Diversity Of Ecotypes Research Articles

Genetic diversity in ecotypes of Tunisian date-palm (Phoenix dactylifera L.) assessed by AFLP markers

SummaryAmplified fragment length polymorphisms (AFLP) were used successfully to survey genetic diversity in 40 ecotypes of date-palm (Phoenix dactylifera L.) collected from oases in Tunisia. Six primer pairs were screened to assess their ability to detect polymorphism in this tree crop. As a result, a total of 428 AFLPs have been generated and used to estimate genetic distances which ranged from 0.07 – 0.63. A large, and typically continuous, range of genetic diversity characterises Tunisian date-palm germplasm. In addition, the UPGMA dendrogram derived from these data exhibited two clusterings of ecotypes independent of their geographic origin or the sex of the trees. These data corroborate the hypothesis of the origin of date-palm domestication being in Mesopotamia. Moreover, taking into account the high percentage of polymorphic bands, together with their resolving power (Rp), all the primer pairs tested contributed to the discrimination of date-palm genotypes, suggesting that the AFLP method is efficient in assessing genetic diversity in this crop. The data are discussed in relation to the use of AFLP molecular markers in the management and improvement of date-palm.

Distribution, composition, and orientation of down deadwood in riparian old-growth woodlands of Zoar Valley Canyon, western New York State, USA

During 2005, we catalogued down deadwood (DDW) in forty-one 30-m × 30-m quadrats on 10 riparian upper terraces within the minimally disturbed Zoar Valley Canyon of western New York State. Woodlands on these former floodplains represent late-successional stages of a diversity of broadleaf ecotypes, with increment core-based stand ages up to 351 years. Volume of DDW averaged 84.9 ± 9.7 (±S.E.) m 3/ha among all quadrats, and ranged up to 145.3 ± 43.2 m 3/ha on individual terraces. Abundance of downed sugar maple reflected this species’ prevalence in the live overstory, but American beech deadwood was markedly overabundant due to beech bark disease mortality. Prevalence of very-shade-tolerant (sugar maple, American beech, eastern hemlock) DDW was modest for northern hardwood old growth (46.4 ± 4.3% among all quadrats), and was not related to stand age. We speculate this may reflect the floodplain origin of these woodlands. Down deadwood volume was positively associated with stand age among terraces ( R 2 = 0.446, P = 0.035), but not at the neighborhood scale of 30-m quadrats ( R 2 = 0.027), where individual tree mortality may obscure broader patterns. Orientation of DDW was non-uniform (Kolmogorov–Smirnov goodness-of-fit, P < 0.05) on five of the ten study terraces, where statistical trends in treefall direction suggested the influence of prevailing westerly winds blowing through the east-west canyon (this DDW orientation was also opposite to stream flow). This was an unexpected result, however, as we otherwise found very limited evidence of episodic wind-throw within the study area.

Genetic diversity and reproductive biology in ecotypes of the facultative apomict Hypericum perforatum L.

Apomixis is a mode of asexual reproduction through seed. Progeny produced by apomixis are clonal replicas of a mother plant. The essential feature of apomixis is that embryo sacs and embryos are produced in ovules without meiotic reduction or egg cell fertilisation. Thus, apomixis fixes successful gene combinations and propagates high fitness genotypes across generations. A more profound knowledge of the mechanisms that regulate reproductive events in plants would contribute fundamentally to understanding the evolution and genetic control of apomixis. Molecular markers were used to determine levels of genetic variation within and relationship among ecotypes of the facultative apomict Hypericum perforatum L. (2n = 4x = 32). All ecotypes were polyclonal, being not dominated by a single genotype, and characterised by different levels of differentiation among multilocus genotypes. Flow cytometric analysis of seeds indicated that all ecotypes were facultatively apomictic, with varying degrees of apomixis and sexuality. Seeds set by haploid parthenogenesis and/or by fertilisation of aposporic egg cells were detected in most populations. The occurrence of both dihaploids and hexaploids indicates that apospory and parthenogenesis may be developmentally uncoupled and supports two distinct genetic factors controlling apospory and parthenogenesis in this species. Cyto-embryological analysis showed that meiotic and aposporic processes do initiate within the same ovule: the aposporic initial often appeared evident at the time of megaspore mother cell differentiation. Our observations suggest that the egg cell exists in an active metabolic state before pollination, and that its parthenogenetic activation leading to embryo formation may occur before fertilisation and endosperm initiation.

Molecular characterization of genetic diversity in European germplasm of perennial ryegrass

Perennial ryegrass (Lolium perenne L.) is the most important grass species for temperate grassland agriculture. The level and distribution of genetic variation in gene bank ecotype collections is still largely unknown but of great interest for the planning of breeding programs. The objectives of this study were to (i) assess the molecular diversity of Polish ecotypes of perennial ryegrass, and (ii) compare the relationship between this group and German ecotypes and European cultivars investigated previously. A total number of 166 polymorphic marker bands were detected among the 171 individual plants of the 9 Polish ecotypes. In a joint analysis with 9 Polish and 22 German ecotypes, and 22 European cultivars 172 polymorphic RAPD markers could be found. Genetic distance among the Polish ecotypes ranged from 0.31 to 0.51, while for all 53 populations a broader range was detected (0.25–0.67). An analysis of molecular variance (AMOVA) revealed a much larger variation within populations (71%) than among them (29%). The Polish ecotypes contained the highest within population variation (74%). The largest among group difference (15%) was found between the Polish ecotypes versus all other accessions. We conclude that the Polish ecotypes represent a valuable genetic resource for enlarging the genetic variation in the West European germplasm pool of perennial ryegrass.

Reclassification of salt-water Bdellovibrio sp. as Bacteriovorax marinus sp. nov. and Bacteriovorax litoralis sp. nov.

Bdellovibrios are unique, predatory bacteria with an intraperiplasmic growth and multiplication phase within their prey, which consists of many Gram-negative bacteria. Until recently, all bacteria that exhibited these traits were included in the genus Bdellovibrio. However, analysis of 16S rDNA sequences and other studies have demonstrated substantial genotypic, phenotypic and ecotypic diversity among the organisms in this genus (Baer et al., 2000; Snyder et al., 2002). This has resulted in reclassification of Bdellovibrio stolpii and Bdellovibrio starrii into the newly constructed genus Bacteriovorax (Baer et al., 2000). In this study, examination of marine isolates of Bdellovibrio (designated SJT, AQ and JS5T) has revealed them to be related more closely to the newly designated genus Bacteriovorax. Phylogenetic analysis of 16S rRNA gene sequences revealed that marine isolates SJT, AQ and JS5T clustered in a separate clade from Bdellovibrio bacteriovorus 100T as part of the clade that contains Bacteriovorax spp., indicating a much closer taxonomic relationship to the latter. DNA-DNA hybridization experiments also demonstrated <5 % similarity between Bdellovibrio bacteriovorus 100T and the marine isolates. Distinct differences between the salt-water group and Bdellovibrio spp. were also observed by determination of DNA G+C content, salinity growth testing and antibiotic sensitivity analysis. On the basis of the results from the studies described above, it is proposed that marine isolates SJT (=ATCC BAA-682T=DSM 15412T) and JS5T (=ATCC BAA-684T=DSM 15409T) should be classified within the genus Bacteriovorax as the type strains of Bacteriovorax marinus sp. nov. and Bacteriovorax litoralis sp. nov., respectively.

Productivity, trophic structure, and energy flow in the steady-state ecosystems of Silver Springs, Florida

Animals originated in the oceans and evolved there for hundreds of millions of years before adapting to terrestrial environments. Today, oceans cover more than two-thirds of Earth and generate as much primary production as land. The path from the first macrobiota to modern marine biodiversity involved parallel increases in terrestrial nutrient input, marine primary production, species’ abundance, metabolic rates, ecotypic diversity and taxonomic diversity. Bottom-up theories of ecosystem cascades arrange these changes in a causal sequence. At the base of marine food webs, nutrient fluxes and atmosphere–ocean chemistry interact with phytoplankton to regulate production. First-order consumers (e.g., zooplankton) might propagate changes in quantity and quality of phytoplankton to changes in abundance and diversity of larger predators (e.g., nekton). However, many uncertainties remain about the mechanisms and effect size of bottom-up control, particularly in oceans across the entire history of animal life. Here, we review modern and fossil evidence for hypothesized bottom-up pathways, and we assess the ramifications of these processes for four key intervals in marine ecosystems: the Ediacaran–Cambrian (635–485 million years ago), the Ordovician (485–444 million years ago), the Devonian (419–359 million years ago) and the Mesozoic (252–66 million years ago). We advocate for a clear articulation of bottom-up hypotheses to better understand causal relationships and proposed effects, combined with additional ecological experiments, paleontological documentation, isotope geochemistry and geophysical reconstructions. How small-scale ecological change transitions into large-scale evolutionary change remains an outstanding question for empirical and theoretical research.

Spatial distribution of Rhodopseudomonas palustris ecotypes on a local scale.

The number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. Oda et al. (Y. Oda, B. Star, L. A. Huisman, J. C. Gottschal, and L. J. Forney, Appl. Environ. Microbiol. 69:xxx-xxx, 2003) have shown that Rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. To extend these observations, we investigated the clonal diversity of R. palustris in 0.5-g samples taken from the corners and center of a 1-m square. A total of 35 or 36 clones were recovered by direct plating from each sample and were characterized by BOX A1R repetitive element-PCR genomic DNA fingerprinting. Isolates with fingerprint images that were >/=80% similar to each other were defined as the same genotype. Among the 178 isolates studied, 32 genotypes were identified, and each genotype contained between 1 and 40 isolates. These clusters were consistent with minor variations found in 16S rRNA gene sequences. The Shannon indices of the genotypic diversity within each location ranged from 1.08 (5 genotypes) to 2.18 (13 genotypes). Comparison of the rank abundance of genotypes found in pairs of locations showed that strains from three locations were similar to each other, with Morisita-Horn similarity coefficients ranging from 0.59 to 0.71. All comparisons involving the remaining two locations resulted in coefficients between 0 and 0.12. From these results we inferred that the patterns of ecotype diversity at the sampling site are patchy at a 1-m scale and postulated that factors such as mixing, competitive interactions, and microhabitat variability are likely to be responsible for the maintenance of the similarities between some locations and the differences between others.

Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice ( Oryza sativa L.).

Four multiplex panels of fluorescent-labeled rice microsatellite markers were designed to survey allelic diversity at a total of 27 simple sequence repeat loci. Automated fragment detection, size calling and binning were used to identify the microsatellite alleles. The panels were tested on 72 accessions representing the diversity of ecotypes and isozyme groups in cultivated rice ( Oryza sativa L.). Genetic diversity was evaluated by estimating the distribution and range of allele sizes, as well as the polymorphism information content (PIC), for each microsatellite locus. The multiplex panels were shown to be useful for fingerprinting and for clustering rice varieties, and genetic associations determined in this analysis agreed well with previous isozyme- and RFLP-based studies of these genotypes. Because of the wide cross-section of germplasm represented, we expect that the allele size-ranges reported here are close to the maximum for cultivated rice. In the future, panels of microsatellites from each rice chromosome will be made to facilitate the mapping of segregating populations and the identification of genes and QTLs underlying traits of interest.

CARACTERIZACIÓN Y VARIABILIDAD AGRONÓMICA DE 125 ECOTIPOS DE Bromus valdivianus Phil. RECOLECTADOS EN LA PROVINCIA DE VALDIVIA

Bromus valdivianus Phil. is a native species of southern Chile. It can be found on natural pastures of the Xth Region. The evolution of this species has created a wide diversity of ecotypes, which have not been characterized. The objective of this study was to characterize agronomically 125 ecotypes of B. valdivianus Phil., which were collected from four different areas of Valdivia province. Additionally through a multivariate analysis, groups of B. valdivianus Phil. ecotypes with similar agronomic characteristics were determinated. One hundred twenty five B. valdivianus Phil. ecotypes were studied from four different areas (north central valley, south central valley, north foofhills and south foothills). Ten variables were evaluated, from which dry matter was measured on spring, summer and autumn. A randomized block design with three replicatos was used. The average data from the ecotypes for the variables were analyzed by mean of multivariate analysis. The agronomic characterization allowed to show the phenotypic differentiation among ecotypes in relation to forage production. Principal components analysis and cluster analysis were used to observe the nature and degree of divergence of ecotypes, while the discriminant analysis allowed to determine if individuals in each group were well classified. Three principal components were choosen, which explained 56.7% of the total variation. The cluster analysis distinguished four groups clearly related with forage production and leaf morphology. According with discriminant analysis 94,4% of ecotypes were correctly classified and seven ecotypes (5,6%) were not. The geographic origin of the ecotypes did not show relationship with the cluster, because of some plants from different areas were observed in the same group.

Host-specific ecotype diversity of rhizoplane diazotrophs of the perennial glasswort Salicornia virginica and selected salt marsh grasses

The degree of host specificity of most plant root associated bacteria is poorly under- stood. In this study we examined the physiological diversity of oxygen utilizing, culturable dia- zotrophs from the rhizoplane of the high marsh perennial glasswort Salicornia virginica and com- pared them to diazotrophs from other salt marsh plants (tall and short Spartina alterniflora, Juncus roemerianus, and Spartina patens) from the same ecosystem. Forty-six pure culture strains were recovered from the rhizoplane of S. virginica by stab inoculating freshly collected roots into com- bined nitrogen-free semi-solid media, followed by streak plating of clonal outgrowths. The majority of these strains were Gram-negative obligately aerobic or microaerophilic rods, but 3 Gram-positive strains were also isolated and characterized. API 20NE test strips were used for preliminary charac- terization of all strains, yielding 22 physiologically different API strain groups. One representative strain was selected from each API group and tested for the presence of nifH, denoting strains capa- ble of N2-fixation. Seventeen strains (14 Gram-negative, 3 Gram-positive) were nifH-positive and were characterized further using BIOLOG test plates. Four well-supported strain clusters were iden- tified by bootstrapped cluster analysis of the BIOLOG substrate utilization profiles. These clusters differed in utilization of carbohydrates, carboxylic acids, and amino acids. S. virginica diazotrophs were physiologically quite different from rhizoplane diazotrophs from the low marsh plants S. alterni- flora and J. roemerianus, but much more similar to diazotrophs from another high marsh plant, S. patens. We hypothesize that the observed physiological differentiation between high marsh and low marsh diazotrophs reflects differences in selection pressures in the rhizoplane microenvironment produced by plants with differing abilities to ventilate the rhizosphere. In addition, high and low marsh branches were further resolved into host-specific strain clusters, which also implies a strong impact of other host features, such as the suite of carbon exudate compounds produced, on the dis- tributions of specific diazotroph strains. These findings imply endemic, host-specific distributions of salt marsh diazotrophs and are consistent with the great diversity of diazotrophs that have been observed in this ecosystem to date.

Mangroves of the United Arab Emirates: ecotypic diversity in cuticular waxes at the bioclimatic extreme

Scattered populations of Avicennia marina can be found in the Arabian Gulf, occupying one of the driest mangrove habitats in the world, in which salt concentrations may reach levels that are beyond the physiological limit for other species. These ecosystems are poorly known, in particular, what levels of productivity can be attained and whether there are any indications of genetic adaptation to these exceptionally severe conditions. We have estimated standing biomass as varying between 70 and 110 t ha −1 for the tallest stands and between 14 and 65 t ha −1 for shortest stands. Our estimates for litterfall are 7.4–8.5 t ha −1 yr −1 in the tallest stands and 5.1–6.9 t ha −1 yr −1 in the shortest stands. These values of biomass are intermediate between levels reported for the same species in New Zealand and in Australia and the estimate of litterfall is comparable with that obtained from stands in Australia. Thus, despite the harsh ecological conditions, A. marina forms highly productive stands. We have analyzed leaf cuticular hydrocarbon composition, by gas chromatography, as a marker of population differentiation. The dominant alkanes were C 33 and C 31, which are unusually long as compared with the other widespread species Avicennia. germinans. Since longer carbon chain lengths appear to offer an adaptation to minimize cuticular water loss, it would appear that A. marina has evolved under more arid conditions than A. germinans. Our sampled population from the Inner Gulf differed in quantitative cuticular wax composition from the Outer Gulf population, suggesting a possible genetic differentiation between the two populations. Our data indicate the need for more detailed analyses of the possible role of genetic adaptation in the productivity of mangrove ecosystems at the margins of their ecological range.

Isozyme Genotype of Major Cultivar Groups Resistant to Bacterial Blight in Asian Rice.

Isozyme types were determined for six cultivar groups carrying different resistance to rice bacterial blight in Asia. The temporarily proposed Isozyme genotypes would be associated with the differentiation of the reaction of resistance. The predominant type of the Java 14 group was Isozyme type VI-1, and type II-4 was involved as the second predominant type. The majority of the DZ 192 group belonged to type II-1 and II-2. A newly assigned TN 1 group consisted of Isozyme type I and VI / . The predomi-nant occurrence of I-1 and I-2 was common among the TKM 6, Cas 209, Mond Ba and TN I groups. However, frequent involvement of IM-1 and IM-2 were specific to the TKM 6 group. The frequent presence of I-4 and I-5 was the characteristic of the Cas 209 and Mond Ba groups. Based on these observations the ecotypic diversity of each group was discussed.

MODELING THE DEVELOPMENT OF IN-SITU BREAST-CANCER - A CLONAL EVOLUTIONARY APPROACH

We present a speculative hypothesis based on the assumption that a morphological parameter of a tumour in this case the nuclear area as assessed by computerised image analysis can be utilised to predict the number of specific events occurring at a gene or chromosomal level within a tumour given the assumption that the tumour morphology is predictive of the clonal evolution of a tumour and clonal progression of neoplasia. Assuming that the phenotype of the tumour is truly determined by the genotype and that morphological variations within a tumour are not due to other factors such analogous to biotypic or ecotypic diversity in animal species we argue that this may be a valuable model to approach the understanding of tumour biology and clonal evolution of tumour cell populations. Such analyses could in future be important in cytogenetic or microdissection studies of DCIS, and could be applicable to studies of clonal evolution in DCIS and other neoplasms using fluorescent in situ hybridisation.

Mode of Subsistence and Folk Biological Taxonomy [and Comments and Reply

There are significant differences between the folk biological taxonomy and nomenclature of hunter-gatherers and that of small-scale agriculturalists. While foragers possess sizable inventories of labeled plant and animal classes, small-scale farmers tend to have inventories that are considerably larger. Also, binomial names, such as English blue oak and shingle oak, are common in folk taxonomies of cultivators but rare in those of hunter-gatherers. An explanatory framework accounting for these findings is proposed which in part relates the larger taxonomies of farmers to (1) a diversity of ecotypes created by subsistence farming that supports a broadened range of wild organisms, (2) intensive utilization of wild plants and animals as famine foods when crops fail, and (3) the greater health risks of farmers, which motivate exceptional interest in organisms of medicinal value. The common occurrence of binomially labeled classes in taxonomies of agriculturalists is related to the lower salience of those ta...