Mantel Statistics Research Articles

Flowering plant communities mediate the effects of habitat composition and configuration on wild pollinator communities

Abstract There is strong evidence that landscape‐scale factors such as habitat diversity, composition and configuration are important drivers of declines in pollinators and pollination services. However, context and species‐specific responses make it challenging to draw general conclusions about the most important components of landscapes that support diverse and abundant pollinator communities. In this study, we took a functional‐traits approach to community assembly and tested the hypothesis that landscape properties act most strongly on pollinators indirectly, through their influence on flowering plant communities. Using plant and pollinator data from 96 landscapes in Britain, we tested the associations between plant and pollinator communities and local environmental factors, such as habitat cover and configuration, using path analysis based on Mantel and partial Mantel statistics. When all pollinators were considered, we found that the environmental factors had stronger links to the composition of flowering plant communities than to the composition of pollinator communities. Further, the flowering plant community was strongly linked to the pollinator community suggesting a mediating role between land use and pollinators. When separating the pollinator community into taxonomic groups, we found the same result for hoverflies, but wild bees were linked to both environmental factors and flowering plants. We further explored these links with structural equation models using the response‐effect trait framework as a guiding principle. We found strong evidence that land‐use composition and configuration influence the trait distribution and functional diversity of the pollinator community via plant community composition. These findings suggest that the indirect effect of land use on pollinators via flowering plants should be considered in informing the design of pollinator friendly landscapes and in future research of the effects of land use and management on wild pollinators. Read the free Plain Language Summary for this article on the Journal blog.

The Yates, Conover, and Mantel statistics in 2 × 2 tables revisited (and extended)

AbstractAsymptotic inferences about the difference, ratio or odds‐ratio of two independent proportions are very common in diverse fields. This article defines for each parameter eight conditional inference methods. These methods depend on: (1) using a chi‐squared type statistic or a z type one; (2) using the classic Yates continuity correction or the less well‐known Conover one; and (3) whether the p‐value of the test is determined by doubling the one‐tailed p‐value or by the Mantel method (asymmetrical approach). In all cases, the conclusions are: (i) the methods based on the chi‐squared statistic should not be used, as they are too liberal; (ii) for those in favor of using the criterion of doubling the p‐value, the best method is using the z statistic with Conover continuity correction; and (iii) for those in favor of the asymmetrical approach, the best method is based on the z statistic with Conover continuity correction and the Mantel p‐value.

Are urban material gradients transferable between areas?

Urban areas contain a complex mixture of surface materials resulting in mixed pixels that are challenging to handle with conventional mapping approaches. In particular, for spaceborne hyperspectral images (HSIs) with sufficient spectral resolution to differentiate urban surface materials, the spatial resolution of 30 m (e.g. EnMAP HSIs) makes it difficult to find the spectrally pure pixels required for detailed mapping of urban surface materials. Gradient analysis, which is commonly used in ecology to map natural vegetation consisting of a complex mixture of species, is therefore a promising and practical tool for pattern recognition of urban surface material mixtures. However, the gradients are determined in a data-driven manner, so analysis of their spatial transferability is urgently required. We selected two areas—the Ostbahnhof (Ost) area and the Nymphenburg (Nym) area in Munich, Germany—with simulated EnMAP HSIs and material maps, treating the Ost area as the target area and the Nym area as the well-known area. Three gradient analysis approaches were subsequently proposed for pattern recognition in the Ost area for the cases of (i) sufficient samples collected in the Ost area; (ii) some samples in the Ost area; and (iii) no samples in the Ost area. The Ost samples were used to generate an ordination space in case (i), while the Nym samples were used to create the ordination space to support the pattern recognition of the Ost area in cases (ii) and (iii). The Mantel statistical results show that the sample distributions in the two ordination spaces are similar, with high confidence (the Mantel statistics are 0.995 and 0.990, with a significance of 0.001 in 999 free permutations of the Ost and Nym samples). The results of the partial least square regression models and 10-fold cross-validation show a strong relationship (the calculation-validation R2 values on the first gradient among the three approaches are 0.898, 0.892; 0.760, 0.743; and 0.860, 0.836, and those on the second gradient are 0.433, 0.351; 0.698, 0.648; and 0.736, 0.646) between the ordination scores of the samples and their reflectance values. The mapping results of the Ost area from three approaches also show similar patterns (e.g. the distribution of vegetation, artificial materials, water, and ceremony area) and characteristics of urban structures (the intensity of buildings). Therefore, our findings can help assess the transferability of urban material gradients between similar urban areas.

Sensitivity of migratory connectivity estimates to spatial sampling design

BackgroundThe use of statistical methods to quantify the strength of migratory connectivity is commonplace. However, little attention has been given to their sensitivity to spatial sampling designs and scales of inference.MethodsWe examine sources of bias and imprecision in the most widely used methodology, Mantel correlations, under a range of plausible sampling regimes using simulated migratory populations.ResultsAs Mantel correlations depend fundamentally on the spatial scale and configuration of sampling, unbiased inferences about population-scale connectivity can only be made under certain sampling regimes. Within a contiguous population, samples drawn from smaller spatial subsets of the range generate lower connectivity metrics than samples drawn from the range as a whole, even when the underlying migratory ecology of the population is constant across the population. Random sampling of individuals from contiguous subsets of species ranges can therefore underestimate population-scale connectivity. Where multiple discrete sampling sites are used, by contrast, overestimation of connectivity can arise due to samples being biased towards larger between-individual pairwise distances in the seasonal range where sampling occurs (typically breeding). Severity of all biases was greater for populations with lower levels of true connectivity. When plausible sampling regimes were applied to realistic simulated populations, accuracy of connectivity measures was maximised by increasing the number of discrete sampling sites and ensuring an even spread of sites across the full range.ConclusionsThese results suggest strong potential for bias and imprecision when making quantitative inferences about migratory connectivity using Mantel statistics. Researchers wishing to apply these methods should limit inference to the spatial extent of their sampling, maximise their number of sampling sites, and avoid drawing strong conclusions based on small sample sizes.

Sampling Robustness in Gradient Analysis of Urban Material Mixtures

Many studies analyzing spaceborne hyperspectral images (HSIs) have so far struggled to deal with a lack of pure pixels due to complex mixtures of urban surface materials. Recently, an alternative concept of gradients in urban surface material composition has been proposed and successfully applied to map cities with spaceborne HSIs without the requirement for a previous determination of pure pixels. The gradient concept treats all pixels as mixed and aims to describe and quantify gradual transitions in the cover fractions of surface materials. This concept presents a promising approach to tackle urban mapping using spaceborne HSIs. However, since gradients are determined in a data-driven way, their transferability within urban areas needs to be investigated. For this purpose, we analyze the robustness of urban surface material gradients and their dependence across six systematic and three simple random sampling schemes. The results show high similarity between nine sampling schemes in the primary gradient feature space (Pspace) and individual gradient feature spaces (Ispaces). Comparing the Pspace with the Ispaces, the Mantel statistics show the resemblance of samples' distribution in the Pspace, and each Ispace is rather strong with high credibility, as the significance level is P < 0.01. Therefore, it can be concluded that the material gradients defined in the test area are independent of the specific sampling scheme. This study paves the way for subsequent analysis of the stability of urban surface material gradients and the interpretation of material gradients in other urban environments.

Over 80 years without major disturbance, late‐successional Białowieża woodlands exhibit complex dynamism, with coherent compositional shifts towards true old‐growth conditions

Abstract Controversies about successional dynamics of woodland communities have a long history, dating back to the classical debates between Clements and Gleason and continuing into the present. These debates have largely concerned the predictability or convergence of forest developmental trends as well as the relative importance of different mechanisms and forces driving forest succession. However, opportunities for rigorous testing of competing hypotheses are limited, mainly because plot‐based studies of forest vegetation spanning more than a decade are scarce and even fewer concern late‐successional stands. We exploit a unique long‐term dataset from mesic temperate forests of eastern Poland, spanning c. 80 years (1936–2012) in strictly protected, late‐successional woodlands assigned to seven different ‘structural types’. We use non‐metric multidimensional scaling to assess the stability of species composition over the study period. We examine the predictability of composition and change trajectories over time using Mantel statistics, and we examine the changes in distributions of dissimilarity indices to assess convergence or divergence at the examined time and spatial scales. Tree communities in Białowieża Forest have changed substantially over the last eight decades. Several species (aspen, birch, pine, oak, ash, maple and spruce) exhibited large decreases in density, while a few other species (especially hornbeam and lime) have increased in importance across a wide range of initial compositional types. Forest types recognized in earlier periods have become much less distinguishable. Metrics do not yet show clear successional convergence, mainly due to (a) decline in the previously broadly distributed spruce and (b) persistence of large individuals of intermediate, long‐lived species (even though these species lack significant regeneration). Synthesis. Late‐successional woodland communities of Białowieża Forest are clearly dynamic and do not show quasi‐equilibrial properties often assumed of old‐growth forests. Forest types previously recognized as distinct have become progressively less differentiated. Plausible explanations invoke alteration in competitive relationships due to complex changes in environment, including warming climate, N deposition, natural and human disturbance, and ungulate herbivory over 80 years. Hornbeam and lime have been favoured over spruce, pine, oak and birch, although potential successional convergence is far from complete at this time. In the absence of major disturbance, we expect future decades to show continued successional homogenization.

Ecological differentiation, speciation, and rarity: How do they match in Tephroseris longifolia agg. (Asteraceae)?

Tephroseris longifolia agg. is a complex group of outcrossing perennials distributed throughout Central Europe. Recent morphological study revealed six morphotypes corresponding to five previously distinguished subspecies, together with Alpine and Pannonian morphotypes of T. longifolia subsp. longifolia. The delimited morphotypes differ in relative DNA content, geographical range, and rarity. We compared ecological niches of the six morphotypes in order to assess the impact of ecological differentiation on the speciation processes within the T. longifolia agg. Further, we examined whether morphotypes with small range are more ecologically specialized than their widespread relatives. The distribution area of the aggregate includes the Alps, Apennines, Carpathians, and the Pannonian Basin. Ecological variables linked to climate, topography, soil, and vegetation were gathered from 135 circular plots recorded in 35 localities. Related variables were grouped to describe the partial ecological niches: climatic, topographic, pedological, biotic, and coenotic (based either on vascular plants or on bryophytes), each of them visualized as an envelope in the two‐dimensional nonmetric multidimensional scaling ordination space. Each partial ecological niche for a given morphotype was characterized by its position (location of the envelope centroid), breadth (surface of the envelope), and overlaps with envelopes of the other morphotypes. Mantel statistics based on Spearman correlation coefficients were used to quantify differentiation of morphotypes in ecological parameters represented by the partial ecological niches. The significant niche differentiation was confirmed for climatic, topographic, pedological, and vascular plant‐based coenotic niches. Ecological niche differentiation corresponded well to morphological and partially also to karyological differentiation. Narrowly distributed morphotypes occupied more specific habitats and had narrower ecological niches than their widespread relatives. Ecological differentiation could be considered an important driver in allopatric speciation within the T. longifolia agg. Our results demonstrate that quantification of ecological divergence is helpful in assessing evolutionary history of closely related taxa.

A web application to facilitate crop model comparison in ensemble studies

Crop models are reference tools that can be used to evaluate the performances of cropping systems under current and future agro-climatic scenarios. A recent trend is the adoption of multi-model ensembles, as crop model responses vary across pedoclimatic contexts. We present the web application MOBEDIS, aimed at investigating the causes of differences in crop models’ behaviour. MOBEDIS combines non-parametric statistical methods (Spearman correlation, Random Forest, Hierarchical clustering, Mantel statistics) to analyze and cluster crop models according to the relationship between final outputs (e.g., yield) and a set of intermediate outputs related to plant processes. We applied MOBEDIS in three case studies to (1) discuss its capability to facilitate the understanding of the behaviour of two crop models in a simulation experiment, and (2) prove its applicability for model ensemble studies. MOBEDIS is freely available and ready-to-use for understanding single model responses and identifying groups of crop models sharing similar behaviour.

Genetic diversity among synthetic hexaploid wheat accessions (Triticum aestivum) with resistance to several fungal diseases

Synthetic hexaploid wheat (SHW) is known to be an excellent vehicle for transferring large genetic variations especially the many useful traits present in the D genome of Aegilops tauschii Coss. (2n = 2x = 14, DD) for improvement of cultivated wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD). The objectives of the present study were to (1) evaluate genetic diversity among 32 selected SHW accessions with resistance to several fungal diseases using Amplified Fragment Length Polymorphism (AFLP) and Simple Sequence Repeat (SSR) markers and (2) identify diverse SHWs for pyramiding genes conferring resistance to different diseases. These SHWs containing different accessional sources of the D genome were identified from about 1000 SHW accessions developed by the Wheat Wide Crosses program at the International Maize and Wheat Improvement Center, Mexico. Of the 32 SHW accessions eight had resistance to Fusarium head blight (Fusarium graminearum Schw.), seven were resistant to leaf rust (Puccinia triticina Eriks.), eight resistant to Helminthosporium spot blotch [Cochliobolus sativus (Ito et Kurib.) Drechsler ex Dastur (syn.: Bipolaris sorokiniana (Sacc.) Shoem., Helminthosporium sativum Pammel, King et Bakke)], seven resistant to Septoria tritici blotch (Septoria tritici Roberge in Desmaz.), while two were resistant to both Fusarium head blight and leaf rust. Seventeen EcoRI/MseI AFLP primer combinations and 27 highly polymorphic SSR markers including 20 D genome specific markers were screened over all 32 SHW accessions. Among the 703 AFLP fragments scored, 225 were polymorphic across the 32 SHW accessions. Polymorphic information content (PIC) among the SHWs for AFLP ranged from 0.06 to 0.50 with an average PIC of 0.24. Major allelic frequency from SSR analysis ranged from 0.23 to 0.81 with an average of 0.45. Number of alleles per locus for the SSR markers ranged from 3 to 15 with an average allele number of 7.4. Average gene diversity and PIC for the SSR markers was 0.69 and 0.66, respectively, with the highest values being for the D genome specific markers. Cluster analysis showed distinct groups among the SHW accessions studied. Mantel statistics between the distance matrices from AFLP and SSR analyses showed a moderate but significant correlation (r = 0.52**). Our results indicate that the SHW accessions studied possess substantial genetic diversity and are valuable user-friendly pre-breeding materials for breeding improvement of wheat with resistance to Fusarium head blight, leaf rust, Helminthosporium spot blotch, and Septoria tritici blotch. The most diverse SHW accessions can be used for pyramiding resistance genes for different diseases.

Sexual dimorphism in Muzeina Bedouins from South Sinai: Multivariate analysis on dermatoglyphic traits with asymmetry and diversity

The objective of this study is to compare the pattern of sex differences between two different sets of dermatoglyphic traits: 22 quantitative and 40 indices of diversity and asymmetry through Multivariate analyses in Muzeina Bedouins with high inbreeding coefficient of 0.0908 (Kobyliansky and Hershkovitz 1997) from South Sinai. A degree of universality is observed in the “digital pattern size factor” indicate the genetic factor which has more influence on these variables than environmental factors in male and female. Similarity is also observed by the factors- “intra-individual diversity”, “bilateral asymmetry” extracted from 40 traits which also suggests that a common biological validity exists in the underlying component structure. All variables (two groups) scattered into a number of small clusters are mainly categorized into three large and those are markedly similar between sexes. The above similarity was confirmed by the Mantel statistics- the Z values are within the level of non-significance, very good similarities in 22 (0.88) and good similarities in 40 (0.79) traits. Therefore, sex dimorphism is similar between two categories of dermatoglyphic traits which may be used for sex-discrimination in different ethnic populations.

Space Time Clustering and the Permutation Moments of Quadratic Form.

The Mantel and Knox space–time clustering statistics are popular tools to establish transmissibility of a disease and detect outbreaks. The most commonly used null distributional approximations may provide poor fits, and researchers often resort to direct sampling from the permutation distribution. However, the exact first four moments for these statistics are available, and Pearson distributional approximations are often effective. Thus, our first goals are to clarify the literature and make these tools more widely available. In addition, by rewriting terms in the statistics, we obtain the exact first four permutation moments for the most commonly used quadratic form statistics, which need not be positive definite. The extension of this work to quadratic forms greatly expands the utility of density approximations for these problems, including for high-dimensional applications, where the statistics must be extreme in order to exceed stringent testing thresholds. We demonstrate the methods using examples from the investigation of disease transmission in cattle, the association of a gene expression pathway with breast cancer survival, regional genetic association with cystic fibrosis lung disease and hypothesis testing for smoothed local linear regression. © The Authors. Stat published by John Wiley & Sons Ltd.

Large-scale controls on potential respiration and denitrification in riverine floodplains

Restoration measures of deteriorated river ecosystems generally aim at increasing the spatial heterogeneity and connectivity of these systems in order to increase biodiversity and ecosystem stability. While this is believed to benefit overall ecological integrity, consequences of such restoration projects on biogeochemical processes per se (i.e. ecosystem functioning) in fluvial systems are rarely considered. We address these issues by evaluating the characteristics of surface water connection between side arms and the main river channel in a former braided river section and the role and degree of connectivity (i.e. duration of surface water connection) on the sediment biogeochemistry. We hypothesized that potential respiration and denitrification would be controlled by the degree of hydrological connectivity, which was increased after floodplain restoration. We measured potential microbial respiration (SIR) and denitrification (DEA) and compared a degraded floodplain section of the Danube River with a reconnected and restored floodplain in the same river section. Re-establishing surface water connection altered the controls on sediment microbial respiration and denitrification ultimately impacting potential microbial activities. Meta-variables were created to characterize the effects of hydrology, morphology, and the available carbon and nutrient pools on potential microbial processing. Mantel statistics and path analysis were performed and demonstrate a hierarchy where the effects of hydrology on the available substrates and microbial processing are mediated by the morphology of the floodplain. In addition, these processes are highest in the least connected sites. Surface water connection, mediated by morphology regulates the potential denitrification rate and the ratio of N2O to N2 emissions, demonstrating the effects of restoration in floodplain systems.

Genetic diversity in dill (Anethum graveolens L.) populations on the basis of morphological traits and molecular markers

Dill (Anethum graveolens L.) is a green leafy medicinal and aromatic plant belonging to Apiaceae (Umbelliferae) family widely used as spice and medicine. In order to evaluate the genetic diversity in different landraces of dill based on morphological traits and molecular markers, the seeds of 37 accessions collected from different areas of Iran in addition to one European accession were cultured. Based on morphological traits assessment, the highest correlation coefficients were observed among the days to primary and secondary flowers which were 0.98. Cluster analysis classified the accessions of A. graveolens into four main groups. Cluster analysis framed by morphological traits was performed using Ward’s cluster analysis and upon molecular markers the UPGMA and Jaccard’s similarity coefficients was carried out in cluster analysis appeared by amplified fragement length polymorphism (AFLP) markers. Twenty 5-mer primers were used and 355 bands were detected with138 loci (39.8%) polymorphic. Principal coordinates analysis showed that 13 factors justified 69% of data variations. Mantel statistics revealed that the dendrogram was in conformity with similarity matrices (r=0.8). Results of cluster analysis showed that genetic diversity expressed by morphological traits and molecular markers did not completely correlate with geographical region.

Genetic variability and divergence studies in seed and oil parameters of mahua (Madhuca longifolia Koenig) J.F. Macribide accessions

Variability in oil content and seed weight of 37 accessions of mahua (Madhuca longifolia Koenig) J.F. Macribide collected from different part of Tamil Nadu, India were assessed. There were significant differences in 100-seed weight and oil parameters, namely, kernel oil %, palmitic acid, stearic acid, oleic acid and linoleic acid. Maximum seed weight (340 g) was recorded in IC554535 and the least weight (100 g) was recorded in IC554545. Kernel oil ranged from minimum of 44.4% in IC554535 to maximum 61.5% in IC556617. The saturated fatty acid i.e palmitic acid and stearic acid ranged from 11.7–25.9% to 19.1–32.2%, respectively. The oleic acid ranged from 32.9 to 48.7% of the total fatty acid while linoleic acid ranged from 9.4 to 15.4%. High heritability was recorded for all the traits studied. It was maximum for palmitic acid (98.6%) and minimum for linoleic acid (95.8%). The Euclidean pairwise dissimilarities were calculated and clustered by UPGMA based SAHN clustering method. Maximum and minimum Euclidean pairwise dissimilarities observed were 7.01 and 0.46, respectively. All the 37 accessions were grouped into three major clusters. The accessions in cluster II had low palmitic acid and high oleic acid while cluster III had high palmitic acid and low oleic acid content. Normalized Mantel statistics (r = 0.8) and principal component analysis supported cluster analysis. Thus on the basis of present findings it is suggested that hybridization between accessions of cluster II and III will result in wide spectrum of variability in subsequent generations for medicinal, edible applications and biodiesel production.

Entropy‐supported marker selection and Mantel statistics for haplotype sharing analysis

Haplotype sharing analysis is a well-established option for the investigation of the etiology of complex diseases. The statistical power of haplotype association methods depends strongly on how the information of unobserved haplotypes can be captured by multilocus genotypes. In this study we combine an entropy-based marker selection algorithm (EMS), with a haplotype sharing-based Mantel statistics into a new algorithm. Genetic markers are iteratively selected by their multilocus linkage disequilibrium (LD), which is assessed by a normalized entropy difference. The initial marker set is gradually enlarged to increase the available information on the amount of sharing around a potential susceptibility marker. Markers are rejected from joint phasing if they do not increase the multilocus LD. In simulated candidate gene studies, the Mantel statistics combined with the new EMS performs as well or better at detecting the disease single nucleotide polymorphism-or in indirect association analysis its flanking markers-than the Mantel statistics without selection of markers prior to haplotype estimation and the Mantel statistics using sliding windows of size five. It is therefore appealing to apply our selection approach for haplotype-based association analysis, since marker selection driven by the observed data avoids both the arbitrary choice of markers when using a fixed window size, as well as the estimation of haplotype block structure.

Sexual dimorphism in the wing morphology of social vespid wasps – a case study on the genus Polistes Latreille using geometric morphometrics

The variation between the forewings of males and females of three species in the genus Polistes (Hymenoptera) was studied with the help of geometric morphometrics, to determine the extent of sexual dimporphism. Mantel statistics revealed a weak correlation between male and female data sets; however, Goodall’s F-test and canonical variates analyses (using the Integrated Morphometric Package) indicated that there are indeed significant differences between the two sexes. Although visual analysis of the relative warp analysis plots of the two sexes and also CVA analysis plot indicated correlations between sexes of the same species, differences in the position of the clusters (or species) on the plots suggests that sexual dimorphism in wings is present. Results from the thin-plate spline analysis of the mean shape of the male and female data sets revealed which landmarks are responsible for the differences.

Capacidade combinatória, divergência genética entre linhagens de milho e correlação com heterose

Objetivou-se avaliar o desempenho de híbridos simples de milho (Zea mays L.), obtidos de cruzamentos dialélicos entre linhagens divergentes, estimar a capacidade de combinação das linhagens e verificar se a divergência genética entre as linhagens, obtida por marcadores moleculares, é correlacionada com a heterose dos híbridos simples no campo. Trinta e seis híbridos resultantes de um dialelo parcial foram avaliados em Campinas e em Mococa e as 12 linhagens parentais somente em Campinas, a fim de se calcular a heterose dos híbridos. O delineamento experimental empregado foi o de blocos ao acaso, com três repetições e 2 testemunhas comerciais. Avaliaram-se os caracteres: altura da planta (AP), altura da espiga (AE) e massa de grãos (MG). Análises de variância foram efetuadas, sendo as médias comparadas entre si pelo teste de Tukey a 5%. A capacidade de combinação das linhagens foi obtida de acordo com o método de Geraldi e Miranda Filho. Estimaram-se as correlações entre heterose, produtividade e capacidade específica de combinação com divergência genética obtida por AFLP e SSR. Destacou-se o híbrido PM624 x IP398, e as linhagens VER266 e L105 revelaram efeitos positivos da capacidade de combinação para produtividade. As estimativas de heterose variaram de -559 a 6.320 kg ha-1. Não houve correlação entre heterose, capacidade específica de combinação e produtividade dos híbridos com a distância genética por AFLP e SSR, indicando que não é possível fazer inferências sobre o comportamento dos híbridos de milho a partir da divergência genética entre as linhagens parentais.

Comparison of the power of haplotype-based versus single- and multilocus association methods for gene × environment (gene × sex) interactions and application to gene × smoking and gene × sex interactions in rheumatoid arthritis

Accounting for interactions with environmental factors in association studies may improve the power to detect genetic effects and may help identifying important environmental effect modifiers. The power of unphased genotype-versus haplotype-based methods in regions with high linkage disequilibrium (LD), as measured by D', for analyzing gene x environment (gene x sex) interactions was compared using the Genetic Analysis Workshop 15 (GAW15) simulated data on rheumatoid arthritis with prior knowledge of the answers. Stepwise and regular conditional logistic regression (CLR) was performed using a matched case-control sample for a HLA region interacting with sex. Haplotype-based analyses were performed using a haplotype-sharing-based Mantel statistic and a test for haplotype-trait association in a general linear model framework. A step-down minP algorithm was applied to derive adjusted p-values and to allow for power comparisons. These methods were also applied to the GAW15 real data set for PTPN22.For markers in strong LD, stepwise CLR performed poorly because of the correlation/collinearity between the predictors in the model. The power was high for detecting genetic main effects using simple CLR models and haplotype-based methods and for detecting joint effects using CLR and Mantel statistics. Only the haplotype-trait association test had high power to detect the gene x sex interaction.In the PTPN22 region with markers characterized by strong LD, all methods indicated a significant genotype x sex interaction in a sample of about 1000 subjects. The previously reported R620W single-nucleotide polymorphism was identified using logistic regression, but the haplotype-based methods did not provide any precise location information.

Comparison of measures for haplotype similarity

Measuring the association of haplotype similarities with phenotype similarities has been used to develop statistical tests of genetic association. Previously, we applied the general approach of Mantel statistics to correlate genetic and phenotype similarity, where genetic similarity was defined by the number of intervals flanked by markers identical by state for pairs of haplotypes. Here we investigated in the case-control study design the effect on power of the Mantel statistics for five different measures of genetic similarity based on haplotypes: 1) the number of shared intervals, 2) the physical length of the shared intervals, 3) the genetic length of the shared intervals in centimorgans, 4) the genetic length of the shared intervals in linkage disequilibrium units (LDU) and 5) Yu's measure that attaches more weight to the sharing of rare than common alleles. With prior knowledge of the answers of Genetic Analysis Workshop 15 Problem 3, we analyzed the simulated data sets in two genomic regions surrounding the disease loci on chromosomes 6 and 18. For the dense map on chromosome 6, all methods showed a very high power of comparable magnitude. For chromosome 18, we observed a power between 19% and 99% at the pointwise 5% significance level using 1000 cases and 1000 controls for all methods except Yu's measure. While it yielded a much lower power, Yu's measure had 80% power around the disease locus.

Correlação da heterose de híbridos de milho com divergência genética entre linhagens

O objetivo deste trabalho foi avaliar a produtividade de híbridos simples de milho obtidos de cruzamentos dialélicos entre linhagens divergentes, estimar a capacidade de combinação das linhagens e confirmar se a divergência genética entre as linhagens, obtida por marcadores moleculares, é correlacionada com a heterose dos híbridos simples no campo. Trinta e seis híbridos resultantes do dialelo parcial e as 12 linhagens parentais foram avaliadas em Campinas em blocos ao acaso, com três repetições e duas testemunhas. A capacidade de combinação das linhagens foi estimada de acordo com o modelo 4 de Griffing. Estimaram-se a correlação matricial, mediante a estatística de Mantel, entre heterose, produtividade e capacidade específica de combinação com divergência genética por AFLP e SSR. Destacou-se o híbrido PM518 x L111 e as linhagens PM518, IP4035 e L111 apresentaram efeitos positivos da capacidade geral de combinação. As estimativas de heterose variaram de 927 a 6.698 kg ha-1. Houve correlação entre heterose e divergência genética por AFLP e SSR. No entanto, a divergência genética não foi suficiente para determinar a capacidade específica de combinação nem a produtividade dos híbridos.