Polytomies and Bayesian phylogenetic inference

Bayesian phylogenetic analyses are now very popular in systematics and molecular evolution because they allow the use of much more realistic models than currently possible with maximum likelihood methods. There are, however, a growing number of examples in which large Bayesian posterior clade probabilities are associated with very short branch lengths and low values for non-Bayesian measures of support such as nonparametric bootstrapping. For the four-taxon case when the true tree is the star phylogeny, Bayesian analyses become increasingly unpredictable in their preference for one of the three possible resolved tree topologies as data set size increases. This leads to the prediction that hard (or near-hard) polytomies in nature will cause unpredictable behavior in Bayesian analyses, with arbitrary resolutions of the polytomy receiving very high posterior probabilities in some cases. We present a simple solution to this problem involving a reversible-jump Markov chain Monte Carlo (MCMC) algorithm that allows exploration of all of tree space, including unresolved tree topologies with one or more polytomies. The reversible-jump MCMC approach allows prior distributions to place some weight on less-resolved tree topologies, which eliminates misleadingly high posteriors associated with arbitrary resolutions of hard polytomies. Fortunately, assigning some prior probability to polytomous tree topologies does not appear to come with a significant cost in terms of the ability to assess the level of support for edges that do exist in the true tree. Methods are discussed for applying arbitrary prior distributions to tree topologies of varying resolution, and an empirical example showing evidence of polytomies is analyzed and discussed.     

Exploring Component Stability Using Life-Stage Concordance In Sabethine Mosquitoes (Diptera: Culicidae)

Abstract — Morphological characters from sabethine mosquitoes were coded from larvae, pupae and adults, and life-stage partitions were evaluated to determine the contribution of each to the topology of a combined cladogram. Initial tests failed to find congruence between characters partitioned by life stage. However, when components from the combined analysis were tested using reduced taxon sets, a high degree of concordance between partitions was observed. A procedure for assessing individual life-stage contribution is employed, in which exhaustive searches are used to explore all possible arrangements for each of the selected components. Seven of the 10 components examined were able to recover the combined topology with a reduced taxon set. Congruent arrangements of taxa were typically observed for two or more life stages, although partitioned data were less resolved and frequently included aberrant topologies (those not supported by other partitioned or combined reduced taxon tree sets). In addition, none of the partitioned data sets gave robust results for all tests, suggesting that studies which emphasize character data from single life stages may support misleading arrangements of taxa. One component on the combined cladogram was not supported by any of the life-stage partitions when analysed separately. These results are complementary to “total evidence” approach, and demonstrate that partitions of data are useful for examining suits of characters which may cause some components of the “total     

Strange bayes indeed: uniform topological priors imply non-uniform clade priors

While Bayesian analysis has become common in phylogenetics, the effects of topological prior probabilities on tree inference have not been investigated. In Bayesian analyses, the prior probability of topologies is almost always considered equal for all possible trees, and clade support is calculated from the majority rule consensus of the approximated posterior distribution of topologies. These uniform priors on tree topologies imply non-uniform prior probabilities of clades, which are dependent on the number of taxa in a clade as well as the number of taxa in the analysis. As such, uniform topological priors do not model ignorance with respect to clades. Here, we demonstrate that Bayesian clade support, bootstrap support, and jackknife support from 17 empirical studies are significantly and positively correlated with non-uniform clade priors resulting from uniform topological priors. Further, we demonstrate that this effect disappears for bootstrap and jackknife when data sets are free from character conflict, but remains pronounced for Bayesian clade supports, regardless of tree shape. Finally, we propose the use of a Bayes factor to account for the fact that uniform topological priors do not model ignorance with respect to clade probability.     

Reconstructing the prior probabilities of allelic phylogenies

In general when a phylogeny is reconstructed from DNA or protein sequence data, it makes use only of the probabilities of obtaining some phylogeny given a collection of data. It is also possible to determine the prior probabilities of different phylogenies. This information can be of use in analyzing the biological causes for the observed divergence of sampled taxa. Unusually "rare" topologies for a given data set may be indicative of different biological forces acting. A recursive algorithm is presented that calculates the prior probabilities of a phylogeny for different allelic samples and for different phylogenies. This method is a straightforward extension of Ewens' sample distribution. The probability of obtaining each possible sample according to Ewens' distribution is further subdivided into each of the possible phylogenetic topologies. These probabilities depend not only on the identity of the alleles and on 4N(mu) (four times the effective population size times the neutral mutation rate) but also on the phylogenetic relationships among the alleles. Illustrations of the algorithm are given to demonstrate how different phylogenies are favored under different conditions.     

Reanalysis of Murphy et al.'s data gives various mammalian phylogenies and suggests overcredibility of Bayesian trees

Murphy and colleagues reported that the mammalian phylogeny was resolved by Bayesian phylogenetics. However, the DNA sequences they used had many alignment gaps and undetermined nucleotide sites. We therefore reanalyzed their data by minimizing unshared nucleotide sites and retaining as many species as possible (13 species). In constructing phylogenetic trees, we used the Bayesian, maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) methods with different substitution models. These trees were constructed by using both protein and DNA sequences. The results showed that the posterior probabilities for Bayesian trees were generally much higher than the bootstrap values for ML, MP, and NJ trees. Two different Bayesian topologies for the same set of species were sometimes supported by high posterior probabilities, implying that two different topologies can be judged to be correct by Bayesian phylogenetics. This suggests that the posterior probability in Bayesian analysis can be excessively high as an indication of statistical confidence and therefore Murphy et al.'s tree, which largely depends on Bayesian posterior probability, may not be correct.     

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method

An improved Bayesian method is presented for estimating phylogenetic trees using DNA sequence data. The birth-death process with species sampling is used to specify the prior distribution of phylogenies and ancestral speciation times, and the posterior probabilities of phylogenies are used to estimate the maximum posterior probability (MAP) tree. Monte Carlo integration is used to integrate over the ancestral speciation times for particular trees. A Markov Chain Monte Carlo method is used to generate the set of trees with the highest posterior probabilities. Methods are described for an empirical Bayesian analysis, in which estimates of the speciation and extinction rates are used in calculating the posterior probabilities, and a hierarchical Bayesian analysis, in which these parameters are removed from the model by an additional integration. The Markov Chain Monte Carlo method avoids the requirement of our earlier method for calculating MAP trees to sum over all possible topologies (which limited the number of taxa in an analysis to about five). The methods are applied to analyze DNA sequences for nine species of primates, and the MAP tree, which is identical to a maximum-likelihood estimate of topology, has a probability of approximately 95%.      

The parasite capacity of the host population

The estimation of parasitic pressure on the host populations is frequently required in parasitological investigations. The empirical values of prevalence of infection are used for this, however the latter one as an estimation of parasitic pressure on the host population is insufficient. For example, the same prevalence of infection can be insignificant for the population with high reproductive potential and excessive for the population with the low reproductive potential. Therefore the development of methods of an estimation of the parasitic pressure on the population, which take into account the features the host population, is necessary. Appropriate parameters are to be independent on view of the researcher, have a clear biological sense and be based on easily available characteristics. The methods of estimation of parasitic pressure on the host at the organism level are based on various individual viability parameters: longevity, resistance to difficult environment etc. The natural development of this approach for population level is the analysis of viability parameters of groups, namely, the changing of extinction probability of host population under the influence of parasites. Obviously, some critical values of prevalence of infection should exist; above theme the host population dies out. Therefore the heaviest prevalence of infection, at which the probability of host population size decreases during the some period is less than probability of that increases or preserves, can serve as an indicator of permissible parasitic pressure on the host population. For its designation the term "parasite capacity of the host population" is proposed. The real parasitic pressure on the host population should be estimated on the comparison with its parasite capacity. Parasite capacity of the host population is the heaviest possible prevalence of infection, at which, with the generation number T approaching infinity, there exists at least one initial population size ni(0) for which the probability of size decrease through T generations is less than the probability of its increase. [formula: see text] The estimation of the probabilities of host population size changes is necessary for the parasite capacity determination. The classical methods for the estimation of extinction probability of population are unsuitable in this case, as these methods require the knowledge of population growth rates and their variances for all possible population sizes. Thus, the development methods of estimate of extinction probability of population, based on the using of available parameters (sex ratio, fecundity, mortality, prevalence of infection PI) is necessary. The population size change can be considered as the Markov process. The probabilities of all changes of population size for a generation in this case are described by a matrix of transition probabilities of Markov process (pi) with dimensions Nmax x Nmax (maximum population size). The probabilities of all possible size changes for T generations can be calculated as pi T. Analyzing the behaviour matrix of transition at various prevalence of infection, it is possible to determine the parasite capacity of the host population. In constructing of the matrix of transition probabilities, should to be taken into account the features the host population and the influence of parasites on its reproductive potential. The set of the possible population size at a generation corresponds to each initial population size. The transition probabilities for the possible population sizes at a generation can be approximated to the binomial distribution. The possible population sizes at a generation nj(t + 1) can be calculated as sums of the number of survived parents N1 and posterities N2; their probabilities--as P(N1) x P(N2). The probabilities of equal sums N1 + N2 and nj(t + 1) > or = Nmax are added. The number of survived parents N1 may range from 0 to (1-PI) x ni(t). The survival probabilities can be estimated for each N1 as [formula: see text] The number of survived posterities N2 may range from 0 to N2max (the maximum number of posterities). N2max is [formula: see text] and the survival probabilities for each N2, is defined as [formula: see text] where [formula: see text], ni(t) is the initial population size (including of males and infected specimens of host), PI is the prevalence of infection, Q1 is the survival probabilities of parents, Pfemales is the frequency of females in the host population, K is the number of posterities per a female, and Q2 is the survival probabilities of posterities. When constructing matrix of transition probabilities of Markov process (pi), the procedure outlined above should be repeated for all possible initial population size. Matrix of transition probabilities for T generations is defined as pi T. This matrix (pi T) embodies all possible transition probabilities from the initial population sizes to the final population sizes and contains a wealth of information by itself. From the practical point of view, however, the plots of the probability of population size decrease are more suitable for analysis. They can be received by summing the probabilities within of lines of matrix from 0 to ni--1 (ni--the population size, which corresponds to the line of the matrix). Offered parameter has the number of advantages. Firstly, it is independent on a view of researcher. Secondly, it has a clear biological sense--this is a limit of prevalence, which is safe for host population. Thirdly, only available parameters are used in the calculation of parasite capacity: population size, sex ratio, fecundity, mortality. Lastly, with the availability of modern computers calculations do not make large labour. Drawbacks of this parameter: 1. The assumption that prevalence of infection, mortality, fecundity and sex ratio are constant in time (the situations are possible when the variability of this parameters can not be neglected); 2. The term "maximum population size" has no clear biological sense; 3. Objective restrictions exist for applications of this mathematical approach for populations with size, which exceeds 1000 specimens (huge quantity of computing operations--order Nmax 3*(T-1), work with very low probabilities). The further evolution of the proposed approach will allow to transfer from the probabilities of size changes of individual populations to be probabilities of size changes of population systems under the influence of parasites. This approach can be used at the epidemiology and in the conservation biology.     

The probability of topological concordance of gene trees and species trees

The concordance of gene trees and species trees is reconsidered in detail, allowing for samples of arbitrary size to be taken from the species. A sense of concordance for gene tree and species tree topologies is clarified, such that if the "collapsed gene tree" produced by a gene tree has the same topology as the species tree, the gene tree is said to be topologically concordant with the species tree. The term speciodendric is introduced to refer to genes whose trees are topologically concordant with species trees. For a given three-species topology, probabilities of each of the three possible collapsed gene tree topologies are given, as are probabilities of monophyletic concordance and concordance in the sense of N. Takahata (1989), Genetics 122, 957-966. Increasing the sample size is found to increase the probability of topological concordance, but a limit exists on how much the topological concordance probability can be increased. Suggested sample sizes beyond which this probability can be increased only minimally are given. The results are discussed in terms of implications for molecular studies of phylogenetics and speciation.     

Comparing bootstrap and posterior probability values in the four-taxon case

Assessment of the reliability of a given phylogenetic hypothesis is an important step in phylogenetic analysis. Historically, the nonparametric bootstrap procedure has been the most frequently used method for assessing the support for specific phylogenetic relationships. The recent employment of Bayesian methods for phylogenetic inference problems has resulted in clade support being expressed in terms of posterior probabilities. We used simulated data and the four-taxon case to explore the relationship between nonparametric bootstrap values (as inferred by maximum likelihood) and posterior probabilities (as inferred by Bayesian analysis). The results suggest a complex association between the two measures. Three general regions of tree space can be identified: (1) the neutral zone, where differences between mean bootstrap and mean posterior probability values are not significant, (2) near the two-branch corner, and (3) deep in the two-branch corner. In the last two regions, significant differences occur between mean bootstrap and mean posterior probability values. Whether bootstrap or posterior probability values are higher depends on the data in support of alternative topologies. Examination of star topologies revealed that both bootstrap and posterior probability values differ significantly from theoretical expectations; in particular, there are more posterior probability values in the range 0.85-1 than expected by theory. Therefore, our results corroborate the findings of others that posterior probability values are excessively high. Our results also suggest that extrapolations from single topology branch-length studies are unlikely to provide any general conclusions regarding the relationship between bootstrap and posterior probability values.     

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection

Gene tree topologies have proven a powerful data source for various tasks, including species tree inference and species delimitation. Consequently, methods for computing probabilities of gene trees within species trees have been developed and widely used in probabilistic inference frameworks. All these methods assume an underlying multispecies coalescent model. However, when reticulate evolutionary events such as hybridization occur, these methods are inadequate, as they do not account for such events. Methods that account for both hybridization and deep coalescence in computing the probability of a gene tree topology currently exist for very limited cases. However, no such methods exist for general cases, owing primarily to the fact that it is currently unknown how to compute the probability of a gene tree topology within the branches of a phylogenetic network. Here we present a novel method for computing the probability of gene tree topologies on phylogenetic networks and demonstrate its application to the inference of hybridization in the presence of incomplete lineage sorting. We reanalyze a Saccharomyces species data set for which multiple analyses had converged on a species tree candidate. Using our method, though, we show that an evolutionary hypothesis involving hybridization in this group has better support than one of strict divergence. A similar reanalysis on a group of three Drosophila species shows that the data is consistent with hybridization. Further, using extensive simulation studies, we demonstrate the power of gene tree topologies at obtaining accurate estimates of branch lengths and hybridization probabilities of a given phylogenetic network. Finally, we discuss identifiability issues with detecting hybridization, particularly in cases that involve extinction or incomplete sampling of taxa.     

Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics

Using a four-taxon example under a simple model of evolution, we show that the methods of maximum likelihood and maximum posterior probability (which is a Bayesian method of inference) may not arrive at the same optimal tree topology. Some patterns that are separately uninformative under the maximum likelihood method are separately informative under the Bayesian method. We also show that this difference has impact on the bootstrap frequencies and the posterior probabilities of topologies, which therefore are not necessarily approximately equal. Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434, 1996) stated that bootstrap frequencies can, under certain circumstances, be interpreted as posterior probabilities. This is true only if one includes a non-informative prior distribution of the possible data patterns, and most often the prior distributions are instead specified in terms of topology and branch lengths. [Bayesian inference; maximum likelihood method; Phylogeny; support.].     

Improving the analysis of movement data from marked individuals through explicit estimation of observer heterogeneity

Ring re-encounter data, in particular ring recoveries, have made a large contribution to our understanding of bird movements. However, almost every study based on ring re-encounter data has struggled with the bias caused by unequal observer distribution. Re-encounter probabilities are strongly heterogeneous in space and over time. If this heterogeneity can be measured or at least controlled for, the enormous number of ring re-encounter data collected can be used effectively to answer many questions. Here, we review four different approaches to account for heterogeneity in observer distribution in spatial analyses of ring re-encounter data. The first approach is to measure re-encounter probability directly. We suggest that variation in ring re-encounter probability could be estimated by combining data whose re-encounter probabilities are close to one (radio or satellite telemetry) with data whose re-encounter probabilities are low (ring re-encounter data). The second approach is to measure the spatial variation in re-encounter probabilities using environmental covariates. It should be possible to identify powerful predictors for ring re-encounter probabilities. A third approach consists of the comparison of the actual observations with all possible observations using randomization techniques. We encourage combining such randomisations with ring re-encounter models that we discuss as a fourth approach. Ring re-encounter models are based on the comparison of groups with equal re-encounter probabilities. Together these four approaches could improve our understanding of bird movements considerably. We discuss their advantages and limitations and give directions for future research.     

The shape of evolution: systematic tree topology

Three hypotheses that predict probabilities associated with various tree shapes, or topologies, are compared with observed topology frequencies for a large number of 4, 5, 6 and 7-member trees. The united data on these n-member trees demonstrate that both the equiprobable and proportional-to-distinguishable-types hypotheses poorly predict tree topologies, while all observed topology frequencies are similar to predictions of a simple Markovian dichotomous branching hypothesis. Differences in topology frequencies between phenetic and non-phenetic trees are observed, but their statistical significance is uncertain. Relative frequencies of highly asymmetrical topologies are larger, and those of symmetrical topologies are smaller, in phenetic than in non-phenetic trees. The fact that a simple Markovian branching process, which assumes that each species has an equal probability of speciating in each time period, can predict tree topologies offers promise. Refinement of Markovian branching hypotheses to include the possibility of multiple furcations, differential speciation and extinction rates for different groups of organisms as well as for a single group through geological time, hybrid speciation, introgression, and lineage fusion will be necessary to produce realistic models of lineage diversification.     

The combinatorics of tandem duplication trees

We developed a recurrence relation that counts the number of tandem duplication trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the standard unequal recombination (or crossover) model of tandem duplications. The number of rooted duplication trees is exactly twice the number of unrooted trees, which means that on average only two positions for a root on a duplication tree are possible. Using the recurrence, we tabulated these numbers for small values of n. We also developed an asymptotic formula that for large n provides estimates for these numbers. These numbers give a priori probabilities for phylogenies of the repeated sequences to be duplication trees. This work extends earlier studies where exhaustive counts of the numbers for small n were obtained. One application showed the significance of finding that most maximum-parsimony trees constructed from repeat sequences from human immunoglobins and T-cell receptors were tandem duplication trees. Those findings provided strong support to the proposed mechanisms of tandem gene duplication. The recurrence relation also suggests efficient algorithms to recognize duplication trees and to generate random duplication trees for simulation. We present a linear-time recognition algorithm.     

Probability of Mitochondrial Lineage Extinction in Female Offspring,Modern and Paleolithic: Branching Process Analysis

We evaluate the probability of extinction of the female offspring of two populations of women: the one Paleolithic, the other that of Italy today. In both cases it is assumed that possible extinction arises exclusively on account of limitations in the degree of fertility and/or an imbalance in the sex-ratio of the population. The value is obtained as the probability that a Branching Process describing the evolution of the offspring by a progenitor degenerates to a “Blank Generation,” that is, a generation without women. Mathematically, it derives from a solution between 0 and 1 of a linear equation whose coefficients are the probabilities that a single progenitor breeds various integer numbers of daughters. We evaluated such probabilities by consulting literature. The probability of branch extinction is also the probability of extinction of progenitor’s mitochondrial lineage.     

Natural history of cervical intraepithelial neoplasia: a meta-analysis

OBJECTIVE: To determine the probabilities of transition of stages in the cervical cancer by conducting a meta-studies on the topic. STUDY DESIGN: We identified health states of interest in the natural history of cervical precancer, identified all possible papers that could meet selection criteria, developed relevance and acceptability criteria for inclusion, then thoroughly reviewed the selected studies. To determine the transition probability data we used a random effects model. We determined probabilities for 4 health state transitions. The 6-month mean predictive transition probability (95% confidence intervals with "prediction interval" in parentheses) for high grade squamous intraepithelial lesions (HSIL) to cancer was 0.0037 (0.00004, 0.03386), for low grade squamous intraepithelial lesions (LSIL) to HSIL was 0.0362 (0.00055, 0.23220), for HSIL to LSIL was 0.0282 (0.00027, 0.35782), and for LSIL to normal was 0.0740 (0.00119, 0.42672). CONCLUSION: The transition probabilities between cervical cancer health states for 6-month intervals are small; however, the cumulative risk of cervical cancer is significant. Markers to identify the cervical precursors that will lead to the transition to cervical cancer are needed.     

Bayesian estimation of concordance among gene trees

Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species.     

Type I error and the power of the s-test: old lessons from a new,analytically justified statistical test for phylogenies

We present a new procedure for assessing the statistical significance of the most likely unrooted dichotomous topology inferrable from four DNA sequences. The procedure calculates directly a P-value for the support given to this topology by the informative sites congruent with it, assuming the most likely star topology as the null hypothesis. Informative sites are crucial in the determination of the maximum likelihood dichotomous topology and are therefore an obvious target for a statistical test of phylogenies. Our P-value is the probability of producing through parallel substitutions on the branches of the star topology at least as much support as that given to the maximum likelihood dichotomous topology by the aforementioned informative sites, for any of the three possible dichotomous topologies. The degree of statistical significance is simply the complement of this P-value. Ours is therefore an a posteriori testing approach, in which no dichotomous topology is specified in advance. We implement the test for the case in which all sites behave identically and the substitution model has a single parameter. Under these conditions, the P-value can be easily calculated on the basis of the probabilities of change on the branches of the most likely star topology, because under these assumptions, each site can become informative independently from every other site; accordingly, the total number of informative sites of each kind is binomially distributed. We explore the test's type I error by applying it to data produced in star topologies having all branches equally long, or having two short and two long branches, and various degrees of homoplasy. The test is conservative but we demonstrate, by means of a discreteness correction and progressively assumption-free calculations of the P-values, that (1) the conservativeness is mostly due to the discrete nature of informative sites and (2) the P-values calculated empirically are moreover mostly quite accurate in absolute terms. Applying the test to data produced in dichotomous topologies with increasing internal branch length shows that, despite the test's "conservativeness," its power is much higher than that of the bootstrap, especially when the relevant informative sites are few.     

A METHOD FOR TESTING THE CORRELATED EVOLUTION OF TWO BINARY CHARACTERS: ARE GAINS OR LOSSES CONCENTRATED ON CERTAIN BRANCHES OF A PHYLOGENETIC TREE?

A method is presented for assessing whether changes in a binary character are more concentrated than expected by chance on certain branches of a phylogenetic tree. It can be used to test for correlated evolution of two characters by asking whether changes in the first character are significantly concentrated on those branches on which the second character has a specified state. Thus, one could test whether this specified state is associated with, and thus might enable or select, gains or losses in the first character. The probability of achieving a concentration as or more extreme than that observed under the null hypotheses that changes are distributed randomly on the cladogram is obtained by calculating (a) the number of ways that n gains and m losses can be distributed on the cladogram and (b) the number of ways that p gains q losses can be distributed on the branches of interest given n gains and m losses in the cladogram overall. Summing (b) for appropriate p and q then dividing by (a) yields the desired probability. Simulations suggest that biases resulting from errors in parsimony reconstructions of ancestral states are not extreme.     

Spermatozoa of Pseudinae (Amphibia, Anura, Hylidae), with a test of the hypothesis that sperm ultrastructure correlates with reproductive modes in anurans

We describe, for the first time, the sperm ultrastructure of the two genera of Pseudinae. Based on sperm ultrastructure, the five species herein examined can be separated into three groups: one containing Pseudis paradoxa, P. bolbodactyla, and P. tocantins, the second containing P. minuta, and the third containing Lysapsus laevis. The midpiece is similar in all species and auxiliary fibers and the undulating membrane are absent. In Pseudis a subacrosomal cone and a multilaminar structure (P. minuta) or a granular material (P. paradoxa group) are seen above the nucleus. Lysapsus laevis has only remnants of the subacrosomal cone. All species have peripheral fibers associated with the outer doublets of the axoneme. We tested the hypothesis of correlation between the presence of an undulating membrane and fertilization environments in anurans using a concentrated changes test (CCT) based on the Hay et al. (Mol Biol Evol 1995;12:928-937) hypothesis of phylogenetic relationships among anuran families. Only a subset of the resolved topologies derived from the Hay et al. (1995) cladogram, where Ranoidea is the sister-group of Sooglossidae, produced significant probabilities of the CCT. Therefore, support for the correlation between sperm ultrastructure and fertilization environments in anurans is, at best, equivocal.