportional (-1, .. . 0, .. . +1) scale, a corresponding coefficient of raw-scores likeness L = ΢XY/N, and raw-scores principal component analysis. In a normal sample, the approach resulted in a structure dominated by a first principal component, according to which most people are faintly to mildly socially desirable. We hypothesized that a more differentiated structure would arise in a clinical sample. We analyzed the scores of 775 psychiatric clients on the 132 items of the Dutch Personality Questionnaire (NPV). In comparison to a normative sample (N = 3140), the eigenvalue for the first principal component appeared to be 1.7 times as small, indicating that such clients have less personality (social desirability) in common. Still, the match between the structures in the two samples was excellent after oblique rotation of the loadings. We applied the abridged m-dimensional circumplex design, by which persons are typed by their two highest scores on the principal components, to the scores on the first four principal components. We identified five types: Indignant (1-), Resilient (1-2+), Nervous (1-2-), Obsessive-Compulsive (1-3-), and Introverted (1-4-), covering 40% of the psychiatric sample. Some 26% of the individuals had negligible scores on all type vectors. We discuss the potential and the limitations of our approach in a clinical context.

Download Full-text