Quartet-based phylogenetic inference: improvements and limits

We analyze the performance of quartet methods in phylogenetic reconstruction. These methods first compute four-taxon trees (4-trees) and then use a combinatorial algorithm to infer a phylogeny that respects the inferred 4-trees as much as possible. Quartet puzzling (QP) is one of the few methods able to take weighting of the 4-trees, which is inferred by maximum likelihood, into account. QP seems to be widely used. We present weight optimization (WO), a new algorithm which is also based on weighted 4-trees. WO is faster and offers better theoretical guarantees than QP. Moreover, computer simulations indicate that the topological accuracy of WO is less dependent on the shape of the correct tree. However, although the performance of WO is better overall than that of QP, it is still less efficient than traditional phylogenetic reconstruction approaches based on pairwise evolutionary distances or maximum likelihood. This is likely related to long-branch attraction, a phenomenon to which quartet methods are very sensitive, and to inappropriate use of the initial results (weights) obtained by maximum likelihood for every quartet.     

Phylogeny of shorebirds, gulls, and alcids (Aves: Charadrii) from the cytochrome-b gene: parsimony, Bayesian inference, minimum evolution, and quartet puzzling

Charadrii (shorebirds, gulls, and alcids) have exceptional diversity in ecological, behavioral, and life-history traits. A phylogenetic framework is necessary to fully understand the relationships among these traits. Despite several attempts to resolve the phylogeny of the Charadrii, none have comprehensively utilized molecular sequence data. Complete and partial cytochrome-b gene sequences for 86 Charadrii and five Falconides species (as outgroup taxa) were obtained from GenBank and aligned. We analyzed the resulting matrices using parsimony, Bayesian inference, minimum evolution, and quartet puzzling methods. Posterior probabilities, decay indices, and bootstrapping provide strong support for four major lineages consisting of gulls, alcids, plovers, and sandpipers, respectively. The broad structure of the trees differ significantly from all previous hypotheses of Charadrii phylogeny in placing the plovers at the base of the tree below the sandpipers in a pectinate sequence towards a large clade of gulls and alcids. The parsimony, Bayesian, and minimum evolution models provide strong evidence for this phylogenetic hypothesis. This is further corroborated by non-tree based measures of support and conflict (Lento plots). The quartet puzzling trees are poorly resolved and inconclusive.     

Quartets MaxCut: a divide and conquer quartets algorithm

Accurate phylogenetic reconstruction methods are currently limited to a maximum of few dozens of taxa. Supertree methods construct a large tree over a large set of taxa, from a set of small trees over overlapping subsets of the complete taxa set. Hence, in order to construct the tree of life over a million and a half different species, the use of a supertree method over the product of accurate methods, is inevitable. Perhaps the simplest version of this task that is still widely applicable, yet quite challenging, is quartet-based reconstruction. This problem lies at the root of many tree reconstruction methods and theoretical as well as experimental results have been reported. Nevertheless, dealing with false, conflicting quartet trees remains problematic. In this paper, we describe an algorithm for constructing a tree from a set of input quartet trees even with a significant fraction of errors. We show empirically that conflicts in the inputs are handled satisfactorily and that it significantly outperforms and outraces the Matrix Representation with Parsimony (MRP) methods that have previously been most successful in dealing with supertrees. Our algorithm is based on a divide and conquer algorithm where our divide step uses a semidefinite programming (SDP) formulation of MaxCut. We remark that this builds on previous work of ours for piecing together trees from rooted triplet trees. The recursion for unrooted quartets, however, is more complicated in that even with completely consistent set of quartet trees the problem is NP-hard, as opposed to the problem for triples where there is a linear time algorithm. This complexity leads to several issues and some solutions of possible independent interest.     

Fast local fragment chaining using sum-of-pair gap costs

Background

When inferring phylogenetic trees different algorithms may give different trees. To study such effects a measure for the distance between two trees is useful. Quartet distance is one such measure, and is the number of quartet topologies that differ between two trees.

Results

We have derived a new algorithm for computing the quartet distance between a pair of general trees, i.e. trees where inner nodes can have any degree ≥ 3. The time and space complexity of our algorithm is sub-cubic in the number of leaves and does not depend on the degree of the inner nodes. This makes it the fastest algorithm so far for computing the quartet distance between general trees independent of the degree of the inner nodes.

Conclusions

We have implemented our algorithm and two of the best competitors. Our new algorithm is significantly faster than the competition and seems to run in close to quadratic time in practice.     

Actin Phylogeny and Intron Distribution in Bangiophyte Red Algae(Rhodoplantae)

The molecular phylogeny of red algal actin genes, with emphasis on the paraphyletic “Bangiophyceae,” was examined and compared to the rhodophyte SSU rDNA phylogeny. Nineteen new genomic actin sequences and seven SSU rDNA sequences were obtained and subjected to diverse phylogenetic analyses (maximum likelihood, distance/neighbor-joining, maximum parsimony, Bayesian analyses, and, with respect to protein sequences, also quartet puzzling). The actin trees confirmed most of the major clades found in the SSU rDNA phylogenies, although with a lower resolution. An actin gene duplication in the florideophycean lineage is reported, presumably related to an increased complexity of sexual reproduction. In addition, the distribution and characteristics of spliceosomal introns found in some of the actin sequences were examined. Introns were found in almost all florideophycean actin genes, whereas only two bangiophyte sequences contained introns. One intron in the florideophycean actin genes was also found in metazoan, and, shifted by one or two nucleotides, in a glaucocystophyte, a cryptophyte, and two fungal actin genes, and thus may be an ancient intron.[Reviewing Editor: Dr. Yves Van de Peer]     

Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae: Draco) as inferred from mitochondrial DNA sequence data

Phylogenetic analysis of mitochondrial DNA sequence data using maximum parsimony, minimum evolution (of log-determinant distances), and maximum-likelihood optimality criteria provided a robust estimate of Draco phylogenetic relationships. Although the analyses based on alternative optimality criteria were not entirely congruent, non-parametric bootstrap analyses identified many well-supported clades that were common to the analyses under the three altrenative criteria. Relationships within the major clades are generally well resolved and strongly supported, although this is not the case for the Philippine volans subclade. The hypothesis that a clade composed primarily of Philippine species represents a rapid radiation could not be rejected. A revised taxonomy for Draco is provided.     

番茄WOX转录因子家族的鉴定及其进化、表达分析

WUSCHEL相关的同源异型盒(WUSCHEL-related homeobox,WOX)是一类植物特异的转录因子家族,具有调控植物干细胞分裂分化动态平衡等重要功能。本研究利用番茄(Solanum lycopersicum)基因组数据,通过建立隐马尔科夫模型并进行检索,鉴定了番茄10个WOX转录因子家族成员。多序列比对发现,番茄WOX转录因子家族成员具有高度保守的同源异型结构域;以拟南芥WOX转录因子家族成员序列为参照,通过邻接法、极大似然法、贝叶斯法重建了系统发育树,三者呈现出类似的拓扑结构,番茄和拟南芥WOX转录因子家族共25个成员被分为3个进化支(Clade)和9个亚家族(Subgroup);利用MEME和GSDS对WOX转录因子家族成员的蛋白保守结构域和基因结构进行了分析,同一亚家族内的WOX转录因子家族成员的保守结构域的种类、组织形式以及基因结构具有高度的一致性;利用Perl和Orthomcl对家族成员的染色体定位和同源性关系进行分析,结果表明串联重复的SlWOX3a和SlWOX3b可能来源于一次复制事件;利用番茄转录组数据和qRT-PCR进行表达分析,结果显示家族成员在不同组织中的表达存在差异,暗示了WOX家族的不同成员在功能上可能具有多样性。本研究对番茄WOX转录因子家族成员进行GO(Gene Ontology)注释和比较分析,结果表明该家族成员作为转录因子,可能在组织器官发育、细胞间通讯等过程中发挥作用。     

IQPNNI: moving fast through tree space and stopping in time

An efficient tree reconstruction method (IQPNNI) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n(2)) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm. These steps are repeated several times and the best tree, with respect to the likelihood criterion, is considered as the inferred phylogenetic tree. Moreover, we suggest a rule which indicates when to stop the search. Simulations show that IQPNNI gives a slightly better accuracy than other programs tested. Moreover, we applied the approach to 218 small subunit rRNA sequences and 500 rbcL sequences. We found trees with higher likelihood compared to the results by others. A program to reconstruct DNA or amino acid based phylogenetic trees is available online (http://www.bi.uni-duesseldorf.de/software/iqpnni).     

QDist--quartet distance between evolutionary trees

SUMMARY: QDist is a program for computing the quartet distance between two unrooted trees, i.e. the number of quartet topology differences between the trees, where a quartet topology is the topological subtree induced by four species. The program is based on an algorithm with running time O(n log2 n), which makes it practical to compare large trees. Available under GNU license. AVAILABILITY: http://www.birc.dk/Software/QDist     

Nuclear and mtDNA phylogenies of the Trimeresurus complex: implications for the gene versus species tree debate

Phylogenies based on mitochondrial DNA (mtDNA) may represent gene trees that may not be congruent with the equivalent species tree. One solution to this problem is to include additional, independent loci from the nuclear genome. Sequence data from the seventh intron of the beta-fibrinogen gene were generated for 25 specimens of vipers, including 8 nominal species of the Trimeresurus complex of Asian pit vipers. Phylogenetic trees were generated using maximum-parsimony and maximum-likelihood methods. The taxonomic level at which the intron provided significant phylogenetic information was examined and the trees were compared to those produced from previously obtained mtDNA cytochrome b sequences. A variety of different approaches (separate analyses, conditional data combination, and consensus) were used in an attempt to provide a sound organismal phylogeny based on both nuclear and mtDNA data sets. We discuss the implications for the gene tree-species tree debate and its particular relevance to medically important organisms.     

Molecular phylogeny and historical biogeography of the Aphanius (Pisces,Cyprinodontiformes) species complex of central Anatolia,Turkey

Phylogenetic relationships of a subset of Aphanius fish comprising central Anatolia, Turkey, are investigated to test the hypothesis of geographic speciation driven by early Pliocene orogenic events in spite of morphological similarity. We use 3434 aligned base pairs of mitochondrial DNA from 42 samples representing 36 populations of three species and six outgroup species to test this hypothesis. Genes analyzed include those encoding the 12S and 16S ribosomal RNAs; transfer RNAs coding for valine, leucine, isoleucine, glutamine, methionine, tryptophan, alanine, asparagine, cysteine, and tyrosine; and complete NADH dehydrogenase subunits I and II. Distance based minimum evolution and maximum-likelihood analyses identify six well-supported clades consisting of Aphanius danfordii, Aphanius sp. aff danfordii, and four clades of Aphanius anatoliae. Parsimony analysis results in 462 equally parsimonious trees, all of which contain the six well supported clades identified in the other analyses. Our phylogenetic results are supported by hybridization studies (Villwock, 1964), and by the geological history of Anatolia. Phylogenetic relationships among the six clades are only weakly supported, however, and differ among analytical methods. We therefore test and subsequently reject the hypothesis of simultaneous diversification among the six central Anatolian clades. However, our analyses do not identify any internodes that are significantly better supported than expected by chance alone. Therefore, although bifurcating branching order is hypothesized to underlie this radiation, the exact branching order is difficult to estimate with confidence.     

Divergence and support among slightly suboptimal likelihood gene trees

Contemporary phylogenomic studies frequently incorporate two-step coalescent analyses wherein the first step is to infer individual-gene trees, generally using maximum-likelihood implemented in the popular programs PhyML or RAxML . Four concerns with this approach are that these programs only present a single fully resolved gene tree to the user despite potential for ambiguous support, insufficient phylogenetic signal to fully resolve each gene tree, inexact computer arithmetic affecting the reported likelihood of gene trees, and an exclusive focus on the most likely tree while ignoring trees that are only slightly suboptimal or within the error tolerance. Taken together, these four concerns are sufficient for RAxML and Phy ML users to be suspicious of the resulting (perhaps over-resolved) gene-tree topologies and (perhaps unjustifiably high) bootstrap support for individual clades. In this study, we sought to determine how frequently these concerns apply in practice to contemporary phylogenomic studies that use RAxML for gene-tree inference. We did so by re-analyzing 100 genes from each of ten studies that, taken together, are representative of many empirical phylogenomic studies. Our seven findings are as follows. First, the few search replicates that are frequently applied in phylogenomic studies are generally insufficient to find the optimal gene-tree topology. Second, there is often more topological variation among slightly suboptimal gene trees relative to the best-reported tree than can be safely ignored. Third, the Shimodaira–Hasegawa-like approximate likelihood ratio test is highly effective at identifying dubiously supported clades and outperforms the alternative approaches of relying on bootstrap support or collapsing minimum-length branches. Fourth, the bootstrap can, but rarely does, indicate high support for clades that are not supported amongst slightly suboptimal trees. Fifth, increasing the accuracy by which RA xML optimizes model-parameter values generally has a nominal effect on selection of optimal trees. Sixth, tree searches using the GTRCAT model were generally less effective at finding optimal known trees than those using the GTRGAMMA model. Seventh, choice of gene-tree sampling strategy can affect inferred coalescent branch lengths, species-tree topology and branch support.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

基于 rDNA ITS 1序列探讨臂尾轮属轮虫的系统发生关系

本文通过对剪形臂尾轮虫、矩形臂尾轮虫、十指臂尾轮虫、红臂尾轮虫、角突臂尾轮虫、双棘臂尾轮虫、裂足臂尾轮虫和萼花臂尾轮虫等八种臂尾轮虫rDNAITS 1序列分析,并以西氏晶囊轮虫为外群,使用PAUP和贝叶斯软件分别构建臂尾轮属轮虫系统发生树( MP树、NJ树、ML树和贝叶斯树) ,以探讨臂尾轮属的系统发生关系,并解决其中的一些分类问题。结果表明:本研究所涉及的轮虫rDNAITS 1平均序列差异百分比较高,为29 %;海水和淡水臂尾轮虫被明显分为不同的进化枝;除双棘臂尾轮虫外,在淡水臂尾轮虫中具有三对前棘刺且营附着生活的种类与前棘刺少于三对且营浮游生活的种类聚在不同支系中,这与以形态特征为主所进行的系统发生研究结果基本一致;所有的系统树均支持将十指臂尾轮虫作为一个独立的支系分离出来,裂足臂尾轮虫应归入臂尾轮属。     

Molecular phylogenetics of slit‐faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.     

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.     

The phylogeny of <Emphasis Type="Italic">Schistidium</Emphasis> (Bryophyta,Grimmiaceae) based on the primary and secondary structure of nuclear rDNA internal transcribed spacers

Phylogeny of Schistidium (Bryophyta, Grimmiaceae) was studied by comparing the nucleotide sequences of internal transcribed spacers ITS1-2 of nuclear rDNA and the trnT-trnD region of chloroplast DNA. Phylogenetic trees constructed based on nuclear and chloroplast sequences were consistent, comprising a basal grade and two large clades. Morphological characteristics specific for these clades were described. Secondary structures of ITS1 and ITS2 Schistidium species were modeled using thermodynamic criteria. Four different structures of the longest ITS1 hairpin were identified. These results were used to analyze possible paths of Schistidium evolution. Characteristics of the ITS2 secondary structure support the two major clades recognized in the phylogenetic trees.     

Phylogenetic hypotheses for the turtle family Geoemydidae

The turtle family Geoemydidae represents the largest, most diverse, and most poorly understood family of turtles. Little is known about this group, including intrafamilial systematics. The only complete phylogenetic hypothesis for this family positions geoemydids as paraphyletic with respect to tortoises, but this arrangement has not been accepted by many workers. We compiled a 79-taxon mitochondrial and nuclear DNA data set to reconstruct phylogenetic relationships for 65 species and subspecies representing all 23 genera of the Geoemydidae. Maximum parsimony (MP) and maximum-likelihood (ML) analyses and Bayesian analysis produced similar, well-resolved trees. Our analyses identified three main clades comprising the tortoises (Testudinidae), the old-world Geoemydidae, and the South American geoemydid genus Rhinoclemmys. Within Geoemydidae, many nodes were strongly supported, particularly based on Bayesian posterior probabilities of the combined three-gene dataset. We found that adding data for a subset of taxa improved resolution of some deeper nodes in the tree. Several strongly supported groupings within the Geoemydidae demonstrate non-monophyly of some genera and possible interspecific hybrids, and we recommend several taxonomic revisions based on available evidence.     

Higher-level phylogenetic relationships of Homobasidiomycetes (mushroom-forming fungi) inferred from four rDNA regions.

Homobasidiomycetes include approximately 13,000 described species of mushroom-forming fungi and related taxa. The higher-level classification of this ecologically important group has been unsettled for over 100 years. The goals of the present study were to evaluate a recent phylogenetic classification by Hibbett and Thorn that divided the homobasidiomycetes into eight major unranked clades, and to infer the higher-order relationships among these clades. A dataset of 93 species that represent all eight previously recognized clades was assembled, with 3800 bp of sequence data from nuclear and mitochondrial large and small subunit rDNAs for each taxon. Parsimony and maximum-likelihood analyses support the monophyly of the eight major clades recognized by Hibbett and Thorn. Most groups are strongly supported in bootstrapped parsimony analyses, but the polyporoid clade remains weakly supported. For the first time, the sister-group relationship of the euagarics clade and bolete clade is strongly supported, and the Hygrophoraceae is strongly supported as the sister group of the rest of the euagarics clade. Nevertheless, the backbone of the homobasidiomycete phylogeny, and the internal structure of several clades, remain poorly resolved.     

Towards a phylogeny of chitons (Mollusca, Polyplacophora) based on combined analysis of five molecular loci

This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.