Unweighted Pair-group Method Cluster Research Articles

Population variation and island effect in Melipona subnitida (Hymenoptera: Apidae)

We examined the head morphology of island and mainland populations of the stingless bee Melipona subnitida. We employed geometric morphometrics to test for differences in head morphology and analyzed 122 colonies. Head measurements were performed using 25 landmarks and semi-landmarks. For head shape, landmarks were analyzed by generalized procrustes analysis, principal component analysis (PCA), Mahalanobis distance, discriminant function analysis, cross-validation and unweighted pair-group method clustering (UPGMA). For head size, data were analyzed by analysis of variance (ANOVA), followed by the Tukey test. In addition, the relations between head shape, head size, geographical distance and altitude were analyzed using Pearson’s correlation coefficients. Morphological analyses revealed significant differences (p<.01) between mainland and island populations. Moreover, island bees differed in head shape and head size. The first two principal components explained 69.72% of the total variation, and UPGMA revealed that the individuals collected on the Island of Fernando de Noronha differed from the remaining locations, with 100% bootstrap support. Cross-validation correctly classified 84% of the individuals into their respective locations. The results also indicated structuring of those populations introduced to and isolated on the Island of Fernando de Noronha for more than 30 years. The characterization of the studied M. subnitida populations, especially the island populations, alerts us to the fact that isolation may lead to a loss of diversity, or even of the whole population, in M. subnitida and the remaining meliponines, possibly negatively affecting biotic interactions, especially plant–pollinator interactions.Variación poblacional y efecto insular en Melipona subnitida (Hymenoptera: Apidae)Examinamos la morfología de la cabeza de poblaciones insulares y continentales de Melipona subnitida. Empleamos morfometría geométrica para probar las diferencias en la morfología de la cabeza y analizamos 122 colonias. Las mediciones de la cabeza se realizaron utilizando 25 puntos y semi-puntos de referencia. Para la forma de la cabeza, los puntos de referencia se analizaron mediante el análisis procrustal generalizado, el análisis de componentes principales (PCA), la distancia Mahalanobis, el análisis de funciones discriminantes, la validación cruzada y la agrupación de métodos de grupos de pares no ponderados (UPGMA). Para el tamaño de la cabeza, los datos se analizaron mediante el análisis de varianza (ANOVA), seguido de la prueba de Tukey. Además, se analizaron las relaciones entre la forma de la cabeza, el tamaño de la cabeza, la distancia geográfica y la altitud utilizando los coeficientes de correlación de Pearson. Los análisis morfológicos revelaron diferencias significativas (p < 0,01) entre las poblaciones del continente y de las islas. Además, las abejas insulares diferían en la forma y el tamaño de la cabeza. Los dos primeros componentes principales explicaron el 69,72% de la variación total, y la UPGMA reveló que los individuos recolectados en la Isla de Fernando de Noronha difirieron del resto de las localidades, con un 100% de apoyo de bootstrap. La validación cruzada clasificó correctamente al 84% de los individuos en sus respectivas ubicaciones. Los resultados también indicaron la estructuración de las poblaciones introducidas y aisladas en la isla de Fernando de Noronha durante más de 30 años. La caracterización de las poblaciones estudiadas de M. subnitida, especialmente las poblaciones insulares, nos alerta de que el aislamiento puede llevar a una pérdida de diversidad, o incluso de toda la población, en M. subnitida y los meliponinos restantes, afectando posiblemente negativamente a las interacciones bióticas, especialmente las interacciones planta-polinizador.

Assessment of genetic diversity of Iranian Ascochyta rabiei isolates using rep‐PCR markers

AbstractGenetic diversity and population structure among 29 isolates of Ascochyta rabiei (AR) obtained from diseased chickpea plants in six different geographical origins in Iran was characterized by MAT and rep‐PCR (BOX/ERIC/REP) markers. Both mating types were found in all six populations, and the frequencies of mating types were variable between populations. The majority of the isolates belonged to Mat1‐1 (58.12%) with the remainder (41.88%) being Mat1‐2. A dendrogram was calculated with Jaccard's similarity coefficients with unweighted pair group method clustering (UPGMA) for the combination of rep‐PCR results, AR strains were differentiated into four clusters (A–D) at 60% similarity level. ERIC, REP and BOX showed a total of 19, 37 and 24 alleles per locus, respectively. Gene diversity (He) and Shannon's information index (I) were the highest in the REP (He = 0.82; I = 2.11), while the lowest values were estimated for the ERIC (He = 0.42; I = 1.3). Our result showed that among the three techniques studied, REP‐PCR produced the most complex amplified banding patterns, which reflected a high degree of diversity among the Iranian AR strains. ERIC‐PCR was the least discriminating method, and BOX‐PCR was intermediate. To the best our knowledge, this is first study of assessment of genetic diversity of AR isolates by rep‐PCR markers.

Molecular characterization and cultivar identification in Bougainvillea spp. using SSR markers

The present study was undertaken to determine the genetic relatedness and molecular characterization of fifty bougainvillea cultivars that belong to four major species of bougainvillea namely B. glabra, B. spectabilis, B.peruviana and Bougainvillea × buttiana. Five microsatellite (simple sequence repeat; SSR) markers with high PIC values were used to characterize these bougainvillea cultivars. A total of 28 alleles were detected at an average number of alleles of 5.6 alleles /locus. The PIC values varied widely among primers and ranged from 0.364 to 0.891 with an average of 0.716 per locus and the size of the amplified products ranged from 90bp to 250bp. Primer BOUG-1 showed the highest polymorphism index content (0.891) thus reflecting it’s ability to differentiate these cultivars much better at molecular level. A total of 18 rare alleles were identified among which the cultivar (Blondie) had maximum number of rare alleles (3). An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main clusters with Cluster I being the largest one encompassing 18 cultivars while cluster IV and V emerged as the smallest ones comprising 3 cultivars each. The pair wise estimates of genetic distance ranged from 0 (Cherry Blossom to Mary Palmer Special) to 1.0 (Blondie to Shubhra, Partha, Lady Hope, Gloriosus, Red September, Zakiriana, Lady Richards and Spledens). The present investigation is first of its kind in using microsatellite markers for phylogenetic analysis and molecular characterization in bougainvillea cultivars. The study proved the efficiency of SSR markers in documentation, identification and tracing out the molecular origin among unknown cultivars of bougainvillea.

Genetic diversity and genetic similarities between Iranian rose species

SummaryWild rose species were collected from different regions of Iran for a rose breeding programme. They included accessions from Rosa persica, R. foetida, R. pimpinellifolia, R. hemisphaerica, R. canina, R. iberica, R. damascena, R. beggeriana, and R. orientalis. Ten microsatellite (simple sequence repeat; SSR) markers were used to analyse the genetic variation among these rose species. The SSR markers amplified alleles in all species, even if they were from different sections within the genus. An unweighted pair group method cluster analysis (UPGMA) based on similarity values revealed five main Groups. The data showed no support for any distinction between R. canina and R. iberica, as all the accessions were placed in one Group, and accessions of these two species were more closely-related to each other within a Province than to accessions of the same species in other Provinces. Accessions of sect. Pimpinellifoliae were combined with plants from sect. Rosa and Cinnamomeae in two different Groups. Genetically, R. persica clustered distinctly from all others, with few alleles shared with the other taxa. We discuss the use of SSR markers for phylogenetic analysis when these markers are amplified in all species of a genus.

Wide genetic diversity of Rosa damascena Mill. germplasm in Iran as revealed by RAPD analysis

The genetic relationships among 41 Rosa damascena accessions from various cultivation areas of Iran and one accession from Bulgaria were analyzed using 31 RAPD (Randomly Amplified Polymorphic DNA) primers. Each primer exhibited 3–12 banding patterns for a total of 343 scorable and 184 polymorphic bands. The combination of 11 primers was found optimal for discrimination of 42 accessions with very low values of cumulative confusion probability (9.7 × 10 −5); indicating that only one pair from over 10,000 distinct pairs of accessions would be indistinguishable. Unweighted pair group method cluster analysis based on similarity values revealed 10 groups at the distance of 0.85. The Bulgarian genotype grouped with the majority of the Iranian genotypes in a main cluster. Results of molecular variance analysis (AMOVA) indicated that the major proportion (65.7%) of the total genetic variation was within collecting provinces rather than between them. The wide genetic variation seen for R. damascena in Iran indicates that Iran is a center of genetic diversity for this species and that there is a promising future for the breeding.

Molecular Characterization of Olive Cultivars Using RAPD Markers

Forty olive (Olea europaea L.) cultivars from Valencia, Spain, were screened using random amplified-polymorphic DNA (RAPD) markers. Eighteen selected decamer primers produced 34 reproducible amplification fragments that were then used as polymorphic markers. The resulting combinations of these RAPD markers were used to discriminate 40 cultivars. Results were analyzed for similarity among cultivars and the relatedness of polymorphisms obtained between cultivars agreed with previous results using isozymes. Unweighted pair group method cluster analysis of their similarity values revealed two main groups divided according to geographic origin within Valencia. A third group, which included two Spanish cultivars from regions outside of Valencia, was clustered separately from the Valencian cultivars. RAPD technology proved useful in discriminating closely related cultivars. There was no apparent clustering of cultivars by fruit size or other morphological traits.

Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigación y Formación Agraria “Alameda del Obispo” in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar-specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.

Isozyme analysis of population structure and diversity in the puffball species Lycoperdon pyriforme

Isozyme analysis possesses predictive value and may reveal aspects of the natural history of a species that are not otherwise obvious. Working on this premise, isozyme analysis was performed on Ly- coperdon pyriforme to shed light on the attributes of this species that most likely influence the distribution of genetic diversity observed among seven collection sites within the study region (i.e., central Arkansas, northeastern Kansas and northwestern Missouri). Forty-nine unique multilocus isozyme phenotypes were identified from cultures isolated from immature glebal tissue of 310 basidiocarps collected from the surface of decaying logs (-one isozyme phenotype per log). Numerical and cluster analyses to deter- mine similarity of phenotypes indicated that these group out randomly and not according to collection site. Further analyses of isozyme data were per- formed, grouping phenotypes together into popula- tions according to collection site. Isozyme bands were partitioned by locus based on the assumption that these represent alleles and interpreted on the as- sumption that the dikaryotic mycelia of this puffball species are physiologically diploid. Nine of the eleven putative loci examined were polymorphic, with a mean of 3.6 alleles/polymorphic locus. Mean hetero- zygosity for populations varied from 0.200 to 0.345, suggesting the possibility that outcrossing occurs in this species. Unweighted pair group method cluster analysis displayed marginal grouping of populations based on geographic proximity. Genetic diversity sta- tistics indicate that genetic differentiation among populations is low (GST = 0.122). Patterns of varia- tion observed in this species suggest that gene flow has acted as a homogenizing force in this species within the region sampled.