scholarly journals Discrimination ofPicea chihuahuanaMartinez populations on the basis of climatic, edaphic, dendrometric, genetic and population traits

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3452 ◽  
Author(s):  
Iliana Karina Dominguez-Guerrero ◽  
Samantha del Rocío Mariscal-Lucero ◽  
José Ciro Hernández-Díaz ◽  
Berthold Heinze ◽  
José Ángel Prieto-Ruiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Logistic Regression ◽  
Environmental Conditions ◽  
Clustering Algorithm ◽  
Optimal Number ◽  
Ex Situ ◽  
Background Information ◽  
Assisted Migration ◽  
Binomial Logistic Regression ◽  
The Mean

BackgroundPicea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. These populations are fragmented and can be classified into three geographically distinct clusters in the SMO. The total area covered byP. chihuahuanapopulations is less than 300 ha. A recent study suggested assisted migration as an alternative to theex situconservation ofP. chihuahuana, taking into consideration the genetic structure and diversity of the populations and the predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The genetic diversity of populations, which affect vigor, evolution and adaptability of the species, must also be considered. In this study, we examined 14 populations ofP.chihuahuana, with the overall aim of discriminating the populations and form clusters of this species.MethodsEach population was represented by one 50 × 50 m plot established in the center of its respective location. Climate, soil, dasometric, density variables and genetic and species diversities were assessed in these plots for further analyses. The putatively neutral and adaptive AFLP markers were used to calculate genetic diversity. Affinity Propagation (AP) clustering technique andk-means clustering algorithm were used to classify the populations in the optimal number of clusters. Later stepwise binomial logistic regression was applied to test for significant differences in variables of the southern and northernP. chihuahuanapopulations. Spearman’s correlation test was used to analyze the relationships among all variables studied.ResultsThe binomial logistic regression analysis revealed that seven climate variables, the geographical longitude and sand proportion in the soil separated the southern from northern populations. The northern populations grow in more arid and continental conditions and on soils with lower sand proportion. The mean genetic diversity using all AFLP studied ofP. chihuahuanawas significantly correlated with the mean temperature in the warmest month, where warmer temperatures are associated to larger genetic diversity. Genetic diversity ofP. chihuahuanacalculated with putatively adaptive AFLP was not statistically significantly correlated with any environmental factor.DiscussionFuture reforestation programs should take into account that at least two different groups (the northern and southern cluster) ofP. chihuahuanaexist, as local adaptation takes place because of different environmental conditions.

scholarly journals Discrimination of Picea chihuahuana Martinez populations on the basis of numerous dendrometric, climatic and edaphic traits and genetic diversity

2017 ◽  
Author(s):  
Iliana Karina Dominguez-Guerrero ◽  
Samantha Mariscal-Lucero ◽  
José Ciro Hernández-Díaz ◽  
Berthold Heinze ◽  
José Ángel Prieto-Ruiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Discriminant Analysis ◽  
Population Size ◽  
Environmental Conditions ◽  
Diversity Indices ◽  
Ex Situ ◽  
Assisted Migration ◽  
Tree Community ◽  
Southern Central ◽  
The Mean

Background. Picea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. The populations are fragmented and can be classified into three distinct clusters in the SMO of the two States (south, center and north), each group separated by a distance of about 300 km. The total area covered P. chihuahuana trees is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and also predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The vitality and genetic diversity of populations, which affect vigour, evolution and adaptability of the species, must also be considered. In this study, we examined the P. chihuahuana tree community growing in fourteen different locations, with the overall aim of discriminating the populations and clusters of this species using 22 climatic, 27 edaphic and 15 dasometric variables and three genetic diversity indices. Methods. Each location was represented by one 50 x 50 m plot established in the center of the location in which was measured the climate, soil, dasometric and genetic variables. The putative neutral and adaptive AFLP were used to calculate genetic diversity. Multivariate discriminant analysis including cross-validation was considered to test for significant differences in variables in the southern, central and northern populations and locations of the P. chihuahuana tree community. Spearman's correlation test was used to analyze the relationships between genetic diversity, population size, and the climatic, soil and dasometric variables. Results. The discriminant analysis revealed 22 highly significant variables, which separated the southern, central and northern populations. The mean genetic diversity of P. chihuahuana was significantly correlated with the mean temperature in the warmest month. Genetic diversity of P. chihuahuana calculated with putative adaptive AFLP was not statistically significantly correlated with any environmental factor. Finally, no significant correlations were observed between any of the three genetic diversity indices and population size. Discussion. At least three different ecotypes of P. chihuahuana probably exist, as local adaptation may take place because of the different environmental conditions. Therefore, future reforestation programs should take into account these different ecotypes and environmental conditions.

scholarly journals Discrimination of Picea chihuahuana Martinez populations on the basis of numerous dendrometric, climatic and edaphic traits and genetic diversity

2017 ◽  
Author(s):  
Iliana Karina Dominguez-Guerrero ◽  
Samantha Mariscal-Lucero ◽  
José Ciro Hernández-Díaz ◽  
Berthold Heinze ◽  
José Ángel Prieto-Ruiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Discriminant Analysis ◽  
Population Size ◽  
Environmental Conditions ◽  
Diversity Indices ◽  
Ex Situ ◽  
Assisted Migration ◽  
Tree Community ◽  
Southern Central ◽  
The Mean

Background. Picea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. The populations are fragmented and can be classified into three distinct clusters in the SMO of the two States (south, center and north), each group separated by a distance of about 300 km. The total area covered P. chihuahuana trees is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and also predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The vitality and genetic diversity of populations, which affect vigour, evolution and adaptability of the species, must also be considered. In this study, we examined the P. chihuahuana tree community growing in fourteen different locations, with the overall aim of discriminating the populations and clusters of this species using 22 climatic, 27 edaphic and 15 dasometric variables and three genetic diversity indices. Methods. Each location was represented by one 50 x 50 m plot established in the center of the location in which was measured the climate, soil, dasometric and genetic variables. The putative neutral and adaptive AFLP were used to calculate genetic diversity. Multivariate discriminant analysis including cross-validation was considered to test for significant differences in variables in the southern, central and northern populations and locations of the P. chihuahuana tree community. Spearman's correlation test was used to analyze the relationships between genetic diversity, population size, and the climatic, soil and dasometric variables. Results. The discriminant analysis revealed 22 highly significant variables, which separated the southern, central and northern populations. The mean genetic diversity of P. chihuahuana was significantly correlated with the mean temperature in the warmest month. Genetic diversity of P. chihuahuana calculated with putative adaptive AFLP was not statistically significantly correlated with any environmental factor. Finally, no significant correlations were observed between any of the three genetic diversity indices and population size. Discussion. At least three different ecotypes of P. chihuahuana probably exist, as local adaptation may take place because of the different environmental conditions. Therefore, future reforestation programs should take into account these different ecotypes and environmental conditions.

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

scholarly journals Comparison of two approaches for an estimation of the mean annual flood at ungauged sites in Slovakia

2020 ◽  
Vol 15 (2) ◽  
pp. 130-141
Author(s):  
Zuzana Németová ◽  
Silvia Kohnová ◽  
Romana Marková
Keyword(s):  
Clustering Algorithm ◽  
Optimal Number ◽  
Flood Frequency ◽  
Flood Frequency Analysis ◽  
Ungauged Sites ◽  
Index Flood ◽  
Regional Flood Frequency Analysis ◽  
The Mean ◽  
Essential Problem ◽  
Observation Period

AbstractRegional flood frequency analysis is considered to be an important and popular method for estimating different hydrological variables at ungauged sites. The estimation of the index flood is the essential problem when this method is applied. The objective of the study is a comparison of the estimation of the mean annual flood (or index flood) by using two approaches based on the ‘so-called’ index flood method and top-kriging. The concept behind these methods permits estimating the mean annual flood at ungauged locations using information taken from gauged sites located within the same homogeneous pooling groups. The study area comprises 104 gauging stations on the whole territory of Slovakia. The observation period of the annual maximum discharges of the selected stations was from 1961-2010. The identification of the homogeneous pooling group was performed using a non-hierarchical k-means clustering algorithm. The optimal number of clusters is determined by the Silhouette method. As a result, eight homogeneous pooling group clusters were identified. Finally, the results of the estimated mean annual floods using the index flood method and top-kriging were compared with the observed data. Top-kriging provided better results than the classical index flood method for estimating the mean annual flood at ungauged sites.

scholarly journals Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia

2021 ◽  
Vol 22 (10) ◽  
Author(s):  
Zulfahmi Zulfahmi ◽  
Parjanto Parjanto ◽  
Edi Purwanto ◽  
Ahmad Yunus
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Gene Diversity ◽  
In Situ Conservation ◽  
Genetic Material ◽  
Ex Situ ◽  
Breeding Programs ◽  
The Mean

Abstract. Zulfahmi, Parjanto, Purwanto E, Yunus A. 2021. Genetic diversity and population structure of Eurycoma apiculata in Eastern Sumatra, Indonesia. Biodiversitas 22: 4431-4439. Information on genetic variation within and among populations of Eurycoma apiculata plants is important to develop strategies for their conservation, sustainable use, and genetic improvement. To date, no information on genetic variation within and among populations of the E. apiculata has been reported. This study aims to assess genetic diversity within and among populations of E. apiculata based on RAPD markers, and to determine populations to collect E. apiculata genetic material for conservation and breeding programs. Young leaves of E. apiculata were collected from six natural populations. Fifteen RAPD primers were used to assess the genetic diversity of each population. The data obtained were analyzed with POPGEN and Arlequin software. The amplification results of 15 selected primers produced 3-16 loci with all primers 100% polymorphic. At the species level, the mean allele per locus (Na), number of effective alleles (Ne), percentage of polymorphic loci (PPL), Nei’s gene diversity index (He) and Shannon information index (I) were 2.000, 1.244, 100%, 0.167, and 0.286, respectively. At the population level, the mean values for Na, Ne, PPL, He and I were 1.393, 1.312, 39.27%, 0.119, and 0.186, respectively. The highest value of gene diversity within population (He) was found in the Lingga-1 population and the lowest value was found in the Rumbio population. The value of genetic differentiation among populations (GST) of E. apiculata is 0.284, consistent with the results of the AMOVA analysis which found that genetic variation among populations was 23.14%, indicates that the genetic variation of E. apiculata was more stored within populations than among populations. The gene flow (Nm) value of E. apiculata was 1.259 migrants per generation among populations. The Nm value of this species was high category, and could inhibit genetic differentiation among populations. The clustering of E. apiculata population based on the UPGMA dendrogram and PCA was inconsistent with its geographic distribution, reflecting the possibility that genes migration occurred between islands in the past. The main finding of this study was the genetic variation of the E. apiculata mostly stored within the population. Therefore, the population with the highest genetic diversity is a priority for in-situ conservation, and collection of E. apiculata genetic material for ex-situ conservation and breeding programs should be carried out minimum from Lingga-1 and Pokomo populations.

scholarly journals Genetic diversity of bushy cashew (Anacardium humile A. St.-Hil.) based on characteristics of fruits

2019 ◽  
Vol 41 (5) ◽  
Author(s):  
Laísse Danielle Pereira ◽  
Danielle Fabíola Pereira da Silva ◽  
Lásara Kamila Ferreira de Souza ◽  
Erick Tiago Lino Pereira ◽  
Hildeu Ferreira da Assunção ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Euclidean Distance ◽  
Descriptive Analysis ◽  
Physicochemical Characteristics ◽  
Ex Situ ◽  
Physical Chemical ◽  
Abstract Knowledge ◽  
The Mean ◽  
Measure Of Similarity ◽  
Selection Of

Abstract Knowledge of the genetic variability among genotypes of bushy cashew is important to establish strategies for pre-breeding and use in breeding program. The objective of this study was to evaluate the genetic diversity of bushy cashew by means of the evaluation of physical, chemical and physicochemical characteristics of cashew apples and cashew nuts. The work was carried out with cashew nuts and cashew apples collected in the harvest of 2016 of genotypes in the “ex situ” biological collection of Anacardium humile A. St.-Hil. in the area of genetic resources of the Universidade Federal de Goiás - Regional Jataí. The results were submitted to descriptive analysis and multivariate analysis, estimating the mean Euclidean distance obtained from the fruiting attributes analyzed. The measure of similarity and custering of the provenances was done by the optimization algorithm of Tocher and dendrograma UPGMA. There was a coincidence of clusters, which confirms the distribution of genetic diversity of the genotypes in the germplasm bank of Anacardium humileA. St.-Hil. evaluated. The results obtained can be used for the selection of individuals of the species in future works of breeding and conservation of the specie.

COLONY OF THE FUNGUS Aspergillus oryzae AND SELF-AFFINE FRACTAL GEOMETRY OF GROWTH FRONTS

Fractals ◽  
1993 ◽  
Vol 01 (01) ◽  
pp. 11-19 ◽  
Author(s):  
SHU MATSUURA ◽  
SASUKE MIYAZIMA
Keyword(s):  
Aspergillus Oryzae ◽  
Environmental Conditions ◽  
Fractal Geometry ◽  
Nutrient Concentration ◽  
Incubation Temperature ◽  
Characteristic Exponent ◽  
Growth Front ◽  
Favorable Condition ◽  
The Self ◽  
The Mean

A variety of colony shapes of the fungus Aspergillus oryzae under varying environmental conditions such as the nutrient concentration, medium stiffness and incubation temperature are obtained, ranging from a homogeneous Eden-like to a ramified DLA-like pattern. The roughness σ(l, h) of the growth front of the band-shaped colony, where h is the mean front height within l of the horizontal range, satisfies the self-affine fractal relation under favorable environmental conditions. In the most favorable condition of our experiments, its characteristic exponent is found to be a little larger than that of the 2-dimensional Eden model.

scholarly journals Recombination and Gene Conversion in a 170-kb Genomic Region of Arabidopsis thaliana

Genetics ◽  
2002 ◽  
Vol 161 (3) ◽  
pp. 1269-1278 ◽  
Author(s):  
Bernhard Haubold ◽  
Jürgen Kroymann ◽  
Andreas Ratzka ◽  
Thomas Mitchell-Olds ◽  
Thomas Wiehe
Keyword(s):  
Genetic Diversity ◽  
Arabidopsis Thaliana ◽  
Linkage Disequilibrium ◽  
Gene Conversion ◽  
Genomic Sequence ◽  
Genomic Region ◽  
Resistance To Herbivory ◽  
Linkage Disequilibria ◽  
Coalescent Simulations ◽  
The Mean

Abstract Arabidopsis thaliana is a highly selfing plant that nevertheless appears to undergo substantial recombination. To reconcile its selfing habit with the observations of recombination, we have sampled the genetic diversity of A. thaliana at 14 loci of ~500 bp each, spread across 170 kb of genomic sequence centered on a QTL for resistance to herbivory. A total of 170 of the 6321 nucleotides surveyed were polymorphic, with 169 being biallelic. The mean silent genetic diversity (πs) varied between 0.001 and 0.03. Pairwise linkage disequilibria between the polymorphisms were negatively correlated with distance, although this effect vanished when only pairs of polymorphisms with four haplotypes were included in the analysis. The absence of a consistent negative correlation between distance and linkage disequilibrium indicated that gene conversion might have played an important role in distributing genetic diversity throughout the region. We tested this by coalescent simulations and estimate that up to 90% of recombination is due to gene conversion.

scholarly journals COVID-19-Related Changes in Perceived Household Food Waste in the United States: A Cross-Sectional Descriptive Study

2021 ◽  
Vol 18 (3) ◽  
pp. 1104
Author(s):  
Kelly Cosgrove ◽  
Maricarmen Vizcaino ◽  
Christopher Wharton
Keyword(s):  
Logistic Regression ◽  
Food Waste ◽  
The United States ◽  
Food Groups ◽  
Related Factors ◽  
Cross Sectional ◽  
Household Level ◽  
Binomial Logistic Regression ◽  
Household Food ◽  
Fresh Vegetables

Food waste contributes to adverse environmental and economic outcomes, and substantial food waste occurs at the household level in the US. This study explored perceived household food waste changes during the COVID-19 pandemic and related factors. A total of 946 survey responses from primary household food purchasers were analyzed. Demographic, COVID-19-related household change, and household food waste data were collected in October 2020. Wilcoxon signed-rank was used to assess differences in perceived food waste. A hierarchical binomial logistic regression analysis was conducted to examine whether COVID-19-related lifestyle disruptions and food-related behavior changes increased the likelihood of household food waste. A binomial logistic regression was conducted to explore the contribution of different food groups to the likelihood of increased food waste. Perceived food waste, assessed as the estimated percent of food wasted, decreased significantly during the pandemic (z = −7.47, p < 0.001). Food stockpiling was identified as a predictor of increased overall food waste during the pandemic, and wasting fresh vegetables and frozen foods increased the odds of increased food waste. The results indicate the need to provide education and resources related to food stockpiling and the management of specific food groups during periods of disruption to reduce food waste.

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