Testing a covariotide model of DNA substitution

The concomitantly variable codons hypothesis of DNA substitution argues that at any time only a fraction of the codons in a gene are capable of accepting a mutation. However, as mutations are fixed at some positions in a gene, the sites that are potentially variable also change because of changed functional constraints. This hypothesis has been termed the "covarion" hypothesis or when the model is applied to nucleotides, the "covariotide" hypothesis. The covarion-covariotide model has proven to be remarkably difficult to test. Here I examine a covariotide hypothesis for 11 genes using a likelihood ratio test. I show that in nine of the genes examined a covariotide model provides a better explanation of the data than a model that does not allow constraints to change over time.     

Revisit on the evolutionary relationship between alternative splicing and gene duplication

Gene duplications and alternative splicing (AS) isoforms are two widespread types of genetic variations that can facilitate diversification of protein function. A number of studies claimed that after gene duplication, two AS isoforms with differential functions can be 'fixed', respectively, in each of the duplicate copies. This simple 'functional-sharing' hypothesis was recently challenged by Roux and Robinson-Rechavi (2011). Instead, they proposed a more sophisticated hypothesis, invoking that less alternative splicing genes tend to be duplicated more frequently, and single-copy genes are younger than duplicate genes, or the 'duplicability-age' hypothesis for short. In this letter, we show that all these genome-wide analyses of AS isoforms actually did not provide clear-cut evidence to nullify the basic idea of functional-sharing hypothesis. After updating our understanding of genome-wide alternative splicing, duplicability and CNV (copy number variation), we argue that the foundation of the duplicability-age hypothesis remains to be justified carefully. Finally, we suggest that a better approach to resolving this controversy is the correspondence analysis of indels (insertions and deletions) between duplicate genes to the genomic exon-intron structure, which can be used to experimentally test the effect of functional-sharing hypothesis.     

Test Procedures in Configural Frequency Analysis (CFA) Controlling the Local and Multiple Level

The test statistics used until now in the CFA have been developed under the assumption of the overall hypothesis of total independence. Therefore, the multiple test procedures based on these statistics are really only different tests of the overall hypothesis. If one likes to test a special cell hypothesis, one should only assume that this hypothesis is true and not the whole overall hypothesis. Such cell tests can then be used as elements of a multiple test procedure. In this paper it is shown that the usual test procedures can be very anticonservative (except of the two-dimensional, and, for some procedures, the three-dimensional case), and corrected test procedures are developed. Furthermore, for the construction of multiple tests controlling the multiple level, modifications of Holm's (1979) procedure are proposed which lead to sharper results than his general procedure and can also be performed very easily.     

生态学假说试验验证的原假说困境

试验方法是生态学假说的主要验证方法之一,但也存在由原假说引发的质疑.Quinn和Dunham(1983)通过对Platt(1964)的假说-演绎模型进行分析,主张生态学不可能存在可以严格被试验验证的原假说.Fisher的证伪主义与Neyman-Pearson(N-P)的非判决性使得统计学原假说不能被严格验证;而生态过程中存在的不同于经典物理学的原假说H₀(α=1,β=0)与不同的备假说H₁′(α′=1,β′=0)的情况,使得生态学原假说也很难得到严格的实验验证.通过降低P值、谨慎选择原假说、对非原假说采取非中心化和双侧验证可分别缓解上述的原假说困境.但统计学的原假说显著性验证(NHST)不应等同于生态学假说中有关因果关系的逻辑证明方法.因此,现有大量基于NHST的生态学假说的方法研究和试验验证的结果与结论都不是绝对的逻辑可靠的.     

On the Number of Rays in Starfish

Multiradiate starfish evolved independently in fourteen livingfamilies. Twenty living families are strictly 5-rayed. The FIVE-PLUShypothesis is that supernumerary rays develop separately fromthe five primary rays. The ontogeny of the primary rays is proposedto be highly integrated ("en bloc" hypothesis), closely timed(synchronic hypothesis) and a developmental constraint ("tamper-proof"hypothesis). The "en bloc" hypothesis postulates that the fiveprimary rays develop as a unit. The deep structure of this unitis believed to be a 2-1-2, BA-A-BA, organization. The synchronichypothesis postulates that there is only a brief time at metamorphosisduring which the "en bloc" pathway operates. There is a pausebefore the development of supernumerary rays. The "tamper-proof"hypothesis postulates that the "en bloc" pathway has no heritablevariation and cannot be co-opted for the production of supernumeraryrays. There is diversity of timing and pattern in the developmentof supernumerary rays. Postgeneration of rays in the rudimentand intercalary regeneration of rays in the imago are independentray-producing pathways that may have been co-opted variouslyand recurrently in the multiple origins of multiradiate starfish.     

Birds Flush Early and Avoid the Rush: An Interspecific Study

Since 1986, studies about the escape decisions made by prey are grounded in optimal escape theory (OET) which states that prey will initiate escape when the risk of remaining and the costs of leaving are equal. However, a recent hypothesis, Flush Early and Avoid the Rush (FEAR), acknowledged that the cost of monitoring approaching predators might be a ubiquitous cost. The FEAR hypothesis predicts that prey will generally flee soon after they detect a predator so as to minimize the costs incurred by monitoring the predator. Knowing whether animals flee to reduce monitoring costs is of applied interest because wildlife managers use escape behavior to create set-back zones to reduce human-wildlife conflict. Here we provide the most comprehensive assessment of the FEAR hypothesis using data collected from 178 bird species representing 67 families from two continents. The FEAR hypothesis explains escape behavior in 79% of studied species. Because the FEAR hypothesis is a widespread phenomenon that drives escape behavior in birds, alert distance must be systematically incorporated into the design of set-back zones to protect vulnerable species.     

The epidemiological consequences of leprosy-tuberculosis co-infection

While in antiquity both leprosy and tuberculosis were prevalent in Europe, leprosy declined thereafter and, simultaneously, tuberculosis prevalence increased. Since both diseases are caused by mycobacterial infections, it has been suggested that there might be a causal relationship between both epidemics.Chaussinand observed the inverse prevalence of leprosy and tuberculosis and suggested that individuals with a latent tuberculosis infection are protected from acquiring leprosy. His cross-immunity hypothesis has been countered more recently by a co-infection hypothesis. The latter suggestion, proposed by Donoghue, states that people being infected with multi-bacillary leprosy are more susceptible to tuberculosis, which leads to increased mortality from the disease.This study utilizes mathematical modeling to explore the epidemiological consequences of the co-infection hypothesis for realistically confined parameter values. While the co-infection hypothesis appears plausible at first glance, a second thought reveals that it comprises also substantial consequences for tuberculosis epidemics: if co-infection raises the mortality rate above that of purely tuberculosis infected persons, then tuberculosis might as well be eradicated by leprosy. It is the specific interplay of both increased susceptibility towards tuberculosis and increased death rate when co-infected that determines the epidemiological fate.As a result of this analysis, it is shown that there is a large parameter region where the eventual disappearance of leprosy could indeed be explained by co-infection. This parameter region is considerably larger than that predicted by the cross-immunity hypothesis. This shows that the co-infection hypothesis should be considered a significant alternative to the cross-immunity hypothesis. The time scales at which the effects of co-infection are observed depend critically on the spatial distribution of the individuals but reach epidemiologically realistic values for rather immobile individuals with local interaction.     

Patterns of species richness among North Carolina hardwood forests: tests of two hypotheses

The number of species (species richness) and 13 soil variables were determined in 30 0.1 ha plots in the Duke Forest, Durham and Orange Counties, North Carolina, in order to test whether variability in species richness can be accounted for by the environmental variability hypothesis, or the sampling effect hypothesis. The environmental variability hypothesis predicts a positive correlation between the variance in factors which are ecologically important and species richness. However, the variabilities of environmental factors are unrelated to richness. The sampling effect hypothesis predicts that more rare species will be found in species-rich sites. However, as richness increases, the number of species in all abundance classes increases. Both the environmental variability hypothesis and the sampling effect hypothesis are therefore unlikely to account for the substantial variability in species richness which exists in the Duke Forest.     

An assessment of the impact of hafting on Paleoindian point variability

It has long been argued that the form of North American Paleoindian points was affected by hafting. According to this hypothesis, hafting constrained point bases such that they are less variable than point blades. The results of several studies have been claimed to be consistent with this hypothesis. However, there are reasons to be skeptical of these results. None of the studies employed statistical tests, and all of them focused on points recovered from kill and camp sites, which makes it difficult to be certain that the differences in variability are the result of hafting rather than a consequence of resharpening. Here, we report a study in which we tested the predictions of the hafting hypothesis by statistically comparing the variability of different parts of Clovis points. We controlled for the potentially confounding effects of resharpening by analyzing largely unused points from caches as well as points from kill and camp sites. The results of our analyses were not consistent with the predictions of the hypothesis. We found that several blade characters and point thickness were no more variable than the base characters. Our results indicate that the hafting hypothesis does not hold for Clovis points and indicate that there is a need to test its applicability in relation to post-Clovis Paleoindian points.     

森林生态系统中植食性昆虫与寄主的互作机制、假说与证据

围绕"多样性稳定性"假说、"联合抗性假说"、"生长势假说"、"胁迫假说"、以及下调、上调和推拉等机制与假说提出的背景与实验验证的证据,力图辨析其概念以及它们之间的相互关系。作者认为,多样性-稳定性机制关注森林生态系统的功能,是基于群落甚至景观层次。多样性条件下的联合抗性机制和联合易感性应属于稳定性中的抵抗力范畴。联合抗性机制的主要基础是基于资源集中假说和天敌假说,这些观点在种群层次上更易理解;上调力和下调力机制是以食物网底部的资源与顶端的天敌来探讨这种互作关系。因此,资源集中与上调力有着对应关系,而天敌假说只是下调力机制中的一个层面而已。植物生长势假说和植物胁迫假说力图从植物个体或种的群体的生长状态出发解析植食性动物的对寄主的选择趋势。上述有关植食性昆虫与寄主互作的机制、假说与证据是基于不同的层面提出的,因而在解析研究目标时,由于基本面的差异有可能会得出不同的结论。以近年来的研究进展和研究成果为依据有针对性地阐述这些理论对森林有害生物生态调控技术的指导作用,其中,联合抗性和联合易感性理论对指导森林有害生物生态控制具有更直接的指导作用。进一步提出了相应的亟待解决的科学问题。     

小型哺乳动物种群周期性波动的外因调节假说

对小型哺乳动物种群数量周期性波动的外因调节假说进行介绍 ,概述了食物假说、捕食假说和复合因子假说的主要内容和研究进展。在少数生存环境严酷的小型哺乳动物种群中 ,食物假说能解释它们的周期性数量波动现象 ,可能作为调节因子起作用 ,但难以说明低数量期的确切机制 ,对于大多数小型哺乳动物而言 ,它更可能作为限制因子。捕食假说解释了北欧芬诺斯坎底亚地区某些种群的周期性波动 ,尤其是捕食的间接效应已引起许多学者的关注 ,但也有不支持该假说的证据。对于复合因子假说 ,近年颇受学者重视 ,其中验证食物和捕食交互及累加作用的实验证据较多 ,有的研究还包括气候、种间竞争、空间或社会行为等因素。有关复合因子的实验研究 ,尽管工作是困难和艰巨的 ,花费也是巨大的 ,但所得结果却极有价值 ,为深入理解种群动态调节理论提供了一个合理而有效的手段     

Using phylogeographic analyses of gene trees to test species status and processes

A gene tree is an evolutionary reconstruction of the genealogical history of the genetic variation found in a sample of homologous genes or DNA regions that have experienced little or no recombination. Gene trees have the potential of straddling the interface between intra- and interspecific evolution. It is precisely at this interface that the process of speciation occurs, and gene trees can therefore be used as a powerful tool to probe this interface. One application is to infer species status. The cohesion species is defined as an evolutionary lineage or set of lineages with genetic exchangeability and/or ecological interchangeability. This species concept can be phrased in terms of null hypotheses that can be tested rigorously and objectively by using gene trees. First, an overlay of geography upon the gene tree is used to test the null hypothesis that the sample is from a single evolutionary lineage. This phase of testing can indicate that the sampled organisms are indeed from a single lineage and therefore a single cohesion species. In other cases, this null hypothesis is not rejected due to a lack of power or inadequate sampling. Alternatively, this null hypothesis can be rejected because two or more lineages are in the sample. The test can identify lineages even when hybridization and lineage sorting occur. Only when this null hypothesis is rejected is there the potential for more than one cohesion species. Although all cohesion species are evolutionary lineages, not all evolutionary lineages are cohesion species. Therefore, if the first null hypothesis is rejected, a second null hypothesis is tested that all lineages are genetically exchangeable and/or ecologically interchangeable. This second test is accomplished by direct contrasts of previously identified lineages or by overlaying reproductive and/or ecological data upon the gene tree and testing for significant transitions that are concordant with the previously identified lineages. Only when this second null hypothesis is rejected is a lineage elevated to the status of cohesion species. By using gene trees in this manner, species can be identified with objective, a priori criteria with an inference procedure that automatically yields much insight into the process of speciation. When one or more of the null hypotheses cannot be rejected, this procedure also provides specific guidance for future work that will be needed to judge species status.     

Theory of the effect of externally applied voltage on membrane oxidation kinetics

Lund recently demonstrated that application of an external electrical potential across a membrane changes the rate of enzymatic oxidation in the membrane. This is a qualitative confirmation of a prediction derived from the hypothesis that membrane potentials are due to redox potentials, with electron conduction across the membrane through its solid matrix. In the present paper, equations relating membrane oxidation rates to applied external potential are derived from the above hypothesis so that this hypothesis may be testedquantitatively by experiments of the type performed by Lund.     

Testing the generalized neutrality hypothesis

Various tests of the hypothesis of selective neutrality based on gene frequency are now available. These tests take as null hypothesis the concept of “strict neutrality”: all new mutants are required to be selectively identical to each other. For evolutionary questions, however, (as opposed to those of genetic polymorphism), a wider null hypothesis might be of interest. Since deleterious alleles have essentially no evolutionary importance, one might wish to test the null hypothesis that only neutral or deleterious mutations occur. The principal alternative to this hypothesis is that there exists heterotic selection of some form for some alleles tending to maintain a level of genetic polymorphism higher than that under neutrality. In this paper an assessment is made of the usefulness of a test of strict neutrality first proposed by this author (Ewens, 1972) as a test of null hypothesis of “generalized neutrality,” i.e. that only neutral or deleterious alleles occur. At the same time some remarks will be made about estimation of the fundamental parameter θ defining these processes.     

On the Ordered Development of Plants 2. Self-thinning in Plant Communities

It is shown that the hypothesis that a growing point on a vegetativeplant requires a minimum rate of supply of assimilate to continuegrowth can quantitatively describe self-thinning in communitiesof Trifolium subterraneum. The hypothesis can also be used toexplain the different relationships observed between mean plantweight and plant density when plants are grown in full daylight,70 per cent shade, and transferred between the two light environments.The implications of the hypothesis to self-thinning in naturalplant communities are discussed. Self-thinning, assimilate, plant development     

The Evolution of Large Testes: Sperm Competition or Male Mating Rate?

A positive relationship across species between the extent to which females mate with more than one male and relative testes mass has been demonstrated in a wide range of vertebrate taxa and certain insects. At least two hypotheses, which are not necessarily mutually exclusive, could account for this pattern: (1) the numerical sperm competition hypothesis, which assumes that larger testes enable the male to transfer more sperm to each female, giving the male an advantage in sperm competition and (2) the male mating rate hypothesis, which proposes that larger testes allow the male to produce a greater number of (potentially smaller) ejaculates to engage in frequent copulations with different females. Of these hypotheses, the former has won broad acceptance, while the latter has tended to be dismissed. Here, we argue that the lines of evidence commonly used to support the numerical sperm competition hypothesis in favour of the male mating rate hypothesis are not as clear cut or generally applicable as they are purported to be and that, consequently, the male mating rate hypothesis cannot be excluded with confidence on the basis of the current evidence. Furthermore, some evidence, such as the finding that ejaculate mass and/or sperm number is negatively correlated with testes mass across species in some insects and that larger testes in Drosophila can evolve in response to an increase in the number of females available for mating in the laboratory, provides support for the male mating rate hypothesis. Further work is needed to disentangle the relative effects of these selective pressures on the evolution of testes size.     

The enemy release hypothesis as a hierarchy of hypotheses

In ecology, a hypothesis is usually not discarded if a few studies reject it, as long as there are other studies supporting it. How to assess the usefulness of ecological hypotheses is therefore not straightforward. Using the enemy release hypothesis as an example, we show how creating a hierarchy of hypotheses (HoH) can help reviewing and evaluating evidence for and against an ecological hypothesis. In a HoH, a broad, overarching hypothesis branches into more specific and better testable sub‐hypotheses. The enemy release hypothesis is a major hypothesis in invasion ecology and posits that the absence of enemies in the exotic range of an alien species is a cause of its invasion success. Based on a systematic review of empirical tests of this hypothesis, we divided it into sub‐hypotheses, differentiating among 1) indicators for enemy release, 2) types of comparisons, and 3) types of enemies. We identified 176 empirical tests and weighted each test according to the number of alien species studied and the research method (experimental vs observational, field vs enclosure vs laboratory). For the broadly formulated enemy release hypothesis, we found nearly as much supporting (36%) as questioning evidence (43%). At the sub‐hypotheses level, however, we found that some sub‐hypotheses are strongly supported by empirical evidence, whereas others receive hardly any support. These differences are further emphasized for some types of habitat and focal taxonomic groups. Our findings suggest that several specific formulations (i.e. sub‐hypotheses) of the broad enemy release hypothesis are useful, whereas other formulations should be viewed more critically. In general, the approach outlined here can help evaluate major ecological hypotheses and their specific sub‐hypotheses. Our study also highlights the need for a scientific debate on how much supporting evidence is sufficient to consider an ecological hypothesis to be useful.     

Do homoiologies impede phylogenetic analyses of the fossil hominids? An assessment based on extant papionin craniodental morphology

Homoiologies are phylogenetically misleading resemblances among taxa that can be attributed to phenotypic plasticity. Recently, it has been claimed that homoiologies are widespread in the hominid skull, especially in those regions affected by mastication-related strain, and that their prevalence is a major reason why researchers have so far been unable to obtain a reliable estimate of hominid phylogeny. To evaluate this "homoiology hypothesis", we carried out analyses of a group of extant primates for which a robust molecular phylogeny is available-the papionins. We compiled a craniometric dataset from measurements that differ in their susceptibility to mastication-related strain according to developmental considerations and experimental evidence. We used the coefficient of variation and analysis of variance with post hoc least significant difference comparisons in order to evaluate the variability of the measurements. The prediction from the homoiology hypothesis was that dental measurements, which do not remodel in response to strain, should be less variable than low-to-moderate-strain measurements, and that the latter should be less variable than high-strain measurements. We then performed phylogenetic analyses using characters derived from the measurements and compared the resulting phylogenetic hypotheses to the group's consensus molecular phylogeny. The prediction was that, if the homoiology hypothesis is correct, the agreement between the craniometric and molecular phylogenies would be best in the analyses of dental characters, intermediate in the analyses of low-to-moderate-strain characters, and least in the analyses of high-strain characters. The results of this study support the suggestion that mastication-related mechanical loading can result in variation in hominid cranial characters. However, they do not support the hypothesis that homoiology is a major reason why phylogenetic analyses of hominid crania have so far yielded conflicting and weakly supported hypotheses of relationship. These findings are consistent with a recent test of the homoiology hypothesis using craniodental data from extant hominoids, and cast doubt on the validity of the homoiology hypothesis, as originally formulated.