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Principal Coordinate Analysis (principal + coordinate_analysis)
Selected AbstractsAnalysis of the morphological attributes of a sweetpotato collectionANNALS OF APPLIED BIOLOGY, Issue 2 2010M.M. Manifesto The knowledge about the distribution of descriptors of a collection constitutes a useful tool for the management of genetic resources. The object of this work was to evaluate the composition and morphological characterisation of the ,in vitro' collection kept at the Gene Bank of the Biological Resources Institute (IRB), INTA Castelar, Argentina, to establish conservation criteria and make available useful data for breeding programmes. This collection, comprising 310 sweetpotato clones, includes landraces, worldwide clones, commercial varieties and breeding material. The descriptors, which presented the highest correlation values, were leaf lobe types, the shape of central leaf lobes and general leaf outline. Cluster analyses showed eight major groups with an average similarity of 0.42 (SE ± 0.005). About 76% of the clones presented unique morphology, whereas 34% of them were distributed in 22 groups that could not be distinguished with this technique. Worldwide germplasm formed a separate group with values of diversity higher than those of the Argentinean clones and no duplicates. A projection of the phenotypic variation among cultivars was obtained through Principal Coordinate Analysis (PCoorA), which confirmed the results obtained by UPGMA analysis, predominant skin colour, secondary skin colour, number of leaf lobes, general leaf outline, petiole pigmentation and predominant colour of vine were the variables that made the highest contribution. Collection composition in reference to flesh and skin colour was also analysed. [source] Seasonal and substrate preferences of fungi colonizing leaves in streams: traditional versus molecular evidenceENVIRONMENTAL MICROBIOLOGY, Issue 2 2005Liliya G. Nikolcheva Summary Aquatic hyphomycetes are the main fungal decomposers of plant litter in streams. We compared the importance of substrate (three leaf species, wood) and season on fungal colonization. Substrates were exposed for 12 4-week periods. After recovery, mass loss, fungal biomass and release of conidia by aquatic hyphomycetes were measured. Fungal communities were characterized by counting and identifying released conidia and by extracting and amplifying fungal DNA (ITS2), which was subdivided into phylotypes by denaturing gradient gel electrophoresis (DGGE) and terminal-restriction fragment length polymorphism (T-RFLP). Mass loss, fungal biomass and reproduction were positively correlated with stream temperature. Conidial diversity was highest between May and September. Numbers of different phylotypes were more stable. Principal coordinate analyses (PCO) and canonical analyses of principal coordinates (CAP) of presence/absence data (DGGE bands, T-RFLP peaks and conidial species) showed a clear seasonal trend (P, 0.002) but no substrate effect (P, 0.88). Season was also a significant factor when proportional similarities of conidial communities or relative intensities of DGGE bands were evaluated (P, 0.003). Substrate was a significant factor determining DGGE band intensities (P = 0.002), but did not significantly affect conidial communities (P = 0.50). Both traditional and molecular techniques suggest that strict exclusion of fungi by substrate type is rare, and that presence of different species or phylotypes is governed by season. Biomasses of the various taxa (based on DGGE band intensities) were related to substrate type. [source] Who were the Meroites?INTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY, Issue 4 2010A biological investigation into the Nubian post-hiatus group Abstract Scholars have identified a hiatus in the archaeological record of Lower Nubia that spans approximately 1000 years. This interval may represent a desertion of Lower Nubia by its inhabitants. Evidence of occupation did not reappear in the area until the Meroitic time period. However, the identity of the returning people has been the subject of speculation. In order to determine who the Meroites of Lower Nubia were, 20 cranial non-metric traits were observed on six Nubian groups, representing five time periods. Two groups date to time periods immediately before (Kerma) and immediately after (X-Group) the Meroitic period. Three additional Nubian groups (two Christian samples from different sites and Sesebi, a contemporary sample) were utilised as outgroups to elucidate a clearer picture of the relationship among the six samples. Mahalanobis D2 with a tetrachoric matrix was employed for calculating biological distances among the groups. Principal coordinates analysis produced two clusters of Nubians, where the Meroitics clustered with other Nubian groups. Specific distance scores indicate the Meroites were biologically similar to individuals from the time periods prior to and after their arrival in Lower Nubia. The Meroites therefore appear to be a Nubian group returning to Lower Nubia after its desertion. Copyright © 2009 John Wiley & Sons, Ltd. [source] Genetic structure of Hypochaeris uniflora (Asteraceae) suggests vicariance in the Carpathians and rapid post-glacial colonization of the Alps from an eastern Alpine refugiumJOURNAL OF BIOGEOGRAPHY, Issue 12 2007Patrik Mráz Abstract Aim, The range of the subalpine species Hypochaeris uniflora covers the Alps, Carpathians and Sudetes Mountains. Whilst the genetic structure and post-glacial history of many high-mountain plant taxa of the Alps is relatively well documented, the Carpathian populations have often been neglected in phylogeographical studies. The aim of the present study is to compare the genetic variation of the species in two major European mountain systems , the Alps and the Carpathians. Location, Alps and Carpathians. Methods, The genetic variation of 77 populations, each consisting of three plants, was studied using amplified fragment length polymorphism (AFLP). Results, Neighbour joining and principal coordinate analyses revealed three well-supported phylogeographical groups of populations corresponding to three disjunct geographical regions , the Alps and the western and south-eastern Carpathians. Moreover, two further clusters could be distinguished within the latter mountain range, one consisting of populations from the eastern Carpathians and the second consisting of populations from the southern Carpathians. Populations from the Apuseni Mountains had an intermediate position between the eastern and southern Carpathians. The genetic clustering of populations into four groups was also supported by an analysis of molecular variance, which showed that most genetic variation (almost 46%) was found among these four groups. By far the highest within-population variation was found in the eastern Carpathians, followed by populations from the southern and western Carpathians. Generally, the populations from the Alps were considerably less variable and displayed substantially fewer region-diagnostic markers than those from the south-eastern Carpathians. Although no clear geographical structure was found within the Alps, based on neighbour joining or principal coordinate analyses, some trends were obvious: populations from the easternmost part were genetically more variable and, together with those from the south-western part, exhibited a higher proportion of rare AFLP fragments than populations in other areas. Moreover, the total number of AFLP fragments per population, the percentage of polymorphic loci and the proportion of rare AFLP fragments significantly decreased from east to west. Main conclusions, Deep infraspecific phylogeographical gaps between the populations from the Alps and the western and south-eastern Carpathians suggest the survival of H. uniflora in three separate refugia during the last glaciation. Our AFLP data provide molecular evidence for a long-term geographical disjunction between the eastern and western Carpathians, previously suggested from the floristic composition at the end of 19th century. It is likely that Alpine populations survived the Last Glacial in the eastern part of the Alps, from where they rapidly colonized the rest of the Alps after the ice sheet retreated. Multiple founder effects may explain a gradual loss of genetic variation during westward colonization of the Alps. [source] The usefulness of amplified fragment length polymorphism markers for taxon discrimination across graduated fine evolutionary levels in Caribbean Anolis lizardsMOLECULAR ECOLOGY, Issue 3 2002R. Ogden Abstract Fine-level taxon discrimination is important in biodiversity assessment and ecogeographical research. Genomic markers are often required for studies on closely related taxa, however, most existing mitochondrial and nuclear markers require prior knowledge of the genome and are impractical for use in small conservation projects. This study describes the application of amplified fragment length polymorphism (AFLP) to discriminate at four progressively finer evolutionary levels of Caribbean Anolis lizards from the central Lesser Antilles. AFLP is shown to be a rapid and effective method for discriminating between species. Separation increases with primer pair number and choice of primer combination appears to be noncritical. Initial population-level results show markedly less discriminatory power. A screening technique for the identification of population informative markers combining principal component and principal coordinate analyses is presented and assessed. Subsequent results show selected conspecific AFLP data to be remarkably congruent with those of mitochondrial DNA, microsatellite and morphological markers. The use of AFLP as a low-cost nuclear marker in species-level taxon discrimination is supported, whereas population level application demands further consideration. [source] A prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei, Atherinopsidae) from Southern BrazilACTA ZOOLOGICA, Issue 2 2010Maria Cristina Da Silva Cortinhas Abstract Da Silva Cortinhas, M. C., Glienke, C., Prioli, A. J., Noleto, R. B., Matoso, D. A. and Cestari, M. M. 2010. A prime inference on genetic diversity (RAPDs) in the marine fish Atherinella brasiliensis (Teleostei, Atherinopsidae) from Southern Brazil. ,Acta Zoologica (Stockholm) 91: 242,248 As a result of the importance of Atherinella brasiliensis in estuarine environments, random amplified polymorphic DNA (RAPD) markers were used to verify the genetic diversity in A. brasiliensis from two different places in Paranaguá Bay (Paraná State) and one from the Conceição Lagoon (Santa Catarina State). Cytogenetic data have shown a high karyotypic diversity in some populations, although in others this peculiarity demonstrates rearrangements such as heterochromatinization. In the present study, a low level of genetic structuring between the samples from Conceição Lagoon compared with the others was observed through principal coordinate analysis (PCO), analysis of molecular variance and Mantel test according to 79 RAPD markers. As this specie does not perform horizontal migration and the individuals of Conceição Lagoon are isolated, three hypotheses are proposed to explain the results: (i) similar environments may show homogeneous populations not depending on the geographical distance, (ii) because vicariant events that formed the bays occurred in a recent period, the fragmentation effects over the structuring of the genetic diversity may still be low and not totally detectable by the RAPD technique and (iii) the isolation time or the number of generations may not be enough to promote a possible differentiation and genetic structuring between the specimens of these three places. The specimens of these places present a low level of differentiation and genetic structuring so we can consider them as a unique homogeneous population. [source] Genetic structure of Euphrasia stricta on the Baltic island of Gotland, SwedenECOGRAPHY, Issue 4 2005Anna-Karin Kolseth Genetic differentiation between and within five varieties of Euphrasia stricta (var. brevipila, var. gotlandica, var. stricta, var. suecica and var. tenuis) on Gotland was investigated, using amplified fragment length polymorphism, AFLP. The varieties are described in the literature by morphology and association to habitat type. We wanted to investigate whether the varieties are locally adapted populations to the typical habitat type for each variety or if they are preadapted to certain habitat types and have colonized Gotland in their present form. A constrained principal coordinate analysis revealed three genetically differentiated subunits within the species. The two early-flowering varieties suecica and tenuis each formed a distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta together formed the third group. A phylogenetic tree confirms the partitioning into three groups. Within the group containing the late-flowering varieties there are populations that pair as each other's closest relatives, but belong to different varieties. These pairs are also geographically adjacent. The phylogenetic tree had a "star-like" appearance indicating a stronger divergence between populations than between varieties. The same pattern was seen in the partitioning of genetic diversity, with a lower amount of genetic variation occurring between varieties, FST=0.14, than between populations within the varieties, FST ranging from 0.26 to 0.60. In Euphrasia stricta the varieties suecica and tenuis and the group containing the varieties stricta/gotlandica/brevipila are likely to have a phylogeographical history outside Gotland, or an ancient and concealed local origin on the island. Within the group stricta/gotlandica/brevipila local evolutionary events seem to determine the variety identity, probably through local adaptation. [source] Environmental change and the phenology of European aphidsGLOBAL CHANGE BIOLOGY, Issue 8 2007RICHARD HARRINGTON Abstract Aphids, because of their short generation time and low developmental threshold temperatures, are an insect group expected to respond particularly strongly to environmental changes. Forty years of standardized, daily data on the abundance of flying aphids have been brought together from countries throughout Europe, through the EU Thematic Network ,EXAMINE'. Relationships between phenology, represented by date of first appearance in a year in a suction trap, of 29 aphid species and environmental data have been quantified using the residual maximum likelihood (REML) methodology. These relationships have been used with climate change scenario data to suggest plausible changes in aphid phenology. In general, the date of first record of aphid species in suction traps is expected to advance, the rate of advance varying with location and species, but averaging 8 days over the next 50 years. Strong relationships between aphid phenology and environmental variables have been found for many species, but they are notably weaker in species living all year on trees. Canonical variate analysis and principal coordinate analysis were used to determine ordinations of the 29 species on the basis of the presence/absence of explanatory variables in the REML models. There was strong discrimination between species with different life cycle strategies and between species feeding on herbs and trees, suggesting the possible value of trait-based groupings in predicting responses to environmental changes. [source] Genetic Diversity and Association Analysis for Salinity Tolerance, Heading Date and Plant Height of Barley Germplasm Using Simple Sequence Repeat MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2008Lilia Eleuch Abstract The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers. Four of the 22 markers (Bmac316, scssr03907, HVM67 and Bmag770) were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H, bin 13) in two different environments with common significant alleles (175, 177), whereas the HVHOTR1 marker (2H, bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398. [source] A new genotype 2 subcluster identified among GBV-C strains circulating in the Lisbon metropolitan area of PortugalJOURNAL OF MEDICAL VIROLOGY, Issue 3 2010Cristina Branco Abstract The rate of infection by the GBV-C virus was investigated in a group of 214 individuals at high risk of infection with parenterally transmitted viruses, and all living in the Lisbon metropolitan area (Portugal). RNA was extracted from plasma samples, and a fragment of the 5,-UTR was amplified by RT-PCR, disclosing a high prevalence of infection (40.7%). Most probably due to similar modes of viral transmission, the majority of GBV-C (+) individuals were found to be coinfected with HIV and/or HCV. A genomic region covering part of the E1/E2 glycoprotein coding sequence was amplified from approximately half of the GBV-C positive samples (44/87). Phylogenetic analysis of nucleotide sequences showed segregation of Portuguese GBV-C strains with genotype 1 (G1, n,=,10) and genotype 2 (G2, n,=,24) references. Genotype 1 was significantly associated with the African descent of those infected. Curiously, some of the strains assigned to genotype 2 were shown to form a separate cluster (designated G2*) in both neighbor-joining and Bayesian phylogenetic trees, which was confirmed by multivariate principal coordinate analysis. However, analysis of the distribution of intra- and intergenotype genetic distances support the hypothesis that rather than corresponding to a new viral genotype, G2* is a geographical subcluster within the genotype 2 radiation. J. Med. Virol. 82:452,459, 2010. © 2010 Wiley-Liss, Inc. [source] Long-term changes in the chromosomal inversion polymorphism of Drosophila subobscura.JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2004Abstract The chromosomal polymorphism of 13 European populations of Drosophila subobscura has been compared with that of the same populations collected 15,35 years ago. The chromosomal polymorphism of the old populations differs significantly from that of the new populations, mainly for chromosomes U and O. There is a very good agreement between the geographical space and the genetic space as shown by a graphical representation of the 26 statistical populations (13 old and 13 new) obtained by a principal coordinate analysis. This reflects both the existence of significant latitudinal clines for the frequencies of some chromosomal arrangements in the old and new samples and systematic changes that have taken place in these populations during the period that elapsed between the two surveys. An increase in the frequency of those arrangements typical of southern latitudes and a decrease for those common in northern latitudes is observed in all populations , Mediterranean, Atlantic and Central European. Furthermore, the genetic distances of the new populations to a southern population of reference have decreased in comparison with those of the old populations. These changes could be the result of climatic factors that are correlated with latitude. In particular, the assumption that global warming is responsible for all the changes observed appears rather likely. Whether these systematic changes of the chromosomal polymorphism are a consequence of local adaptations or have been produced by migration from the south remains an open question. Zusamennfassung Der gegenwärtige chromosomale Inversionspolymorphismus in 13 europäischen Populationen von Drosophila subobscura wurde mit dem Zustand in denselben Populationen verglichen, die vor 15 bis 35 Jahren untersucht worden waren. Der Chromosomenpolymorphismus der ,,alten'' Populationen unterscheidet sich signifikant von dem der ,,neuen'' Populationen, besonders für die Chromosomen U und O. Eine sehr gute Übereinstimmung zeigt sich zwischen der geographischen Komponente und der genetischen Komponente bei einer graphischen Darstellung der 26 Populationen (13 alte und 13 neue Populationen) durch eine Koordinatenanalyse. Das spiegelt beides wider, die Existenz von signifikanten breitenabhängigen Klinen in der Häufigkeit einiger chromosomaler Strukturtypen in den alten und den neuen Populationen, aber auch die systematischen Änderungen, die sich bei diesen Populationen im Laufe der Zeit zwischen den beiden Untersuchungen ereignet haben. Eine Zunahme in den Häufigkeiten jener Chromosomenstrukturen, die typisch für südliche Breiten sind, und eine Abnahme solcher Strukturen, die häufig in nördliche Breiten sind, konnte beobachtet werden - in den mediterranen, den atlantischen und den mitteleuropäischen Populationen in der gleichen Weise. Außerdem haben die genetischen Distanzen der neuen Populationen zu einer südlichen Referenzpopulation im Vergleich zu denen der alten Populationen abgenommen. Diese Veränderungen wurden vermutlich von klimatischen Faktoren bestimmt, die mit der geographischen Breite korreliert sind. Insbesonders erscheint die Annahme, daß die globale Erwärmung für die Veränderungen des Chromosomenpolymorphismus dafür verantwortlich ist, ziemlich wahrscheinlich. Ob diese systematischen Transformationen des Chromosomenpolymorphismus ein Konsequenz lokaler Anpassungen oder auf Migration aus dem Süden zurückzuführen sind, bleibt eine offene Frage. [source] Detection and visualization of spatial genetic structure in continuous Eucalyptus globulus forestMOLECULAR ECOLOGY, Issue 4 2007TIM H. JONES Abstract Visualizing the pattern of variation using microsatellites within a Eucalyptus globulus forest on the island of Tasmania provided surprising insights into the complex nature of the fine-scale spatial genetic structure that resides in these forests. We used spatial autocorrelation and principal coordinate analysis to compare fine-scale genetic structure between juvenile and mature cohorts in a study area, 140 m in diameter, located within a typical, continuous E. globulus forest. In total, 115 juvenile and 168 mature individuals were genotyped with eight highly polymorphic microsatellite loci. There was no significant difference in the level of genetic diversity between cohorts. However, there were differences in the spatial distribution of the genetic variation. Autocorrelation analysis provided clear evidence for significant spatial genetic structure in the mature cohort and significant, but weaker, structure in the juvenile cohort. The spatial interpolation of principal coordinate axes, derived from ordination of the genetic distance matrix between individuals, revealed a spatially coherent family group which was evident in both cohorts. Direct comparison of the genetic structure within each cohort allowed visualization of a shift in the spatial distribution of genetic variation within the population of approximately 10 m. As the shift coincided with the direction of prevailing winds, it is hypothesized that this phenomenon is due to downwind dispersal of seeds and is indicative of the important role of prevailing winds in forcing eastward gene flow in these high-latitude forests. [source] Clonal genetic diversity and populational genetic differentiation in Phragmites australis distributed in the Songnen Prairie in northeast China as revealed by amplified fragment length polymorphism and sequence-specific amplification polymorphism molecular markersANNALS OF APPLIED BIOLOGY, Issue 1 2009M. Li Abstract Genetic variation within and between four naturally occurring Phragmites australis land populations, DBS, QG, SS1 and SS2 (named after locality), which colonise distinct habitats (different edaphic conditions) in the Songnen Prairie in northeast China, were investigated by amplified fragment length polymorphism (AFLP) and sequence-specific amplification polymorphism (S-SAP) markers. It was found that the selected primer combinations of both markers were highly efficient in revealing the inter-clonal genetic diversity and inter-populational genetic differentiation in P. australis from a molecular ecological perspective. Cluster analysis categorised the plants into distinct groups (DBS, QG and SS groups), which were in line with their localities, albeit the two SS group populations (SS1 and SS2) showed a lower degree of inter-populational differentiation. These results were strongly supported by multiple statistical analysis including Mantel's test, principal coordinate analysis, allocation test and analysis of molecular variance, which further suggested that gene flow, genetic drift and differences in as yet unidentified edaphic factors may all underpin the inter-clonal genetic diversity and inter-populational differentiation at the nucleotide sequence level. Analysis of intra-population clonal diversity also revealed that the QG population harboured a strikingly lower amount of within-population variation compared with those of the other three populations, presumably being caused by genetic drift and followed by physical and/or biological isolation. Homology analysis of a subset of population-specific or population-private AFLP and S-SAP bands suggested that regulatory genes and retroelements might play important roles in the ecological adaptation and differentiation of the P. australis populations. Possible causes for and implications of the extensive genetic variability in P. australis were discussed for its future genetic conservation and use in ecological revegetation. [source] The genetic diversity of perennial Leymus chinensis originating from ChinaGRASS & FORAGE SCIENCE, Issue 1 2007Z. P. Liu Summary Leymus chinensis is an economically and ecologically important grass that is widely distributed across eastern areas of the Eurasian steppe. A better knowledge of genetic diversity of L. chinensis could be valuable in the efficient utilization, conservation and management of germplasm collections. Genetic diversity in thirty-seven morphological characters of 293 accessions was assessed in three successive years. Based on these qualitative and quantitative characters, the genetic diversity indices (Shannon indices) of traits and geographical populations were estimated, and a principal coordinates analysis and a path analysis were undertaken. Compared with the yellow-green type of L. chinensis, the grey-green type had significantly (P < 0·05) more genetic diversity. In addition, the path analysis suggested that the combined effects of genetic diversity and vegetative traits could explain 0·206 of the total variance in plant reproductive traits. The highest Shannon genetic diversity index of accessions (H = 2·252) was observed in accessions from the region of longitude of 124,128°E, suggesting the most abundant germplasm of L. chinensis in this region. [source] Contrasting patterns of nuclear microsatellite genetic structure of Fraxinus mandshurica var. japonica between northern and southern populations in JapanJOURNAL OF BIOGEOGRAPHY, Issue 6 2010Li-Jiang Hu Abstract Aim, The aim of this study is to detect extant patterns of population genetic structure of Fraxinus mandshurica var. japonica in Japan, and to provide insights into the post-glacial history of this species during the Holocene. Location, Hokkaido and Honshu islands, Japan (including the Oshima and Shimokita peninsulas). Methods, We examined nine polymorphic nuclear microsatellite loci to assess genetic variation within and among 15 populations across almost the entire range of the species in Japan. Extant patterns of geographical structure were analysed using Bayesian clustering, Monmonier's algorithm, analysis of molecular variance, Mantel tests and principal coordinates analysis. Recent bottlenecks within populations and regional genetic variation were also assessed. Results, Northern populations (Hokkaido Island and the Shimokita Peninsula) formed a single homogeneous deme, maintaining the highest level of allelic diversity on the Oshima Peninsula. By contrast, southern populations (Honshu Island) demonstrated strong substructure on both coasts. Specifically, populations on the Pacific side of Honshu exhibited significant bottlenecks and erosion of allelic diversity but preserved distinct subclusters diverging from widespread subclusters on the Japan Sea side of this island. Main conclusions, Genetic evidence and life history traits suggest that F. mandshurica occupied cryptic northern refugia on the Oshima Peninsula during the Last Glacial Maximum, which is reflected in the species' extant northern distribution. Strong geographical structure in southern populations, in agreement with fossil pollen records, suggests geographical isolation by mountain ranges running north,south along Honshu. Given that this tree species is cold-adapted and found in riparian habitats, populations on the Pacific side of Honshu probably contracted into higher-elevation swamps during warm post-glacial periods, leading to a reduction of effective population sizes and rare allelic richness. [source] Contrasting phylogeographies inferred for the two alpine sister species Cardamine resedifolia and C. alpina (Brassicaceae)JOURNAL OF BIOGEOGRAPHY, Issue 1 2009Judita Lihová Abstract Aim, We use Cardamine alpina and C. resedifolia as models to address the detailed history of disjunctions in the European alpine system. These species grow on siliceous bedrock: C. alpina in the Alps and Pyrenees, and C. resedifolia in several mountain ranges from the Sierra Nevada to the Balkans. We explore differentiation among their disjunct populations as well as within the contiguous Alpine and Pyrenean ranges, and compare the phylogeographical histories of these diploid sister species. We also include samples of the closely related, arctic diploid C. bellidifolia in order to explore its origin and post-glacial establishment. Location, European alpine system, Norway and Iceland. Methods, We employed amplified fragment length polymorphisms (AFLPs). AFLP data were analysed using principal coordinates analysis, neighbour joining and Bayesian clustering, and measures of diversity and differentiation were computed. Results, For the snow-bed species C. alpina (27 populations, 203 plants) we resolved two strongly divergent lineages, corresponding to the Alps and the Pyrenees. Although multiple glacial refugia were invoked in the Pyrenees, we inferred only a single one in the Maritime Alps , from which rapid post-glacial colonization of the entire Alps occurred, accompanied by a strong founder effect. For C. resedifolia (33 populations, 247 plants), which has a broader ecological amplitude and a wider distribution, the genetic structuring was rather weak and did not correspond to the main geographical disjunctions. This species consists of two widespread and largely sympatric main genetic groups (one of them subdivided into four geographically more restricted groups), and frequent secondary contacts exist between them. Main conclusions, The conspicuously different histories of these two sister species are likely to be associated with their different ecologies. The more abundant habitats available for C. resedifolia may have increased the probability of its gradual migration during colder periods and also of successful establishment after long-distance dispersal, whereas C. alpina has been restricted by its dependence on snow-beds. Surprisingly, the arctic C. bellidifolia formed a very divergent lineage with little variation, contradicting a scenario of recent, post-glacial migration from the Alps or Pyrenees. [source] Genetic diversity revealed by morphological traits and ISSR markers in hazelnut germplasm from northern SpainPLANT BREEDING, Issue 4 2010J. J. Ferreira With 3 figures and 4 tables Abstract Hazelnut (Corylus avellana L.) has been a traditional crop in northern Spain. As a result of germplasm exploration over 3 years (2003,05), 90 trees were selected in this region. This study describes phenotypic variation in nut and husk traits and investigates genetic relationships among selections and cultivars using inter simple sequences repeat (ISSR) markers. The local selections were phenotypically diverse and many had characteristics appreciated by the market. Eleven ISSR primers, which generated 66 polymorphic bands, were used in the analysis. The graph from principal coordinates analysis of the molecular marker data showed two main groups, one for the local selections and the other for the standard cultivars. The dendrogram generated from UPGMA cluster analysis showed the same two main groups. The results suggest that the local accessions are closely related to each other, but are relatively distant from the standard cultivars of eastern Spain, Italy and the USA. Selections from northern Spain may be directly useful as new cultivars or alternatively as parents in breeding programmes. The collection and preservation of this genetic diversity is important. [source] Assessment of genetic diversity in clover species from Sardinia, Italy, using AFLP analysisPLANT BREEDING, Issue 4 2003S. J. Bennett Abstract Two species, Trifolium glomeratum and T. nigrescens, from Sardinia, Italy, were analysed for genetic diversity using amplified fragment length polymorphism (AFLP). Variation between and within populations was compared between the inbreeder, T. glomeratum, and the outbreeder, T. nigrescens. Four AFLP primer combinations resulted in a total of 292 loci, of which 75% were polymorphic in T. glomeratum and 85% in Trifolium nigrescens. Variation was highest between populations in both species, but the difference between populations was greater in T. glomeratum (Fst = 0.17), compared with T. nigrescens (Fst = 0.02). Cluster analysis and principal coordinates analysis were used to verify the relationships found. The high level of genetic variation within populations in both species is attributed to the movement of sheep between paddocks, the existence of both species in Sardinia for thousands of years and the persistence of a long-lived seedbank due to the production of large numbers of small seeds with high levels of hard seededness. [source] Horse-mounted invaders from the Russo-Kazakh steppe or agricultural colonists from western Central Asia?AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2004A craniometric investigation of the Bronze Age settlement of Xinjiang Abstract Numerous Bronze Age cemeteries in the oases surrounding the Täklamakan Desert of the Tarim Basin in the Xinjiang Uyghur Autonomous Region, western China, have yielded both mummified and skeletal human remains. A dearth of local antecedents, coupled with woolen textiles and the apparent Western physical appearance of the population, raised questions as to where these people came from. Two hypotheses have been offered by archaeologists to account for the origins of Bronze Age populations of the Tarim Basin. These are the "steppe hypothesis" and the "Bactrian oasis hypothesis." Eight craniometric variables from 25 Aeneolithic and Bronze Age samples, comprising 1,353 adults from the Tarim Basin, the Russo-Kazakh steppe, southern China, Central Asia, Iran, and the Indus Valley, are compared to test which, if either, of these hypotheses are supported by the pattern of phenetic affinities possessed by Bronze Age inhabitants of the Tarim Basin. Craniometric differences between samples are compared with Mahalanobis generalized distance (d2), and patterns of phenetic affinity are assessed with two types of cluster analysis (the weighted pair average linkage method and the neighbor-joining method), multidimensional scaling, and principal coordinates analysis. Results obtained by this analysis provide little support for either the steppe hypothesis or the Bactrian oasis hypothesis. Rather, the pattern of phenetic affinities manifested by Bronze Age inhabitants of the Tarim Basin suggests the presence of a population of unknown origin within the Tarim Basin during the early Bronze Age. After 1200 B.C., this population experienced significant gene flow from highland populations of the Pamirs and Ferghana Valley. These highland populations may include those who later became known as the Saka and who may have served as "middlemen" facilitating contacts between East (Tarim Basin, China) and West (Bactria, Uzbekistan) along what later became known as the Great Silk Road. Am J Phys Anthropol, 2003. © 2003 Wiley-Liss, Inc. [source] Multivariate analysis of morphological variation in Cineraria deltoidea (Asteraceae, Senecioneae)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2007GLYNIS V. CRON Cluster analysis and principal coordinates analysis were used to investigate phenetic variation in Cineraria deltoidea, a species that ranges from near sea level in KwaZulu-Natal, South Africa, to 4300 m a.s.l. on the mountains of East Africa and Ethiopia. Earlier taxonomic revisions reduced nine previously recognized species to synonyms of C. deltoidea. Two closely related species, C. decipiens and C. atriplicifolia, were also included in the analyses. Thirty-six morphological characters were examined on 111 specimens. Phenograms and scattergrams show partial clusters of specimens of C. deltoidea from individual mountains or geographical regions, but no groups are sufficiently distinct to warrant formal recognition at any rank. The East African specimens from 3000 m a.s.l. and higher tend to cluster together. Growth at high altitude in East Africa is correlated with fewer, larger capitula on longer peduncles, and an absence of a cobwebby indumentum comprising long, narrow-based trichomes. Cineraria deltoidea is thus a highly variable species with geographical and clinal variation evident throughout its range. Cineraria atriplicifolia and C. decipiens are maintained as distinct species, distinguished from C. deltoidea by their growth form, life span and auricle shape. © 2007 University of the Witwatersrand, Johannesburg. Journal compilation © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154, 497,521. [source] Application of RAPDs to the critical taxonomy of the English endemic elm Ulmus plotii DaceBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2000MAX COLEMAN The taxonomy of the British elms is notoriously complicated and a satisfactory consensus classification remains elusive. This taxonomic complexity appears to be attributable to the reproductive biology of the species. Ulmus glabra Huds. reproduces sexually and its taxonomic status is widely (albeit not universally) accepted. In contrast, the suckering elms of the U. minor complex (U. minor Mill. emend. Richens sensu latissimo) rarely reproduce by seed in Britain. Instead they perpetuate predominantly by vegetative reproduction; arguments regarding their taxonomy are legion. We have used molecular markers (RAPDs) to investigate the amounts and partitioning of clonal diversity and taxon inter-relationships in the British elms, focusing on a particularly enigmatic suckering elm, U. plotii Druce. Our molecular data suggest that all samples of U. plotii that precisely match the type description are ramets of a single genet, the distribution of which is attributable to human planting. Morphologically similar samples, which have many but not all of the U. plotii diagnostic characters, do not cluster with U. plotii when the RAPD data are analysed using principal coordinates analysis (PCO). Instead, they are scattered on the PCO plots throughout the broader range of variability of the U. minor complex. The implications of these results for the taxonomy of the British elms are discussed, and the need to combine knowledge of population structure with taxonomic pragmatism is emphasized. [source] | |||||||||||||||||||||||||