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DNA Diversity (dna + diversity)
Kinds of DNA Diversity Selected AbstractsChloroplast and microsatellite DNA diversities reveal the introduction history of Brazilian peppertree (Schinus terebinthifolius) in FloridaMOLECULAR ECOLOGY, Issue 12 2005DEAN A. WILLIAMS Abstract Brazilian peppertree (Schinus terebinthifolius) is a woody perennial that has invaded much of Florida. This native of northeastern Argentina, Paraguay, and Brazil was brought as an ornamental to both the west and east coasts of Florida at the end of the 19th century. It was recorded as an invader of natural areas in the 1950s, and has since extended its range to cover over 280 000 ha. Our goals were to understand the history of this invasion, as one step toward understanding why this exotic was so successful, and ultimately to improve development of biological control agents. We sampled plants from the native and exotic ranges, particularly Florida, and genotyped these individuals at nuclear and chloroplast loci. Nuclear microsatellite and cpDNA loci reveal strong genetic population structure consistent with limited dispersal in the introduced and native ranges. Bayesian clustering of microsatellite data separates the east and west coast plants in Florida into distinct populations. The two chloroplast haplotypes found in Florida are also concordant with this separation: one predominates on the east coast, the other on the west coast. Analysis of samples collected in South America shows that haplotypes as distinct as the two in Florida are unlikely to have come from a single source population. We conclude that the genetic evidence supports two introductions of Brazilian peppertree into Florida and extensive hybridization between them. The west coast genotype likely came from coastal Brazil at about 27° south, whereas the east coast genotype probably originated from another, as yet unidentified site. As a result of hybridization, the Florida population does not exhibit low genetic variation compared to populations in the native range, possibly increasing its ability to adapt to novel environments. Hybridization also has important consequences for the selection of biocontrol agents since it will not be possible to identify closely co-adapted natural enemies in the native range, necessitating more extensive host testing. [source] Mitochondrial control region variation in bank voles (Clethrionomys glareolus) is not related to Chernobyl radiation exposureENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 2 2007Heather N. Meeks Abstract ,Three previous studies at Chernobyl, Ukraine, documented elevated mitochondrial DNA diversity in bank voles (Clethrionomys glareolus) from radioactively contaminated sites. Little evidence was found to link patterns of diversity in contaminated areas to radiation exposure, but the experimental design precluded discriminating among alternative explanations for elevated diversity in exposed groups. Reference sites selected for the studies were relatively distant from contaminated sites and, additionally, were separated from contaminated sites by large river systems; thus, we hypothesized that differences among sites were correlated with geographic isolation rather than with radiation exposure. For the present study, we added three reference sites, which were selected based on minimal radioactive contamination, proximity to contaminated sites, and absence of obvious barriers to dispersal. We hypothesized that neighboring reference sites should exhibit levels and patterns of diversity similar to those of contaminated sites if the previously detected differences were, in fact, caused by geographic isolation. Indeed, levels of diversity in nearby reference sites are comparable to levels in contaminated sites. Additionally, nearby reference sites contain several haplotypes not observed at other study sites. Our results suggest that levels of diversity in contaminated regions are more plausibly explained by ecological and historical factors than by increased mutational pressure resulting from exposure to Chernobyl radiation. [source] Effects of environmental pollution on microsatellite DNA diversity in wood mouse (Apodemus sylvaticus) populationsENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 11 2005Veerle Berckmoes Abstract Ten microsatellite DNA loci were surveyed to investigate the effects of heavy metal pollution on the genetic diversity and population genetic structure of seven wood mouse (Apodemus sylvaticus) populations along a heavy metal pollution gradient away from a nonferrous smelter in the south of Antwerp (Flanders, Belgium). Analysis of soil heavy metal concentrations showed that soil Ag, As, Cd, Cu, and Pb decreased with increasing distance from the smelter. Genetic analyses revealed high levels of genetic variation in all populations, but populations from the most polluted sites in the gradient did not differ from those of less-polluted sites in terms of mean observed and expected heterozygosity level and mean allelic richness. No correlation was found between measures of genetic diversity and the degree of heavy metal pollution. However, an analysis of molecular variance and a neighbor-joining tree suggested a contamination-related pattern of genetic structuring between the most polluted and less polluted sites. Pairwise FST values indicated that populations were significantly genetically differentiated, and assignment tests and direct estimates of recent migration rates suggested restricted gene flow among populations. Additionally, genetic differentiation increased significantly with geographical distance, which is consistent with an isolation-by-distance model. We conclude that, at least for our microsatellite DNA markers, genetic diversity in the studied wood mouse populations is not affected greatly by the heavy metal pollution. [source] Different Helicobacter pylori Strains Colonize the Antral and Duodenal Mucosa of Duodenal Ulcer PatientsHELICOBACTER, Issue 2 2000Ann-Catrin E. Thoreson Background. We have investigated the possibility that the same patients may be colonized by Helicobacter pylori strains of different genotypes or phenotypes in the antrum as compared to in the duodenum. The strains were typed for DNA fingerprints, different lipopolysaccharides (LPS), and Lewis antigen expression on the O,side chains of LPS. Materials and Methods. Polymerase chain reaction (PCR) amplifications using primer sequences (i.e., the Enterobacterial Repetitive Intergenic Consensus [ERIC]) and randomly amplified polymorphic DNA (RAPD) elements were performed to asses chromosomal DNA diversity between H. pylori strains. The expression of different LPS types and Lewis antigens in the various H. pylori isolates were determined by whole bacterial enzyme-linked immunosorbent assays using monoclonal antibodies. Results. Duodenal ulcer patients had different H. pylori genotypes in the duodenum as compared to in the antrum as shown by ERIC-PCR (44%) and by RAPD-PCR (75%). Different DNA patterns were found among the strains that were isolated from various regions of the duodenum in 4 of 16 patients (25%) as shown by ERIC-PCR and in 8 of 16 patients (50%) as shown by RAPD-PCR. Sixty-three percent of the duodenal ulcer patients had H. pylori strains with a different Lewis antigen phenotype in the duodenum as compared to in the antrum, and 3 of 16 patients (19%) had strains with different Lewis antigens expressed by strains from different duodenal biopsies from the same patient. Conclusion. The results suggest that a mixed population of different H. pylori strains with marked variation, both genotypically and phenotypically, colonize the same patient. [source] How mitochondrial DNA diversity can help to understand the dynamics of wild-cultivated complexes.MOLECULAR ECOLOGY, Issue 12 2001The case of Medicago sativa in Spain Abstract In order to clarify the relationships (genetic exchange and shared ancestry) between natural and cultivated populations of alfalfa (Medicago sativa L.) in Spain, we investigated the patterns of mitochondrial DNA variation (characterized through restriction fragment length polymorphism) for 248 individuals in seven natural and six cultivated populations of this species. Mitochondrial variation was evidenced in both natural and cultivated populations of M. sativa. Among the seven mitotypes idengified in the species, two were specific of the natural populations, a result attesting the fact that the Spanish wild form of M. sativa is an original genetic pool compared to the cultivated one. Other mitotypes were observed in both natural and cultivated populations, suggesting the occurrence of gene flow through seeds from cultivated towards natural populations. Comparisons with previously gathered nuclear and phenotypic data give insights into the different evolutionary forces acting on the different kinds of Spanish natural populations examined so far. [source] Genetic structure and random amplified polymorphic DNA diversity of the rapidly declining Angelica palustris (Apiaceae) in Eastern Germany in relation to population size and seed productionPLANT SPECIES BIOLOGY, Issue 3 2005ANKE DITTBRENNER Abstract Angelica palustris (Besser) Hoffm. (Apiaceae) is a rare wetland community species that is currently rapidly declining because of changes in land use. In the present study, we analyzed patterns of random amplified polymorphic DNA (RAPD) variation among nine populations of A. palustris in Germany to assess its overall genetic condition. We aimed to examine the level of genetic diversity as well as its local differentiation in relation to population size and geographic distancing between populations. Results achieved from ,ST statistics and amova indicated that most of the variability is distributed among individuals within the populations (57.7%), whereas among-population variation accounted for 30.2% of the variation. Variation between regions was 12.1%. This corresponds to the results of a multivariate analysis based on the asymmetric Soerensen similarity, which also suggested a strong population differentiation, as would be expected from a short-lived species with limited seed dispersal capacities that had never covered extensive areas in Eastern Germany. Consistently the geographic differentiation was not reflected in the RAPD profile. Significant correlations were noted between population size and the percentage of polymorphic loci (P < 0.05) and genetic diversity (P < 0.05). An analysis of seed production showed positive relationships between average seed number and levels of genetic variation. Our results support concerns regarding the loss of genetic diversity in endangered plant populations because this process might have harmful effects on reproductive fitness. [source] Human DNA sequences: More variation and less raceAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2009Jeffrey C. Long Abstract Interest in genetic diversity within and between human populations as a way to answer questions about race has intensified in light of recent advances in genome technology. The purpose of this article is to apply a method of generalized hierarchical modeling to two DNA data sets. The first data set consists of a small sample of individuals (n = 32 total, from eight populations) who have been fully resequenced for 63 loci that encode a total of 38,534 base pairs. The second data set consists of a large sample of individuals (n = 928 total, from 46 populations) who have been genotyped at 580 loci that encode short tandem repeats. The results are clear and somewhat surprising. We see that populations differ in the amount of diversity that they harbor. The pattern of DNA diversity is one of nested subsets, such that the diversity in non-Sub-Saharan African populations is essentially a subset of the diversity found in Sub-Saharan African populations. The actual pattern of DNA diversity creates some unsettling problems for using race as meaningful genetic categories. For example, the pattern of DNA diversity implies that some populations belong to more than one race (e.g., Europeans), whereas other populations do not belong to any race at all (e.g., Sub-Saharan Africans). As Frank Livingstone noted long ago, the Linnean classification system cannot accommodate this pattern because within the system a population cannot belong to more than one named group within a taxonomic level. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc. [source] Nuclear integrations of mitochondrial DNA in gorillasAMERICAN JOURNAL OF PRIMATOLOGY, Issue 3 2004Michael I. Jensen-Seaman Abstract Great ape systematics, particularly at the species level and below, is currently under debate, due in part to the recent influx of molecular data. The phylogenies of previously published mitochondrial control region (or D-loop) DNA sequences in gorillas show deep splits within West African gorillas (Gorilla gorilla gorilla), and very high levels of nucleotide diversity in this subspecies. Here we demonstrate that several previously reported D-loop haplotypes from West African gorillas are in all likelihood nuclear integrations of mitochondrial DNA. Revised estimates of the amount and pattern of mitochondrial DNA diversity in gorillas are provided, revealing two reciprocally monophyletic and highly divergent groups of gorillas, concurrent with their geographic distribution. Am. J. Primatol. 63:139,147, 2004. © 2004 Wiley-Liss, Inc. [source] Mitochondrial DNA diversity and origins of South and Central American goatsANIMAL GENETICS, Issue 3 2009M. Amills Summary We have analysed the genetic diversity of South and Central American (SCA) goats by partially sequencing the mitochondrial control region of 93 individuals with a wide geographical distribution. Nucleotide and haplotype diversities reached values of 0.020 ± 0.00081 and 0.963 ± 0.0012 respectively. We have also observed a rather weak phylogeographic structure, with almost 69% of genetic variation included in the within-breed variance component. The topology of a median-joining network analysis including 286 European, Iberian, Atlantic and SCA mitochondrial sequences was very complex, with most of the haplotypes forming part of independent small clusters. SCA sequences showed a scattered distribution throughout the network, and clustering with Spanish and Portuguese sequences occurred only occasionally, not allowing the distinguishing of a clear Iberian signature. Conversely, we found a prominent cluster including Canarian, Chilean, Argentinian and Bolivian mitochondrial haplotypes. This result was independently confirmed by constructing a Bayesian phylogenetic tree (posterior probability of 0.97). Sharing of mitochondrial haplotypes by SCA and Canarian goats suggests that goat populations from the Atlantic archipelagos, where Spanish and Portuguese ships en route to the New World used to stow food and supplies, participated in the foundation of SCA caprine breeds. [source] Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goatANIMAL GENETICS, Issue 3 2009L. J. Royo Summary To date, no comprehensive study has been performed on mitochondrial genetic diversity of the West African goat. Here, we analysed a 481-bp fragment of the HVI region of 111 goats representing four native West African populations, namely the three main Burkina Faso breeds, zoo-farm kept Dwarf goats and endangered Spanish goat breeds used as the outgroup. Analyses gave 83 different haplotypes with 102 variable sites. Most haplotypes (65) were unique. Only three haplotypes were shared between populations. Haplotypes were assigned to cluster A except for H45 (belonging to the Spanish Bermeya goat) which was assigned to cluster C. amova analysis showed that divergence between groups (,CT) was not statistically significant regardless of whether the partition in two hierarchical levels that was fitted included Spanish samples or not. The West African goat scenario shown here is consistent with that previously reported for the species: haplogroup A is predominant and has a very high haplotype diversity regardless of the geographic area or sampled breed. The large phenotypic differences observable between the West African Dwarf and Sahelian long-legged goat populations are not detectable with mitochondrial markers. Moreover, a previously suggested introgression of Sahelian goat southwards because of desertification could not be assessed using mtDNA information. [source] Worldwide mitochondrial DNA diversity and phylogeography of pilot whales (Globicephala spp.)BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2009MARC OREMUS Pilot whales (Globicephala spp.) provide an interesting example of recently diverged oceanic species with a complex evolutionary history. The two species have wide but largely non-overlapping ranges. Globicephala melas (long-finned pilot whale; LFPW) has an antitropical distribution and is found in the cold-temperate waters of the North Atlantic and Southern Hemisphere, whereas Globicephala macrorhynchus (short-finned pilot whale; SFPW) has a circumglobal distribution and is found mainly in the tropics and subtropics. To investigate pilot whale evolution and biogeography, we analysed worldwide population structure using mitochondrial DNA (mtDNA) control region sequences (up to 620 bp) from a variety of sources (LFPW = 643; SFPW = 150), including strandings in New Zealand and Tasmania, and whale-meat products purchased on the markets of Japan and Korea. Phylogenetic reconstructions failed to support a reciprocal monophyly of the two species, despite six diagnostic substitutions, possibly because of incomplete lineage sorting or inadequate phylogenetic information. Both species had low haplotype and nucleotide diversity compared to other abundant widespread cetaceans (LFPW, , = 0.35%; SFPW, , = 0.87%) but showed strong mtDNA differentiation between oceanic basins. Strong levels of structuring were also found at the regional level. In LFPW, phylogeographic patterns were suggestive either of a recent demographic expansion or selective sweep acting on the mtDNA. For SFPW, the waters around Japan appear to represent a centre of diversity, with two genetically-distinct forms, as well as a third population of unknown origin. The presence of multiple unique haplotypes among SFPW from South Japan, together with previously documented morphological and ecological differences, suggests that the southern form represents a distinct subspecies and/or evolutionary significant unit. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 729,744. [source] | ||||||||||