scholarly journals GENETIC DISTANCES BASED ON QUANTITATIVE TRAITS

Genetics ◽  
1985 ◽  
Vol 111 (4) ◽  
pp. 945-962
Author(s):  
A Camussi ◽  
E Ottaviano ◽  
T Calinski ◽  
Z Kaczmarek
Keyword(s):  
Evolutionary Biology ◽  
Genetic Parameters ◽  
Distance Matrix ◽  
Genetic Distances ◽  
Point Of View ◽  
Linear Functions ◽  
Morphological Data ◽  
Phenotypic Data ◽  
Statistical Estimates ◽  
Distance Analysis

ABSTRACT Morphological data showing continuous distributions, polygenically controlled, may be particularly useful in intergroup classification below the species level; an appropriate distance analysis based on these traits is an important tool in evolutionary biology and in plant and animal breeding.—The interpretation of morphological distances in genetic terms is not easy because simple phenotypic data may lead to biased estimates of genetic distances. Convenient estimates can be obtained whenever it is possible to breed populations according to a suitable crossing design and to derive information from genetic parameters.—A general method for determining genetic distances is proposed. The procedure of multivariate analysis of variance is extended to estimate appropriate genetic parameters (genetic effects). Not only are optimal statistical estimates of parameters obtained but also the procedure allows the measurement of genetic distances between populations as linear functions of the estimated parameters, providing an appropriate distance matrix that can be defined in terms of these parameters. The use of the T  2 statistic, defined in terms of the vector of contrasts specifying the distance, permits the testing of the significance of any distance between any pair of populations that may be of interest from a genetic point of view.—A numerical example from maize diallel data is reported in order to illustrate the procedure. In particular, heterosis effects are used as the basis for estimates of genetic divergence between populations.

scholarly journals Species Relationship and Population Differentiation In Stellaria L. (Caryophyllaceae) Of Iran Using Scot Molecular Marker and Morphological Data

2021 ◽  
Vol 28 (2) ◽  
pp. 317-328
Author(s):  
Jialing Li ◽  
Xin Yang ◽  
Shadi Hajrasouliha
Keyword(s):  
Genetic Parameters ◽  
Genetic Distances ◽  
Morphological Data ◽  
Jaccard Similarity ◽  
Descriptive Data ◽  
Broad Distribution ◽  
Species Relationship ◽  
Genetic Characteristics ◽  
Plant Taxon ◽  
Morphological Research

Recognition of species is essential in a variety of domains, most remarkably biology, biogeography, ecology, as well as conservation. The genus Stellaria L. (Caryophyllaceae) has over 120 species spread across Europe and Asia's temperate zones. According to the most remarkable current treatments, nine species recognize Stellaria in Iran. These species are categorized into two types. Despite the broad distribution of several Stellaria species in Iran, no research on their genetic variability, method of divergence, or dispersion trends is accessible. As a result, we conducted genetic and morphological research on six Stellaria species and two of their closest relatives gathered from various habitats in Iran. This research aims to 1) Can SCoT markers be utilized to recognize Stellaria species? 2) What are the genetic characteristics of the mentioned taxa in Iran? and 3) To examine the interrelation of the species. In this research, ten SCoT markers were employed for molecular analysis, and 112 accessions were utilized for morphological study. The genetic distances were calculated using the Jaccard similarity coefficient, and descriptive data on the populations were used to estimate genetic parameters. There were 98 polymorphic bands all over. The integration of morphological and SCoT data demonstrated that the Stellaria species of Iran could be delimited and recognized. The Stellaria species are genetically unique; however, they share some similar alleles, according to AMOVA and STRUCTURE analyses. Bangladesh J. Plant Taxon. 28(2): 317-328, 2021 (December)

Selective statistical estimates of multi-year monthly concentrations of biogenous pollution of small rivers of the Northwest zone of the Russian Federation

2020 ◽  
pp. 9-13
Author(s):  
Sergey Kovalenko
Keyword(s):  
Statistical Processing ◽  
Point Of View ◽  
Small Rivers ◽  
Statistical Parameters ◽  
Monthly Data ◽  
Statistical Estimates ◽  
Scientific Task ◽  
The Russian Federation ◽  
Agricultural Areas

The management of surface watercourses is an urgent scientific task. The article presents the results of statistical processing of long-term monthly data of field observations of hydrological and hydrochemical parameters along the Upper Yerga small river in the Vologda region. Sampling estimates of statistical parameters are obtained, autocorrelation and correlation analyzes are performed. The limiting periods from the point of view of pollution for water receivers receiving wastewater from drained agricultural areas are identified.

scholarly journals Combination of nuclear and mitochondrial markers as a useful tool to identify Ctenophthalmus species and subspecies (Siphonaptera: Ctenophthalmidae)

2021 ◽  
Author(s):  
Antonio Zurita ◽  
Cristina Cutillas
Keyword(s):  
Taxonomic Status ◽  
Molecular Study ◽  
Molecular Data ◽  
Point Of View ◽  
Morphological Data ◽  
Molecular Approach ◽  
Nuclear Marker ◽  
Mitochondrial Markers ◽  
Morphological Criteria ◽  
Mtdna Markers

AbstractCtenophthalmus is considered the largest genus within the Order Siphonaptera. From a morphological point of view, only males of this genus can be identified at species and subspecies levels using morphological keys, whereas there are no morphological criteria in order to classify females at these taxonomical levels. Furthermore, the amount of available molecular and phylogenetic data for this genus is quite scarce so far. The main objective of this work was to assess the utility of the combination of nuclear and mitochondrial markers with respect to their ability to differentiate among different subspecies within the Ctenophthalmus genus. With this purpose, we carried out a comparative morphological and molecular study of three different subspecies (Ctenophthalmus baeticus arvernus, Ctenophthalmus nobilis dobyi, and Ctenophthalmus andorrensis catalaniensis) in order to clarify and discuss its taxonomic status. In addition, our study complemented the molecular data previously provided for Ctenophthalmus baeticus boisseauorum and Ctenophthalmus apertus allani subspecies. We sequenced five different molecular markers: EF1-α, ITS1, ITS2, cox1, and cytb. Our results confirmed that morphological data by themselves are not able to discriminate among Ctenophthalmus female taxa; however, the combination of the nuclear marker EF1-α together with mtDNA markers cytb and cox1 constituted a useful taxonomical and phylogenetic tool to solve this issue. Based on these results, we consider that the use of this molecular approach should be gradually used within Ctenophthalmus genus in order to complement its classical taxonomy and clarifying the complex taxonomy of other congeneric species of fleas.

Methods for Studying Morphological Integration and Modularity

2010 ◽  
Vol 16 ◽  
pp. 213-243 ◽  
Author(s):  
Anjali Goswami ◽  
P. David Polly
Keyword(s):  
Distance Matrix ◽  
Japanese Macaques ◽  
Morphological Integration ◽  
Matrix Analysis ◽  
Euclidean Distance Matrix ◽  
Phenotypic Data ◽  
Graphical Modelling ◽  
Landmark Data ◽  
Competing Models ◽  
Matrix Correlation

Morphological integration and modularity are closely related concepts about how different traits of an organism are correlated. Integration is the overall pattern of intercorrelation; modularity is the partitioning of integration into evolutionarily or developmentally independent blocks of traits. Modularity and integration are usually studied using quantitative phenotypic data, which can be obtained either from extant or fossil organisms. Many methods are now available to study integration and modularity, all of which involve the analysis of patterns found in trait correlation or covariance matrices. We review matrix correlation, random skewers, fluctuating asymmetry, cluster analysis, Euclidean distance matrix analysis (EDMA), graphical modelling, two-block partial least squares, RV coefficients, and theoretical matrix modelling and discuss their similarities and differences. We also review different coefficients that are used to measure correlations. We apply all the methods to cranial landmark data from and ontogenetic series of Japanese macaques,Macaca fuscatato illustrate the methods and their individual strengths and weaknesses. We conclude that the exploratory approaches (cluster analyses of various sorts) were less informative and less consistent with one another than were the results of model testing or comparative approaches. Nevertheless, we found that competing models of modularity and integration are often similar enough that they are not statistically distinguishable; we expect, therefore, that several models will often be significantly correlated with observed data.

scholarly journals Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243853
Author(s):  
Berline Fopa Fomeju ◽  
Dominique Brunel ◽  
Aurélie Bérard ◽  
Jean-Baptiste Rivoal ◽  
Philippe Gallois ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Genetic Distances ◽  
Lavandula Angustifolia ◽  
Distance Analysis ◽  
Alternative Medicines ◽  
Dna And Rna ◽  
Snp Development ◽  
High Level

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

scholarly journals Cancer metabolic subtypes and their association with molecular and clinical features

2021 ◽  
Author(s):  
Enrico Moiso ◽  
Paolo Provero
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Tumor Grade ◽  
Point Of View ◽  
General Point ◽  
Protein Abundance ◽  
Phenotypic Data ◽  
Cancer Subtypes ◽  
Molecular Features

Alteration of metabolic pathways in cancer has been investigated for many years, beginning way before the discovery of the role of oncogenes and tumor suppressors, and the last few years have witnessed a renewed interest in this topic. Large-scale molecular and clinical data on tens of thousands of samples allow us today to tackle the problem from a general point of view. Here we show that trancriptomic profiles of tumors can be exploited to define metabolic cancer subtypes, that can be systematically investigated for association with other molecular and clinical data. We find thousands of significant associations between metabolic subtypes and molecular features such as somatic mutations, structural variants, epigenetic modifications, protein abundance and activation; and with clinical/phenotypic data including survival probability, tumor grade, and histological types. Our work provides a methodological framework and a rich database of statistical associations, accessible from https://metaminer.unito.it, that will contribute to the understanding of the role of metabolic alterations in cancer and to the development of precision therapeutic strategies.

scholarly journals Detecting selection with a genetic cross

2020 ◽  
Vol 117 (36) ◽  
pp. 22323-22330
Author(s):  
Hunter B. Fraser
Keyword(s):  
Skin Color ◽  
Evolutionary Biology ◽  
Neutral Evolution ◽  
Sign Test ◽  
Stabilizing Selection ◽  
Mrna Levels ◽  
Effective Population ◽  
Phenotypic Data ◽  
Genetic Cross ◽  
Selected Traits

Distinguishing which traits have evolved under natural selection, as opposed to neutral evolution, is a major goal of evolutionary biology. Several tests have been proposed to accomplish this, but these either rely on false assumptions or suffer from low power. Here, I introduce an approach to detecting selection that makes minimal assumptions and only requires phenotypic data from ∼10 individuals. The test compares the phenotypic difference between two populations to what would be expected by chance under neutral evolution, which can be estimated from the phenotypic distribution of an F2cross between those populations. Simulations show that the test is robust to variation in the number of loci affecting the trait, the distribution of locus effect sizes, heritability, dominance, and epistasis. Comparing its performance to the QTL sign test—an existing test of selection that requires both genotype and phenotype data—the new test achieves comparable power with 50- to 100-fold fewer individuals (and no genotype data). Applying the test to empirical data spanning over a century shows strong directional selection in many crops, as well as on naturally selected traits such as head shape in HawaiianDrosophilaand skin color in humans. Applied to gene expression data, the test reveals that the strength of stabilizing selection acting on mRNA levels in a species is strongly associated with that species’ effective population size. In sum, this test is applicable to phenotypic data from almost any genetic cross, allowing selection to be detected more easily and powerfully than previously possible.

scholarly journals Classification of Streptomyces griseus (Krainsky 1914) Waksman and Henrici 1948 and related species and the transfer of ‘Microstreptospora cinerea’ to the genus Streptomyces as Streptomyces yanii sp. nov.

2005 ◽  
Vol 55 (4) ◽  
pp. 1605-1610 ◽  
Author(s):  
Zhiheng Liu ◽  
Yanlin Shi ◽  
Yamei Zhang ◽  
Zhihong Zhou ◽  
Zhitang Lu ◽  
...  
Keyword(s):  
Streptomyces Griseus ◽  
Taxonomic Status ◽  
Morphological Data ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Genus Streptomyces ◽  
Actinomycete Strain ◽  
Soil Actinomycete

A soil actinomycete, strain 80-133T, with the non-validly published name ‘Microstreptospora cinerea’, was the subject of a polyphasic study designed to clarify its taxonomic status. Comparative 16S rRNA gene sequence studies indicated that the organism belonged to the genus Streptomyces, a result in line with previous chemotaxonomic and morphological data. The strain belonged to the Streptomyces griseus clade, but could be distinguished from representatives of species assigned to this taxon by using DNA–DNA relatedness and phenotypic data. In light of these findings, it is proposed that the organism should be recognized as a novel species of the genus Streptomyces. The name proposed for this taxon is Streptomyces yanii sp. nov., with isolate 80-133T (=AS 4.1146T=JCM 3331T) as the type strain. It was also shown that representative strains of Streptomyces argenteolus, Streptomyces caviscabies, S. griseus and Streptomyces setonii belong to the same genomic species and have key phenotypic properties in common. It is proposed that S. caviscabies and S. setonii should be considered as later heterotypic synonyms of S. griseus and that S. argenteolus AS 4.1693T should also be assigned to this taxon.

Evaluation of genetic distances between pepper inbred lines for cultivar protection purposes: comparison of AFLP, RAPD and phenotypic data

2001 ◽  
Vol 102 (5) ◽  
pp. 741-750 ◽  
Author(s):  
V. Lefebvre ◽  
B. Goffinet ◽  
J. C. Chauvet ◽  
B. Caromel ◽  
P. Signoret ◽  
...  
Keyword(s):  
Inbred Lines ◽  
Genetic Distances ◽  
Phenotypic Data

Phylogeny reconstruction and the tempo of speciation in cheilostome Bryozoa

Paleobiology ◽  
1994 ◽  
Vol 20 (4) ◽  
pp. 407-423 ◽  
Author(s):  
Jeremy B. C. Jackson ◽  
Alan H. Cheetham
Keyword(s):  
Effective Means ◽  
Morphological Variability ◽  
Genetic Distances ◽  
Morphological Data ◽  
Phylogeny Reconstruction ◽  
High Confidence ◽  
Skeletal Morphology ◽  
Living Species ◽  
Cladistic Analyses ◽  
Tight Correlation

We compared phylogenies derived from morphological data for two cheilostome bryozoan genera, Stylopoma and Metrarabdotos, with genetic differences between species (Stylopoma) and the stratigraphic occurrence of fossils (both genera). Correspondence between species of Stylopoma defined by protein electrophoresis and on preservable skeletal morphology is excellent, despite great morphological variability within colonies and the predominance of quantitative over discrete characters. Moreover, agreement between genetic and morphological classifications increased greatly when morphological discrimination was pushed to the limit, despite inability to consistently assign all specimens to species with high confidence. This “splitting” strategy also maximized the correlation between genetic distances and the distances between species in cladistically derived phylogenies.Fossil and living species of both genera are sufficiently abundant and widespread to provide credible limits for inferred ancestral relationships. Inclusion of fossils in cladistic analyses of Stylopoma increased the consistency of cladistic hypotheses by up to 30% and provided a more effective means of rooting trees than comparison with living species of the most closely related genus (“outgroup”). Moreover, in the case of Metrarabdotos, failure to incorporate stratigraphic information turned the cladogram virtually upside down, so that postulated ancestors first appear in the fossil record 6–16 m.y. after their putative descendants became extinct.Stratigraphically rooted trees suggest that most well-sampled Metrarabdotos and Stylopoma species originated fully differentiated morphologically and persisted unchanged for > 1 to > 16 m.y., typically alongside their putative ancestors. Moreover, the tight correlation between phenetic, cladistic, and genetic distances among living Stylopoma species suggests that changes in all three variables occurred together during speciation. All of these observations support the punctuated equilibrium model of speciation.

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