STORM: software for testing hypotheses of relatedness and mating patterns

Storm is a software package that allows users to test a variety of hypotheses regarding patterns of relatedness and patterns of mate choice and/or mate compatibility within a population. These functions are based on four main calculations that can be conducted either independently or in the hypothesis-testing framework: internal relatedness; homozygosity by loci; pairwise relatedness; and a new metric called allele inheritance, which calculates the proportion of loci at which an offspring inherits a paternal allele different from that inherited from its mother. STORM allows users to test four hypotheses based on these calculations and Monte Carlo simulations: (i) are individuals within observed associations or groupings more/less related than expected; (ii) do observed offspring have more/less genetic variability (based on internal relatedness or homozygosity by loci) than expected from the gene pool; (iii) are observed mating pairs more/less related than expected if mating is random with respect to relatedness; and (iv) do observed offspring inherit paternal alleles different from those inherited from the mother more/less often than expected based on Mendelian inheritance.     

Internet: a major resource for toxicologists

Use of the Internet in developing countries is now growing faster. Internet has created a new conduit not only for communication but also in the access, sharing and exchange of information among scientists. The Internet is now viewed as the world's biggest library where retrieval of scientific literature and other information resources are possible within seconds. Large volumes of toxicological information resources are available on the Internet. This review outlines some sites that may be of great importance and useful to the toxicologist.     

Phylogeography of the Western Lyresnake (Trimorphodon biscutatus): testing aridland biogeographical hypotheses across the Nearctic-Neotropical transition

The Western Lyresnake (Trimorphodon biscutatus) is a widespread, polytypic taxon inhabiting arid regions from the warm deserts of the southwestern United States southward along the Pacific versant of Mexico to the tropical deciduous forests of Mesoamerica. This broadly distributed species provides a unique opportunity to evaluate a priori biogeographical hypotheses spanning two major distinct biogeographical realms (the Nearctic and Neotropical) that are usually treated separately in phylogeographical analyses. I investigated the phylogeography of T. biscutatus using maximum likelihood and Bayesian phylogenetic analysis of mitochondrial DNA (mtDNA) from across this species' range. Phylogenetic analyses recovered five well-supported clades whose boundaries are concordant with existing geographical barriers, a pattern consistent with a model of vicariant allopatric divergence. Assuming a vicariance model, divergence times between mitochondrial lineages were estimated using Bayesian relaxed molecular clock methods calibrated using geological information from putative vicariant events. Divergence time point estimates were bounded by broad confidence intervals, and thus these highly conservative estimates should be considered tentative hypotheses at best. Comparison of mtDNA lineages and taxa traditionally recognized as subspecies based on morphology suggest this taxon is comprised of multiple independent lineages at various stages of divergence, ranging from putative secondary contact and hybridization to sympatry of 'subspecies'.     

Experimental models for testing hypotheses about cumulative cultural evolution

The rapid appearance (over evolutionary time) of the cognitive skills and complex inventions of modern humans has been attributed to “cumulative cultural evolution” (CCE), the accumulation of knowledge and skills over generations. To date, researchers have only been able to speculate about the reasons for the apparent absence of this phenomenon in nonhumans, and it has not been possible to test hypotheses regarding the mechanisms underlying it. Here, we show that it is possible to demonstrate CCE under laboratory conditions by simulating generational succession through the repeated removal and replacement of human participants within experimental groups. We created “microsocieties” in which participants were instructed to complete simple tasks using everyday materials. In one of our procedures, participants were instructed to build a paper aeroplane which flew as far as possible, and in the other, they were instructed to construct a tower of spaghetti which was as tall as possible. We show that, in both cases, information accumulates within the groups such that later generations produce designs which are more successful than earlier ones. These methods offer researchers a window to understanding CCE, allowing for experimental manipulation and hypothesis testing.     

The inheritance procedure: multiple testing of tree-structured hypotheses

Hypotheses tests in bioinformatics can often be set in a tree structure in a very natural way, e.g. when tests are performed at probe, gene, and chromosome level. Exploiting this graph structure in a multiple testing procedure may result in a gain in power or increased interpretability of the results.We present the inheritance procedure, a method of familywise error control for hypotheses structured in a tree. The method starts testing at the top of the tree, following up on those branches in which it finds significant results, and following up on leaf nodes in the neighborhood of those leaves. The method is a uniform improvement over a recently proposed method by Meinshausen. The inheritance procedure has been implemented in the globaltest package which is available on www.bioconductor.org.     

Holotestoid: a computational model for testing hypotheses about echinoid skeleton form and growth

Regular echinoid skeletons, or tests, comprise plate patterns and overall shapes that have proven challenging to analyse solely on the basis of any one approach or process. Herein, we present a computational model, Holotestoid, that emulates four macrostructural ontogenic processes involved in test growth (plate growth, plate addition, plate interaction, and plate gapping). We devise a geometric representation for analysing tests and describe how we use analogies (bubble interactions and close-packing) to emulate the processes. In the computational model, the emulated processes are used to determine the plate size and plate shape and combined to simulate a growth zone. We simulated growth zones for Arbacia punctulata and for Strongylocentrotus franciscanus by changing the value for one parameter, the ambulacral column angle. We quantitatively compared morphological features for simulated forms to those for real specimens to test the computational model. Additionally, we simulated growth zones for A. punctulata, S. franciscanus, Eucidaris thouarsii, and Mellita quinquiesperforata by changing three parameters, ambulacral column angle, peristome radius to apical system radius ratio, and apical system radius to column length ratio. Holotestoid can be used to explain morphological disparity among echinoid tests.     

Extending conventional priors for testing general hypotheses in linear models

We consider that observations come from a general normal linearmodel and that it is desirable to test a simplifying null hypothesisabout the parameters. We approach this problem from an objectiveBayesian, model-selection perspective. Crucial ingredients forthis approach are ‘proper objective priors’ to beused for deriving the Bayes factors. Jeffreys-Zellner-Siow priorshave good properties for testing null hypotheses defined byspecific values of the parameters in full-rank linear models.We extend these priors to deal with general hypotheses in generallinear models, not necessarily of full rank. The resulting priors,which we call ‘conventional priors’, are expressedas a generalization of recently introduced ‘partiallyinformative distributions’. The corresponding Bayes factorsare fully automatic, easily computed and very reasonable. Themethodology is illustrated for the change-point problem andthe equality of treatments effects problem. We compare the conventionalpriors derived for these problems with other objective Bayesianproposals like the intrinsic priors. It is concluded that bothpriors behave similarly although interesting subtle differencesarise. We adapt the conventional priors to deal with nonnestedmodel selection as well as multiple-model comparison. Finally,we briefly address a generalization of conventional priors tononnormal scenarios.     

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.     

Choosing appropriate genetic markers and analytical methods for testing landscape genetic hypotheses

Landscape genetics and phylogeography both examine population‐level microevolutionary processes, such as population structure and gene flow, in the context of environmental and geographic variation. They differ in terms of the spatial and temporal scales they typically investigate, meaning that different genetic markers and analytical methods are better suited for testing the different hypotheses typically posed by each discipline. In a recent comment, Bohonak & Vandergast (2011) argue that I overlooked the value of mtDNA for landscape genetics in an article I published last year in Molecular Ecology (Wang 2010) and that a gap between landscape genetics and phylogeography, which I outlined, does not exist. Here, I clarify several points in my original article and summarize the commonly held viewpoint that different genetic markers are appropriate for drawing inferences at different temporal scales.     

Note on the choice of statistic for testing hypotheses regarding seasonality

The Kolmogorov-Smirnov one-sample test and the Pearson chi-square test are discussed regarding their application for testing hypotheses of seasonality in births. This paper addresses some points mentioned in an earlier paper by McCullough and argues that the chi-square procedure may be the better test.     

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.     

Sexual segregation in western grey kangaroos: testing alternative evolutionary hypotheses

In sexually dimorphic ungulates, sexual segregation is hypothesized to have evolved because of sex-specific differences in body size and/or reproductive strategies. We tested these alternative hypotheses in kangaroos, which are ecological analogues of ungulates. Kangaroos exhibit a wide range of body sizes, particularly among mature males, and so the effects of body size and sex can be distinguished. We tested predictions derived from these hypotheses by comparing the distribution of three sex–sex size classes of western grey kangaroos Macropus fuliginosus , in different habitats, and the composition of groups of kangaroos, across seasons. In accordance with the predation risk-reproductive strategy hypothesis, during the non-breeding season, females, which were more susceptible to predation than larger males, and were accompanied by vulnerable young-at-foot, were over-represented in secure habitats. Large males, which were essentially immune to predation, occurred more often than expected in nutrient-rich habitat, and small males, which faced competing demands of predator avoidance and feeding, were intermediate between females and large males in their distribution across habitats. During the breeding season, females continued to be over-represented in secure habitats when their newly emerged pouch young were most vulnerable to predation. All males occupied these same habitats to maximize their chances of securing mates. Consistent with the social hypotheses, groups composed of individuals of the same sex, irrespective of body size, were over-represented in the population during the non-breeding season, while during the breeding season all males sought females so that mixed-sex groups predominated. These results indicate that body size and reproductive strategies are both important, yet independent, factors influencing segregation in western grey kangaroos.     

Novel coaggregating microbial consortium: testing strength for field applications

Acinetobacter johnsonii S35 has an ability to coaggregate with Oligotropha carboxidovorans S23 when grown with favorable carbon substrate and nutrient-rich growth media. However, nutrient-deficient situations or poorly accessible carbon substrates in waste streams could trigger changes in the cell surface properties and thus modify the coaggregation behavior. Thus, in the present study, we test the stability of these novel interactions under various stresses that might transpire in the waste streams. The effect of mineral-component deficiency and shortage of substrate on the growth, cell surface hydrophobicity and coaggregation ability of S35 and O. carboxidovorans S23 has been investigated. As compared to the control, growth of S35 was adversely affected in mineral-deficient medium; the cells had lower hydrophobicity but displayed only slightly lower aggregation index (AI, 75-84%) as compared to control (92%). S35 grown on marginally supplemented Sterile Filtrate of Activated Sludge (SFAS) could also grow well and form larger stable coaggregates with S23. S35 grown with mineral-deficient medium and with the supplemented SFAS still posses the ability to coaggregate with S23. Hence the coaggregation ability of S35 strain is constitutive and is not significantly affected by environmental factors. It would be desirable to work out suitable formulations of such robust and environmentally relevant microbes.