Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology

The statistical testing of alternative phylogenetic trees is central to evaluating competing evolutionary hypotheses. Fleming proposed that the New Zealand cicada species Maoricicada iolanthe is the sister species to the major radiation of both low-altitude and montane Maoricicada species. However, using 1,520 bp of mitochondrial DNA sequence data from the cytochrome oxidase subunit I, tRNA aspartic acid, and the ATPase subunit 6 and 8 genes, we inferred that both M. iolanthe and another low-altitude species, Maoricicada campbelli, are nested within the montane Maoricicada radiation. Therefore, we examined the stability of the inferred phylogenetic placement of these two species using the newly developed Shimodaira-Hasegawa test (SH test) implemented in a maximum-likelihood framework. The SH test has two advantages over the more commonly used Kishino-Hasegawa (KH) and Templeton tests. First, the SH test simultaneously compares multiple topologies and corrects the corresponding P: values to accommodate the multiplicity of testing. Second, the SH test is correct when applied to a posteriori hypotheses, unlike the KH test, because it readjusts the expectation of the null hypothesis (that two trees are not different) accordingly. The comparison of P: values estimated under the assumptions of both the KH test and the SH test clearly demonstrate that the KH test has the potential to be misleading when the issue of comparing of a posteriori hypotheses is ignored and when multiple comparisons are not taken into account. The SH test, in combination with a variety of character-weighting schemes applied to our data, reveals a surprising amount of ambiguity in the phylogenetic placement of M. iolanthe and M. campbelli.     

The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes

The complete sequence of the 16,539 nucleotide mitochondrial genome from the single species of the catfish family Cranoglanididae, the helmet catfish Cranoglanis bouderius, was determined using the long and accurate polymerase chain reaction (LA PCR) method. The nucleotide sequences of C. bouderius mitochondrial DNA have been compared with those of three other catfish species in the same order. The contents of the C. bouderius mitochondrial genome are 13 protein-coding genes, two ribosomal RNA and 22 transfer RNA genes, and a non-coding control region, the gene order of which is identical to that observed in most other vertebrates. Phylogenetic analyses for 13 otophysan fishes were performed using Bayesian method based on the concatenated mtDNA protein-coding gene sequence and the individual protein-coding gene sequence data set. The competing otophysan topologies were then tested by using the approximately unbiased test, the Kishino-Hasegawa test, and the Shimodaira-Hasegawa test. The results show that the grouping ((((Characiformes, Gymnotiformes), Siluriformes), Cypriniformes), outgroup) is the most likely but there is no significant difference between this one and the other alternative hypotheses. In addition, the phylogenetic placement of the family Cranoglanididae among siluriform families was also discussed.     

An approximately unbiased test of phylogenetic tree selection

An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.     

Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

A widely held view of land plant relationships places liverworts as the first branch of the land plant tree, whereas some molecular analyses and a cladistic study of morphological characters indicate that hornworts are the earliest land plants. To help resolve this conflict, we used parsimony and likelihood methods to analyze a 6, 095-character data set composed of four genes (chloroplast rbcL and small-subunit rDNA from all three plant genomes) from all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes, ferns (including PSILOTUM: and EQUISETUM:), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in which all positions were included and weighted equally. However, in parsimony and likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts were placed as sister to all other land plants, with mosses and liverworts jointly forming the second deepest lineage. Decay analyses and Kishino-Hasegawa tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, including the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone recovered essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terrestrial plants.     

POOR STATISTICAL PERFORMANCE OF THE MANTEL TEST IN PHYLOGENETIC COMPARATIVE ANALYSES

The Mantel test, based on comparisons of distance matrices, is commonly employed in comparative biology, but its statistical properties in this context are unknown. Here, we evaluate the performance of the Mantel test for two applications in comparative biology: testing for phylogenetic signal, and testing for an evolutionary correlation between two characters. We find that the Mantel test has poor performance compared to alternative methods, including low power and, under some circumstances, inflated type‐I error. We identify a remedy for the inflated type‐I error of three‐way Mantel tests using phylogenetic permutations; however, this test still has considerably lower power than independent contrasts. We recommend that use of the Mantel test should be restricted to cases in which data can only be expressed as pairwise distances among taxa.     

Confidence regions and hypothesis tests for topologies using generalized least squares

A confidence region for topologies is a data-dependent set of topologies that, with high probability, can be expected to contain the true topology. Because of the connection between confidence regions and hypothesis tests, implicitly or explicitly, the construction of confidence regions for topologies is a component of many phylogenetic studies. Existing methods for constructing confidence regions, however, often give conflicting results. The Shimodaira-Hasegawa test seems too conservative, including too many topologies, whereas the other commonly used method, the Swofford-Olsen-Waddell-Hillis test, tends to give confidence regions with too few topologies. Confidence regions are constructed here based on a generalized least squares test statistic. The methodology described is computationally inexpensive and broadly applicable to maximum likelihood distances. Assuming the model used to construct the distances is correct, the coverage probabilities are correct with large numbers of sites.     

Using a nonrecursive formula to determine cladogram probabilities

Three properties of bifurcating branching diagrams that are used for representing a specific number of taxa are (1) the number of possible arrangements, (2) the number of possible topologies, and (3) the probabilities of formation according to particular models of cladogenesis. Of these, the probabilities have received the least attention in the literature. Indeed, many biologists would be astonished by the observation that the probability of a commonly cited cladogram containing 35 phyla of the animal kingdom is < 0.0072% of the value of the average probability taken over all possible cladograms! We reviewed works on cladogram arrangements and topologies and developed a computer-generated table of enumerations that extends and corrects such tables in the literature. We also developed a nonrecursive formula for the determination of cladogram probabilities. This formula facilitates calculation and thereby should promote use of cladogram probabilities, which might provide more accurate null hypotheses for tests of cladogenic events than do considerations of cladogram arrangements or topologies.     

LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference

SUMMARY: LumberJack is a phylogenetic tool intended to serve two purposes: to facilitate sampling treespace to find likely tree topologies quickly, and to map phylogenetic signal onto regions of an alignment in a revealing way. LumberJack creates non-random jackknifed alignments by progressively sliding a window of omission along the alignment. A neighbor-joining tree is built from the full alignment and from each jackknifed alignment, and then the likelihood for each topology (given the original full alignment) is calculated. To determine whether any of the topologies generated is significantly more likely than the others, Kishino-Hasegawa, Shimodaira-Hasegawa and ELW tests are implemented. Availability and SUPPLEMENTARY INFORMATION: http://www.plantbio.uga.edu/~russell/software.html     

Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters

We explore whether phylogenetic analyses of the same sequence data set at the amino acid and nucleotide level are able to recover congruent topologies, as well as the advantages and limitations of both alternative approaches. As a case study, mitochondrial protein-coding genes were used to discern among competing hypotheses on the phylogenetic relationships of major anuran amphibian lineages. To properly address this phylogenetic question, the complete nucleotide sequences of the mitochondrial genomes of two archaeobatrachian species, Ascaphus truei and Pelobates cultripes, were determined anew. Bayesian and maximum likelihood phylogenetic inferences of the same sequence data set were performed based on both amino acid and nucleotide characters, with the latter analysed either as codons or as a reduced data set of first+second (P12) codon positions. In addition, likelihood-based ratio tests were performed to evaluate the support of alternative topologies. The different data sets arrived at congruent and highly supported topologies, suggesting a similar phylogenetic resolving power of the two character types provided that correctly selected sites and appropriate evolutionary models are used. The reconstructed anuran mitochondrial phylogeny supports the paraphyly of Archaeobatrachia, with Ascaphus as sister group to all the remaining anurans, and Pelobates as sister group of Neobatrachia. However, the employed tree reconstruction methods and likelihood-based ratio tests seemed to be negatively affected by the fast evolving sequences of neobatrachians, suggesting that the phylogeny of Anura here presented is not definitive, and needs further investigation using an extended taxon sampling.     

Measuring and comparing the accuracy of species distribution models with presence–absence data

Species distribution models have been widely used to predict species distributions for various purposes, including conservation planning, and climate change impact assessment. The success of these applications relies heavily on the accuracy of the models. Various measures have been proposed to assess the accuracy of the models. Rigorous statistical analysis should be incorporated in model accuracy assessment. However, since relevant information about the statistical properties of accuracy measures is scattered across various disciplines, ecologists find it difficult to select the most appropriate ones for their research. In this paper, we review accuracy measures that are currently used in species distribution modelling (SDM), and introduce additional metrics that have potential applications in SDM. For the commonly used measures (which are also intensively studied by statisticians), including overall accuracy, sensitivity, specificity, kappa, and area and partial area under the ROC curves, promising methods to construct confidence intervals and statistically compare the accuracy between two models are given. For other accuracy measures, methods to estimate standard errors are given, which can be used to construct approximate confidence intervals. We also suggest that as general tools, computer‐intensive methods, especially bootstrap and randomization methods can be used in constructing confidence intervals and statistical tests if suitable analytic methods cannot be found. Usually, these computer‐intensive methods provide robust results.     

Using distance matrices to choose between competing theories and an application to the origin of modern humans

This paper examines competing theories for cases in which both the data and the hypotheses can be represented as distance matrices. A test due to Dow & Cheverud has been used for such comparisons in anthropology, but when data are spatially, temporally, or phylogenetically autocorrelated, this test may be far too liberal. We examine a classification procedure based on ratios of probabilities obtained from Mantel tests of the competing hypotheses and find that design matrices describing only lag-one connections and those eliminating common connections of competing hypotheses are the most informative. We apply this method to simulated gene-frequency data in a 7×7 chessboard representing a stepping-stone model and discriminate between alternative theories with a 7% misclassification rate. We also apply these techniques to the current controversy concerning the origin of anatomically modern humans by testing design matrices representing regional continuity and single African origins. The outcome for lag-one matrices and those showing only unique lag-one differences indicate that the single African origin of anatomically modern humans fits the distance matrix based on 165 characters of 83 fossil crania better than the competing theory. However, we also tested a design matrix describing single origin out of southwest Asia. This design matrix was clearly most similar to the data in all tested cases. These results make the regional-continuity theory a less likely explanation for the observed cranial differences than the two single-origin theories. Of these, single southwest Asian origins seems the more likely interpretation of the data.     

DISENTANGLING THE EFFECTS OF MATING PROPENSITY AND MATING CHOICE IN DROSOPHILA

Incipient sexual isolation between genotypes, lines, or populations of the same species is commonly measured in Drosophila by choice tests. Results of these tests are known to be influenced, in an undetermined manner, by the mating propensity of competitors and by discriminatory factors during courtship. We have approached the problem by measuring male and female propensities in separate, independent tests, and by examining whether these estimates could explain the results of the choice tests. First, male and female choice tests were used to measure sexual isolation between populations of Drosophila melanogaster and between populations of D. simulans. Significant deviations from random mating occurred in 31 out of 48 tests, in agreement with the propensity values of the tested genotypes. We conclude that mating propensity instead of discrimination is directly involved in the estimation of sexual isolation in our populations, and advise against the application of male and female choice tests to assess intraspecific isolation without a proper knowledge of the mating propensities of competing individuals. Second, multiple choice tests were used to assess isolation between D. melanogaster populations. In examining the dynamics of matings throughout the test, we show that if competing individuals differ in mating propensities and tests are long enough to allow most matings to happen, a spurious sexual isolation can appear. We recommend that multiple choice tests be terminated once 50 percent of matings had been observed.     

Partitioned likelihood support and the evaluation of data set conflict

In simultaneous analyses of multiple data partitions, the trees relevant when measuring support for a clade are the optimal tree, and the best tree lacking the clade (i.e., the most reasonable alternative). The parsimony-based method of partitioned branch support (PBS) "forces" each data set to arbitrate between the two relevant trees. This value is the amount each data set contributes to clade support in the combined analysis, and can be very different to support apparent in separate analyses. The approach used in PBS can also be employed in likelihood: a simultaneous analysis of all data retrieves the maximum likelihood tree, and the best tree without the clade of interest is also found. Each data set is fitted to the two trees and the log-likelihood difference calculated, giving "partitioned likelihood support" (PLS) for each data set. These calculations can be performed regardless of the complexity of the ML model adopted. The significance of PLS can be evaluated using a variety of resampling methods, such as the Kishino-Hasegawa test, the Shimodiara-Hasegawa test, or likelihood weights, although the appropriateness and assumptions of these tests remains debated.     

Bootstrap method of interior-branch test for phylogenetic trees

Statistical properties of the bootstrap test of interior branch lengths of phylogenetic trees have been studied and compared with those of the standard interior-branch test in computer simulations. Examination of the properties of the tests under the null hypothesis showed that both tests for an interior branch of a predetermined topology are quite reliable when the distribution of the branch length estimate approaches a normal distribution. Unlike the standard interior-branch test, the bootstrap test appears to retain this property even when the substitution rate varies among sites. In this case, the distribution of the branch length estimate deviates from a normal distribution, and the standard interior-branch test gives conservative confidence probability values. A simple correction method was developed for both interior- branch tests to be applied for testing the reliability of tree topologies estimated from sequence data. This correction for the standard interior-branch test appears to be as effective as that obtained in our previous study, though it is much simpler. The bootstrap and standard interior-branch tests for estimated topologies become conservative as the number of sequence groups in a star-like tree increases.      

Most Powerful Permutation Invariant Tests for Relatedness Hypotheses Using Genotypic Data

The problem of inferring kinship structure among a sample of individuals using genetic markers is considered with the objective of developing hypothesis tests for genetic relatedness with nearly optimal properties. The class of tests considered are those that are constrained to be permutation invariant, which in this context defines tests whose properties do not depend on the labeling of the individuals. This is appropriate when all individuals are to be treated identically from a statistical point of view. The approach taken is to derive tests that are probably most powerful for a permutation invariant alternative hypothesis that is, in some sense, close to a null hypothesis of mutual independence. This is analagous to the locally most powerful test commonly used in parametric inference. Although the resulting test statistic is a U-statistic, normal approximation theory is found to be inapplicable because of high skewness. As an alternative it is found that a conditional procedure based on the most powerful test statistic can calculate accurate significance levels without much loss in power. Examples are given in which this type of test proves to be more powerful than a number of alternatives considered in the literature, including Queller and Goodknight's (1989) estimate of genetic relatedness, the average number of shared alleles (Blouin, 1996), and the number of feasible sibling triples (Almudevar and Field, 1999).     

Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach

The most commonly used method in evolutionary biology for combining information across multiple tests of the same null hypothesis is Fisher's combined probability test. This note shows that an alternative method called the weighted Z-test has more power and more precision than does Fisher's test. Furthermore, in contrast to some statements in the literature, the weighted Z-method is superior to the unweighted Z-transform approach. The results in this note show that, when combining P-values from multiple tests of the same hypothesis, the weighted Z-method should be preferred.     

Cucurbit biotechnology-the importance of virus resistance

Summary The cucurbit family includes a number of valuable crop species (melon, cucumber, squash/pumpkin, watermelon). Much of this review is concerned with transgenic resistance to viruses, shown to be the major application of biotechnology in the cucurbit family. Progress made with the production of transgenic cucurbit crops is discussed. Published data on field tests of transgenic cucurbits are reviewed, showing that much progress has been made with multiple virus-resistant cucurbit crops which can be productive without chemical control of insect virus vectors. Modes of virus resistance in trangenic cucurbits are discussed, as is the bio-safety of such crops. For the first time a detailed analysis has been made of world-wide and US field test applications for cucurbit crops. World-wide, most field test applications were for melon (54%), followed by squash (32%). World-wide most field test applications were for virus resistance (84%), and most applications (77%) were in the USA. Two transgenic multiple virus-resistant squash crops have been deregulated (released for sale). Additionally, the analysis shows that there are transgenic multiple virus-resistant crops in all major cucurbit species already available, for which several different companies have applied for field tests. This would imply that such crops are ready to be marketed should conditions permit, which would have an impact world-wide in reduction of ecological damage due to chemical control of the insect viral vectors.     

Testing goodness-of-fit in logistic case-control studies

We present a goodness-of-fit test for the logistic regressionmodel under case-control sampling. The test statistic is constructedvia a discrepancy between two competing kernel density estimatorsof the underlying conditional distributions given case-controlstatus. The proposed goodness-of-fit test is shown to comparevery favourably with previously proposed tests for case-controlsampling in terms of power. The test statistic can be easilycomputed as a quadratic form in the residuals from a prospectivelogistic regression maximum likelihood fit. In addition, theproposed test is affine invariant and has an alternative representationin terms of empirical characteristic functions.     

Reassortment and concerted evolution in banana bunchy top virus genomes

The nanovirus Banana bunchy top virus (BBTV) has six standard components in its genome and occasionally contains components encoding additional Rep (replication initiation protein) genes. Phylogenetic network analysis of coding sequences of DNA 1 and 3 confirmed the two major groups of BBTV, a Pacific and an Asian group, but show evidence of web-like phylogenies for some genes. Phylogenetic analysis of 102 major common regions (CR-Ms) from all six components showed a possible concerted evolution within the Pacific group, which is likely due to recombination in this region. The CR-M of additional Rep genes is close to that of DNA 1 and 2. Comparison of tree topologies constructed with DNA 1 and DNA 3 coding sequences of 14 BBTV isolates showed distinct phylogenetic histories based on Kishino-Hasegawa and Shimodaira-Hasegawa tests. The results of principal component analysis of amino acid and codon usages indicate that DNA 1 and 3 have a codon bias different from that of all other genes of nanoviruses, including all currently known additional Rep genes of BBTV, which suggests a possible ancient genome reassortment event between distinctive nanoviruses.     

Molecular phylogeny and evolutionary habitat transition of the flower bugs (Heteroptera: Anthocoridae)

We performed a molecular phylogenetic study of the Anthocoridae, the flower bugs, based on maximum likelihood, maximum parsimony, and Bayesian analyses of ～ 3000 base pairs (bp) of DNA sequence from the mitochondrial 16S rRNA and nuclear 18S rRNA and 28S rRNA genes for 44 taxa. Our phylogenetic analyses indicates that (i) the tribe Cardiastethini (Dufouriellini) could be a paraphyletic group, as the genera Amphiareus and Dysepicritus are not included in the tribe; (ii) the main subgroups, Oriini and Anthocorini, are monophyletic within Anthocoridae; (iii) three tribes of Blaptostethini, Xylocorini, and Scolopini are separated from the main anthocorid clade which is composed of Anthocorini, Cardiastethini, and Oriini, suggesting that Anthocoridae could not be monophyletic. We compared our molecular phylogeny to previous hypotheses of evolutionary relationships within Cimicoidea based on different anthocorid classification systems using alternative hypothesis tests (Kishino-Hasegawa and Shimodaira-Hasegawa tests). BayesTraits were used to examine the ancestral character states inferring historical habitat patterns of the Anthocoridae. Reconstruction of the ancestral habitat patterns of the Anthocoridae suggests that dead plants may have served as an important habitat for the common ancestor of anthocorids. The biological events such as diversification of angiosperms and anthocorid prey might have provided anthocorids with more habitat options, such as living plants; thereafter, Anthocorini and Amphiareus appeared to have evolved increasingly specialized habitat relationships.