Home About us Contact
|
Home About us Contact | ||
|
|
||
Pairwise Differences (pairwise + difference)
Selected AbstractsPopulation genetics analysis of the origin of the Oriental fruit fly, Bactrocera dorsalis Hendel (Diptera: Tephritidae), in northern Yunnan Province, ChinaENTOMOLOGICAL SCIENCE, Issue 1 2007Jianhong LIU Abstract We examined genetic variation in the Oriental fruit fly, Bactrocera dorsalis (Hendel), using six populations in two regions of Yunnan Province, China, to determine the distribution and likely mechanism for the dispersal of this fly. A 501-bp portion of the mitochondrial cytochrome oxidase gene was sequenced from a minimum of eight individuals from each population, and 43 haplotypes were observed in the six Bactrocera dorsalis populations. When comparing the genetic diversity of populations in the northern and southern regions, which differ with respect to elevation, climate and plant phenology, we found a significantly greater haplotype diversity in the southern region (permutation test; P < 0.05), suggesting that the northern populations, those at Kunming and Qujing, probably originated from somewhere in the southern region. FST and number of pairwise differences revealed a high level of differentiation between the Panxi population and the other populations (permutation test; P < 0.05). Although the difference was marginally insignificant, the Shuitang population seemed to have differentiated from both northern populations. The Mantel test did not detect any isolation due to geographic distance. An amova analysis found that 2.56% of the variance was caused by the Panxi population. Haplotype network analysis showed that none of the six populations had a specific genetic lineage. Together, these analyses suggest that long-distance dispersal has occurred for this species, and the species most probably took advantage of both a mountain pass and prevailing air currents. The Panxi population was significantly isolated from the others, probably because of its distinguishing habitat features, host plants or the recent reduction of the population size. [source] Non-homogeneous infinitely many sites discrete-time model with exact coalescentMATHEMATICAL METHODS IN THE APPLIED SCIENCES, Issue 6 2010Adam Bobrowski Abstract Kingman's coalescent is among the most fertile concepts in mathematical population genetics. However, it only approximates the exact coalescent process associated with the Wright,Fisher model, in which the ancestry of a sample does not have to be a binary tree. The distinction between the approximate and exact coalescent becomes important when population size is small and time has to be measured in discrete units (generations). In the present paper, we explore the exact coalescent, with mutations following the infinitely many sites model. The methods used involve random point processes and generating functionals. This allows obtaining joint distributions of segregating sites in arbitrary intervals or collections of intervals, and generally in arbitrary Borel subsets of two or more chromosomes. Using this framework it is possible to find the moments of the numbers of segregating sites on pairs of chromosomes, as well as the moments of the average of the number of pairwise differences, in the form that is more general than usually. In addition, we demonstrate limit properties of the first two moments under a range of demographic scenarios, including different patterns of population growth. This latter part complements results obtained earlier for Kingman's coalescent. Finally, we discuss various applications, including the analysis of fluctuation experiments, from which mutation rates of biological cells can be inferred. Copyright © 2009 John Wiley & Sons, Ltd. [source] Molecular evidence for a founder effect in invasive house finch (Carpodacus mexicanus) populations experiencing an emergent disease epidemicMOLECULAR ECOLOGY, Issue 1 2006DANA M. HAWLEY Abstract The impact of founder events on levels of genetic variation in natural populations remains a topic of significant interest. Well-documented introductions provide a valuable opportunity to examine how founder events influence genetic diversity in invasive species. House finches (Carpodacus mexicanus) are passerine birds native to western North America, with the large eastern North American population derived from a small number of captive individuals released in the 1940s. Previous comparisons using amplified fragment length polymorphism (AFLP) markers found equivalent levels of diversity in eastern and western populations, suggesting that any genetic effects of the founder event were ameliorated by the rapid growth of the newly established population. We used an alternative marker system, 10 highly polymorphic microsatellites, to compare levels of genetic diversity between four native and five introduced house finch populations. In contrast to the AFLP comparisons, we found significantly lower allelic richness and heterozygosity in introduced populations across all loci. Three out of five introduced populations showed significant reductions in the ratio of the number of alleles to the allele size range, a within-population characteristic of recent bottlenecks. Finally, native and introduced populations showed significant pairwise differences in allele frequencies in every case, with stronger isolation by distance within the introduced than native range. Overall, our results provide compelling molecular evidence for a founder effect during the introduction of eastern house finches that reduced diversity levels at polymorphic microsatellite loci and may have contributed to the emergence of the Mycoplasma epidemic which recently swept the eastern range of this species. [source] Genetic Heterogeneity of IcelandersANNALS OF HUMAN GENETICS, Issue 1 2003E. Árnason Summary Recently statements have been made about a special ,genetic homogeneity' of the Icelanders that are at variance with earlier work on blood groups and allozymes. To validate these claims an extensive reanalysis was undertaken of mtDNA variation by examining primary data from original sources on 26 European populations. The results show that Icelanders are among the most genetically heterogeneous Europeans by the mean number of nucleotide differences as well as by estimates of , parameters of the neutral theory. The distribution of pairwise differences in general has the same shape as European populations and shows no evidence of bottlenecks of numbers in Iceland. The allelic frequency distribution of Iceland is relatively even with a large number of haplotypes at polymorphic frequencies contrasting with other countries. This is a signature of admixture during the founding or history of Iceland. Assumptions of models used to simulate number of haplotypes at sampling saturation for comparing populations are violated to different degrees by various countries. Anomalies identified in data in previous reports on Icelandic mtDNA variation appear to be due to errors in publicly accessible databases. This study demonstrates the importance of basing analyses on primary data so that errors are not propagated. Claims about special genetic homogeneity of Icelanders are not supported by evidence. [source] Controlling the False Discovery Rate with Constraints: The Newman-Keuls Test RevisitedBIOMETRICAL JOURNAL, Issue 1 2007Juliet Popper Shaffer Abstract The Newman-Keuls (NK) procedure for testing all pairwise comparisons among a set of treatment means, introduced by Newman (1939) and in a slightly different form by Keuls (1952) was proposed as a reasonable way to alleviate the inflation of error rates when a large number of means are compared. It was proposed before the concepts of different types of multiple error rates were introduced by Tukey (1952a, b; 1953). Although it was popular in the 1950s and 1960s, once control of the familywise error rate (FWER) was accepted generally as an appropriate criterion in multiple testing, and it was realized that the NK procedure does not control the FWER at the nominal level at which it is performed, the procedure gradually fell out of favor. Recently, a more liberal criterion, control of the false discovery rate (FDR), has been proposed as more appropriate in some situations than FWER control. This paper notes that the NK procedure and a nonparametric extension controls the FWER within any set of homogeneous treatments. It proves that the extended procedure controls the FDR when there are well-separated clusters of homogeneous means and between-cluster test statistics are independent, and extensive simulation provides strong evidence that the original procedure controls the FDR under the same conditions and some dependent conditions when the clusters are not well-separated. Thus, the test has two desirable error-controlling properties, providing a compromise between FDR control with no subgroup FWER control and global FWER control. Yekutieli (2002) developed an FDR-controlling procedure for testing all pairwise differences among means, without any FWER-controlling criteria when there is more than one cluster. The empirical example in Yekutieli's paper was used to compare the Benjamini-Hochberg (1995) method with apparent FDR control in this context, Yekutieli's proposed method with proven FDR control, the Newman- Keuls method that controls FWER within equal clusters with apparent FDR control, and several methods that control FWER globally. The Newman-Keuls is shown to be intermediate in number of rejections to the FWER-controlling methods and the FDR-controlling methods in this example, although it is not always more conservative than the other FDR-controlling methods. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Simultaneous Factor Selection and Collapsing Levels in ANOVABIOMETRICS, Issue 1 2009Howard D. Bondell Summary When performing an analysis of variance, the investigator often has two main goals: to determine which of the factors have a significant effect on the response, and to detect differences among the levels of the significant factors. Level comparisons are done via a post-hoc analysis based on pairwise differences. This article proposes a novel constrained regression approach to simultaneously accomplish both goals via shrinkage within a single automated procedure. The form of this shrinkage has the ability to collapse levels within a factor by setting their effects to be equal, while also achieving factor selection by zeroing out entire factors. Using this approach also leads to the identification of a structure within each factor, as levels can be automatically collapsed to form groups. In contrast to the traditional pairwise comparison methods, these groups are necessarily nonoverlapping so that the results are interpretable in terms of distinct subsets of levels. The proposed procedure is shown to have the oracle property in that asymptotically it performs as well as if the exact structure were known beforehand. A simulation and real data examples show the strong performance of the method. [source] Optical Coherence Tomography: A Noninvasive Method to Assess Wound ReepithelializationACADEMIC EMERGENCY MEDICINE, Issue 5 2007Adam J. Singer MD BackgroundAccurate assessment of wound healing may require invasive tissue biopsies, limiting its clinical usefulness in humans. Optical coherence tomography (OCT) is a novel, high-resolution method using light reflection to obtain noninvasive cross sectional imaging of biological tissues. ObjectivesTo evaluate the utility of OCT for assessing wound reepithelialization in a porcine model. MethodsThe authors conducted an animal study with two domestic pigs. Excisional cutaneous wounds were created over the ventral surface of the animals using an electric dermatome set at a depth of 600 ,m. The wounds were excised two or three days later and precisely marked to guide initial OCT and subsequent tissue slicing and microscopy. Comparing hematoxylin and eosin,stained histologic sections and the corresponding OCT images from each tissue sample permitted identification of the correlative micromorphology. Scatter and Bland,Altman plots were used to present the data. The primary measure of agreement was the standard deviation of the pairwise differences in percent reepithelialization between OCT and histology together with a 95% confidence interval. ResultsIn normal skin, the epidermis was characterized by a thin, bright layer indicating a high degree of light scattering on OCT. The dermis below was characterized by a thicker, darker area indicating less scattering of light. All fresh excisional wounds lacked an outer bright layer of epidermis immediately after injury. At days 2 and 3, the wounds were partially reepithelialized. A new bright layer with intense light scattering was present on OCT corresponding to the neoepidermis on hematoxylin and eosin,stained sections. The correlation between percent reepithelialization measured with OCT and histology was 0.66 (p < 0.001), and the standard deviation of the differences was 11.0% (95% confidence interval = 8.4% to 16.1%). ConclusionsOCT accurately detects the presence or absence of the epidermal layer of skin, allowing noninvasive tracking of wound reepithelialization. [source] | |||||||||||||