The efficiency of different search strategies in estimating parsimony jackknife,bootstrap, and Bremer support

Background  

For parsimony analyses, the most common way to estimate confidence is by resampling plans (nonparametric bootstrap, jackknife), and Bremer support (Decay indices). The recent literature reveals that parameter settings that are quite commonly employed are not those that are recommended by theoretical considerations and by previous empirical studies. The optimal search strategy to be applied during resampling was previously addressed solely via standard search strategies available in PAUP*. The question of a compromise between search extensiveness and improved support accuracy for Bremer support received even less attention. A set of experiments was conducted on different datasets to find an empirical cut-off point at which increased search extensiveness does not significantly change Bremer support and jackknife or bootstrap proportions any more.     

Phylogenetic utility of mitochondrial COI and nuclear Gpdh genes in Drosophila

Phylogenetic utility of the mitochondrial COI (cytochrome oxidase subunit I) and nuclear Gpdh (glycerol-3-phosphate dehydrogenase) genes was studied in the Drosophila melanogaster species group. The rate of substitution was higher in the COI gene than in the Gpdh gene. In addition, multiple substitutions, not only for transitional but also for transversional substitutions, occurred faster in the COI gene. None of the trees obtained using the COI gene supported the well-established monophyly of the ananassae subgroup. In addition, the incongruence length difference test, Templeton test, and partitioned Bremer support revealed that the trees based on the COI data are considerably different from those based on the Gpdh and the combined data set. Thus, the COI gene did not show good phylogenetic performance in the melanogaster group. The present analyses based on the Gpdh gene and the combined data set revealed that the ananassae subgroup branched off first in the melanogaster group followed by the montium subgroup and further by the melanogaster subgroup in contrast to the most recent phylogenetic hypothesis based on Amy multigenes.     

Measuring Support for Phylogenies: The "Proportional Support Index"

The total support index (Bremer, 1994), a measure of cladogram support, is influenced both by character incongruence and by uninformative characters. A modified version of this index is therefore proposed—the proportional support index. This index measures the actual support for a cladogram relative to the maximum potential support as determined by the number of informative characters. This index is not distorted by uninformative characters and is thus a more accurate means to compare the strength of phylogenetic signals in different data sets.     

Image analysis shows that variations in actin crossover spacings are random, not compensatory.

A recent paper by Bremer et al. (1991. J. Cell Biol. 115:689-703) has argued that the random angular disorder model for actin is wrong, and that the variations in crossover spacing observed in electron micrographs of F-actin filaments can be best explained by a compensatory disorder caused by the lateral slipping of the twin (or two-start) strands which comprise the actin filament. We have analyzed the images of F-actin presented in Bremer et al. and show that their data argues against compensatory disorder and in favor of random disorder, independent of the cause of the disorder. We also revise our estimate of the angular component and show that the magnitude of this disorder is about 5-6 degrees per subunit, which is less than the 10-12 degrees that we originally proposed.     

Resampling measures of group support: a reply to Grant and Kluge

Grant and Kluge (2003) associated resampling measures of group support with the aim of evaluating statistical stability, confidence, or the probability of recovering a true phylogenetic group. This interpretation is not necessary to methods such as jackknifing or bootstrapping, which are better interpreted as measures of support from the current dataset. Grant and Kluge only accepted the absolute Bremer value as a measure of group support, and considered resampling methods as irrelevant to phylogenetic inference. It is shown that under simple circumstances resampling indices better reflect the degree of support than Bremer values. Grant and Kluge associated the resampling methods (and the use of measures of group support in general) with what they call a “verificationist agenda”, where strongly supported groups are first detected, and then protected against additional testing. They propose that identifying weakly supported groups, and then concentrating additional tests on them, will better serve science. Both programs are actually equivalent, and inert as to the selection of methods to estimate group support. The ranking of groups under a range of resampling strength is proposed as an additional criterion to evaluate resampling methods. A reexamination of the slope of symmetric resampling frequency as a function of resampling strength suggest that slopes can be problematic as well as a measure of group support. © The Willi Hennig Society 2005.     

Evaluating the clade size effect in alternative measures of branch support

The clade size effect refers to a bias that causes middle‐sized clades to be less supported than small or large‐sized clades. This bias is present in resampling measures of support calculated under maximum likelihood and maximum parsimony and in Bayesian posterior probabilities. Previous analyses indicated that the clade size effect is worst in maximum parsimony, followed by maximum likelihood, while Bayesian inference is the least affected. Homoplasy was interpreted as the main cause of the effect. In this study, we explored the presence of the clade size effect in alternative measures of branch support under maximum parsimony: Bremer support and symmetric resampling, expressed as absolute frequencies and frequency differences. Analyses were performed using 50 molecular and morphological matrices. Symmetric resampling showed the same tendency that bootstrap and jackknife did for maximum parsimony and maximum likelihood. Few matrices showed a significant bias using Bremer support, presenting a better performance than resampling measures of support and comparable to Bayesian posterior probabilities. Our results indicate that the problem is not maximum parsimony, but resampling measures of support. We corroborated the role of homoplasy as a possible cause of the clade size effect, increasing the number of random trees during the resampling, which together with the higher chances that medium‐sized clades have of being contradicted generates the bias during the perturbation of the original matrix, making it stronger in resampling measures of support.     

A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data

The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.     

Influence of data conflict and molecular phylogeny of major clades in Cimicomorphan true bugs (Insecta: Hemiptera: Heteroptera)

Cimicomorpha, which consists of 16 families representing more than 19,400 species, is the largest infraorder in Heteroptera, Insecta. We present the first molecular phylogenetic investigation of family relationships of Cimicomorpha, including 46 taxa from 12 of 16 Cimicomorphan families. Three genes, with a total of 3277 bp of sequence data (nuclear 18S rDNA: 2022 bp, 28S rDNA: 755 bp, and mitochondrial 16S rDNA: 498 bp) were analyzed. Data partitions were analyzed separately and in combination, by employing ML (maximum likelihood), MP (maximum parsimony), and Bayesian methods. As saturation was detected in substitutions of 16S rDNA, influence of data conflict in combined analyses was further explored by three methods: the incongruence length difference (ILD) test, the partitioned Bremer support (PBS), and the partition addition bootstrap alteration approach (PABA). PBS and PABA approaches suggested that 16S rDNA was not very suitable for addressing relationships at this level in Cimicomorpha. Our results also supported the nabid-cimicoid lineage for Cimicoidea proposed by Schuh and Stys [Schuh, R.T., Stys, P., 1991. Phylogenetic analysis of Cimicomorphan family relationships (Heteroptera). J. NY Entomol. Soc. 99 (3), 298-350]. Data incongruence and the utility of the three genes were briefly discussed.     

Phylogenetic Studies on Didelphid Marsupials I. Introduction and Preliminary Results from Nuclear IRBP Gene Sequences

We report and analyze nucleotide sequence variation in the first exon (1158 bp) of the nuclear gene encoding the Interphotoreceptor Retinoid Binding Protein (IRBP) among 21 species representing all 15 currently recognized genera of living didelphids. Six previously published IRBP sequences representing five nondidelphimorph marsupial orders were also analyzed to test didelphid monophyly, and 12 published sequences representing ten placental orders were used as outgroups. No gaps (indels) are necessary to align didelphid sequences, but one short region (35 bp) is alignment-ambiguous among nondidelphids. Uncorrected pairwise sequence divergence ranges from 0.7 to 5.7% among nonconspecific didelphids, from 9.2 to 15.3% between didelphids and nondidelphid marsupials, and from 24.9 to 32.1% between marsupials and placentals. Neither transitions nor transversions exhibit saturation for any codon position at any level of taxonomic comparison. Parsimony analyses of these data provide strong support (bootstrap values >95%, Bremer values 7) for the monophyly of (1) Didelphidae ("caluromyines" + Didelphinae); (2) a group containing Caluromys and Caluromysiops; (3) Didelphinae; (4) a group of large opossums that includes Metachirus; (5) a group containing the remaining large opossums (with 2N = 22 chromosomes); (6) a group containing Marmosa and Micoureus; (7) a group containing Thylamys, Lestodelphys, and Gracilinanus; and (8) a group containing the last three genera plus a monophyletic Marmosops. In addition, we found moderate support (bootstrap values >80%, Bremer values 2) for the monophyly of Thylamys + Lestodelphys and for a sister-group relationship between Monodelphis and Marmosa + Micoureus. Sensitivity analysis suggests that all of these clades, together with their associated levels of bootstrap and Bremer support, are robust to alternative hypotheses of positional homology within the ambiguously alignable region. Although some of the relationships supported by IRBP are not consistent with the results of published morphological analyses, our reassessment of the morphological data suggests that many conflicts are more apparent than real.     

Phylogeny of the Drosophila saltans species group based on combined analysis of nuclear and mitochondrial DNA sequences

Nucleotide sequences from two nuclear loci, alcohol dehydrogenase and internal transcribed spacer-1 of the nuclear ribosomal DNA repeats, and two mitochondrial genes, cytochrome oxidase I and cytochrome oxidase II, were determined from nine species in the Drosophila saltans species group. The partition homogeneity test and partitioned Bremer support were used to measure incongruence between phylogenetic hypotheses generated from individual partitions. Individual loci were generally congruent with each other and consistent with the previously proposed morphological hypothesis, although they differed in level of resolution. Since extreme conflict between partitions did not exist, the data were combined and analyzed simultaneously. The total evidence method gave a more resolved and highly supported phylogeny, as indicated by bootstrap proportions and decay indices, than did any of the individual analyses. The cordata and elliptica subgroups, considered to have diverged early in the history of the D. saltans group, were sister taxa to the remainder of the saltans group. The sturtevanti subgroup, represented by D. milleri and D. sturtevanti, occupies an intermediate position in this phylogeny. The saltans and parasaltans subgroups are sister clades and occupy the most recently derived portion of the phylogeny. As with previous morphological studies, phylogenetic relationships within the saltans subgroup were not satisfactorily resolved by the molecular data.      

Lijndenia, a re–established paleotropical genus of the Melastomataceae–Memecyleae

The genus Lijndenia Zoll. & Mor. is re–established and emended to include four species, L. laurina Zoll. & Mor. from W Malesia and Java, L. capitellata (Arn.) Bremer from Ceylon, L. gardneri (Thw.) Bremer from Ceylon, and L. barteri (Hook. f.) Bremer from tropical W Africa. The latter three names are new combinations.     

Molecular phylogeny of the tribe Sphodrini (Coleoptera: Carabidae) based on mitochondrial and nuclear markers

A phylogenetic analysis of 6.4 kb of nucleotide sequence data from seven genes (mitochondrial cox1-cox2 and tRNA(leu), and nuclear Ef-1alpha C0, Ef-1alpha C1, 28S, and 18S) was done to reconstruct the phylogenetic relationships of the ground-beetle tribe Sphodrini. Gene regions of variable nucleotide length were aligned using both a secondary structure model, Clustal W, and a combination of the two. Sensitivity analysis was performed in order to explore the effect of alignment methods. The ribosomal and protein-coding genes were largely congruent based on the ILD test and partitioned Bremer support measures. MtDNA analysis provided high resolution and high support for most clades. The tribe Sphodrini and the related tribes Platynini, Pterostichini and Zabrini made up monophyletic clades, but the relationship between them was weakly resolved and sensitive to alignment strategy. Previously suggested relationships between subtribes of Sphodrini were not corroborated, and only the subtribe Atranopsina revealed high support as the sister clade to the other subtribes. The analyses clearly demonstrated the importance of exploring effects of alignment methods that may become particularly important in resolving polytomies and nodes with low support.     

Phylogeny of the African murid tribe Otomyini (Rodentia), based on morphological and allozyme evidence

Based on a cladistic analysis of 45 morphological (craniodental) and 46 binary allozyme characters, previous systematic treatments of the African murid tribe, Otomyini (laminate-toothed rats), are reviewed. Cladistic analysis of the craniodental data, involving eight outgroup taxa, confirmed the monophyly of the Otomyini, and suggested Pelomys to represent the sister genus of the Otomyini. Craniodental synapomorphies provided strong support for certain basal relationships among Otomyini rodents, reinforcing available palaeontological evidence. However, poor statistical (Bremer decay index) support was obtained for terminal relationships. The data presented revealed a 'mesic clade' of southern and eastern African species, with Otomys sloggetti basal to this group. The arid-adapted, southern Africa-endemic species, Parotomys littledalei , P. brantsii and O. unisulcatus , were all placed basal to the 'mesic clade', but did not form a separate 'arid clade', as suggested by earlier biochemical studies. Two allozyme synapomorphies supported the existence of the 'mesic clade', separate from arid-adapted southern African species. A strict cladistic interpretation of the present data did not support the existence of two genera in the tribe, and the two species of Parotomys (whistling rats) should be transferred to Otomys . At the species level, specific identity of O. lacustris and O. barbouri , distinct from O. anchietae , was supported by several autapomorphies, and O. tropicalis burtoni was shown to be included in O. angoniensis rather than O. tropicalis , extending the range of the former species into West Africa.     

Attempted tests of the surrogacy value of the ED environmental diversity measures highlight the need for corroboration assessment of surrogacy hypotheses

A recent paper in this journal (Hortal et al., 2009) claimed to have evaluated the ED biodiversity surrogates methods of Faith and Walker, 1994, Faith and Walker, 1996, and to have provided evidence for poor performance of the continuous ED method. In fact, their study neither used nor evaluated the continuous ED method. Here, I document their misrepresentation. I then discuss some constructive lessons emerging from their study and other recent studies that have attempted tests of ED surrogacy value. The need to consider the actual degree of support that observed evidence provides for a hypothesis about surrogacy raises general issues for evaluations of indicators’ performance, and suggests a greater role for corroboration assessments. Guidelines for achieving this cover three aspects of surrogates testing: experimental design of tests, ongoing corroboration assessment of evidence produced by tests, and accumulation of lessons learned from multiple test studies over time.     

cpDNA intergene sequences corroborate restriction site data for reconstructingRubiaceae phylogeny

Representatives of seven genera from five tribes ofRubiaceae have been compared in respect to a non-coding intergene cpDNA region of about 1000 bp, situated between the atpB and the rbcL genes. The resulting most parsimonious PAUP cladogram corresponds very well with one based on total cpDNA restriction site data obtained byBremer & Jansen (1991). The two different molecular analyses thus corroborate each other and contribute to an improved systematic arrangement of the large family, e.g., in respect to placing the tribeHedyotideae clearly into the subfamilyRubioideae, closer toRubieae than toPsychotrieae.     

Is REP a measure of “objective support”?

Grant and Kluge have recently stated that Bremer support and their own REP (“relative explanatory power”), are the only objective measures of group support. This paper discusses their claim, showing that their philosophical arguments have no basis, and that their own numerical examples actually serve to illustrate shortcomings of REP.     

Phylogeny of Drosophilinae (Diptera: Drosophilidae), with comments on combined analysis and character support

Drosophilidae (Diptera) is a diverse, cosmopolitan family of flies. Here, we present a combined analysis phylogeny of Drosophilinae, one of the two subfamilies of Drosophilidae, based on data from six different data partitions, including both molecular and morphological characters. Although our data show support for the monophyly of the Hawaiian Drosophilidae, and the subgenus Sophophora, neither the genus Drosophila nor the subgenus Drosophila is monophyletic. Partitioned Bremer support (PBS) indicates that morphological data taken from Grimaldi's monograph (Grimaldi, 1990a), as well as sequences from the mitochondrial (mt) 16S rDNA and the nuclear Adh gene, lend much support to our tree's topology. This is particularly interesting in the case of Grimaldi's data, since his published hypothesis conflicts with ours in significant ways. Our combined analysis cladogram phylogeny reflects the catch-all designation that the name Drosophila has become, in that the cladogram does not support the monophyly of either the genus or subgenus Drosophila.     

Molecular phylogenetics of the tribeInuleae s. str.(Asteraceae), based on ITS sequences of nuclear ribosomal DNA

The sequences of the internal transcribed spacer (ITS) region of 18S–26S nrDNA for a sample of 16 taxa from theInuleae s. str. and two outgroup taxa are analysed cladistically with PAUP. A consensus tree of the four most parsimonious cladograms is presented. Three different tests of cladogram stability are conducted (Bremer support, parsimony jackknifing and bootstrapping); all tests indicate a high degree of support for the basal nodes of the tree. The ITS phylogeny of the tribe is compared with previous hypotheses based on morphological data. The position ofAnisopappus as sister group to the rest of the tribe is supported by the molecular data, but the proposed subdivision ofInuleae s. str. into a paleate grade group and an epaleate clade is not. The interpretation of the character evolution of, e.g. receptacular paleae and pappus features within the tribe is discussed.     

Phylogeny of theCyclanthaceae

The affinities ofCyclanthaceae are discussed, and it is concluded that the sister-group to this family is most probablyPandanaceae. A hypothesis of generic relationships inCyclanthaceae, based on cladistic methods, is presented. Bootstrap analysis and Bremer support (decay index) have been used to test the strength of individual clades, and the result is compared with previously made phylogenetic analyses. TheSphaeradenia group (Chorigyne, Stelestylis, Sphaeradenia, andLudovia) is supported as monophyletic and acceptably resolved, while theAsplundia group (remaining genera inCarludovicoideae) may be paraphyletic, with largely uncertain relationships. A formal recognition of these groups is therefore not justified. The probable character evolution inCarludovicoideae is discussed.     

Morphology versus molecules: resolution of the positions of Nymphalis, Polygonia, and related genera (Lepidoptera: Nymphalidae)

The debate on whether to combine different data sets for simultaneous analysis has continued to the present day unabated. We have studied the effects of combining one morphological data set with four molecular data sets (two mitochondrial gene sequences and two nuclear gene sequences) for a group of butterflies belonging to the tribe Nymphalini using partitioned Bremer support. We particularly focus our attention on a group of species belonging to the genera Aglais, Inachis, Roddia, Nymphalis, Kaniska, and Polygonia. We find that, despite significant incongruence between most data partitions, all data partitions contribute positively to the support of most nodes in the most parsimonious trees found for the combined data set. We also find that the morphological data set resolves one particular node (Kaniska basal to Polygonia) with good support, while the molecular data sets are ambiguous about the existence of this node. We suggest that partitioned Bremer support allows one to critically appraise the robustness of each node in a given tree and thereby identify nodes that may change with the addition of new data and nodes that are likely to remain unchanged with new data. We also suggest that morphological data are still crucial to our being able to understand the relationships of extant organisms, despite published views to the contrary. Based on our results we suggest that Inachis should be synonymized with Aglais, Roddia with Nymphalis, and Kaniska with Polygonia.