Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability

Owing to the exponential growth of genome databases, phylogenetic trees are now widely used to test a variety of evolutionary hypotheses. Nevertheless, computation time burden limits the application of methods such as maximum likelihood nonparametric bootstrap to assess reliability of evolutionary trees. As an alternative, the much faster Bayesian inference of phylogeny, which expresses branch support as posterior probabilities, has been introduced. However, marked discrepancies exist between nonparametric bootstrap proportions and Bayesian posterior probabilities, leading to difficulties in the interpretation of sometimes strongly conflicting results. As an attempt to reconcile these two indices of node reliability, we apply the nonparametric bootstrap resampling procedure to the Bayesian approach. The correlation between posterior probabilities, bootstrap maximum likelihood percentages, and bootstrapped posterior probabilities was studied for eight highly diverse empirical data sets and were also investigated using experimental simulation. Our results show that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated on bootstrapped character matrices. Moreover, simulations corroborate empirical observations in suggesting that, being more conservative, the bootstrap approach might be less prone to strongly supporting a false phylogenetic hypothesis. Thus, apparent conflicts in topology recovered by the Bayesian approach were reduced after bootstrapping. Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared.     

A contribution to sedentary polychaete phylogeny using 18S rRNA sequence data

The phylogenetic position of Annelida as well as its ingroup relationships are a matter of ongoing debate. A molecular phylogenetic study of sedentary polychaete relationships was conducted based on 70 sequences of 18S rRNA, including unpublished sequences of 18 polychaete species. The data set was analysed with maximum parsimony and maximum likelihood methods. Clade robustness was estimated by parsimony-bootstrapping and jackknifing, decay index, and clade support, as well as a posteriori probability tests using Bayesian inference. Irrespective of the applied method, some traditional sedentary polychaete taxa, such as Cirratulidae, Opheliidae, Orbiniidae, Siboglinidae and Spionidae, were recovered by our phylogenetic reconstruction. A close relationship between Orbiniidae and Questa received a particularly strong support. Echiura appears to be a polychaete ingroup taxon which is closely related to Dasybranchus (Capitellidae). As in previous molecular analyses, no support was found for the monophyly of Annelida nor for that of Polychaeta. However, we suggest that an increase in taxon sampling may yield additional resolution in the reconstruction of polychaete ingroup phylogeny, although the difficulties in reconstructing the basal phylogenetic relationships within Annelida may be due to their rapid radiation.     

Inference of bacterial microevolution using multilocus sequence data

We describe a model-based method for using multilocus sequence data to infer the clonal relationships of bacteria and the chromosomal position of homologous recombination events that disrupt a clonal pattern of inheritance. The key assumption of our model is that recombination events introduce a constant rate of substitutions to a contiguous region of sequence. The method is applicable both to multilocus sequence typing (MLST) data from a few loci and to alignments of multiple bacterial genomes. It can be used to decide whether a subset of isolates share common ancestry, to estimate the age of the common ancestor, and hence to address a variety of epidemiological and ecological questions that hinge on the pattern of bacterial spread. It should also be useful in associating particular genetic events with the changes in phenotype that they cause. We show that the model outperforms existing methods of subdividing recombinogenic bacteria using MLST data and provide examples from Salmonella and Bacillus. The software used in this article, ClonalFrame, is available from http://bacteria.stats.ox.ac.uk/.     

A multigene phylogeny of the Gelidiales including nuclear large-subunit rRNA sequence data

Partial sequences (1032 bp) of the nuclear-encoded large ribosomal RNA gene (LSU) were determined for 16 gelidialean species, and analyzed separately and in combination with plastid rbcL and nuclear SSU gene sequences. The number of informative characters and levels of sequence divergence among taxa are intermediate in LSU sequences as compared to that for rbcL and SSU. Analyses of the separate LSU, and a combined LSU, SSU, and rbcL data sets have identified early-diverging lineages within the Gelidiales including Gelidiella, Pterocladia, Pterocladiella, and a lineage including Gelidium and species classified in other genera. The relationships among most gelidialean taxa are well-resolved and well-supported by analyses of the combined data; however, the relationships of Ptilophora and Capreolia remain unclear. It is speculated that these two lineages have diverged from a common ancestor over an evolutionarily short period of time. This revised version was published online in June 2006 with corrections to the Cover Date.     

A method for molecular phylogeny construction by direct use of nucleotide sequence data

Summary A method for molecular phylogeny construction is newly developed. The method, called the stepwise ancestral sequence method, estimates molecular phylogenetic trees and ancestral sequences simultaneously on the basis of parsimony and sequence homology. For simplicity the emphasis is placed more on parsiomony than on sequence homology in the present study, though both are certainly important. Because parsimony alone will sometimes generate plural candidate trees, the method retains not one but five candidates from which one can then single out the final tree taking other criteria into account.The properties and performance of the method are then examined by simulating an evolving gene along a model phylogenetic tree. The estimated trees are found to lie in a narrow range of the parsimony criteria used in the present study. Thus, other criteria such as biological evidence and likelihood are necessary to single out the correct tree among them, with biological evidence taking precedence over any other criterion. The computer simulation also reveals that the method satisfactorily estimates both tree topology and ancestral sequences, at least for the evolutionary model used in the present study.     

Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny

The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite‐host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.     

An upgraded comprehensive multilocus phylogeny of the Tardigrada tree of life

Providing accurate animals’ phylogenies rely on increasing knowledge of neglected phyla. Tardigrada diversity evaluated in broad phylogenies (among phyla) is biased towards eutardigrades. A comprehensive phylogeny is demanded to establish the representative diversity and propose a more natural classification of the phylum. So, we have performed multilocus (18S rRNA and 28S rRNA) phylogenies with Bayesian inference and maximum likelihood. We propose the creation of a new class within Tardigrada, erecting the order Apochela (Eutardigrada) as a new Tardigrada class, named Apotardigrada comb. n. Two groups of evidence support its creation: (a) morphological, presence of cephalic appendages, unique morphology for claws (separated branches) and wide‐elongated buccopharyngeal apparatus without placoids, and (b) phylogenetic support based on molecular data. Consequently, order Parachela is suppressed and its superfamilies erected as orders within Eutardigrada, maintaining their current names. We propose a new classification within the family Echiniscidae (Echiniscoidea, Heterotardigrada) with morphological and phylogenetic support: (a) subfamily Echiniscinae subfam. n., with two tribes Echiniscini tribe n. and Bryodelphaxini tribe n.; (b) subfamily Pseudechiniscinae subfam. n., with three tribes Cornechiniscini tribe n., Pseudechiniscini tribe n. and Anthechiniscini tribe n.; and (c) subfamily Parechiniscinae subfam. n., with two tribes Parechiniscini tribe n. and Novechiniscini tribe n. Reliable biodiversity selection for tardigrades in broad phylogenies is proposed due to biased analyses performed up to now. We use our comprehensive molecular phylogeny to evaluate the evolution of claws in the clawless genus Apodibius and claw reduction across the Tardigrada tree of life. Evolutionary consequences are discussed.     

Molecular phylogeny of Pottiaceae (Musci) based on chloroplast rps4 sequence data

Comparative sequencing of the chloroplast rps4 gene was used to reconstruct the phylogenetic relationships within the family Pottiaceae (Musci). The results confirm that Ephemerum spinulosum, Splachnobryum obtusum, Goniomitrium acuminatum and Cinclidotus fontinaloides are clearly positioned within the Pottiaceae and that Hypodontium dregei is not a member. At subfamily level, the data support the subfamily Pottioideae as being a monophyletic clade. The Trichostomoideae are probably paraphyletic. Neither the subfamily Chionolomideae, represented in this study by Pseudosymblepharis schimperiana, nor the subfamily Erythrophyllopsoideae, represented by both known species, Erythrophyllastrum andinum and Erythrophyllopsis fuscula, are supported by the sequence data. The Timmielloideae should be excluded from the Pottiaceae. The Merceyoideae, represented in this study by Scopelophila cataractae, might form a sister clade to all other Pottiaceae, but their position is not fully resolved. At the genus level, Barbula is clearly polyphyletic since Barbula bolleana and Barbula indica appear in a clade clearly separated from Barbula unguiculata. Pottiopsis caespitosa and Leptobarbula berica are placed within the Trichostomoideae. Likewise, the genera Gymnostomum and Anoectangium are excluded from the Pottioideae and placed within the Trichostomoideae. Leptophascum leptophyllum is closely related with Syntrichia; Aloina is not closely related to Tortula or Crossidium. Evidence of a clade within the Pottioideae, formed of Leptodontium and Triquetrella, is provided.     

Reconstruction of molecular phylogeny of extant hominoids from DNA sequence data

Evolutionary distance matrices of the extant hominoids are computed from DNA sequence data, and hominoid DNA phylogenies are reconstructed by applying the neighbor-joining method to these distance matrices. The chimpanzee is clustered with the human in most of the phylogenetic trees thus obtained. The proportion of the distance between human and chimpanzee to that between human/chimpanzee and orangutan is estimated. Both mitochondrial DNA and nuclear DNA show a similar value (0.44), which is close to values derived from DNA-DNA hybridization data.     

Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF

The chloroplast gene ndhF was used to study phylogenetic relationships of the Polemoniaceae at two levels: among members of the Ericales and among genera of the family. Sequence data for interfamilial analyses consisted of 2266 bp for 14 members of the Ericales, including four species of the Polemoniaceae, plus three outgroup taxa. The Polemoniaceae were found to be related to Diospyros, Fouquieria, the Primulales, Rhododendron, and Impatiens, but relationships among taxa were generally not well supported. The precise position of the Polemoniaceae within the Ericales remains obscure. Data for intrafamilial analyses consisted of 1031 bp for 27 species of the Polemoniaceae, including at least one species from most genera of the family, plus five outgroup taxa. A single most parsimonious tree was identified. The analyses suggested that subfamily Cobaeoideae, excluding Loeselia, is monophyletic and that Huthia is sister to Cantua. Acanthogilia was sister to the remainder of subfamily Cobaeoideae. Subfamily Polemonioideae plus Loeselia formed four subclades that were strongly supported as monophyletic and represent the major lineages of the subfamily.     

Prokaryote phylogeny based on ribosomal proteins and aminoacyl tRNA synthetases by using the compositional distance approach

In order to show that the newly developed K-string composition distance method, based on counting oligopeptide frequencies, for inferring phylogenetic relations of prokaryotes works equally well without requiring the whole proteome data, we used all ribosomal proteins and the set of aminoacyl tRNA synthetases for each species. The latter group has been known to yield inconsistent trees if used individually. Our trees are obtained without making any sequence alignment. Altogether 16 Archaea, 105 Bacteria and 2 Eucarya are represented on the tree. Most of the lower branchings agree well with the latest, 2003, Outline of the second edition of the Bergey’s Manual of Systematic Bacteriology and the trees also suggest some relationships among higher taxa.     

Prokaryote phylogeny based on ribosomal proteins and aminoacyl tRNA synthetases by using the compositional distance approach

1 Introduction The systematics of prokaryotes has been a chal-lenge in microbiology as there are too few morpho-logical characteristics that can be used for classifica-tion[1]. A major breakthrough took place in the 1970s when Carl Woese[2] and coworkers aligned the small subunit ribosomal RNA (SSU rRNA) sequences to infer phylogenetic relations. The recognition of Ar-chaea as a third domain of life in addition to Bacteria and Eukarya and the support to the endosymbiotic origin of chlor…     

Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data

The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes （mitogenomes）. Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with ＂Cambrian explosion＂ revealed by paleontologists. It was the 520-million-year＇s evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship.     

Estimating the phylogeny in mollusc Littorina saxatilis (Olivi) from enzyme data: methodological considerations

The evolutionary history of 19 populations of Littorina saxatilis (Olivi) was estimated by four different approaches. Three of these operate upon a population by population matrix of genetic distances: average linkage clustering, and two versions of the Fitch-Margoliash method. The fourth method was a maximum likelihood estimate based on differences in allele frequencies between populations. The study aims to assess how well each method estimates the phylogeny by including seven populations of the closely related species L. arcana Hannaford Ellis. The rationale behind this is that a good estimation technique should be able to separate these two monophyletic taxa.The results show that, by our criteria, the maximum likelihood method yields the best estimate and the unconstrained Fitch-Margoliash technique gives reasonable estimates. Both average-linkage clustering and the Fitch-Margoliash method with evolutionary clock perform less well. We argue that this is expected since both these techniques are based on probably unrealistic assumptions such as the overall rate of evolutionary divergence being homogeneous over phyletic lines.     

The blood alga: phylogeny of Haematococcus (Chlorophyceae) inferred from ribosomal RNA gene sequence data

The status of the green algal genera Haematococcus and Stephanosphaera has been a source of debate among algal systematists. A phylogenetic alliance between Haematococcus (sensu lato) and the colonial Stephanosphaera was affirmed by earlier molecular phylogenetic investigations. Although the data suggested that the genus Haematococcus may not be a monophyletic group, taxon sampling limited the scope of any potential taxonomic revision. Results from new molecular phylogenetic analyses of data from the 18S and 26S rRNA genes support the establishment of a separate genus, Balticola, as originally proposed by Droop in 1956. Haematococcus remains as a valid genus, with H. pluvialis as its only member. The monotypic status of H. pluvialis is supported both by molecular phylogenetic analyses of the ribosomal RNA genes and assessments of molecular evolution in the ITS2 sequences of H. pluvialis strains. The near-complete absence of compensatory base changes in a sequence-structure analysis of the highly variable ITS2 gene from more than 40 geographically diverse isolates of H. pluvialis corroborates the unity of the species inferred from molecular phylogenetic analyses of 18S and 26S rRNA gene sequence data.     

Molecular phylogeny and evogenomics of heterocystous cyanobacteria using rbcl gene sequence data

Taxonomic affiliations and molecular diversity of 41 heterocystous cyanobacteria representing 12 genera have been assessed on an evolutionary landscape using rbcl gene sequence data-based phylogenomics and evogenomics approaches. Phylogenetic affiliations have clearly demonstrated the polyphyly of the true branching cyanobacteria, along with a frequent intermixing amongst the heterocystous cyanobacteria. The monophyletic origin of the heterocystous cyanobacteria was also quite evident from maximum parsimony and neighbor joining analyses. Incongruency with the traditional scheme of cyanobacterial taxonomy was frequently observed, thus advocating towards some re-amendments in the cyanobacterial classificatory schemes. Evogenomics analyses of gene sequence data gave a clear indication about the greater evolutionary pace of the unbranched cyanobacteria as compared to the branched forms. It was evident that the order Nostocales would be controlling the future pace of evolution of heterocystous cyanobacteria. The cyanobacteria Nostoc was found to have the greatest genetic heterogeneity amongst the studied genera, along with some evidence towards events of lateral gene transfer amongst the heterocystous cyanobacteria in case of the rbcl gene. Thus, heterocystous cyanobacteria were found to be a fast evolving group, with estimates of gene conversion tracts pointing towards the unbranched heterocystous cyanobacteria being at the base of evolutionary diversifications of the complete heterocystous lineage.     

基于COI与ITS序列的杂鳞库蚊复组 ( 双翅目: 蚊科) 分子系统发育

使用杂鳞库蚊复组COI部分序列和ITS序列构建分子发育树,并基于COI序列计算该复组种内和种间的Kimura-two-Parameter(K2P)距离,探讨环带库蚊的分类地位和杂鳞库蚊复组内各亲缘种的系统发育关系。环带库蚊和杂鳞库蚊的种间K2P距离为0.24%-0.72%,支持"环带库蚊是杂鳞库蚊的同物异名"这一观点;杂鳞库蚊(环带库蚊)和伪杂鳞库蚊、三带喙库蚊的种间K2P距离为4.41%-9.68%,同时分子系统树显示各个种分别聚类,互为姐妹群,再次证明三者互为独立的种;环带库蚊和杂鳞库蚊聚类的分支最接近树的端部,三带喙库蚊分支最接近树的基部,提示三带喙库蚊最早发生分化,而杂鳞库蚊(环带库蚊)最晚发生分化;采集自日本的三带喙库蚊种内K2P距离为0.48%-2.68%,而它们与采集自中国、印度的该种K2P距离为4.17%-6.76%,日本产三带喙库蚊聚集成一支,并与中印产地的聚类分支互为姐妹群,这些结果提示日本的三带喙库蚊有种下,甚至种级分化的趋势。     

Mitochondrial sequence data reveals the phylogeny of the Asian Helice group of crabs (Decapoda: Brachyura: Varunidae)

The taxonomy of the Helice s. l. crabs has been recently revised, subdividing the Asian species in three genera, Helice , Helicana and Pseudohelice . The last one is widespread throughout the Indo-West Pacific Ocean and a single species, Pseudohelice subquadrata , is found in Asia. The other two genera appear to be endemic to Asia. However, phylogenetic affinities among the Asian representatives of Helice s. l. are poorly understood, and different morphology-based hypotheses of relationships remain untested. In this study, we used sequence data from a mitochondrial gene-block spanning three different genes [16S rDNA- trnL ₁ - IGS -nad1 ] to perform phylogenetic analyses. The results provide independent molecular evidence supporting the splitting of the Asian species into Helice and Helicana . Helice is suggested to be paraphyletic with respect to P. subquadrata . In addition, the heterogeneity of the genus Pseudohelice is shown when including the East Asian and East African counterparts. We propose that the two genera, Helice and Pseudohelice , are not monophyletic in their current composition.     

Convergence and coevolution in a mutualism: evidence from a molecular phylogeny of Ficus

Abstract.— The interaction between Ficus (Moraceae) and their pollinating wasps (Chalcidoidea: Agaonidae; more than 700 species-specific couples) is one of the most specialized mutualisms found in nature. Both partners of this interaction show extensive variation in their respective biology. Here we investigate Ficus life-history trait evolution and fig/fig wasp coadaptation in the context of a well-resolved molecular phylogeny. Mapping out variations in Ficus life-history traits on an independently derived phylogeny constructed from ribosomal DNA sequences (external and internal transcribed spacer) reveals several parallel transitions in Ficus growth habit and breeding system. Convergent trait evolution might explain the discrepancies between morphological analyses and our molecular reconstruction of the genus. Morphological characters probably correlate with growth habit and breeding system and could therefore be subject to convergent evolution. Furthermore, we reconstruct the evolution of Ficus inflorescence characters that are considered adaptations to the pollinators. Our phylogeny reveals convergences in ostiole shape, stigma morphology, and stamen:ovule ratio. Statistical tests taking into account the phylogenetic relationship of the species show that transitions in ostiole shape are correlated with variation in wasp pollinator head shape, and evolutionary changes in stigma morphology and stamen:ovule ratio correlate with changes in the pollination behavior of the associated wasp. These correlations provide evidence for reciprocal adaptations of morphological characters between these mutualistic partners that have interacted over a long evolutionary time. In light of previous ecological studies on mutualism, we discuss the adaptive significance of these correlations and what they can tell us about the coevolutionary process occurring between figs and their pollinators.