Amei

Evaluating the role of contracting and expanding rainforest in initiating cycles of speciation across the Isthmus of Panama

Climatic and geological changes across time are presumed to have shaped the rich biodiversity of tropical regions. However, the impact climatic drying and subsequent tropical rainforest contraction had on speciation has been controversial because of inconsistent palaeoecological and genetic data. Despite the strong interest in examining the role of climatic change on speciation in the Neotropics there has been few comparative studies, particularly, those that include non-rainforest taxa. We used bird species that inhabit humid or dry habitats that dispersed across the Panamanian Isthmus to characterize temporal and spatial patterns of speciation across this barrier. Here, we show that these two assemblages of birds exhibit temporally different speciation time patterns that supports multiple cycles of speciation. Evidence for these cycles is further corroborated by the finding that both assemblages consist of ‘young’ and ‘old’ species, despite dry habitat species pairs being geographically more distant than pairs of humid habitat species. The matrix of humid and dry habitats in the tropics not only allows for the maintenance of high species richness, but additionally this study suggests that these environments may have promoted speciation. We conclude that differentially expanding and contracting distributions of dry and humid habitats was probably an important contributor to speciation in the tropics.

Cancer incidence among Asian American populations in the United States, 2009-2011

Cancer incidence disparities exist among specific Asian American populations. However, the existing reports exclude data from large metropoles like Chicago, Houston and New York. Moreover, incidence rates by subgroup have been underestimated due to the exclusion of Asians with unknown subgroup. Cancer incidence data for 2009 to 2011 for eight states accounting for 68% of the Asian American population were analyzed. Race for cases with unknown subgroup was imputed using stratified proportion models by sex, age, cancer site and geographic regions. Age‐standardized incidence rates were calculated for 17 cancer sites for the six largest Asian subgroups. Our analysis comprised 90,709 Asian and 1,327,727 non‐Hispanic white cancer cases. Asian Americans had significantly lower overall cancer incidence rates than non‐Hispanic whites (336.5 per 100,000 and 541.9 for men, 299.6 and 449.3 for women, respectively). Among specific Asian subgroups, Filipino men (377.4) and Japanese women (342.7) had the highest overall incidence rates while South Asian men (297.7) and Korean women (275.9) had the lowest. In comparison to non‐Hispanic whites and other Asian subgroups, significantly higher risks were observed for colorectal cancer among Japanese, stomach cancer among Koreans, nasopharyngeal cancer among Chinese, thyroid cancer among Filipinos, and liver cancer among Vietnamese. South Asians had remarkably low lung cancer risk. Overall, Asian Americans have a lower cancer risk than non‐Hispanic whites, except for nasopharyngeal, liver and stomach cancers. The unique portrayal of cancer incidence patterns among specific Asian subgroups in this study provides a new baseline for future cancer surveillance research and health policy.

A comparative study on the uptake of polycyclic aromatic hydrocarbons by Anodonta californiensis

Uptake of polycyclic aromatic hydrocarbons (PAHs) by the freshwater bivalve mollusc Anodonta californiensis was examined in the presence and absence of surfactant in order to gain further insight into mixture toxicity and to predict whether certain mixtures have negative and/or positive effects on aquatic organisms. In the presence of surfactant, the uptake of anthracene or chrysene was higher than that of naphthalene, given the same concentration in the solution. In the absence of surfactant, the trend was similar, but the uptakes were increased by approximately 100% compared to those in the presence of surfactant. On the uptake of naphthalene, the presence of anthracene showed only minor influence. The uptake of anthracene was affected by both naphthalene and chrysene. The uptake of chrysene was influenced by neither naphthalene nor anthracene. There was no observable displacement of divalent cations from the surface of the gill membrane by any of the PAHs studied.

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Mutation frequencies can be modeled as a Poisson random field (PRF) to estimate speciation times and the degree of selection on newly arisen mutations. This approach provides a quantitative theory for comparing intraspecific polymorphism with interspecific divergence in the presence of selection and can be used to estimate population genetic parameters. Although the original PRF model has been extended to more general biological settings to make statistical inference about selection and divergence among model organisms, it has not been incorporated into phylogeographic studies that focus on estimating population genetic parameters for nonmodel organisms. Here, we modified a recently developed time-dependent PRF model to independently estimate genetic parameters from a nuclear and mitochondrial DNA data set of 22 sister pairs of birds that have diverged across a biogeographic barrier. We found that species that inhabit humid habitats had more recent divergence times and larger effective population sizes than those that inhabit drier habitats, and divergence time estimated from the PRF model were similar to estimates from a coalescent species-tree approach. Selection coefficients were higher in sister pairs that inhabited drier habitats than in those in humid habitats, but overall the mitochondrial DNA was under weak selection. Our study indicates that PRF models are useful for estimating various population genetic parameters and serve as a framework for incorporating estimates of selection into comparative phylogeographic studies.

A TIME-DEPENDENT POISSON RANDOM FIELD MODEL FOR POLYMORPHISM WITHIN AND BETWEEN TWO RELATED BIOLOGICAL SPECIES

We derive a Poisson random field model for population site polymorphisms differences within and between two species that share a relatively recent common ancestor. The model can be either equilibrium or time inhomogeneous. We first consider a random field of Markov chains that describes the fate of a set of individual mutations. This field is approximated by a Poisson random field from which we can make inferences about the amounts of mutation and selection that have occurred in the history of observed aligned DNA sequences.

Statistical inference of selection and divergence from a time-dependent Poisson random field model.

We apply a recently developed time-dependent Poisson random field model to aligned DNA sequences from two related biological species to estimate selection coefficients and divergence time. We use Markov chain Monte Carlo methods to estimate species divergence time and selection coefficients for each locus. The model assumes that the selective effects of non-synonymous mutations are normally distributed across genetic loci but constant within loci, and synonymous mutations are selectively neutral. In contrast with previous models, we do not assume that the individual species are at population equilibrium after divergence. Using a data set of 91 genes in two Drosophila species, D. melanogaster and D. simulans, we estimate the species divergence time (or 1.68 million years, assuming the haploid effective population size years) and a mean selection coefficient per generation . Although the average selection coefficient is positive, the magnitude of the selection is quite small. Results from numerical simulations are also presented as an accuracy check for the time-dependent model.

A modified Friedman test for randomized complete block designs

Abstract The Friedman test is often used for a randomized complete block design when the normality assumption is not satisfied or the data are ordinal. The Friedman test can be viewed as an extension of the sign test for multiple measurements within each subject or block. We propose a modified Friedman test based on the Wilcoxon sign rank approach. Coincidentally, Tukey proposed a test statistic similar to our proposed test, but blocks are ranked by the minimum difference within each block. In the proposed test, we use the variance of block to rank the blocks, with the least variance being ranked the smallest. In both Tukey test and the modified Friedman test, linear ranks are used for blocks and treatments. The Tukey test belongs to the family of weighted-ranking test from Quade (1979).The modified Friedman test, the Friedman test and the Tukey test are compared under various conditions and the results indicate that the proposed test is generally more powerful than the Friedman test and the Tukey test when the number of groups is small.

Efficient Noninferiority Testing Procedures for Simultaneously Assessing Sensitivity and Specificity of Two Diagnostic Tests

Sensitivity and specificity are often used to assess the performance of a diagnostic test with binary outcomes. Wald-type test statistics have been proposed for testing sensitivity and specificity individually. In the presence of a gold standard, simultaneous comparison between two diagnostic tests for noninferiority of sensitivity and specificity based on an asymptotic approach has been studied by Chen et al. (2003). However, the asymptotic approach may suffer from unsatisfactory type I error control as observed from many studies, especially in small to medium sample settings. In this paper, we compare three unconditional approaches for simultaneously testing sensitivity and specificity. They are approaches based on estimation, maximization, and a combination of estimation and maximization. Although the estimation approach does not guarantee type I error, it has satisfactory performance with regard to type I error control. The other two unconditional approaches are exact. The approach based on estimation and maximization is generally more powerful than the approach based on maximization.

Statistical Inference of Selection and Divergence of the Rice Blast Resistance Gene Pi-ta

The resistance gene Pi-ta has been effectively used to control rice blast disease, but some populations of cultivated and wild rice have evolved resistance. Insights into the evolutionary processes that led to this resistance during crop domestication may be inferred from the population history of domesticated and wild rice strains. In this study, we applied a recently developed statistical method, time-dependent Poisson random field model, to examine the evolution of the Pi-ta gene in cultivated and weedy rice. Our study suggests that the Pi-ta gene may have more recently introgressed into cultivated rice, indica and japonica, and U.S. weedy rice from the wild species, O. rufipogon. In addition, the Pi-ta gene is under positive selection in japonica, tropical japonica, U.S. cultivars and U.S. weedy rice. We also found that sequences of two domains of the Pi-ta gene, the nucleotide binding site and leucine-rich repeat domain, are highly conserved among all rice accessions examined. Our results provide a valuable analytical tool for understanding the evolution of disease resistance genes in crop plants.