Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping.

Linkage disequilibrium (LD) is of great interest for gene mapping and the study of population history. We propose a multilocus model for LD, based on the decay of haplotype sharing (DHS). The DHS model is most appropriate when the LD in which one is interested is due to the introduction of a variant on an ancestral haplotype, with recombinations in succeeding generations resulting in preservation of only a small region of the ancestral haplotype around the variant. This is generally the scenario of interest for gene mapping by LD. The DHS parameter is a measure of LD that can be interpreted as the expected genetic distance to which the ancestral haplotype is preserved, or, equivalently, 1/(time in generations to the ancestral haplotype). The method allows for multiple origins of alleles and for mutations, and it takes into account missing observations and ambiguities in haplotype determination, via a hidden Markov model. Whereas most commonly used measures of LD apply to pairs of loci, the DHS measure is designed for application to the densely mapped haplotype data that are increasingly available. The DHS method explicitly models the dependence among multiple tightly linked loci on a chromosome. When the assumptions about population structure are sufficiently tractable, the estimate of LD is obtained by maximum likelihood. For more-complicated models of population history, we find means and covariances based on the model and solve a quasi-score estimating equation. Simulations show that this approach works extremely well both for estimation of LD and for fine mapping. We apply the DHS method to published data sets for cystic fibrosis and progressive myoclonus epilepsy.     

Transmission/disequilibrium test based on haplotype sharing for tightly linked markers

Studies using haplotypes of multiple tightly linked markers are more informative than those using a single marker. However, studies based on multimarker haplotypes have some difficulties. First, if we consider each haplotype as an allele and use the conventional single-marker transmission/disequilibrium test (TDT), then the rapid increase in the degrees of freedom with an increasing number of markers means that the statistical power of the conventional tests will be low. Second, the parental haplotypes cannot always be unambiguously reconstructed. In the present article, we propose a haplotype-sharing TDT (HS-TDT) for linkage or association between a disease-susceptibility locus and a chromosome region in which several tightly linked markers have been typed. This method is applicable to both quantitative traits and qualitative traits. It is applicable to any size of nuclear family, with or without ambiguous phase information, and it is applicable to any number of alleles at each of the markers. The degrees of freedom (in a broad sense) of the test increase linearly as the number of markers considered increases but do not increase as the number of alleles at the markers increases. Our simulation results show that the HS-TDT has the correct type I error rate in structured populations and that, in most cases, the power of HS-TDT is higher than the power of the existing single-marker TDTs and haplotype-based TDTs.     

Little loss of information due to unknown phase for fine-scale linkage-disequilibrium mapping with single-nucleotide-polymorphism genotype data

We present the results of a simulation study that indicate that true haplotypes at multiple, tightly linked loci often provide little extra information for linkage-disequilibrium fine mapping, compared with the information provided by corresponding genotypes, provided that an appropriate statistical analysis method is used. In contrast, a two-stage approach to analyzing genotype data, in which haplotypes are inferred and then analyzed as if they were true haplotypes, can lead to a substantial loss of information. The study uses our COLDMAP software for fine mapping, which implements a Markov chain-Monte Carlo algorithm that is based on the shattered coalescent model of genetic heterogeneity at a disease locus. We applied COLDMAP to 100 replicate data sets simulated under each of 18 disease models. Each data set consists of haplotype pairs (diplotypes) for 20 SNPs typed at equal 50-kb intervals in a 950-kb candidate region that includes a single disease locus located at random. The data sets were analyzed in three formats: (1). as true haplotypes; (2). as haplotypes inferred from genotypes using an expectation-maximization algorithm; and (3). as unphased genotypes. On average, true haplotypes gave a 6% gain in efficiency compared with the unphased genotypes, whereas inferring haplotypes from genotypes led to a 20% loss of efficiency, where efficiency is defined in terms of root mean integrated square error of the location of the disease locus. Furthermore, treating inferred haplotypes as if they were true haplotypes leads to considerable overconfidence in estimates, with nominal 50% credibility intervals achieving, on average, only 19% coverage. We conclude that (1). given appropriate statistical analyses, the costs of directly measuring haplotypes will rarely be justified by a gain in the efficiency of fine mapping and that (2). a two-stage approach of inferring haplotypes followed by a haplotype-based analysis can be very inefficient for fine mapping, compared with an analysis based directly on the genotypes.     

Estimation of haplotype frequencies,linkage-disequilibrium measures,and combination of haplotype copies in each pool by use of pooled DNA data

Inference of haplotypes is important for many genetic approaches, including the process of assigning a phenotype to a genetic region. Usually, the population frequencies of haplotypes, as well as the diplotype configuration of each subject, are estimated from a set of genotypes of the subjects in a sample from the population. We have developed an algorithm to infer haplotype frequencies and the combination of haplotype copies in each pool by using pooled DNA data. The input data are the genotypes in pooled DNA samples, each of which contains the quantitative genotype data from one to six subjects. The algorithm infers by the maximum-likelihood method both frequencies of the haplotypes in the population and the combination of haplotype copies in each pool by an expectation-maximization algorithm. The algorithm was implemented in the computer program LDPooled. We also used the bootstrap method to calculate the standard errors of the estimated haplotype frequencies. Using this program, we analyzed the published genotype data for the SAA (n=156), MTHFR (n=80), and NAT2 (n=116) genes, as well as the smoothelin gene (n=102). Our study has shown that the frequencies of major (frequency >0.1 in a population) haplotypes can be inferred rather accurately from the pooled DNA data by the maximum-likelihood method, although with some limitations. The estimated D and D' values had large variations except when the /D/ values were >0.1. The estimated linkage-disequilibrium measure rho2 for 36 linked loci of the smoothelin gene when one- and two-subject pool protocols were used suggested that the gross pattern of the distribution of the measure can be reproduced using the two-subject pool data.     

Medullary cystic kidney disease type 1: mutational analysis in 37 genes based on haplotype sharing

Medullary cystic kidney disease type 1 (MCKD1) is an autosomal dominant, tubulo-interstitial nephropathy that causes renal salt wasting and end-stage renal failure in the fourth to seventh decade of life. MCKD1 was localized to chromosome 1q21. We demonstrated haplotype sharing and confirmed the telomeric border by a recombination of D1S2624 in a Belgian kindred. Since the causative gene has been elusive, high resolution haplotype analysis was performed in 16 kindreds. Clinical data and blood samples of 257 individuals (including 75 affected individuals) from 26 different kindreds were collected. Within the defined critical region mutational analysis of 37 genes (374 exons) in 23 MCKD1 patients was performed. In addition, for nine kindreds RT-PCR analysis for the sequenced genes was done to screen for mutations activating cryptic splice sites. We found consistency with the haplotype sharing hypothesis in an additional nine kindreds, detecting three different haplotype subsets shared within a region of 1.19 Mb. Mutational analysis of all 37 positional candidate genes revealed sequence variations in 3 different genes, AK000210, CCT3, and SCAMP3, that were segregating in each affected kindred and were not found in 96 healthy individuals, indicating, that a single responsible gene causing MCKD1 remains elusive. This may point to involvement of different genes within the MCKD1 critical region.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Regression modelling of HLA haplotype sharing in affected siblings

A link between the HLA system and disease susceptibility can be assessed through the observation of families containing two or more affected siblings. Departures from Mendelian inheritance of the parental haplotypes among the affected siblings are an indication of such a relationship. Other variables, such as environmental factors, may also be related to disease susceptibility. An approach to examining the degree of haplotype sharing and the effect of other variables of interest on observed sharing is presented and two examples analyzed.     

A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder

Autism spectrum disorder (ASD) is a highly heritable disorder of complex and heterogeneous aetiology. It is primarily characterized by altered cognitive ability including impaired language and communication skills and fundamental deficits in social reciprocity. Despite some notable successes in neuropsychiatric genetics, overall, the high heritability of ASD (~90%) remains poorly explained by common genetic risk variants. However, recent studies suggest that rare genomic variation, in particular copy number variation, may account for a significant proportion of the genetic basis of ASD. We present a large scale analysis to identify candidate genes which may contain low-frequency recessive variation contributing to ASD while taking into account the potential contribution of population differences to the genetic heterogeneity of ASD. Our strategy, homozygous haplotype (HH) mapping, aims to detect homozygous segments of identical haplotype structure that are shared at a higher frequency amongst ASD patients compared to parental controls. The analysis was performed on 1,402 Autism Genome Project trios genotyped for 1 million single nucleotide polymorphisms (SNPs). We identified 25 known and 1,218 novel ASD candidate genes in the discovery analysis including CADM2, ABHD14A, CHRFAM7A, GRIK2, GRM3, EPHA3, FGF10, KCND2, PDZK1, IMMP2L and FOXP2. Furthermore, 10 of the previously reported ASD genes and 300 of the novel candidates identified in the discovery analysis were replicated in an independent sample of 1,182 trios. Our results demonstrate that regions of HH are significantly enriched for previously reported ASD candidate genes and the observed association is independent of gene size (odds ratio 2.10). Our findings highlight the applicability of HH mapping in complex disorders such as ASD and offer an alternative approach to the analysis of genome-wide association data.     

High haplotype diversity with fine-scale structure in a recently established population of an endangered orchid

New populations of endangered plants may establish outside of protected areas if a suitable habitat becomes available. However, it is unclear whether such populations are genetically uniform, as a result of a founder effect, or whether they contain genetic variation resulting from continuous gene flow from source populations, and subsequent recruitment after establishment. We addressed this by examining haplotype variation in the endangered orchid, Anacamptis robusta, which has formed a new population outside of its protected area within the past 20 years. To assess population growth, the number of A. robusta flowering plants were counted every year for 22 years in both the new population and populations within the reserve. Haplotype diversity and fine-scale structure were examined with spatial autocorrelation analysis, both in the new population and representative populations from the protected area. The number of flowering individuals in the new population increased from 9 to 2,277 between 2003 and 2012, whereas within the reserve flowering population sizes varied between years. Seventeen of 23 haplotypes detected for A. robusta were detected in the new population, with seven of these occurring more frequently in the new population than reserve populations. In the new population, there was strong fine-scale spatial structure of haplotypes, similar to patterns found in large populations from the protected area, suggesting multiple colonization events and subsequent local recruitment. This highlights that ongoing demographic and genetic monitoring of plant populations is vital to improve our understanding of population colonization and the conservation of narrow endemics.     

A haplotype inference algorithm for trios based on deterministic sampling

Background

The three-dimensional shape of grain, measured as grain length, width, and thickness (GL, GW, and GT), is one of the most important components of grain appearance in rice. Determining the genetic basis of variations in grain shape could facilitate efficient improvements in grain appearance. In this study, an F_7:8 recombinant inbred line population (RIL) derived from a cross between indica and japonica cultivars (Nanyangzhan and Chuan7) contrasting in grain size was used for quantitative trait locus (QTL) mapping. A genetic linkage map was constructed with 164 simple sequence repeat (SSR) markers. The major aim of this study was to detect a QTL for grain shape and to fine map a minor QTL, qGL7.

Results

Four QTLs for GL were detected on chromosomes 3 and 7, and 10 QTLs for GW and 9 QTLs for GT were identified on chromosomes 2, 3, 5, 7, 9 and 10, respectively. A total of 28 QTLs were identified, of which several are reported for the first time; four major QTLs and six minor QTLs for grain shape were also commonly detected in both years. The minor QTL, qGL7, exhibited pleiotropic effects on GL, GW, GT, 1000-grain weight (TGW), and spikelets per panicle (SPP) and was further validated in a near isogenic F₂ population (NIL-F₂). Finally, qGL7 was narrowed down to an interval between InDel marker RID711 and SSR marker RM6389, covering a 258-kb region in the Nipponbare genome, and cosegregated with InDel markers RID710 and RID76.

Conclusion

Materials with very different phenotypes were used to develop mapping populations to detect QTLs because of their complex genetic background. Progeny tests proved that the minor QTL, qGL7, could display a single mendelian characteristic. Therefore, we suggested that minor QTLs for traits with high heritability could be isolated using a map-based cloning strategy in a large NIL-F₂ population. In addition, combinations of different QTLs produced diverse grain shapes, which provide the ability to breed more varieties of rice to satisfy consumer preferences.     

The influence of temperature and fine-scale resource distribution on resource sharing and domination in an ant community

Abstract.  1. In order to coexist in sympatry, subordinate species must somehow obtain resources that dominant taxa may generally control. This study examines the response of an ant community to fine-scale variation in resource distribution, as a mechanism enabling resource acquisition by subordinates in the presence of dominant taxa. Food (6 g) was portioned as one, eight, or 64 items in a 0.4-m² area, centred on nests of Monomorium sydneyense Forel, considered the most dominant ant in the area. This ant is a newly established exotic species in our study site of Tauranga, New Zealand.
2. As the number of food items increased, a significant increase in the number of species utilising the food was observed, associated with an increase in the non-utilised proportion of food items.
3. The changing occupation rates of food items by M. sydneyense and three other species were modelled against soil surface temperature and the varying dispersion rates of the food resource. Significant main effects of food density, site, species, and temperature were observed on the probability of food being occupied by a species. However, there were also significant interaction effects, making it impossible to interpret the main effects in isolation. Monomorium sydneyense dominated a smaller proportion of resources in trials with increased resource distribution and cooler temperatures, allowing more species to access resources.
4. There was considerable variation between species in their responses to variation in temperature and food distribution. Although most species were able to respond to increasing resource dispersion, species that were in low abundance apparently could not. However, even species that could respond to increasing resource dispersion were limited in the number of resources they could secure.     

The extent of linkage disequilibrium and haplotype sharing around a polymorphic site

Various expressions related to the length of a conserved haplotype around a polymorphism of known frequency are derived. We obtain exact expressions for the probability that no recombination has occurred in a sample or subsample. We obtain an approximation for the probability that no recombination that could give rise to a detectable recombination event (through the four-gamete test) has occurred. The probabilities can be used to obtain approximate distributions for the length of variously defined haplotypes around a polymorphic site. The implications of our results for data analysis, and in particular for detecting selection, are discussed.     

A comparative measure of biodiversity based on species composition

In conservation planning, species richness and species endemism are the most often used metrics for describing the biodiversity importance of areas. However, when it comes to prioritizing regions for conservation actions these measures alone are insufficient because they do not reveal how similar or different the actual composition of species may be from one area to another. For comparative analysis an additional useful metric would be one that indicates the degree to which the species assemblage in one area is also represented in—or is distinct from—species assemblages of other areas. Here we describe a method for quantifying the compositional representativeness of species assemblages among geographic regions. The method generates asymmetric pairwise similarity coefficients that are then used to calculate separate measures for the representativeness and the distinctiveness of species assemblages in the regions being compared. We demonstrate the method by comparing fish communities among freshwater ecoregions of the Mississippi Basin, and then among smaller hydrological units within two individual freshwater ecoregions. At both scales of analysis, our measures of representativeness and distinctiveness reveal patterns of fish species composition that differ from patterns of species richness. This information can enhance conservation planning processes by ensuring that priority-setting explicitly consider the most representative and distinctive species assemblages.     

基于湿度分布特征的小尺度土壤碳通量空间采样策略

由于土壤碳通量的空间异质性很强,传统的随机抽样方法无法对区域土壤碳通量进行准确估算,而多点采样需耗费大量的人力及设备成本,因此确定适当的采样点数量及分布策略对于区域土壤碳通量的测算非常重要。提出一种基于湿度空间分布特征的小尺度土壤碳通量空间采样策略:首先利用无线传感网密集测量区域的土壤湿度,根据湿度数据的空间分布特征划分监测区域,通过Hammond Mc Cullagh方程计算各子区域内的最优采样点数量,最终确定整个监测区域的空间采样点部署策略。提出的方法考虑了各子区域间土壤碳通量空间分布的差异,使得采样点的部署位置与土壤碳通量的分布具有较好的相关性。研究结果证明:土壤碳通量部署策略能够获得比均匀部署策略、随机部署策略更高的区域土壤碳通量估算准确度。     

Mitosis: taking the measure of spindle length

Recent studies have investigated the mechanisms responsible for setting spindle length - and how spindle length changes over the course of development.     

Pedigree analysis and haplotype sharing within diverse groups of Zea mays L. inbreds

The objectives of this study were the examination of genetic similarities in a diverse group of maize inbreds and an investigation of the incidence of shared haplotypes within closely related groups. Size polymorphisms from 218 mapped simple-sequence repeats (SSR) for 57 entries were detected with the ABI377 Prism system and scored with Genotyper software. The standard error for the estimated size of identical PCR products was 0.13 base pairs. Size estimates were used to examine genetic relationships among the Iodent, flint, corn belt dent, sweet corn and popcorn groups in Zea mays L. inbreds. Cluster analysis of SSR distance data from 57 entries showed similarity between the European flints (F2, F7 and EP1), CO109 and the su1 sweet corns developed in the United States. The inbred F64 from Argentina was distinct from all other entries. Close examination of two sources of B37 revealed that the Purdue University version of B37 contains a set of alleles characteristic of B73. Five groups (Iodents, European flints, the B73 group of corn belt dents, su1 sweet corn, popcorn) show persistent within-group haplotypes. Received: 17 July 2000 / Accepted: 5 January 2001     

A score test for linkage analysis of ordinal traits based on IBD sharing

Statistical methods for linkage analysis are well established for both binary and quantitative traits. However, numerous diseases including cancer and psychiatric disorders are rated on discrete ordinal scales. To analyze pedigree data with ordinal traits, we recently proposed a latent variable model which has higher power to detect linkage using ordinal traits than methods using the dichotomized traits. The challenge with the latent variable model is that the likelihood is usually very complicated, and as a result, the computation of the likelihood ratio statistic is too intensive for large pedigrees. In this paper, we derive a computationally efficient score statistic based on the identity-by-decent sharing information between relatives. Using simulation studies, we examined the asymptotic distribution of the test statistic and the power of our proposed test under various levels of heritability. We compared the computing time as well as power of the score test with the likelihood ratio test. We then applied our method for the Collaborative Study on the Genetics of Alcoholism and performed a genome scan to map susceptibility genes for alcohol dependence. We found a strong linkage signal on chromosome 4.     

A biomechanical perspective on the use of forelimb length as a measure of sexual selection in frogs

Differences in forelimb length between male and female frogs and between amplexing and non-amplexing males have been interpreted to be the results of sexual selection on forelimb length. The causal feature of the forelimb that has been posited to cause such selection is the observation that non-amplexing males attempt to disrupt breeding by prying amplexing males from females. A biomechanical model of forelimb function suggests that total length per se may not be the most appropriate measure to use. There are more functionally significant aspects of forelimb morphology, such as lever arm lengths, that should influence amplexing ability and may make measures of overall forelimb length misleading. This example highlights the relevance of functional analysis to current questions in evolutionary biology that rely on postulated roles for morphological structures under selection.     

A phylogeny of Darwin's finches based on microsatellite DNA length variation

Allele length variation at 16 microsatellite loci was used to estimate the phylogeny of 13 out of the 14 species of Darwin''s finches. The resulting topology was similar to previous phylogenies based on morphological and allozyme variation. An unexpected result was that genetic divergence among Galápagos Island populations of the warbler finch (Certhidea olivacea) predates the radiation of all other Darwin''s finches. This deep split is surprising in view of the relatively weak morphological differentiation among Certhidea populations and supports the hypothesis that the ancestor of all Darwin''s finches was phenotypically similar to Certhidea. The results also resolve a biogeographical problem: the Cocos Island finch evolved after the Galápagos finch radiation was under way, supporting the hypothesis that this distant island was colonized from the Galápagos Islands. Monophyletic relationships are supported for both major groups, the ground finches (Geospiza) and the tree finches (Camarhynchus and Cactospiza), although the vegetarian finch (Platyspiza crassirostris) appears to have diverged prior to the separation of ground and tree finches. These results demonstrate the use of microsatellites for reconstructing phylogenies of closely related species and interpreting their evolutionary and biogeographic histories.     

Impact of missing genotype data on Monte-Carlo simulation based haplotype analysis

In the context of haplotype association analysis of unphased genotype data, methods based on Monte-Carlo simulations are often used to compensate for missing or inappropriate asymptotic theory. Moreover, such methods are an indispensable means to deal with multiple testing problems. We want to call attention to a potential trap in this usually useful approach: The simulation approach may lead to strongly inflated type I errors in the presence of different missing rates between cases and controls, depending on the chosen test statistic. Here, we consider four different testing strategies for haplotype analysis of case-control data. We recommend to interpret results for data sets with non-comparable distributions of missing genotypes with special caution, in case the test statistic is based on inferred haplotypes per individual. Moreover, our results are important for the conduction and interpretation of genome-wide association studies.