Polyhedral Combinatorics of UPGMA Cones

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the normalized volumes of the UPGMA cones for small n. Keywords: phylogenetic trees, polyhedral combinatorics, partition lattic

Genetic dissimilarities between wild olives by random amplified polymorphic DNA (RAPD) assay

Olive, being a fruit of subtropical climate and recognized to have significant importance in terms of human health, is being investigated with different aspects. Wild olives are valuable in the sense that they contain the sources of stability and they can be separated by using random amplified polymorphic DNA (RAPD) technique. In this study, a total of 59 primers were used for the purpose of determining the DNA fingerprints of 12 wild olives obtained from different provinces of Aegean region, and 92 polymorphic bands were yielded. Mean number of polymorphic bands per individual was calculated as 7.67 and number of polymorphic bands per scorable primer was calculated as 4.6. Specific DNA markers are important for determining the genetic relation among wild subspecies in olives. The purpose of this study is to identify the wild olives by using RAPD analysis. In conclusion, the genetic relation between wild olives were determined through Jaccard, Sorensen Dice, Simple Matching coefficients, (unweighted pair group method with arithmetic averages) UPGMA and neighbor joining method by using the data obtained with RAPD.Keywords: Random amplified polymorphic DNA (RAPD), Olea europaea, arbitrary primers, Jaccard, Sorensen Dice, Simple Matching, unweighted pair group method with arithmetic averages, neighbor joinin

Molecular Characterization of Three Cultivars of Tomato (Lycopersicon Esculentum L.) in South-West Nigeria Using SSR Markers

Molecular characterisation of local tomato cultivars – Ibadan Local (IbL), Ife and JM94/46 (JM) were assessed using simple sequence repeat (SSR) markers. Out of ten SSR primer pairs used, three primer pairs were able to differentiate amplified genomic DNA of the cultivars. Unweighted Pair Group Method Using Arithmetic Average (UPGMA) cluster analysis of the data showed a close relationship between IbL and Ife with a genetic distance (GD) of 0.067; Ife and JM had GD of 0.2 and JM and Ife had GD of 0.25

Conformation of phylogenetic relationship of penaeidae shrimp based on Morphometric and Molecular investigations

Understanding of accurate phylogenetic relationship among Penaeidae shrimp is important for academic and fisheries industry. The Morphometric and Randomly Amplified Polymorphic DNA (RAPD) analysis was used to make the phylogenetic relationsip among 13 Penaeidae shrimp. For morphometric analysis forty variables and total lengths of shrimp were measured for each species, and removed the effect of size variation. The size normalized values obtained was subjected to UPGMA (Unweighted Pair-Group Method with Arithmetic Mean) cluster analysis. For RAPD analysis, the four primers showed reliable differentiation between species, and used correlation coefficient between the DNA banding patterns of 13 Penaeidae species to construct UPGMA dendrogram. Phylogenetic relationship from morphometric and molecular analysis for Penaeidae species found to be congruent. We concluded that as the results from morphometry investigations concur with molecular one, phylogenetic relationship obtained for the studied Penaeidae are considered to be reliable.Понимание точных филогенетических отношений у креветок Penaeidae важно как с общенаучной точки зрения, так и для рыбной промышленности. RAPD анализ был использован для установления филогенетических связей 13 видов креветок Penaeidae. Для морфометрических анализов измерены 40 переменных и общих длин креветок для каждого вида и устранен эффект вариабельности размера. Показатели нормализованного размера обработаны с помощью кластерного анализа UPGMA (Unweighted Pair-Group Method with Arithmetic Mean). При RAPD анализе четыре праймера показали достоверные различия между видами. Коэффициенты корреляции между паттернами ДНК использованы для построения UPGMA дендрограмм. Филогенетические связи, построенные на основе морфометрических и молекулярных анализов, совпали, что позволило сделать вывод об их достоверности

Genetic diversity analysis of Nardostachys jatamansi DC, an endangered medicinal plant of Central Himalaya, using random amplified polymorphic DNA (RAPD) markers

The genetic diversity analysis of eight populations of Nardostachys jatamansi DC. collected from different altitude of Central Himalaya has been attempted using 24 sets of random amplified polymorphic DNA (RAPD) primers. These sets of RAPD marker generated a total of 346 discernible and reproducible bands across the analysed population with 267 polymorphic and 75 monomorphic bands. The unweighted pair group method with arithmetic average (UPGMA) cluster analysis revealed three distinct clusters: I, II and III. The cluster I was represented by N. jatamansi population collected from Panwali Kantha (3200 m asl) and Kedarnath (3584 m asl), India together with Jumla (2562 m asl) from Nepal. Cluster II included collections from Har Ki Doon (3400 m asl) and Tungnath (3600 m asl) from India while Cluster III was represented by collections from Munsiyari (2380 m asl), Dayara (3500 m asl) and Valley of Flowers (3400 m asl) from India. The clustering of these populations was independent of variations in altitude and geographical locations. The genetic variations observed in different populations of Jatamansi might be due to environmental influences (biotic and abiotic), rather than altitude level differences. The abiotic (geographical or climatic differentiation) and biotic (pollination between population and seed dispersal) factors might be responsible for the genetic variations among these accessions of Jatamansi.Keywords: Genetic diversity, random amplified polymorphic DNA (RAPD), Nardostachys jatamansi, Central Himalaya, unweighted pair group method with arithmetic average (UPGMA)African Journal of Biotechnology Vol. 12(20), pp. 2816-282

Extensión del algoritmo para análisis filogenético UPGMA (Unweighted Pair Group Method using Arithmetic Averages) aplicado a bases de datos

Tesis (Ingeniero de Sistemas)La aparición del virus de inmunodeficiencia humana (VIH) ha significado un gran reto para la comunidad científica debido a su capacidad de mutar, lo que conlleva a la aparición de múltiples subtipos del mismo, los cuales varían dependiendo de la región donde estos se desarrollen. Por lo cual es de vital importancia llevar a cabo la clasificación de cada uno de ellos. Una manera de hacerlo es implementando algoritmos de análisis filogenético para la determinación de patrones que permitan una clasificación de muestras de virus obtenidas en distintas regiones. El presente proyecto pretende el diseño y la implementación de una interfaz de software que permita el análisis filogenético de un gran número de secuencias genéticas que se encuentran almacenadas en una bases de datos, implementando para ello el algoritmo para análisis filogenético UPGMA (Unweighted Pair Group Method using Arithmetic averages). Como resultado de este proyecto de grado, se generará una interfaz de software que no solo permite llevar a cabo el análisis filogenético de un gran número de secuencias genéticas, las cuales se encuentran almacenadas en una base datos, utilizando para ello el método para análisis filogenético UPGMA, sino que además se incluye una función extra que permite a los investigadores obtener una predicción de asociación a partir de una secuencia de ADN entrante, utilizando para ello un método conocido como GraphDatabases.Universidad del Norte. Programa de Ingeniería de Sistema

Genetic diversity analysis using molecular marker in Terminalia chebula

Terminalia chebula is an important medicinal plant, extensively used in Ayurveda, Unani and Homoeopathic medicines. The present study was aimed to reveal its genetic diversity based on molecular markers from twelve T. chebula accessions. Molecular diversity was studied using RAPD markers. A total of 8 polymorphic primers produced 314 polymorphic bands and 195 monomorphic bands. Unweighted Pair Group Method with Arithmetic Mean (UPMGA) dendrogram divided the accessions into 2 major clusters. Accession IIHRTc2 and IIHRTc10 showed maximum genetic diversity with 55% similarity. This characterization based on molecular markers will help in identification of economically useful accessions for further crop improvement programme

Annual dune plant communities in the Southwest coast of Europe

This study presents an updated sintaxonomic review of the annual communities from coastal dunes in the Southwest coast of Europe, specifically in the Iberian Peninsula, including both types: directly influenced by the sea salt spray and not affected by this influence. The floristic segregation of the different plant associations was obtained by statistical agglomerative processes (UPGMA, Unweighted Pair Group Method with Arithmetic Mean) plus principal coordinate analysis (PCoA) and discussed based on the interpretation of phytosociological tables. Three new communities in central western Portugal were found and are described: Pseudorlayo minusculae-Polycarpietum alsinifoli, Cerastio diffusae-Vulpietum fontqueranae and Omphalodo kunzinskyanae-Evacietum ramosissimae

Molecular diversity in persimmon (Diospyros kaki L.) cultivars growing around Hatay province in Turkey

Genetic relationships among Diospyros kaki L. growing around Hatay province in Turkey were assessed by randomly amplified polymorphic DNA (RAPD) assay. Ten decamer primers were selected from 50 primers. These primers yielded a total of 155 bands and 126 of them were recorded aspolymorphic. Pairwise genetic distances of the samples were used to construct dendograms using Unweighted Pair-Group Method of Arithmetic Average (UPGMA). The study suggests that the morphological differences among cultivars of persimmon might be the result of genetic differencesrather than the ecological or growing conditions. The study forms a basic contribution to the characterization of D. kaki population in Turkey