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Microsatellite Genotypes (microsatellite + genotype)
Selected AbstractsImplications of phenotypic variation of Myzus persicae (Hemiptera: Aphididae) for biological control on greenhouse pepper plantsJOURNAL OF APPLIED ENTOMOLOGY, Issue 7 2009D. R. Gillespie Abstract Variation in vulnerability to natural enemies, reproductive rate and insecticide resistance among phenotypes of Myzus persicae (Sulzer) has been shown to have the potential to disrupt biological control and IPM of this species, and movement of particularly troublesome phenotypes in international horticultural trade could be cause for concern. Three important components of fitness, vulnerability to parasitoids, reproduction and insecticide resistance were determined in three clones of M. persicae originating from prevalent phenotype populations on pepper crops in greenhouses in British Columbia, Canada. One of these phenotypes appeared to be consistently involved in outbreaks in commercial operations. These clones were also characterized for their DNA microsatellite genotype and compared with genotypes of M. persicae from Europe. The clone involved in outbreaks in commercial greenhouses showed reduced vulnerability to parasitoids, and a higher reproductive rate compared to the other two clones suggesting that these traits may have been involved in outbreaks. As in M. persicae European clones, a higher reproductive rate was correlated with a lack of esterase-based resistance (primarily to organophosphates and, to some extent, to carbamates and pyrethroids). However, microsatellite analysis demonstrated that the three clones investigated in British Columbia had unique genotypes, and therefore there was no evidence for their movement in international trade. [source] Clonal composition of the peach-potato aphid Myzus persicae (Homoptera: Aphididae) in France and Scotland: Comparative analysis with IGS fingerprinting and microsatellite markersANNALS OF APPLIED BIOLOGY, Issue 3 2003B FENTON Summary Fourteen colonies of the peach-potato aphid, Myzus persicae, were taken either from French peach trees or weeds in 2001. Thirty five apomictic parthenogenetic lineages (APLs) were established. Ribosomal DNA intergenic spacer (IGS) fingerprinting was used to characterise these and 28 fingerprints were duly obtained. Those lineages with different fingerprints were considered different genotypes and those with the same fingerprint as the same. The genetic identity of APLs was further tested using four microsatellite loci. APLs that differed by IGS fingerprint had distinct microsatellite allele combinations and those that had the same IGS fingerprint had the same microsatellite allele combinations. The results confirmed that IGS types corresponded to different aphid genotypes. Independent APLs with identical IGS and microsatellite genotype were therefore considered different representatives of the same clone. APLs from M. persicae found on Scottish crops in 1995, 1996 and 2001, as well as a long-term laboratory line were also examined by the same methods. Their IGS fingerprints were similar or identical suggesting that they all belonged to the same clone. Microsatellite markers also suggested that these lineages were derived from a single clone. Some field lineages exhibited slight modifications to their IGS fingerprints confirming that the IGS evolves more rapidly than these microsatellite alleles. Thus, IGS will continue to provide a useful marker for aphid fieldwork. [source] Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studiesECOGRAPHY, Issue 6 2008Melanie A. Murphy Landscape genetics, an emerging field integrating landscape ecology and population genetics, has great potential to influence our understanding of habitat connectivity and distribution of organisms. Whereas typical population genetics studies summarize gene flow as pairwise measures between sampling localities, landscape characteristics that influence population genetic connectivity are often continuously distributed in space. Thus, there are currently gaps in both the ability to analyze genotypic data in a continuous spatial context and our knowledge of expected of landscape genetic structure under varying conditions. We present a framework for generating continuous "genetic surfaces", evaluate their statistical properties, and quantify statistical behavior of landscape genetic structure in a simple landscape. We simulated microsatellite genotypes under varying parameters (time since vicariance, migration, effective population size) and used ancestry (q) values from STRUCTURE to interpolate a genetic surface. Using a spatially adjusted Pearson's correlation coefficient to test the significance of landscape variable(s) on genetic structure we were able to detect landscape genetic structure on a contemporary time scale (,5 generations post vicariance, migration probability ,0.10) even when population differentiation was minimal (FST,0.00015). We show that genetic variation can be significantly correlated with geographic distance even when genetic structure is due to landscape variable(s), demonstrating the importance of testing landscape influence on genetic structure. Finally, we apply genetic surfacing to analyze an empirical dataset of black bears from northern Idaho USA. We find black bear genetic variation is a function of distance (autocorrelation) and habitat patch (spatial dependency), consistent with previous results indicating genetic variation was influenced by landscape by resistance. These results suggest genetic surfaces can be used to test competing hypotheses of the influence of landscape characteristics on genetic structure without delineation of categorical groups. [source] DISPERSAL, PHILOPATRY, AND INFIDELITY: DISSECTING LOCAL GENETIC SWTRUCTURE IN SUPERB FAIRY-WRENS (MALURS CYANEUS)EVOLUTION, Issue 3 2005M. C. Double Abstract Dispersal influences evolution, demography, and social characteristics but is generally difficult to study. Here we combine long-term demographic data from an intensively studied population of superb fairy-wrens(Malurus cyaneus) and multivariate spatial autocorrelation analyses of microsatellite genotypes to describe dispersal behavior in this species. The demographic data revealed: (1) sex-biased dispersal: almost all individuals that dispersed into the study area over an eight-year period were female (93%; n 5 153); (2) high rates of extragroup infidelity (66% of offspring), which also facilitated local gene dispersal; and (3) skewed lifetime reproductive success in both males and females. These data led to three expectations concerning the patterns of fine-scale genetic structure: (1) little or no spatial genetic autocorrelation among females, (2) positive spatial genetic autocorrelation among males, and (3) a heterogeneous genetic landscape. Global autocorrelation analysis of the genotypes present in the study population confirmed the first two expectations. A novel two-dimensional local autocorrelation analysis confirmed the third and provided new insight into the patterns of genetic structure across the two-dimensional landscape. We highlight the potential of autocorrelation analysis to infer evolutionary processes but also emphasize that genetic patterns in space cannot be fully understood without an appropriate and intensive sampling regime and detailed knowledge of the individuals genotyped. [source] Stock structure of pallid sturgeon analyzed with microsatellite lociJOURNAL OF APPLIED ICHTHYOLOGY, Issue 4 2007A. W. Schrey Summary Recovery efforts for the endangered pallid sturgeon (Scaphirhynchus albus) include supplementation of wild stocks with hatchery reared progeny. Identifying the extent of genetic stock structure, which has previously been detected in samples from the range extremes, will help to determine whether stock transfers might be harmful. DNA microsatellite genotypes were screened in pallid sturgeon from the upper Missouri River, lower Missouri River, middle Mississippi River and Atchafalaya River and analyzed using a combination of Bayesian model-based and more traditional F-statistic based methods to characterize genetic differentiation. Scaphirhynchus specimens were collected by researchers active in the recovery effort and genotypes were screened at 16 microsatellite loci. Because there is considerable genetic and morphological overlap between pallid sturgeon, shovelnose sturgeon, and their hybrids, a combination of morphological and genetic techniques were used to eliminate shovelnose and possible hybrids from the sample. Genetic differentiation was detected among samples (overall , = 0.050, P = 0.001). Pairwise ,, genetic distances, and Bayesian assignment testing reveal that pallid sturgeon from the upper Missouri River are the most distinct group with pairwise comparisons of pallid sturgeon among all the remaining samples exhibiting lower , values, higher genetic distances, and self assignment scores. Our results indicate that using local broodstock, when available, should be used for pallid sturgeon propagation. If local broodstock are not available, geographically proximate individuals would limit genetic differences between native and stocked individuals. [source] Does character displacement initiate speciation?JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2010Evidence of reduced gene flow between populations experiencing divergent selection Abstract Character displacement , trait evolution stemming from selection to lessen resource competition or reproductive interactions between species , has long been regarded as important in finalizing speciation. By contrast, its role in initiating speciation has received less attention. Yet because selection for character displacement should act only where species co-occur, individuals in sympatry will experience a different pattern of selection than conspecifics in allopatry. Such divergent selection might favour reduced gene flow between conspecific populations that have undergone character displacement and those that have not, thereby potentially triggering speciation. Here, we explore these ideas empirically by focusing on spadefoot toads, Spea multiplicata, which have undergone character displacement, and for which character displacement appears to cause post-mating isolation between populations that are in sympatry with a heterospecific and those that are in allopatry. Using mitochondrial sequence data and nuclear microsatellite genotypes, we specifically asked whether gene flow is reduced between populations in different selective environments relative to that between populations in the same selective environment. We found a slight, but statistically significant, reduction in gene flow between selective environments, suggesting that reproductive isolation, and potentially ecological speciation, might indeed evolve as an indirect consequence of character displacement. Generally, character displacement may play a largely underappreciated role in instigating speciation. [source] Genetic marker investigation of the source and impact of predation on a highly endangered speciesMOLECULAR ECOLOGY, Issue 6 2003Sam C. Banks Abstract In September and October 2000, the remains of a number of apparently predated northern hairy-nosed wombats (Lasiorhinus krefftii) were discovered in Epping Forest National Park, the site of the only known population of this highly endangered species. Analysis of DNA recovered from six carcasses and a section of intestine found nearby was carried out using microsatellite and Y-specific primers. This identified seven individual wombats, the identity of three of which was inferred from a genotype database prepared from animals sampled during trapping programmes. Six victims were male and one female, suggesting that female-biased predation rates are unlikely to be the cause of the current male-biased population sex ratio. DNA isolated from four canid faeces found in the vicinity revealed three distinct canid microsatellite genotypes with very high probabilities of belonging to dingoes (Canis familiaris dingo). A wombat genotype matching that of one of the dead individuals was identified from scats of two of the dingoes. In addition, two macropod microsatellites were amplified from two dingo scats. These observations provided vital information regarding predation on northern hairy-nosed wombats, and prompted the permanent exclusion of dingoes from the park by the erection of a dingo-proof fence. [source] High proportion of protected minke whales sold on Japanese markets is due to illegal, unreported or unregulated exploitationANIMAL CONSERVATION, Issue 5 2009V. Lukoschek Abstract Whale meat products sold on Japanese markets originate from two stocks of North Pacific (NP) minke whales Balaenoptera acutorostrata scammoni: the depleted J-stock, which has been protected since 1986 but continues to be killed as fisheries ,bycatch', and the more abundant O-stock, which is hunted under special permit (scientific whaling). We investigated the geographic distribution and temporal changes in stock composition of NP minke whale products sold on Japanese markets between December 1997 and June 2004. From nearly 1200 ,whale meat' products purchased during this time, 250 were identified as NP minke whales by phylogenetic analysis of mitochondrial DNA (mtDNA) sequences. The 250 NP minke whale products were found to represent 201 unique ,market individuals' after exclusion of replicate products using microsatellite genotypes. Market individuals were further classified into four mtDNA haplogroups, three of which are characteristic of the J-stock (J-type) and one characteristic of the O-stock (O-type). There were moderate differences in the proportions of J-type individuals found in coastal prefectures, perhaps reflecting regional differences in the sale of local bycatch, but no significant difference across time. The absence of a change over time was inconsistent with the four- to fivefold increase in reported bycatch, from an average of 25,122 whales year,1, following a 2001 regulation allowing commercial sale of whales taken as bycatch. Using a mixed-stock analysis based on haplogroup frequencies over the entire survey period, we estimated that 46.1% (se, 4.2%) of all market individuals originated from the J-stock. This estimate of illegal, unreported or unregulated (IUU) exploitation is higher than expected from the officially reported bycatch, suggesting either large-scale under-reporting and/or unrecognized takes of J-stock minke whales from Pacific coastal waters by the scientific hunt. Our estimates of the true level of IUU exploitation have important implications for recovery of this depleted coastal stock. [source] Investigation into the Ability of SNP Chipsets and Microsatellites to Detect Association with a Disease LocusANNALS OF HUMAN GENETICS, Issue 4 2008D. Curtis Summary We wished to investigate the ability of different SNP chipsets to detect association with a disease and to investigate the linkage disequilibrium (LD) relationships between microsatellites and nearby SNPs in order to assess their potential usefulness to detect association. SNP genotypes were obtained from HapMap and microsatellite genotypes from CEPH. 5000 SNPs were simulated as disease genes which increased penetrance from 0.01 to 0.02 in a sample of 400 cases and 400 controls. The power of flanking SNPs to detect association was tested using sets of 1, 2, 3 or 4 markers analysed with haplotype analysis or logistic regression and using either all HapMap markers or those from the Affymetrix 500K, Illumina 300K or Illumina 550K chipsets. Additionally, LD relationships between 10 microsatellites and SNPs within 2Mb of each other were studied. The power for one of the markers to detect association at p = 0.001 was around 0.4. Power was slightly better for logistic regression than haplotype analysis and for two-marker as opposed to single marker analysis but analysing with larger numbers markers had little benefit. The Illumina 550K marker set was better able to detect association than the other two and was almost as powerful as using all HapMap markers. Microsatellites had detectable LD with only a small number of nearby SNPs and the pattern of LD was very variable. Available chipsets have quite good ability to detect association although obviously results will be critically dependent on the nature of the genetic effect on risk, sample size and the actual LD relationships of the susceptibility polymorphisms involved. Microsatellites seem ill-suited for systematic studies to detect association. [source] | ||||||||||