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1.
At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide polymorphism (SNP) marker map has been constructed. Many of the SNPs on this map, however, were identified by sampling a small number of chromosomes from a single population, and inferences drawn from studies using such SNPs may be influenced by ascertainment bias (AB). Through extensive simulations, we have found that AB is a potentially significant problem in estimating and comparing LD within and between populations. Specifically, the magnitude of AB is a function of the SNP discovery strategy, number of chromosomes used for SNP discovery, population genetic characteristics of the particular genomic region considered, amount of gene flow between populations, and demographic history of the populations. We demonstrate that a balanced SNP discovery strategy (where equal numbers of chromosomes are sampled from multiple subpopulations) is the optimal study design for generating broadly applicable SNP resources. Finally, we validate our theoretical predictions by comparing our results to publicly available data from ten genes sequenced in 24 African American and 23 European American individuals.  相似文献   

2.
  • Li X-Y.1992.Studies on germplasm of Glycyrrhiza by using different taxonomic methods.Advances in Plant Taxonomy in Northwest China 1:7-24.
  • Li X-Y.1993.A study of the system and new taxa of genus Glycyrrhiza L.Bulletin of Botanical Research 13(1):14-43.
  • Turrill WB.1937.Glycyrrhizopsis syriaca Turrill.Bulletin of Miscellaneous Information 2:79.
  • >>更多...  相似文献   


    3.
        
    Although discordance between taxonomic diversity and morphological disparity is common, little is known about the underlying dynamics that drive this decoupling. Early in the history of the Cambrian trilobite family Pterocephaliidae, there was an increase in taxonomic diversity and morphological diversity. As taxonomic diversity declined in the later history of the clade, range of variation stayed high and disparity continued to increase. However, per‐branch rates of morphological evolution estimated from a recent phylogeny decreased with time. Neither within‐trait nor within‐species variation increased or decreased, suggesting that the declining rates of morphological evolution were more likely related to ecological opportunity or niche partitioning, rather than increasing intrinsic constraints. This is further supported by evidence for increased biofacies associations throughout the time period. Thus, the high disparity seen at low taxonomic diversity late in the history of this clade was due to extinction – either random or targeting mean forms – rather than increased rates of morphological evolution. This pattern also provides a scenario that could account for instances of low taxonomic diversity but high morphological disparity in modern groups.  相似文献   

    4.
    Microsatellites are DNA-fragments containing short repetitive motifs with 2–10 bp. They are highly variable in most species and distributed throughout the whole genome. It is broadly accepted that their high degree of variability is closely associated with mispairing of DNA-strands during the replication phase, termed slippage, although recombination is also observed. The aim of this study is to demonstrate evidence that non-reciprocal recombination processes changing the total genomic structure are common in microsatellites and flanking regions. We sequenced DNA fragments from birds in which microsatellites are located, and analyzed the structure of the microsatellites and their flanking regions. Additionally, other data and those from literature of three microsatellite regions of primates coding for the Ataxin-2, the Huntingtin and the TATA-box binding protein were analyzed. The structures of seven avian and three primate microsatellites support the hypothesis that non-reciprocal recombination is a common process that may also contribute considerably to the variation at microsatellite loci. We conclude that results of population genetic studies that are analyzed statistically with methods based on stepwise mutation models should be interpreted with caution if no detailed information on the allelic variation of microsatellites is available.  相似文献   

    5.
    Species-specific differences in microsatellite locus length and ascertainment bias have both been proposed to explain differences in microsatellite variability and length usually observed when loci isolated in one species are used to survey variation in a related species. Here we provide a simple algebraic approach to independently estimate the contributions of true species-specific length differences and ascertainment bias. We apply this approach to a reciprocal-isolation microsatellite study and show contributions of both ascertainment bias and a true longer average microsatellite length in Drosophila melanogaster compared with D. simulans.  相似文献   

    6.
    The allometric-constraint hypothesis states that evolutionary divergence of morphological traits is restricted by integrated growth regulation. In this study, we test this hypothesis on a time-calibrated and well-documented palaeontological sequence of dental measurements on the Pleistocene arvicoline rodent species Mimomys savini from the Iberian Peninsula. Based on 507 specimens representing nine populations regularly spaced over 600 000 years, we compare static (within-population) and evolutionary (among-population) allometric slopes between the width and the length of the first lower molar. We find that the static allometric slope remains evolutionary stable and predicts the evolutionary allometry quite well. These results support the hypothesis that the macroevolutionary divergence of molar traits is constrained by static allometric relationships.  相似文献   

    7.
        
    Body morphology is a valuable feature for distinguishing teleostean fishes. However, the utility of character variation in separate body regions has yet to be tested. The taxonomy of the Gerreidae family is controversial due to character overlapping among its fish species. This work aims to analyze and compare the body shape variation in three regions, cephalic, trunk, and caudal peduncle, using landmark data and geometric morphometric methods in 17 species and five genera of the family Gerreidae. The pattern of shape variation for the cephalic region consisted of well-defined character states exclusive of each species analyzed. Shape variation in the trunk and caudal peduncle regions does not distinguish all species in this study. This study showed that the dorsal cephalic profile is highly variable among the species, therefore, shape variation in this region is useful for distinguishing Gerreidae species. In contrast, some species within the same genus share similar shape states in the trunk and caudal peduncle regions, with the most shape variation in the dorsal profile and anal fin for the trunk and in the middle of the caudal peduncle.  相似文献   

    8.
        
    Abstract The pollen morphology of 11 species of the genus Glycyrrhiza L. with one from each of the genera Glycyrrhizopsis Boiss. & Bal. and Meristotropis Fisch. & C. A. Mey. was investigated by scanning electron microscopy. In pollen morphology, the main differences between Glycyrrhizopsis and Glycyrrhiza are: Glycyrrhizopsis—pollen grains 36.63 × 40.42 μm in size, oblate spheroidal in shape; and Glycyrrhiza—pollen grains 24.47–33.18 × 23.82–31.83 μm in size, prolate spheroidal in shape. Glycyrrhizopsis and Glycyrrhiza should be recognized as two distinct genera based on palynological and morphological characters. Meristotropis and Glycyrrhiza are similar in many important palynological and morphological characters, suggesting that the two should be merged. In Glycyrrhiza, two types of pollen grains, 3‐lobed‐circular or subtriangular in polar view, are found in different species, in accordance with morphological differences in the two groups, shedding light on the classification and evolution of the genus.  相似文献   

    9.
    The inference of population divergence times and branching patterns is of fundamental importance in many population genetic analyses. Many methods have been developed for estimating population divergence times, and recently, there has been particular attention towards genome-wide single-nucleotide polymorphisms (SNP) data. However, most SNP data have been affected by an ascertainment bias caused by the SNP selection and discovery protocols. Here, we present a modification of an existing maximum likelihood method that will allow approximately unbiased inferences when ascertainment is based on a set of outgroup populations. We also present a method for estimating trees from the asymmetric dissimilarity measures arising from pairwise divergence time estimation in population genetics. We evaluate the methods by simulations and by applying them to a large SNP data set of seven East Asian populations.  相似文献   

    10.
        
    Ecological theories of adaptive radiation predict that ecological opportunity (EO) stimulates cladogenesis through entry into a novel environment and/or release of competition pressures. Due to its dynamic paleoclimatic and geological history, the Australo‐Papuan region constitutes an opportune scenario to study patterns of diversification in relation to the colonization of new ecological niches. Here, we employ a comparative framework using the Australasian robins (Petroicidae) as a model system to test whether the diversification of this bird family fulfils a niche‐filling process as predicted by the EO model, and to test whether the observed morphological similarity is described by a pattern of phylogenetic niche conservatism (PNC) or convergence. Although we detected an early‐burst, we did not find a slowdown in speciation or morphological evolution as expected in a niche‐filling scenario. Divergence in tarsus length and tail length (PC1) was consistent with a multi‐peak model, in which PC1 represents a convergent trait among distantly related clades sharing the same foraging strategy. Our study thus shows that convergence rather than PNC seems to explain the existence of morphological similarity across independent lineages in the Petroicidae. We also found a low level of PNC regarding annual variations in temperature and precipitation, which is in agreement with the hypothesis that diversification within the Petroicidae involved repeated radiations. We suggest two non‐mutually exclusive hypotheses to explain the overall lack of density‐dependent cladogenesis. First, the extreme spatial and temporal heterogeneity of this region may have generated a pattern of repeated ecological opportunity over time and, second, this family may not yet have reached equilibrium diversity.  相似文献   

    11.
        
    Abstract:  The distribution of organic forms is clumpy at any scale from populations to the highest taxonomic categories, and whether considered within clades or within ecosystems. The fossil record provides little support for expectations that the morphological gaps between species or groups of species have increased through time as it might if the gaps were created by extinction of a more homogeneous distribution of morphologies. As the quantitative assessments of morphology have replaced counts of higher taxa as a metric of morphological disparity, numerous studies have demonstrated the rapid construction of morphospace early in evolutionary radiations, and have emphasized the difference between taxonomic measures of morphological diversity and quantitative assessments of disparity. Other studies have evaluated changing patterns of disparity across mass extinctions, ecomorphological patterns and the patterns of convergence within ecological communities, while the development of theoretical morphology has greatly aided efforts to understand why some forms do not occur. A parallel, and until recently, largely separate research effort in evolutionary developmental biology has established that the developmental toolkit underlying the remarkable breadth of metazoan form is largely identical among Bilateria, and many components are shared among all metazoa. Underlying this concern with disparity is a question about temporal variation in the production of morphological innovations, a debate over the relative significance of the generation of new morphologies vs. differential probabilities of their successful introduction, and the relative importance of constraint, convergence and contingency in the evolution of form.  相似文献   

    12.
        
    We analysed the ecomorphological relationships in four species of Anolis lizard that occur in the Choco' region in Colombia. The region is one of the most diverse of the Neotropical lowlands. The species were assigned to traditionally recognized Greater Antillean ecomorph categories based on habitat use data. Principal component analyses were carried out to examine correlations between the morphological traits, body size, and habitat use. We found that species are separated in morphological space principally by body size and lamella number. Upon removal of the effect of body size, correlations between morphology and habitat use became apparent. However, when compared with Greater Antillean ecomorphs, we found little evidence of morphological convergence in species occupying similar habitats. The species of the Choco' region are, however, clearly separated in the multidimensional morphological space from the Antillean taxa, and appear to form a separate cluster differentiating principally in body size and the number of lamellae. Mainland species clearly constitute an ecomorphological radiation but apparently this is independent of that of the West Indian fauna. More studies are needed to understand the causes for the independence of evolutionary trajectories on the mainland and the Greater Antilles, and to obtain a better understanding of the ecological and evolutionary processes underlying the radiation of these faunas.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 29–39.  相似文献   

    13.
    A rich source of markers may be overlooked by screening for polymorphism in the source species only. We screened 129 microsatellite loci isolated from the powerful owl (Ninox strenua) against two closely related species; Ninox connivens and Ninox novaeseelandiae. From the screening effort 20 polymorphic markers were isolated, including six loci which were originally discarded as they were monomorphic in the source species. Further cross-species amplification of all 20 loci across species from two families, Strigidae and Tytonidae, revealed unusually high levels of polymorphism within closely related species, and limited success within phylogenetically distant species. Routine screening of multiple species during the marker development phase can yield a wider range of polymorphic markers which can subsequently enhance cross-species amplification attempts.  相似文献   

    14.
        
    We propose a likelihood ratio test to assess that sampling has been completed in closed population size estimation studies. More precisely, we assess if the expected number of subjects that have never been sampled is below a user-specified threshold. The likelihood ratio test statistic has a nonstandard distribution under the null hypothesis. Critical values can be easily approximated and tabulated, and they do not depend on model specification. We illustrate in a simulation study and three real data examples, one of which involves ascertainment bias of amyotrophic lateral sclerosis in Gulf War veterans.  相似文献   

    15.
    Surveys of variability of homologous microsatellite loci among species reveal an ascertainment bias for microsatellite length where microsatellite loci isolated in one species tend to be longer than homologous loci in related species. Here, we take advantage of the availability of aligned human and chimpanzee genome sequences to compare length difference of homologous microsatellites for loci identified in humans to length difference for loci identified in chimpanzees. We are able to quantify ascertainment bias for a range of motifs and microsatellite lengths. Because ascertainment bias should not exist if a microsatellite selected in one species is as likely to be longer as it is to be shorter than its homologue, we propose that the nature of ascertainment bias can provide evidence for understanding how microsatellites evolve. We show that bias is greater for longer microsatellites but also that many long microsatellites have short homologues. These results are consistent with the notion that growth of long microsatellites is constrained by an upper length boundary that, when reached, sometimes results in large deletions. By evaluating ascertainment bias separately for interrupted and uninterrupted repeats we also show that long microsatellites tend to become interrupted, thereby contributing a second component of ascertainment bias. Having accounted for ascertainment bias, in agreement with results published elsewhere, we find that microsatellites in humans are longer on average than those in chimpanzees. This length difference is similar among repeat motifs but surprisingly comprises two roughly equal components, one associated with the repeats themselves and one with the flanking sequences. The differences we find can only be explained if microsatellites are both evolving directionally under a biased mutation process and are doing so at different rates in different closely related species.  相似文献   

    16.
    The endemic land snail species Mandarina hahajimana has undergone extensive habitat and morphological diversification within the Hahajima islands in the Bonin archipelago. This species has diversified into populations with ground, arboreal and semi-arboreal life histories. In addition, arboreal populations and semi-arboreal populations show diversification in preferences of species and positions of the tree on which they are found. Shell morphologies of M. hahajimana exhibit remarkable geographical variation, and they have a clear relationship with their life histories. The morphological variation of M. hahajimana results from adaptation to different lifestyles. The habitats of these populations influence the relationships with other species of Mandarina coexisting with M. hahajimana. This suggests that the morphological and ecological divergence within M. hahajimana has been induced by competitive interaction with other species of Mandarina. Character displacement may have played an important role in promoting adaptive radiation of Mandarina in the Bonin Islands.  相似文献   

    17.
        
    The endemic land snail genus Mandarina of the Ogasawara Islands provides an excellent model system to investigate adaptive radiation. Previously, it has been shown that coexisting species of the islands segregate by microhabitat, so that they are either predominantly found on the ground in relatively wet and sheltered sites, dry and exposed sites, or else are arboreal. Moreover, shell morphology correlates with microhabitat, so that species in wet and sheltered sites tend to have high-spired shells with a high aperture, and those in dry and exposed sites tend to have relatively low-spired shells with a wide aperture. We have now found that on Hahajima, Mandarina polita have variable shell morphology, and there is a correlation between morphology and the depth of leaf litter, as well as the presence/absence of other terrestrial species. Specifically, when high-spired terrestrial Mandarina ponderosa is present, M. polita tend to be low-spired and have a large aperture, indicative of character displacement. When M. ponderosa is absent, the shell shape of M. polita is much more variable, the overall spire is higher, individuals are found in deeper litter, and there is a strong correlation between litter depth and spire height. We argue that these patterns are due to local adaptation, but it remains possible that they are an artefact due to the 'ghost of species past'.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 91 , 149–159.  相似文献   

    18.
        
    Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as \"living fossils\" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods.  相似文献   

    19.
        
    Although case-control association studies have been widely used, they are insufficient for many complex diseases, such as Alzheimer's disease and breast cancer, since these diseases may have multiple subtypes with distinct morphologies and clinical implications. Many multigroup studies, such as the Alzheimer's Disease Neuroimaging Initiative (ADNI), have been undertaken by recruiting subjects based on their multiclass primary disease status, while extensive secondary outcomes have been collected. The aim of this paper is to develop a general regression framework for the analysis of secondary phenotypes collected in multigroup association studies. Our regression framework is built on a conditional model for the secondary outcome given the multigroup status and covariates and its relationship with the population regression of interest of the secondary outcome given the covariates. Then, we develop generalized estimation equations to estimate the parameters of interest. We use both simulations and a large-scale imaging genetic data analysis from the ADNI to evaluate the effect of the multigroup sampling scheme on standard genome-wide association analyses based on linear regression methods, while comparing it with our statistical methods that appropriately adjust for the multigroup sampling scheme. Data used in preparation of this article were obtained from the ADNI database.  相似文献   

    20.
    Microsatellite variability is widely used to infer levels of genetic diversity in natural populations. However, the ascertainment bias caused by typically selecting only the most polymorphic markers in the genome may lead to reduced sensitivity for judging genome-wide levels of genetic diversity. To test this potential limitation of microsatellite-based approaches, we assessed the degree of nucleotide diversity in noncoding regions of eight different carnivore populations, including inbred as well as outbred populations, by sequencing 10 introns (5.4–5.7 kb) in 20 individuals of each population (wolves, coyotes, wolverines and lynxes). Estimates of nucleotide diversity varied 30-fold (7.1 × 10−5 –2.1 × 10−3), with densities of one single nucleotide polymorphism every 112–5446 bp. Microsatellite genotyping (10–27 markers) of the same animals revealed mean multilocus heterozygosities of 0.54–0.78, a 1.4-fold difference among populations. There was a positive yet not perfect ( r 2  = 0.70) correlation between microsatellite marker heterozygosity and nucleotide diversity at the population level. For example, point estimates of nucleotide diversity varied in some cases with an order of magnitude despite very similar levels of microsatellite marker heterozygosity. Moreover, at the individual level, no significant correlation was found. Our results imply that variability at microsatellite marker sets typically used in population studies may not accurately reflect the underlying genomic diversity. This suggests that researchers should consider using resequencing-based approaches for assessing genetic diversity when accurate inference is critical, as in many conservation and management contexts.  相似文献   

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