scholarly journals Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

2000 ◽  
Vol 23 (4) ◽  
pp. 739-743 ◽  
Author(s):  
Mariana Pires de Campos Telles ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Stochastic Process ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Small Sample ◽  
Group Method ◽  
Gene Frequencies ◽  
Exponential Relationship ◽  
Local Populations ◽  
Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

scholarly journals Hierarchical structure of genetic distances: Effects of matrix size, spatial distribution and correlation structure among gene frequencies

1998 ◽  
Vol 21 (2) ◽  
pp. 233-240 ◽  
Author(s):  
Flávia Melo Rodrigues ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Genetic Distance ◽  
Dimensional Space ◽  
Correlation Coefficients ◽  
Genetic Distances ◽  
Group Method ◽  
First Eigenvalue ◽  
Gene Frequencies ◽  
Cophenetic Correlation ◽  
Local Populations ◽  
Distance Matrices

Geographic structure of genetic distances among local populations within species, based on allozyme data, has usually been evaluated by estimating genetic distances clustered with hierarchical algorithms, such as the unweighted pair-group method by arithmetic averages (UPGMA). The distortion produced in the clustering process is estimated by the cophenetic correlation coefficient. This hierarchical approach, however, can fail to produce an accurate representation of genetic distances among populations in a low dimensional space, especially when continuous (clinal) or reticulate patterns of variation exist. In the present study, we analyzed 50 genetic distance matrices from the literature, for animal taxa ranging from Platyhelminthes to Mammalia, in order to determine in which situations the UPGMA is useful to understand patterns of genetic variation among populations. The cophenetic correlation coefficients, derived from UPGMA based on three types of genetic distance coefficients, were correlated with other parameters of each matrix, including number of populations, loci, alleles, maximum geographic distance among populations, relative magnitude of the first eigenvalue of covariance matrix among alleles and logarithm of body size. Most cophenetic correlations were higher than 0.80, and the highest values appeared for Nei's and Rogers' genetic distances. The relationship between cophenetic correlation coefficients and the other parameters analyzed was defined by an "envelope space", forming triangles in which higher values of cophenetic correlations are found for higher values in the parameters, though low values do not necessarily correspond to high cophenetic correlations. We concluded that UPGMA is useful to describe genetic distances based on large distance matrices (both in terms of elevated number of populations or alleles), when dimensionality of the system is low (matrices with large first eigenvalues) or when local populations are separated by large geographical distances.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

AFLP-based assessment of genetic diversity among nine alfalfa germplasms using bulk DNA templates

Genome ◽  
2003 ◽  
Vol 46 (1) ◽  
pp. 51-58 ◽  
Author(s):  
A Segovia-Lerma ◽  
R G Cantrell ◽  
J M Conway ◽  
I M Ray
Keyword(s):  
Genetic Diversity ◽  
Medicago Sativa ◽  
High Throughput ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Analysis ◽  
Dna Templates ◽  
Arithmetic Average ◽  
Pair Group ◽  
Large Numbers

Improving commercial utilization of perennial Medicago collections requires developing approaches that can rapidly and accurately characterize genetic diversity among large numbers of populations. This study evaluated the potential of using amplified fragment length polymorphism (AFLP) DNA markers, in combination with DNA bulking over multiple genotypes, as a strategy for high-throughput characterization of genetic distances (D) among alfalfa (Medicago sativa L.) accessions. Bulked DNA templates from 30 genotypes within each of nine well-recognized germplasms (African, Chilean, Flemish, Indian, Ladak, Medicago sativa subsp. falcata, Medicago sativa subsp. varia, Peruvian, and Turkistan) were evaluated using 34 primer combinations. A total of 3754 fragments were identified, of which 1541 were polymorphic. The number of polymorphic fragments detected per primer combination ranged from 20 to 85. Pairwise D estimates among the nine germplasms ranged from 0.52 to 1.46 with M. sativa subsp. falcata being the most genetically dissimilar. Unweighted pair-group method arithmetic average (UPGMA) analysis of the marker data produced two main clusters, (i) M. sativa subsp. sativa and M. sativa subsp. varia, and (ii) M. sativa subsp. falcata. Cluster-analysis results and D estimates among the Chilean, Peruvian, Flemish, and M. sativa subsp. varia germplasms supported the hypothesis that Peruvian was more similar to original Spanish introductions into Central and South America than Chilean. Hierarchical arrangement of the nine germplasms was supported by their respective geographic, subspecific, and intersubspecific hybrid origins. Subsets of as few as seven highly informative primer pairs were identified that produced comparable D estimates and similar heirarchical arrangements compared with the complete dataset. The results indicate that use of primer-pair subsets for AFLP analysis of bulk DNA templates could serve as a high-throughput system for accurately characterizing genetic diversity among large numbers of alfalfa populations.Key words: Medicago sativa, DNA bulking, genetic distance.

scholarly journals Partial diallel and genetic divergence analyses in maize inbred lines

2020 ◽  
Vol 43 ◽  
pp. e53540
Author(s):  
Maria Fernanda de Souza Dias Maioli ◽  
Ronald José Barth Pinto ◽  
Tereza Aparecida da Silva ◽  
Diego Ary Rizzardi ◽  
Robson Akira Matsuzaki ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genetic Divergence ◽  
Block Design ◽  
Inbred Lines ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Maize Inbred Lines ◽  
Randomized Block Design ◽  
Partial Diallel

In this study, we aimed to estimate general and specific combining abilities (GCA and SCA, respectively) and to verify genetic divergence (Rogers distance, Unweighted Pair-Group Method Using Arithmetic Average - UPGMA) using microsatellite markers in maize inbred lines. Using a partial diallel scheme, a total of 19 inbred lines were crossed as (9 x 10), which were derived from the single hybrids SG6015 and P30F53, respectively. The 90 hybrids were evaluated in an incomplete randomized block design with common checks and three replications during the 2017-2018 growing season. Flowering time, average plant height, ear height insertion, average ear diameter, ear length, number of lodged and broken plants, mass of 100 grains and grain yield were measured. According to the analysis of variance, GCA, and SCA were significant (p < 0.05) in all the measured traits; inbred line B as well as 1 and 8, derived from the single hybrids SG6015 and P30F53, respectively, were selected due to their higher GCA values in grain yield to be used in crosses as testers, while the single cross hybrid (B x 1) was selected due to their higher SCA value in grain yield to be used in future breeding programs. The molecular marker analysis divided the inbred lines into two groups, where the highest dissimilarity (0.74) was observed between lines A and 9; however, these did not result in a high SCA value, therefore the hybrids obtained by such crossings were not selected for grain yield.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

scholarly journals Allozyme analysis of geographical and seasonal variation of Illex coindetii (Cephalopoda: Ommastrephidae) from central Mediterranean and Iberian Atlantic

2005 ◽  
Vol 85 (1) ◽  
pp. 177-184 ◽  
Author(s):  
P. Martínez ◽  
P. Belcari ◽  
A. Sanjuan ◽  
A. Guerra
Keyword(s):  
Minimum Spanning Tree ◽  
Geographical Area ◽  
Genetic Distances ◽  
Group Method ◽  
Central Mediterranean ◽  
Homogeneous Population ◽  
Pair Group ◽  
Morphological Studies ◽  
Temporal Variance ◽  
Population Pattern

Previous morphological studies of Illex coindetii from the Mediterranean have shown both juvenile and mature individuals all year round suggesting an homogeneous population pattern, however, seasonal spawning variation seems to exist varying with geographical area. Present work analysed 240 individuals from the northern Tyrrhenian and Atlantic Iberian waters at the four year-round seasons using 33 presumptive enzyme-coding loci to compare geographical and temporal variances. Genetic variability was low (Ho=0·02–0·04). Moderate variation at some loci was found due to both temporal and geographical factors (12% of total genetic variance) and to temporal variance (FST=0·004–0·015). Unweighted pair-group method using arithmetric averages (UPGMA) and Multidimensional scaling–minimum spanning tree (MDS–MST) analyses after Cavalli-Sforza & Edwards (1967) chord genetic distances showed the summer Italian and the spring Atlantic samples as the most divergent among the whole.

scholarly journals Genetic Divergence Among a Breeding Population of Hancornia Speciosa Gomes (Mangabeira) as Determined by Multivariate Statistical Methods

2018 ◽  
Vol 14 (15) ◽  
pp. 421
Author(s):  
Maria Clideana Cabral Maia ◽  
Mirian Fernandes Carvalho Araújo ◽  
Lucio Borges de Araújo ◽  
Carlos Tadeu dos Santos Dias ◽  
Luís Cláudio de Oliveira ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Breeding Population ◽  
Group Method ◽  
Multivariate Techniques ◽  
Multivariate Statistical ◽  
Arithmetic Average ◽  
Group Iii ◽  
Pair Group ◽  
Upgma Cluster Analysis ◽  
Hancornia Speciosa

The mangabeira its figure out among the mains native fruit tree explored by extractivism in Brasil. The objective evaluate the genetic divergence of landraces in orientation of crosses using multivariate techinics. The complete random blocks experimental design with four repetitions was used to evaluate twelve quantitative characteristics from twelve genotypes elite of mangabeiras concerning to divergence genetic using the software R (2012). Three groups genetically divergent were composed by biplot graphic and stored by UPGMA cluster analysis (Unweighted Pair-Group Method using Arithmetic Average / Weighted Clustering Method not using the Arithmetic Mean) showing genetic diversity and variability among 12 mangabeira accesses. Forty-four possible crosses are planned among genotypes of genetically dissimilar three groups and six among individuals in group III. Multivariate techniques were appropriate in the study of genetic divergence.

scholarly journals Detecting DNA Polymorphism and Genetic Diversity in a Wide Pistachio Germplasm: Comparison of AFLP, ISSR, and RAPD Markers

2006 ◽  
Vol 131 (4) ◽  
pp. 522-529 ◽  
Author(s):  
Salih Kafkas ◽  
Hakan Ozkan ◽  
Bekir Erol Ak ◽  
Izzet Acar ◽  
Halit Seyfettin Atli ◽  
...  
Keyword(s):  
Correlation Coefficients ◽  
Genetic Distances ◽  
Group Method ◽  
Aflp Data ◽  
Breeding Programs ◽  
Center Of Origin ◽  
Financial Investment ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
The Mediterranean

There are limited numbers of pistachio (Pistacia vera L.) cultivars in the world and their phenotypic appearance and productivity are variable. Understanding such variation would facilitate their use in cultivar breeding programs. Therefore, in this study, 69 pistachio cultivars and genotypes originating from seven countries were characterized by randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and amplified fragment-length polymorphism (AFLP) markers. The results showed that all three marker systems were able to reveal variability between pistachio cultivars and genotypes. The correlation coefficients for genetic distances were statistically significant among all three molecular marker types. The correlation between RAPD and AFLP data was the highest (r = 0.73) and the value between RAPD and ISSR data was the lowest (r = 0.58). AFLP proved to be the best technique among them. ISSR and AFLP assays were reliable and produced reproducible bands. ISSR was preferred over RAPD, especially when financial investment and technical knowledge are limited. The constructed unweighted pair group method with arithmetic averages (UPGMA) dendrogram obtained from combined data separated the genotypes into two main clusters: one cluster (“Iranian”) included genotypes originating from Iran and the second cluster (“Mediterranean”) contained most other genotypes. The “Mediterranean” cluster further divided into three subclusters: one (“Siirt”) consisted of the cultivars Siirt and Hacireso with a few other selections; the second subcluster (“Turkish”) included Turkish cultivars; and the third subcluster contained Syrian, Italian, and the remaining cultivars. The closeness of the clusters was “Iranian” - “Siirt” - “Turkish”/“Syrian.” These findings reveal a new understanding in the diffusion of pistachio cultivation from its center of origin, the Iranian-Caspian region, via southeastern Turkey to Syria, the Mediterranean region of Europe, and northern Africa.

scholarly journals GENETIC DIVERSITY ASSESSMENT AMONG TALL COCONUT PALM

2018 ◽  
Vol 31 (1) ◽  
pp. 28-39 ◽  
Author(s):  
KAMILA MARCELINO BRITO SOBRAL ◽  
MANOEL ABÍLIO DE QUEIROZ ◽  
CARLOS ALBERTO DA SILVA LEDO ◽  
CARINA MENDES LOIOLA ◽  
JÉSSICA BARROS ANDRADE ◽  
...  
Keyword(s):  
Genetic Divergence ◽  
Cocos Nucifera ◽  
Fruit Weight ◽  
West African ◽  
Group Method ◽  
Eastern Region ◽  
Agronomic Characteristics ◽  
The North ◽  
Pair Group ◽  
Diversity Assessment

ABSTRACT The tall coconut (Cocos nucifera L.) has great socioeconomic importance in Brazil and was first introduced on the coast of the north-eastern region, where it has been exploited in a semi-extractivist manner. The goal of this study was to quantify the genetic divergence between accessions introduced and preserved at the International Coconut Genebank for Latin America and the Caribbean, estimate the efficiency of descriptors used in the discrimination of the accessions, and indicate the essential descriptors for the activities of characterisation and evaluation. The accessions used were: Polynesia Tall; Tonga Tall; West African Tall; Rennel Tall; Rotuma Tall; Vanuatu Tall; Malayan Tall and Brazilian Tall Praia-do-Forte. Thirty-five quantitative descriptors recommended for the species were used. Genetic divergence was estimated by the Mahalanobis’s generalised distance and the cluster analysis was performed using the unweighted pair group method with arithmetic mean (UPGMA). The relative importance of the descriptors was measured according to Singh and Jolliffe’s methods, and the variables were selected taking into consideration the matching information in the two methods, eliminating those that were discarded in the two procedures. The agronomic characteristics indicated that the first canonical variable explained 90.25% of total variance. The most efficient descriptors for detecting the genetic divergence were: fruit equatorial circumference; nut polar and equatorial circumference; quantity of liquid endosperm; total fruit weight; nut weight; stem height; girth of stem at 1,5m height; number of leaflets; and number of bunches. The most dissimilar accessions according to the agronomic characteristics were Rotuma Tall and West African Tall, which can be primarily indicated as genitors for the formation of segregating populations in breeding programmes.

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