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Pairwise Distances (pairwise + distance)
Selected AbstractsThe divergence of two independent lineages of an endemic Chinese gecko, Gekko swinhonis, launched by the Qinling orogenic beltMOLECULAR ECOLOGY, Issue 12 2010JIE YAN Abstract The genetic structure and demographic history of an endemic Chinese gecko, Gekko swinhonis, were investigated by analysing the mitochondrial cytochrome b gene and 10 microsatellite loci for samples collected from 27 localities. Mitochondrial DNA data provided a detailed distribution of two highly divergent evolutionary lineages, between which the average pairwise distance achieved was 0.14. The geographic division of the two lineages coincided with a plate boundary consisting of the Qinling and Taihang Mts, suggesting a historical vicariant pattern. The orogeny of the Qinling Mts, a dispersal and major climatic barrier of the region, may have launched the independent lineage divergence. Both lineages have experienced recent expansion, and the current sympatric localities comprised the region of contact between the lineages. Individual-based phylogenetic analyses of nucDNA and Bayesian-clustering approaches revealed a deep genetic structure analogous to mtDNA. Incongruence between nucDNA and mtDNA at the individual level at localities outside of the contact region can be explained by the different inheritance patterns and male-biased dispersal in this species. High genetic divergence, long-term isolation and ecological adaptation, as well as the morphological differences, suggest the presence of a cryptic species. [source] Use of RAPD and killer toxin sensitivity in Saccharomyces cerevisiae strain typingJOURNAL OF APPLIED MICROBIOLOGY, Issue 3 2005L. Corte Abstract Aims:, Two different strain characterization techniques, random amplified polymorphic DNA (RAPD) and killer toxin sensitivity (KTS), were compared to assess their typing performance using a set of 30 certified Saccharomyces cerevisiae strains. Methods and Results:, A sequential random resampling procedure was employed to subdivide the 32 descriptors in eight sets, in order to compare the differential performances of the two techniques with diverse number of characters. Results showed that RAPD performs better than killer, although the complete differentiation of the strains under study could be obtained only by combining profiles from the two techniques Conclusions:, The combination of different typing techniques was useful when discriminating similar organisms. In such cases, the introduction of a second typing technique can be more advantageous than increasing the number of characters obtained with a single method. Significance and Impact of the Study:, The distribution of among-strains pairwise distances and the relative performance of the two techniques has implications for the study of biodiversity, taxonomy and microbial ecology. [source] Taxonomic homogenization and differentiation across Southern Ocean Islands differ among insects and vascular plantsJOURNAL OF BIOGEOGRAPHY, Issue 2 2010Justine D. Shaw Abstract Aim, To investigate taxonomic homogenization and/or differentiation of insect and vascular plant assemblages across the Southern Ocean Islands (SOI), and how they differ with changing spatial extent and taxonomic resolution. Location, Twenty-two islands located across the Southern Ocean, further subdivided into five island biogeographical provinces. These islands are used because comprehensive data on both indigenous and non-indigenous insect and plant species are available. Methods, An existing database was updated, using newly published species records, identifying the indigenous and non-indigenous insect and vascular plant species recorded for each island. Homogenization and differentiation were measured using Jaccard's index (JI) of similarity for assemblages across all islands on a pairwise basis, and for island pairs within each of the biogeographical provinces. The effects of taxonomic resolution (species, genus, family) and distance on levels of homogenization or differentiation were examined. To explore further the patterns of similarity among islands for each of the taxa and groupings (indigenous and non-indigenous), islands were clustered based on JI similarity matrices and using group averaging. Results, Across the SOI, insect assemblages have become homogenized (0.7% increase in similarity at species level) while plant assemblages have become differentiated at genus and species levels. Homogenization was recorded only when pairwise distances among islands exceeded 3000 km for insect assemblages, but distances had to exceed 10,000 km for plant assemblages. Widely distributed non-indigenous plant species tend to have wider distributions across the SOI than do their insect counterparts, and this is also true of the indigenous species. Main conclusions, Insect assemblages across the SOI have become homogenized as a consequence of the establishment of non-indigenous species, while plant assemblages have become more differentiated. The likely reason is that indigenous plant assemblages are more similar across the SOI than are insect assemblages, which show greater regionalization. Thus, although a suite of widespread, typically European, weedy, non-indigenous plant species has established on many islands, the outcome has largely been differentiation. Because further introductions of insects and vascular plants are probable as climates warm across the region, the patterns documented here are likely to change through time. [source] The pattern of linkage disequilibrium in German Holstein cattleANIMAL GENETICS, Issue 4 2010S. Qanbari Summary This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein,Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein,Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r2 statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r2 = 0.30 ± 0.32 was observed in pairwise distances of <25 kb and it dropped to 0.20 ± 0.24 at 50,75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r2 , 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance ,100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 ± 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r2. It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r2 estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to Ne = 103 up to ,4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed. [source] | ||||||||||