Gene flow in complex landscapes: testing multiple hypotheses with causal modeling

Predicting population-level effects of landscape change depends on identifying factors that influence population connectivity in complex landscapes. However, most putative movement corridors and barriers have not been based on empirical data. In this study, we identify factors that influence connectivity by comparing patterns of genetic similarity among 146 black bears (Ursus americanus), sampled across a 3,000-km(2) study area in northern Idaho, with 110 landscape-resistance hypotheses. Genetic similarities were based on the pairwise percentage dissimilarity among all individuals based on nine microsatellite loci (average expected heterozygosity=0.79). Landscape-resistance hypotheses describe a range of potential relationships between movement cost and land cover, slope, elevation, roads, Euclidean distance, and a putative movement barrier. These hypotheses were divided into seven organizational models in which the influences of barriers, distance, and landscape features were statistically separated using partial Mantel tests. Only one of the competing organizational models was fully supported: patterns of genetic structure are primarily related to landscape gradients of land cover and elevation. The alternative landscape models, isolation by barriers and isolation by distance, are not supported. In this black bear population, gene flow is facilitated by contiguous forest cover at middle elevations.     

A multiple testing procedure for clinical trials.

A multiple testing procedure is proposed for comparing two treatments when response to treatment is both dichotomous (i.e., success or failure) and immediate. The proposed test statistic for each test is the usual (Pearson) chi-square statistic based on all data collected to that point. The maximum number (N) of tests and the number (m1 + m2) of observations collected between successive tests is fixed in advance. The overall size of the procedure is shown to be controlled with virtually the same accuracy as the single sample chi-square test based on N(m1 + m2) observations. The power is also found to be virtually the same. However, by affording the opportunity to terminate early when one treatment performs markedly better than the other, the multiple testing procedure may eliminate the ethical dilemmas that often accompany clinical trials.     

The inheritance of doubleness in Matthiola and Petunia I. The hypotheses

Ohne Zusammenfassung

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The inheritance of doubleness in Matthiola and Petunia I. The hypotheses

     

The 'species problem' and testing macroevolutionary hypotheses

Species lists change for a variety of reasons, including new information and preferences for different species concepts. Uncertainty over species numbers is potentially damaging to tests of proposed correlates of species richness, particularly if taxonomic changes are biased toward some clades over others. We investigate the effects of this error and bias by testing the same suite of macroevolutionary hypotheses in seven different arrangements of primate taxonomy. This is the first time that the effects of the ‘species problem’ have been systematically investigated in this way. Primates are an excellent model system for examining the effects of taxonomic uncertainty: species numbers have doubled in the past two decades, with the fastest growth in the Neotropics. We found that different variables were significantly associated with species richness in each taxonomic arrangement. However, there were no significant differences among taxonomies in the regression slopes for any predictor variable. We found no tendency for significant correlations to occur in taxonomies with more species, suggesting that the results cannot be explained by a lack of power in the smaller taxonomies. The findings are discussed with reference to the wider implications for testing macroevolutionary hypotheses.     

Towards accurate estimation of the proportion of true null hypotheses in multiple testing

BACKGROUND: Biomedical researchers are now often faced with situations where it is necessary to test a large number of hypotheses simultaneously, eg, in comparative gene expression studies using high-throughput microarray technology. To properly control false positive errors the FDR (false discovery rate) approach has become widely used in multiple testing. The accurate estimation of FDR requires the proportion of true null hypotheses being accurately estimated. To date many methods for estimating this quantity have been proposed. Typically when a new method is introduced, some simulations are carried out to show the improved accuracy of the new method. However, the simulations are often very limited to covering only a few points in the parameter space. RESULTS: Here I have carried out extensive in silico experiments to compare some commonly used methods for estimating the proportion of true null hypotheses. The coverage of these simulations is unprecedented thorough over the parameter space compared to typical simulation studies in the literature. Thus this work enables us to draw conclusions globally as to the performance of these different methods. It was found that a very simple method gives the most accurate estimation in a dominantly large area of the parameter space. Given its simplicity and its overall superior accuracy I recommend its use as the first choice for estimating the proportion of true null hypotheses in multiple testing.     

The use of parsimony in testing phylogenetic hypotheses

With the advance of cladistic theory differences in principle between it and other systematic techniques are few but of fundamental importance. In the mechanics of classification they are confined to ranking and the rejection of paraphyletic taxa. In cladistic analysis, leading to cladograms, trees and phylogeny reconstruction, inconsistencies in apparent synapomorphies are said to be resolved using Popper's hypothetico-deductive method together with the principle of parsi However, not only do cladists not use Popper's methodology, which is inconsistent with parsimony, but their use of parsimony is invalid as a test of phylo The only accepted extrinsic test of a classification is that enunciated by John Stuart Mill. It has been claimed that cladistic classifications yield the best results when judged by Mill's criteria, but this is only possibly the case with analytic classifications produced by numerical techniques. No satisfactory test exists in normal (synthetic) cladism for distinguishing synapomorphy from homoplasy. The effects of this are particularly dire in cladograms and classifications involving fossils in which a Stufenreihe arrangement is adopted.     

The selectivity of K+ ion channels: testing the hypotheses

How K⁺ channels are able to conduct certain cations yet not others remains an important but unresolved question. The recent elucidation of the structure of NaK, an ion channel that conducts both Na⁺ and K⁺ ions, offers an opportunity to test the various hypotheses that have been put forward to explain the selectivity of K⁺ ion channels. We test the snug-fit, field-strength, and over-coordination hypotheses by comparing their predictions to the results of classical molecular dynamics simulations of the K⁺ selective channel KcsA and the less selective channel NaK embedded in lipid bilayers. Our results are incompatible with the so-called strong variant of the snug-fit hypothesis but are consistent with the over-coordination hypothesis and neither confirm nor refute the field-strength hypothesis. We also find that the ions and waters in the NaK selectivity filter unexpectedly move to a new conformation in seven K⁺ simulations: the two K⁺ ions rapidly move from site S4 to S2 and from the cavity to S4. At the same time, the selectivity filter narrows around sites S1 and S2 and the carbonyl oxygen atoms rotate 20°−40° inwards toward the ion. These motions diminish the large structural differences between the crystallographic structures of the selectivity filters of NaK and KcsA and appear to allow the binding of ions to S2 of NaK at physiological temperature.     

Dangers in testing statistical hypotheses

Most experiments are intended for the estimation of the size of effects rather than for the testing of a hypothesis of whether or not an effect occurs. Hypothesis testing is often inapplicable, is over-used and is likely to lead to misinterpretations of results. The two types of error possible in hypothesis testing are discussed. Whereas Type I error is usually examined as a matter of course, Type II error is almost always ignored. Investigations in which zero differences are important should recognise the possibility of Type II error in their interpretation. A nonsignificant result should not be interpreted as evidence of a lack of effect. Statistical significance is not synonymous with economic or scientific importance. The importance of choosing the most appropriate design is emphasised and some suggestions are made as to how important sources of error can be avoided.     

A powerful truncated tail strength method for testing multiple null hypotheses in one dataset

This article re-analyses a prey-predator model with a refuge introduced by one of the founders of population ecology Gause and his co-workers to explain discrepancies between their observations and predictions of the Lotka-Volterra prey-predator model. They replaced the linear functional response used by Lotka and Volterra by a saturating functional response with a discontinuity at a critical prey density. At concentrations below this critical density prey were effectively in a refuge while at a higher densities they were available to predators. Thus, their functional response was of the Holling type III. They analyzed this model and predicted existence of a limit cycle in predator-prey dynamics. In this article I show that their model is ill posed, because trajectories are not well defined. Using the Filippov method, I define and analyze solutions of the Gause model. I show that depending on parameter values, there are three possibilities: (1) trajectories converge to a limit cycle, as predicted by Gause, (2) trajectories converge to an equilibrium, or (3) the prey population escapes predator control and grows to infinity.     

The inheritance of resistance alleles in multiple sclerosis

Multiple sclerosis (MS) is a complex trait in which alleles at or near the class II loci HLA-DRB1 and HLA-DQB1 contribute significantly to genetic risk. HLA-DRB1*15 and HLA-DRB1*17-bearing haplotypes and interactions at the HLA-DRB1 locus increase risk of MS but it has taken large samples to identify resistance HLA-DRB1 alleles. In this investigation of 7,093 individuals from 1,432 MS families, we have assessed the validity, mode of inheritance, associated genotypes, and the interactions of HLA-DRB1 resistance alleles. HLA-DRB1*14-, HLA-DRB1*11-, HLA-DRB1*01-, and HLA-DRB1*10-bearing haplotypes are protective overall but they appear to operate by different mechanisms. The first type of resistance allele is characterised by HLA-DRB1*14 and HLA-DRB1*11. Each shows a multiplicative mode of inheritance indicating a broadly acting suppression of risk, but a different degree of protection. In contrast, a second type is exemplified by HLA-DRB1*10 and HLA-DRB1*01. These alleles are significantly protective when they interact specifically in trans with HLA-DRB1*15-bearing haplotypes. HLA-DRB1*01 and HLA-DRB1*10 do not interact with HLA-DRB1*17, implying that several mechanisms may be operative in major histocompatibility complex-associated MS susceptibility, perhaps analogous to the resistance alleles. There are major practical implications for risk and for the exploration of mechanisms in animal models. Restriction of antigen presentation by HLA-DRB1*15 seems an improbably simple mechanism of major histocompatibility complex-associated susceptibility.     

The choice of a statistic for testing hypotheses regarding seasonality

This paper discusses statistical methods for testing hypotheses of seasonality in births across one year, using monthly frequencies. It argues that the Freedman test, a variant of the Kolmogorov-Smirnov one-sample test, and the Edwards test and its modifications are most appropriate for this purpose. These tests take into account the order of the monthly frequencies and have a higher power than the ordinary chi-square goodness-of-fit test, regarding seasonality. The paper addresses some points mentioned in earlier papers by McCullough, and O'Brien and Holbert.     

The origins of premating reproductive isolation: testing hypotheses in the grasshopper Chorthippus parallelus

There are many proposed routes for the origin of premating reproductive isolation, but few systematic studies aimed at testing their relative importance. Accumulated information about the biogeographical history of the European meadow grasshopper, Chorthippus parallelus, has allowed us to make a planned series of comparisons among populations aimed at distinguishing the contributions of some of these hypotheses. We have compared the effects on assortative mating of long-term isolation in glacial refugia, founder events during postglacial colonization, and sympatry with a closely related species. A likelihood-based analysis allowed us to separate effects of variation in male and female mating propensity among populations from variation in mate choice leading to assortative mating. All three effects contributed significantly to the overall variation in mating pattern in a set of 21 pairwise comparisons among seven populations. Male cuticular composition, but not other candidate signals, was significantly associated with the level of assortative mating. Of the hypotheses for the origin of reproductive isolation, only the predictions of the founder hypothesis explained a significant amount of the variation in assortative mating. This does not rule out the possiblity that there may be some other explanation. Having established the pattern of divergence, it is possible to generate hypotheses that explain our results at least as well as the founder hypothesis. However, because many such post hoc hypotheses are possible, they cannot be tested with this dataset. On this basis, our results favor the hypothesis that some aspect of the colonization process tends to accelerate divergence in mating signals leading to premating reproductive isolation. This could be accomplished through any one of several mechanisms. Colonization involves many bottlenecks as new populations are established at the edge of the range by long-distance migrants. Genetic effects may be important, but these bottlenecks may also alter the conditions under which mates are found and chosen, as suggested by Kaneshiro. At the same time, the colonizing populations may encounter novel environmental challenges.     

Chronic CO inhalation and carotid body catecholamines: testing of hypotheses

The purpose of this study was twofold: one concerns carotid blood flow and tissue PO2 and the other the effect of chronic hypoxic hypoxia on enhanced catecholamine content. The rationale was that chronic CO inhalation would not mimic the effect of hypoxia on the carotid body if its tissue blood flow is sufficiently high to counteract the effect of CO on O2 delivery and, hence, on tissue PO2. The differential effects of CO on the carotid body and erythropoietin-producing tissue would also indicate that the effect of hypoxic hypoxia on the carotid body is the result of a direct action of a local low O2 stimulus rather than secondary to a systemic effect initiated by other O2-sensing tissues. To test these alternatives we studied the effects of chronic CO inhalation on carotid body catecholamine content and hematocrit in the rats, which were exposed to an inspired PCO of 0.4-0.5 Torr at an inspired PO2 of approximately 150 Torr for 22 days. The hematocrit of CO-exposed rats was 75 +/- 1.1% compared with 48 +/- 0.7% in controls. Dopamine and norepinephrine content of the carotid bodies (per pair) was 5.88 +/- 0.91 and 3.02 +/- 0.19 ng, respectively, in the CO-exposed rats compared with 6.20 +/- 1.0 and 3.29 +/- 0.6 ng, respectively, in the controls. Protein content of the carotid bodies (per pair) was 18.4 +/- 1.6 and 20.5 +/- 0.9 micrograms, respectively. Thus, despite a vigorous erythropoietic response, the CO-exposed rats failed to show any significant stimulation of carotid body in terms of the content of either catecholamine or protein. The results suggest that carotid body tissue PO2 is not compromised by moderate carboxyhemoglobinemia because of its high tissue blood flow and that the chronic effect of hypoxic hypoxia on carotid body is direct.