Female prairie voles do not choose males based on their frequency of scent marking

We conducted an experiment to test three alternative hypotheses for the function of frequency of scent marking in male prairie voles, MICROTUS OCHROGASTER: (1) sexual attraction (to advertise male quality for mating); (2) reproductive competition; and (3) self-advertisement or individual identity. In laboratory experiments, males deposited scent on all areas of a bare substrate, and more in an area next to a stimulus animal than other areas, regardless of the stimulus animal's sex. Females did not choose mates based on their frequency of scent marking and scent marking did not antagonize or stimulate aggression between males. The frequency of scent marking by males supports the individual identity hypothesis, and is less consistent with the sexual attraction or reproductive competition hypotheses. Mate choice is likely based on a complex suite of characters, but at least in prairie voles, the frequency of scent marking by males does not appear to be one of them.     

Experiments in ecology and management: Their logics,functions and interpretations

Experimental tests of clearly articulated hypotheses are an increasingly widespread feature of modern marine ecology. Increased use of experiments has not, however, been accompanied by increased understanding of the logical structure of falsificationist tests. Most observations can be explained by several different models or theories. To distinguish among these requires demonstration of the falsity of the consequences or predictions of incorrect models. This is best achieved by deriving from each model one or more hypotheses (predictions) about the type, form or nature of observations that should occur in some not-yet-examined set of circumstances. Because of logical constraints on the possibility of proving the correctness of such hypotheses, they must be inverted to form logical null hypotheses which comprise all alternative possibilities to those predicted in the hypotheses. Correctness or not of null hypotheses can then be ascertained by an appropriately designed experiment (or test), leading to unambiguous rejection or retention of the null hypotheses. The former corroborates the hypotheses and provides support for the correctness of the explanatory model for the original observations. In contrast, retention of a null hypothesis identifies an incorrect model. The growth of knowledge is thus the elimination of false models, theories and explanations. Ecological experiments usually require statistical procedures for determining whether or not null hypotheses should be retained. Construction of statistical null hypotheses (i.e. definitions of parameters of frequency distributions of test statistics) sometimes requires that these be identical to logical hypotheses (and not to the logical nulls). This leads to irrational acceptance of hypotheses and the models or theories from which they were derived. It also poses immense problems for determinations of statistical power of experiments. Ecological experiments are analysed to reveal the nature of, and linkages between, their components in relation to falsificationism, statistical procedures and the logical properties and interpretations of ecological theories.     

Detecting the molecular signature of social conflict: theory and a test with bacterial quorum sensing genes

Extending social evolution theory to the molecular level opens the door to an unparalleled abundance of data and statistical tools for testing alternative hypotheses about the long-term evolutionary dynamics of cooperation and conflict. To this end, we take a collection of known sociality genes (bacterial quorum sensing [QS] genes), model their evolution in terms of patterns that are detectable using gene sequence data, and then test model predictions using available genetic data sets. Specifically, we test two alternative hypotheses of social conflict: (1) the "adaptive" hypothesis that cheaters are maintained in natural populations by frequency-dependent balancing selection as an evolutionarily stable strategy and (2) the "evolutionary null" hypothesis that cheaters are opposed by purifying kin selection yet exist transiently because of their recurrent introduction into populations by mutation (i.e., kin selection-mutation balance). We find that QS genes have elevated within- and among-species sequence variation, nonsignificant signatures of natural selection, and putatively small effect sizes of mutant alleles, all patterns predicted by our evolutionary null model but not by the stable cheater hypothesis. These empirical findings support our theoretical prediction that QS genes experience relaxed selection due to nonclonality of social groups, conditional expression, and the individual-level advantage enjoyed by cheaters. Furthermore, cheaters are evolutionarily transient, persisting in populations because of their recurrent introduction by mutation and not because they enjoy a frequency-dependent fitness advantage.     

TRAB: testing whether mutation frequencies are above an unknown background

To rigorously determine whether a gene or a set of genes have alterations that are involved in carcinogenesis requires a comparison of the prevalence of identified changes to a control mutation frequency present in tumor DNA. To facilitate this task, we develop a testing approach and the associated R library, called TRAB, that evaluates whether the frequency of somatic mutation in a given gene is higher than that observed in a control group of genes. Specifically, we test the null hypothesis that the frequency belongs to a control population of frequencies, against the alternative hypothesis that the frequency is higher. Mutation frequencies in the control group are themselves allowed to be variable. TRAB computes the a posteriori probability and the Bayes factor for the hypothesis using a hierarchical Bayesian approach.     

Maintenance of a female-limited polymorphism in Ischnura ramburi (Zygoptera: Coenagrionidae)

Colour polymorphisms can be maintained in a population if all morphs have equal fitness on average, if fitness is frequency dependent or if fitness functions cross for some environmental or social variable. We studied female-limited colour polymorphism in the Rambur's forktail damselfly, Ischnura ramburi, in which one female morph looks like the male. The most commonly cited hypotheses to explain this polymorphism involve an advantage to andromorphs of avoiding costly matings through male mimicry. An alternative hypothesis argues that males learn the most common morph and that the polymorphism is maintained by a rare-morph advantage of mating avoidance, irrespective of male mimicry. We tested predictions of the male mimicry hypothesis, learned mate recognition hypothesis (LMR) and two new hypotheses. We used censuses and a mark-resight study to estimate density, sex ratio, morph frequency and mating frequencies. We observed interactions to test for male mimicry and female competition and to evaluate the frequency of mating attempts. Andromorphs were less likely than gynomorphs to receive mating attempts in encounters with males, but did not mate less frequently, or attack males or interrupt oviposition by other females more frequently. Contrary to the LMR hypothesis, the rarer morph was more likely to receive mating attempts. Andromorph frequency was greater in older females than in younger females, suggesting higher mortality or dispersal of gynomorphs. Our results support a modification of the male mimicry hypothesis, the signal detection hypothesis. Together with past studies, our results suggest that the female morphs may be alternative mating avoidance strategies.     

Methods and criteria for deciding whether specific-locus mutation-rate data in mice indicate a positive,negative, or inconclusive result

The binomial approximation of the UMPU (uniformly most powerful unbiased) test for the equality of 2 binomial proportions is shown to be a highly accurate and easily applied method for testing the hypothesis that a given mouse specific-locus mutation frequency is not higher than the spontaneous mutation frequency (43 mutations in 801 406 offspring, for males). Critical sample sizes have been calculated that show at a glance whether P < 0.05.The first hypothesis that the mutation frequency (induced + spontaneous) of treated mice is not higher than the spontaneous mutation frequency is combined with the second hypothesis that the induced mutation frequency of treated mice is no less than 4 times the historical-control mutation frequency to produce a multiple decision procedure with 4 possible decisions: inconclusive result, negative result, positive result, and weak mutagen. Critical sample sizes for the second hypothesis, also with P < 0.05, are combined with those for the first hypothesis into a grid that permits rapid evaluation of data according to these criterea. The justification for using these criteria in reaching decisions, assuming a high level of exposure has been given, is the practical necessity of rapidly determining which chemicals are potent mutagens.Positive results can become apparent in relatively small samples. Larger samples, of at least 11 166 offspring, are required to obtain a negative result. If samples of 18 000 are routinely collected (unless positive results are found earlier), 75% of tests of chemicals that are non-mutagens will give a negative result. If the question being asked is not whether a chemical induces gene mutations but, rather, whether the exposure received by humans causes any important risk from gene mutations, a much smaller sample size may be acceptable, under certain conditions.A comparison of the relative efficiencies of the specific-locus test (for gene mutations and small deficiencies) and the heritable-translocation test (for transmissible chromosome rearrangements), in detecting the same proportional increases over the spontaneous frequencies of their respective types of genetic damage, shows that less work is involved in reaching a conclusive result in the specific-locus test. Proposed specific-locus tests using biochemical markers are at a considerable statistical disadvantage compared with the standard test (using 7 visible markers) for which there is available a very large historical control showing a very low mutation rate.     

Enhanced Synonymous Site Divergence in Positively Selected VertebrateAntimicrobial Peptide Genes

Nonrandom patterns associated with adaptively evolving genes can shed light on how selection and mutation produce rapid changes in sequences. I examine such patterns in two independent families of antimicrobial peptide genes: those in frogs, which are known to have evolved under positive selection, and those in flatfishes, which I show have also evolved under positive selection. I address two recently proposed hypotheses about the molecular evolution of antimicrobial peptide genes. The first is that the mature peptide region is replicated by an error-prone polymerase that increases the mutation rate and the transversion/transition ratio compared to the signal sequence of the same genes. The second is that mature peptides evolve in a coordinated fashion with their propieces, such that a change in net charge in one molecular region prompts an opposite change in charge in the other region. I test these hypotheses using alternative methods that minimize alignment errors, correct for phylogenetic nonindependence, reduce sequence saturation, and account for differing selection pressures on different regions of the gene. In both gene families I show that divergence at both synonymous and nonsynonymous sites within the mature peptide region is enhanced. However, in neither gene family is there evidence of an increased mutational transversion/transition ratio or coordinated evolution. My observations are consistent with either an elevated mutation rate in an adaptively evolving gene region or widespread selection on “silent” sites. These hypotheses challenge the assumption that mutations are random and can be measured by the synonymous substitution rate. [Reviewing Editor: Dr. Willie J. Swanson]     

Bayesian inferences on umbrella orderings

In regression applications with categorical predictors, interest often focuses on comparing the null hypothesis of homogeneity to an ordered alternative. This article proposes a Bayesian approach for addressing this problem in the setting of normal linear and probit regression models. The regression coefficients are assigned a conditionally conjugate prior density consisting of mixtures of point masses at 0 and truncated normal densities, with a (possibly unknown) changepoint parameter included to accommodate umbrella ordering. Two strategies of prior elicitation are considered: (1) a Bayesian Bonferroni approach in which the probability of the global null hypothesis is specified and local hypotheses are considered independent; and (2) an approach which treats these probabilities as random. A single Gibbs sampling chain can be used to obtain posterior probabilities for the different hypotheses and to estimate regression coefficients and predictive quantities either by model averaging or under the preferred hypothesis. The methods are applied to data from a carcinogenesis study.     

Using novel phylogenetic methods to evaluate mammalian mtDNA,including amino acid-invariant sites-LogDet plus site stripping,to detect internal conflicts in the data,with special reference to the positions of hedgehog,armadillo, and elephant

We look at the higher-order phylogeny of mammals, analyzing in detail the complete mtDNA sequences of more than 40 species. We test the support for several proposed superordinal relationships. To this end, we apply a number of recently programmed methods and approaches, plus better-established methods. New pairwise tests show highly significant evidence that amino acid frequencies are changing among nearly all the genomes studied when unvaried sites are ignored. LogDet amino acid distances, with modifications to take into account invariant sites, are combined with bootstrapping and the Neighbor Joining algorithm to account for these violations of standard models. To weight the more slowly evolving sites, we exclude the more rapidly evolving sites from the data by using "site stripping". This leads to changing optimal trees with nearly all methods. The bootstrap support for many hypotheses varies widely between methods, and few hypotheses can claim unanimous support from these data. Rather, we uncover good evidence that many of the earlier branching patterns in the placental subtree could be incorrect, including the placement of the root. The tRNA genes, for example, favor a split between the group hedgehog, rodents, and primates versus all other sequenced placentals. Such a grouping is not ruled out by the amino acid sequence data. A grouping of all rodents plus rabbit, the old Glires hypothesis, is also feasible with stripped amino acid data, and rodent monophyly is also common. The elephant sequence allows confident rejection of the older taxon Ferungulata (Simpson, 1945). In its place, the new taxa Scrotifera and Fereuungulata are defined. A new likelihood ratio test is used to detect differences between the optimal tree for tRNA versus that for amino acids. While not clearly significant as made, some results indicate the test is tending towards significance with more general models of evolution. Individual placement tests suggest alternative positions for hedgehog and elephant. Congruence arguments to support elephant and armadillo together are striking, suggesting a superordinal group composed of Xenarthra and African endemic mammals, which in turn may be near the root of the placental subtree. Thus, while casting doubt on some recent conclusions, the analyses are also unveiling some interesting new possibilities.     

Determining the role of Tie-dyed1 in starch metabolism: epistasis analysis with a maize ADP-glucose pyrophosphorylase mutant lacking leaf starch

In regions of their leaves, tdy1-R mutants hyperaccumulate starch. We propose 2 alternative hypotheses to account for the data, that Tdy1 functions in starch catabolism or that Tdy1 promotes sucrose export from leaves. To determine whether Tdy1 might function in starch breakdown, we exposed plants to extended darkness. We found that the tdy1-R mutant leaves retain large amounts of starch on prolonged dark treatment, consistent with a defect in starch catabolism. To further test this hypothesis, we identified a mutant allele of the leaf expressed small subunit of ADP-glucose pyrophosphorylase (agps-m1), an enzyme required for starch synthesis. We determined that the agps-m1 mutant allele is a molecular null and that plants homozygous for the mutation lack transitory leaf starch. Epistasis analysis of tdy1-R; agps-m1 double mutants demonstrates that Tdy1 function is independent of starch metabolism. These data suggest that Tdy1 may function in sucrose export from leaves.     

Comparing the strength of modular signal,and evaluating alternative modular hypotheses,using covariance ratio effect sizes with morphometric data

The study of modularity is paramount for understanding trends of phenotypic evolution, and for determining the extent to which covariation patterns are conserved across taxa and levels of biological organization. However, biologists currently lack quantitative methods for statistically comparing the strength of modular signal across datasets, and a robust approach for evaluating alternative modular hypotheses for the same dataset. As a solution to these challenges, we propose an effect size measure () derived from the covariance ratio, and develop hypothesis‐testing procedures for their comparison. Computer simulations demonstrate that displays appropriate statistical properties and low levels of mis‐specification, implying that it correctly identifies modular signal, when present. By contrast, alternative methods based on likelihood (EMMLi ) and goodness of fit (MINT ) suffer from high false positive rates and high model mis‐specification rates. An empirical example in sigmodontine rodent mandibles is provided to illustrate the utility of for comparing modular hypotheses. Overall, we find that covariance ratio effect sizes are useful for comparing patterns of modular signal across datasets or for evaluating alternative modular hypotheses for the same dataset. Finally, the statistical philosophy for pairwise model comparisons using effect sizes should accommodate any future analytical developments for characterizing modular signal.     

Unconditional Non-Asymptotic One-Sided Tests for Independent Binomial Proportions When the Interest Lies in Showing Non-Inferiority and/or Superiority

For two independent binomial proportions Barnard (1947) has introduced a method to construct a non-asymptotic unconditional test by maximisation of the probabilities over the ‘classical’ null hypothesis H₀= {(θ₁, θ₂) ∈ [0, 1]²: θ₁ = θ₂}. It is shown that this method is also useful when studying test problems for different null hypotheses such as, for example, shifted null hypotheses of the form H₀ = {(θ₁, θ₂) ∈ [0, 1]²: θ₂ ≤ θ₁ ± Δ } for non-inferiority and 1-sided superiority problems (including the classical null hypothesis with a 1-sided alternative hypothesis). We will derive some results for the more general ‘shifted’ null hypotheses of the form H₀ = {(θ₁, θ₂) ∈ [0, 1]²: θ₂ ≤ g(θ₁ )} where g is a non decreasing curvilinear function of θ₁. Two examples for such null hypotheses in the regulatory setting are given. It is shown that the usual asymptotic approximations by the normal distribution may be quite unreliable. Non-asymptotic unconditional tests (and the corresponding p-values) may, therefore, be an alternative, particularly because the effort to compute non-asymptotic unconditional p-values for such more complex situations does not increase as compared to the classical situation. For ‘classical’ null hypotheses it is known that the number of possible p-values derived by the unconditional method is very large, albeit finite, and the same is true for the null hypotheses studied in this paper. In most of the situations investigated it becomes obvious that Barnard's CSM test (1947) when adapted to the respective null space is again a very powerful test. A theorem is provided which in addition to allowing fast algorithms to compute unconditional non-asymptotical p-values fills a methodological gap in the calculation of exact unconditional p-values as it is implemented, for example, in Stat Xact 3 for Windows (1995).     

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.     

An exact test for the association between the disease and alleles at highly polymorphic loci with particular interest in the haplotype analysis

The association analysis between the disease and genetic alleles is one of the simple methods for localizing the susceptibility locus in the genes. For revealing the association, several statistical tests have been proposed without discussing explicitly the alternative hypotheses. We therefore specify two types of alternative hypotheses (i.e., there is only one susceptibility allele in the locus, and there is an extension or shortening of alleles associated with the disease) and derive exact tests for the respective hypotheses. We also propose to combine these two tests when the prior knowledge is not sufficient enough to specify one of these two hypotheses. In particular, these ideas are extended to the haplotype analysis of three-way association between the disease and bivariate allele frequencies at two closely linked loci. As a by-product, a factorization of the probability distribution of the three-way cell frequencies under the null hypothesis of no three-way interaction is obtained.     

Bayesian inference in ecology

Bayesian inference is an important statistical tool that is increasingly being used by ecologists. In a Bayesian analysis, information available before a study is conducted is summarized in a quantitative model or hypothesis: the prior probability distribution. Bayes’ Theorem uses the prior probability distribution and the likelihood of the data to generate a posterior probability distribution. Posterior probability distributions are an epistemological alternative to P‐values and provide a direct measure of the degree of belief that can be placed on models, hypotheses, or parameter estimates. Moreover, Bayesian information‐theoretic methods provide robust measures of the probability of alternative models, and multiple models can be averaged into a single model that reflects uncertainty in model construction and selection. These methods are demonstrated through a simple worked example. Ecologists are using Bayesian inference in studies that range from predicting single‐species population dynamics to understanding ecosystem processes. Not all ecologists, however, appreciate the philosophical underpinnings of Bayesian inference. In particular, Bayesians and frequentists differ in their definition of probability and in their treatment of model parameters as random variables or estimates of true values. These assumptions must be addressed explicitly before deciding whether or not to use Bayesian methods to analyse ecological data.     

Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys

Using the strictly neutral model as a null hypothesis, we tested for deviations from expected levels of nucleotide polymorphism at the alcohol dehydrogenase locus (Adh-1) within and among four species of pocket gophers (Geomys bursarius major, G. knoxjonesi, G. texensis llanensis, and G. attwateri). The complete protein-encoding region was examined, and 10 unique alleles, representing both electromorphic and cryptic alleles, were used to test hypotheses (e.g., the neutral model) concerning the maintenance of genetic variation. Nineteen variable sites were identified among the 10 alleles examined, including 9 segregating sites occurring in synonymous positions and 10 that were nonsynonymous. Several statistical methods, including those that test for within-species variation as well as those that examine variation within and among species, failed to reject the null hypothesis that variation (both within and between species of Geomys) at the Adh locus is consistent with the neutral theory. However, there was significant heterogeneity in the ratio of polymorphism to divergence across the gene, with polymorphisms clustered in the first half of the coding region and fixed differences clustered in the second half of the gene. Two alternative hypotheses are discussed as possible explanations for this heterogeneity: an old balanced polymorphism in the first half of the gene or a recent selective sweep in the second half of the gene.      

Statistical Significance of Mutation Frequencies,and the Power of Statistical Testing,Using the Poisson Distribution

The Poisson distribution may be employed to test whether mutation frequencies differ from control frequencies. This paper describes how this testing procedure may be used for either one-tailed or two-tailed hypotheses. It is also shown how the power of the statistical test can be calculated, the power being the probability of correctly concluding the null hypothesis to be false.     

Is it enemy-free space? The evidence for terrestrial insects and freshwater arthropods

Abstract.

• 1 Enemy-free space (EFS) was defined by Jeffries & Lawton (1984) as ‘ways of living that reduce or eliminate a species’ vulnerability to one or more species of natural enemies’. EFS has emerged in the literature as a significant niche-moulding factor. However, the lack of consistency among the empirical studies as to how EFS should be defined, and what hypotheses should be tested in order to evaluate its relative importance, prompted us to review the literature and to propose a working definition that results in a general set of testable hypotheses.
• 2 To test the relative importance of EFS in structuring the communities of organisms, we propose a set of three falsifiable null hypotheses that must be tested sequentially and rejected. Ho1: The fitness of the organism in an original habit (e.g. on an original host plant) in the presence of natural enemies is equal to the fitness of the organism in that habit in the absence of natural enemies. Acceptance of the alternative hypothesis that the fitness of the organism in the presence of natural enemies is less than in the absence of natural enemies is necessary to demonstrate the importance of natural enemies. Ho2: The fitness of the organism in an alternative habit with natural enemies is equal to the fitness of the organism in the original habit with natural enemies. Acceptance of the alternative hypothesis that the fitness of the organism in the alternative habit with natural enemies is greater than that in the original habit with natural enemies is necessary to demonstrate that the alternative habit provides EFS. Ho3: The fitness of the organism in an alternative habit without natural enemies equals the fitness of the organism in the original habit without natural enemies. Acceptance of the alternative hypothesis that the fitness of the organism in an alternative habit without natural enemies is less than in the original habit without natural enemies is necessary to demonstrate the relative importance of EFS compared with other co-occurring niche-moulding factors such as competition or host nutritional quality.
• 3 We searched the literature and evaluated fifty-three references (nineteen references to seventeen different terrestrial systems and thirty-four references to twenty-four different freshwater systems) to test our hypotheses.
• 4 Of the forty-one systems examined, nineteen (46%) tested only for differences in vulnerability of the prey or host species between EFS and non-EFS options (our Ho2); sixteen (39%) tested for the importance of natural enemies and the effectiveness of the alternative habit in providing EFS (our Ho1 and Ho2); and only ten systems (24%) tested for Ho1, Ho2 and the relative importance of EFS in the system as measured by fitness (our Ho3).
• 5 Of the systems that tested for EFS, sixteen of nineteen (84%), thirteen of sixteen (81%) and seven of ten (70%) showed evidence in support of the existence of EFS according to hypothesis Ho2 only, hypotheses Ho1 and Ho2, and our three working hypotheses, respectively.
• 6 These results indicate that very few studies have actually tested for the existence of EFS. Nevertheless, results from this limited number of natural systems suggest that EFS may be important in moulding the niches of arthropods. Because of the large number of claims for EFS in systems where none of the basic hypotheses were investigated, we suggest that authors test for EFS experimentally, be judicious in selecting articles to cite in support of EFS, and exert care in attributing it as a selective force in the evolution of arthropods in specific systems.

     

Advantages of sexual reproduction

Despite the obvious efficiencies of many forms of asexual reproduction, sexual reproduction abounds. Asexual species, for the most part, are relatively short-lived offshoots of sexual ancestors. From the nineteenth century, it has been recognized that, since there is no obvious advantage to the individuals involved, the advantages of sexual reproduction must be evolutionary. Furthermore, the advantage must be substantial; for example, producing males entails a two-fold cost, compared to dispensing with them and reproducing by parthenogenetic females. There are a large number of plausible hypotheses. To me the most convincing of these are two. The first hypothesis, and the oldest, is that sexual reproduction offers the opportunity to produce recombinant types that can make the population better able to keep up with changes in the environment. Although the subject of a great deal of work, and despite its great plausibility, the hypothesis has been very difficult to test by critical observations or experiments. Second, species with recombination can bunch harmful mutations together and eliminate several in a single “genetic death.” Asexual species, can eliminate them only in the same genotype in which they occurred. If the rate of occurrence of deleterious mutations is one or more per zygote, some mechanism for eliminating them efficiently must exist. A test of this mutation load hypothesis for sexual reproduction, then, is to find whether deleterious mutation rates in general are this high-as Drosophila data argue. Unfortunately, although molecular and evolutionary studies can give information on the total mutation rate, they cannot determine what fraction are deleterious. In addition, there are short discussions of the advantages of diploidy, anisogamy, and separate sexes. © 1994 Wiley-Liss, Inc.     

Testing separate families of segregation hypotheses: bootstrap methods.

Aspects of the statistical modeling and assessment of hypotheses concerning quantitative traits in genetics research are discussed. It is suggested that a traditional approach to such modeling and hypothesis testing, whereby competing models are "nested" in an effort to simplify their probabilistic assessment, can be complimented by an alternative statistical paradigm - the separate-families-of-hypotheses approach to segregation analysis. Two bootstrap-based methods are described that allow testing of any two, possibly non-nested, parametric genetic hypotheses. These procedures utilize a strategy in which the unknown distribution of a likelihood ratio-based test statistic is simulated, thereby allowing the estimation of critical values for the test statistic. Though the focus of this paper concerns quantitative traits, the strategies described can be applied to qualitative traits as well. The conceptual advantages and computational ease of these strategies are discussed, and their significance levels and power are examined through Monte Carlo experimentation. It is concluded that the separate-families-of-hypotheses approach, when carried out with the methods described in this paper, not only possesses some favorable statistical properties but also is well suited for genetic segregation analysis.