An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data

Despite the importance of molecular phylogenetics, few of its assumptions have been tested with real data. It is commonly assumed that nonparametric bootstrap values are an underestimate of the actual support, Bayesian posterior probabilities are an overestimate of the actual support, and among-gene phylogenetic conflict is low. We directly tested these assumptions by using a well-supported yeast reference tree. We found that bootstrap values were not significantly different from accuracy. Bayesian support values were, however, significant overestimates of accuracy but still had low false-positive error rates (0% to 2.8%) at the highest values (>99%). Although we found evidence for a branch-length bias contributing to conflict, there was little evidence for widespread, strongly supported among-gene conflict from bootstraps. The results demonstrate that caution is warranted concerning conclusions of conflict based on the assumption of underestimation for support values in real data.     

Synergistic effect on insulin secretion from INS-1 cells of a sulfonylurea and a phosphodiesterase 3 inhibitor

The effects on insulin secretion from INS-1 cells of varying concentrations of the sulfonylurea glyburide and the PDE3 inhibitor milrinone, separately and in combination were measured. Over a range of concentrations the effects of the two drugs in combination were more than additive. A response surface model was fit to the data and was found to describe the data well. From this model, it was apparent that a significant synergistic effect upon insulin secretion existed over a wide range of combinations of the two drugs.     

Abundance estimation from multiple photo surveys: confidence distributions and reduced likelihoods for bowhead whales off Alaska

Maximum likelihood estimates of abundance are obtained from repeated photographic surveys of a closed stratified population with naturally marked and unmarked individuals. Capture intensities are assumed log-linear in stratum, year, and season. In the chosen model, an approximate confidence distribution for total abundance of bowhead whales, with an accompanying likelihood reduced of nuisance parameters, is found from a parametric bootstrap experiment. The confidence distribution depends on the assumed study protocol. A confidence distribution that is exact (except for the effect of discreteness) is found by conditioning in the unstratified case without unmarked individuals.     

Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes

Many early reports of ITS region (ITS 1, 5.8S, and ITS 2) variation in flowering plants indicated that nrDNA arrays within individuals are homogeneous. However, both older and more recent studies have found intra-individual nrDNA polymorphism across a range of plant taxa including presumed non-hybrid diploids. In addition, polymorphic individuals often contain potentially non-functional nrDNA copies (pseudogenes). These findings suggest that complete concerted evolution should not be assumed when embarking on phylogenetic studies using nrDNA sequences. Here we (1). discuss paralogy in relation to species tree reconstruction and conclude that a priori determinations of orthology and paralogy of nrDNA sequences should not be made based on the functionality or lack of functionality of those sequences; (2). discuss why systematists might be particularly interested in identifying and including pseudogene sequences as a test of gene tree sampling; (3). examine the various definitions and characterizations of nrDNA pseudogenes as well as the relative merits and limitations of a subset of pseudogene detection methods and conclude that nucleotide substitution patterns are particularly appropriate for the identification of putative nrDNA pseudogenes; and (4). present and discuss the advantages of a tree-based approach to identifying pseudogenes based on comparisons of sequence substitution patterns from putatively conserved (e.g., 5.8S) and less constrained (e.g., ITS 1 and ITS 2) regions. Application of this approach, through a method employing bootstrap hypothesis testing, and the issues discussed in the paper are illustrated through reanalysis of two previously published matrices. Given the apparent robustness of the test developed and the ease of carrying out percentile bootstrap hypothesis tests, we urge researchers to employ this statistical tool. While our discussion and examples concern the literature on plant systematics, the issues addressed are relevant to studies of nrDNA and other multicopy genes in other taxa.     

Sequential estimation in line transect surveys

This article considers using sequential procedures to determine the amount of survey effort required in a line transect survey in order to achieve a certain precision level in estimating the abundance of a biological population. Sequential procedures are constructed for both parametric and nonparametric animal abundance estimators. The criterion used to derive the stopping rules is the width of confidence intervals for the animal abundance. For each estimator considered, we develop stopping rules based on the asymptotic distributions and the bootstrap. A sequential analysis on an aerial survey of the southern bluefin tuna indicates substantial saving of survey effort can be made by employment of the proposed sequential procedures. This savings of survey effort is also observed in a simulation study designed to evaluate the empirical performance of the proposed sequential procedures.     

MORPHOMETRIC CORRELATION PATTERNS OF ADULT BIRDS (FRINGILLIDAE: PASSERIFORMES AND COLUMBIFORMES) MIRROR THE EXPRESSION OF DEVELOPMENTAL CONTROL GENES

Stimulated by the rapid progress in developmental genetics, recent approaches to evolutionary theory focus on the interface function of developmental processes in the study of genotype-phenotype mapping. From this viewpoint, the main result of the present analysis is that the expression patterns of developmental control genes are reflected in the infraspecific correlation patterns of phenotypic characters in the adult stage. The study is based on 42 logarithmically scaled skeletal measurements of two avian clades, finches (43 species, n = 313) and pigeons (27 species, n = 219). First, for each clade an “observed correlation matrix” was calculated by computing a bias-reduced pooled-species correlation matrix based on the clade-specific pooled within-species variance-covariance matrix between measurements. Second, the expression domains of diverse developmental control genes, that is, Hox, Msx, Pax, Mhox, Shh, Bmp, and Gdf, in characters were represented by “theoretical matrices.” Finally, the observed and the theoretical matrices were compared by Mantel's test to test hypotheses about pattern similarities between phenotypic correlations and the expression of developmental control genes. Seventeen percent of the single matrix comparisons revealed significant (P ≤ 0.05) pattern correspondences in finches, whereas 63% were significant in pigeons. The multiple comparisons revealed correspondences at the highest significance level (P ≤ 0.001) in both clades and disclosed that 15% of the observed matrix patterns are explained in finches versus 22% in pigeons. Presumably, as finches have less pronounced correspondences between gene expression and phenotypic correlation, they are more derived than pigeons. Out of the significant single matrix comparisons, four correspondences are common to both clades: one of them is connected with the Gdf gene expression concerning limb length relations and also harmonizes with the dominant pattern within the infraspecific correlation matrices. The general implication is that the significant correspondences detected here between observed and theoretical matrices are based on a correspondence between phenotypic and genetic modules. Because the phenotypic modules are potential candidates for a direct impact of selection, the important role of genotype-phenotype mapping in molding the body plan becomes apparent.