芍药属牡丹组基于形态学证据的系统发育关系分析

对芍药属牡丹组Paeonia L.sect.Moutan DC.（全部野生种）40个居群进行了基于形态学证据的系统学分析,试图建立组内种间的系统发育关系。利用PAUP （4.0）计算机程序分别构建了建立在25个形态学性状基础上的所有研究类群的距离树（UPGMA、NJ）和最大简约树（MP）。所得树的拓扑结构基本一致,差异只发生在距离树和简约树之间,在由形态和细胞学关系都很近的5个种（牡丹P.suffruticosa、矮牡丹P.jishanensis、卵叶牡丹P.qiui、紫斑牡丹P.rockii和凤丹P.o     

PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA) INFERRED FROM rbcL GENE SEQUENCE DATA

The chloroplast-encoded large subunit of the ribulose-1, 5-bisphosphate carboxylase / oxygenase (rbcL) gene was sequenced from 20 species of the colonial Volvocales (the Volvacaceae, Goniaceae, and Tetrabaenaceae) in order to elucidate phylogenetic relationships within the colonial Volvocales. Eleven hundred twenty-eight base pairs in the coding regions of the (rbcL) gene were analyzed by the neighbor-joining (NJ) method using three kinds of distance estimations, as well as by the maximum parsimony (MP) method. A large group comprising all the anisogamous and oogamous volvocacean species was resolved in the MP tree as well as in the NJ trees based on overall and synonymous substitutions. In all the trees constructed, Basichlamys and Tetrabaena (Tetrabaenaceae) constituted a very robust phylogenetic group. Although not supported by high bootstrap values, the MP tree and the NJ tree based on nonsynonymous substitutions indicated that the Tetrabaenaceae is the sister group to the large group comprising the Volvocaceae and the Goniaceae. In addition, the present analysis strongly suggested that Pandorina and Astrephomene are monophyletic genera whereas Eudorina is nonmonophyletic. These results are essentially consistent with the results of the recent cladistic analyses of morphological data. However, the monophyly of the Volvocaceae previously supported by four morphological synapomorphies is found only in the NJ tree based on nonsynonymous substitutions (with very low bootstrap values). The genus Volvox was clearly resolved as a polyphyletic group with V. rousseletii Pocock separated from other species of Volvox in the rbcL gene comparisons, although this genus represents a monophyletic group in the previous morphological analyses. Furthermore, none of the rbcL gene trees supported the monophyly of the Goniaceae; Astrephomene was placed in various phylogenetic positions .     

NJML: a hybrid algorithm for the neighbor-joining and maximum-likelihood methods

In the reconstruction of a large phylogenetic tree, the most difficult part is usually the problem of how to explore the topology space to find the optimal topology. We have developed a "divide-and-conquer" heuristic algorithm in which an initial neighbor-joining (NJ) tree is divided into subtrees at internal branches having bootstrap values higher than a threshold. The topology search is then conducted by using the maximum-likelihood method to reevaluate all branches with a bootstrap value lower than the threshold while keeping the other branches intact. Extensive simulation showed that our simple method, the neighbor-joining maximum-likelihood (NJML) method, is highly efficient in improving NJ trees. Furthermore, the performance of the NJML method is nearly equal to or better than existing time-consuming heuristic maximum-likelihood methods. Our method is suitable for reconstructing relatively large molecular phylogenetic trees (number of taxa >/= 16).     

Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data.

The relative efficiencies of the maximum-parsimony (MP), UPGMA, and neighbor-joining (NJ) methods in obtaining the correct tree (topology) for restriction-site and restriction-fragment data were studied by computer simulation. In this simulation, six DNA sequences of 16,000 nucleotides were assumed to evolve following a given model tree. The recognition sequences of 20 different six-base restriction enzymes were used to identify the restriction sites of the DNA sequences generated. The restriction-site data and restriction-fragment data thus obtained were used to reconstruct a phylogenetic tree, and the tree obtained was compared with the model tree. This process was repeated 300 times. The results obtained indicate that when the rate of nucleotide substitution is constant the probability of obtaining the correct tree (Pc) is generally higher in the NJ method than in the MP method. However, if we use the average topological deviation from the model tree (dT) as the criterion of comparison, the NJ and MP methods are nearly equally efficient. When the rate of nucleotide substitution varies with evolutionary lineage, the NJ method is better than the MP method, whether Pc or dT is used as the criterion of comparison. With 500 nucleotides and when the number of nucleotide substitutions per site was very small, restriction-site data were, contrary to our expectation, more useful than sequence data. Restriction-fragment data were less useful than restriction-site data, except when the sequence divergence was very small. UPGMA seems to be useful only when the rate of nucleotide substitution is constant and sequence divergence is high.     

Evolutionary relationships of human populations on a global scale

Using gene frequency data for 29 polymorphic loci (121 alleles), we conducted a phylogenetic analysis of 26 representative populations from around the world by using the neighbor-joining (NJ) method. We also conducted a separate analysis of 15 populations by using data for 33 polymorphic loci. These analyses have shown that the first major split of the phylogenetic tree separates Africans from non-Africans and that this split occurs with a 100% bootstrap probability. The second split separates Caucasian populations from all other non-African populations, and this split is also supported by bootstrap tests. The third major split occurs between Native American populations and the Greater Asians that include East Asians (mongoloids), Pacific Islanders, and Australopapuans (native Australians and Papua New Guineans), but Australopapuans are genetically quite different from the rest of the Greater Asians. The second and third levels of population splitting are quite different from those of the phylogenetic tree obtained by Cavalli- Sforza et al. (1988), where Caucasians, Northeast Asians, and Ameridians from the Northeurasian supercluster and the rest of non- Africans form the Southeast Asian supercluster. One of the major factors that caused the difference between the two trees is that Cavalli-Sforza et al. used unweighted pair-group method with arithmetic mean (UPGMA) in phylogenetic inference, whereas we used the NJ method in which evolutionary rate is allowed to vary among different populations. Bootstrap tests have shown that the UPGMA tree receives poor statistical support whereas the NJ tree is well supported. Implications that the phylogenetic tree obtained has on the current controversy over the out-of-Africa and the multiregional theories of human origins are discussed.      

Accuracy of phylogenetic trees estimated from DNA sequence data

The relative merits of four different tree-making methods in obtaining the correct topology were studied by using computer simulation. The methods studied were the unweighted pair-group method with arithmetic mean (UPGMA), Fitch and Margoliash's (FM) method, thd distance Wagner (DW) method, and Tateno et al.'s modified Farris (MF) method. An ancestral DNA sequence was assumed to evolve into eight sequences following a given model tree. Both constant and varying rates of nucleotide substitution were considered. Once the DNA sequences for the eight extant species were obtained, phylogenetic trees were constructed by using corrected (d) and uncorrected (p) nucleotide substitutions per site. The topologies of the trees obtained were then compared with that of the model tree. The results obtained can be summarized as follows: (1) The probability of obtaining the correct rooted or unrooted tree is low unless a large number of nucleotide differences exists between different sequences. (2) When the number of nucleotide substitutions per sequence is small or moderately large, the FM, DW, and MF methods show a better performance than UPGMA in recovering the correct topology. The former group of methods is particularly good for obtaining the correct unrooted tree. (3) When the number of substitutions per sequence is large, UPGMA is at least as good as the other methods, particularly for obtaining the correct rooted tree. (4) When the rate of nucleotide substitution varies with evolutionary lineage, the FM, DW, and MF methods show a better performance in obtaining the correct topology than UPGMA, except when a rooted tree is to be produced from data with a large number of nucleotide substitutions per sequence.(ABSTRACT TRUNCATED AT 250 WORDS)      

Estimating species trees from unrooted gene trees

In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.     

Accuracy of estimated phylogenetic trees from molecular data

Summary The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.     

TOPIARY PRUNING AND WEIGHTING REINFORCE AN AFRICAN ORIGIN FOR THE HUMAN MITOCHONDRIAL DNA TREE

A method is presented for removing recent homoplastic events from a phylogenetic tree. This “topiary pruning” method produces a series of progressively modified duplicates of the original set of data, from which more and more of the most recent substitutions have been removed. The edited sets of data have increased amounts of information per remaining taxon, while similar but randomized data sets subjected to topiary pruning do not. The ability of topiary pruning to “unscramble” artificial data sets that have high levels of homoplasy is demonstrated, and is shown to be similar in its effects to the weighting method of Kluge and Farris (1969), although with the additional advantage of reducing the number of taxa to the point where bootstrapping is feasible. Pruning and weighting used together produce closer approximations to the “true” tree than either method used separately. It is further shown that in these artificial data sets midpoint rooting is more likely to be accurate than outgroup rooting. When pruning and weighting are applied to the extensive sets of mitochondrial DNA data of Cann et al. (1987) and Vigilant et al. (1991), trees result that have deep branch points, some of which lead to entirely African branches. In the case of the Vigilant et al. data, the three African branches have bootstrap values between 0.94 and 1.0, and the consensus and bootstrap midpoint roots also have high bootstrap values and occur on these African branches near their junction. An African origin of the human mitochondrial tree is not proved by this approach, particularly since sequences from non-African groups are underrepresented in current data sets, but it is rendered more likely.     

Accuracy of estimated phylogenetic trees from molecular data

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's f theta, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogenetic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.     

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two approaches by means of computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, and transition/transversion rate bias. In these simulations, we emphasized a worst-case scenario analysis in which 100 replicate datasets for each evolutionary parameter set (gene) were generated, and the replicate dataset that produced a tree topology showing the largest number of phylogenetic errors was selected to represent that parameter set. Both randomly selected and worst-case replicates were utilized to compare the consensus and concatenation approaches primarily using the neighbor-joining (NJ) method. We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very different substitution patterns and no attempts are made to accommodate these differences while inferring phylogenies. These results appear to hold true for parsimony and likelihood methods as well. The concatenation approach shows >95% accuracy with only 10 genes. However, this gain in accuracy is sometimes accompanied by reinforcement of certain systematic biases, resulting in spuriously high bootstrap support for incorrect partitions, whether we employ site, gene, or a combined bootstrap resampling approach. Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support.     

拓扑树间的通经拓扑距离

给出了一种新的系统树间的拓扑距离,使用NJ,MP,UPGMA等3种方法对13种动物的线粒体中14个基因（含组合的）DNA序列数据进行系统树的构建,利用分割拓扑距离和本文给出的通经拓扑距离对这14种系统树这间及其与真树进行比较。结果显示,NJ法对获得已知树的有效率最高,MP法次之,UPGMA法最低。这14种DNA序列所构建的系统树与已知树的拓扑距离基本上是随其DNA序列长度增加而减小,但两者的相关系数并未达到显著水平,分割拓扑距离在总体上可反映树间的拓扑结构差异,但其测度精确度比通经拓扑距离要低。     

基于Cyt b基因探讨羚羊亚科原羚属系统发生关系

原羚属物种在羚羊亚科中的分类地位尚存在很多争议。本文测定了原羚属的黄羊和藏原羚细胞色素b基因全序列(1140bp),并与牛科其它属31个种的同源序列进行比较,对其碱基组成变异情况及核苷酸序列差异进行了分析。基于细胞色素b基因全序列,用简约法(MP)、邻接法(NJ)和似然法(ML)构建了系统进化树。结果表明：黄羊和藏原羚的序列差异为3．78％,颠换数目近乎为0,其突变远未饱和;原羚属内黄羊和藏原羚为不同种,单系发生;原羚属与赛加羚羊属、犬羚属及跳羚属等并系发生,原羚属隶属于羚羊亚科,应为独立属;羚羊亚科组成属间多为并系起源。根据序列差异值2％／百万年的细胞色素6分子钟,推测黄羊和藏原羚分歧时间大约为1～2百万年;原羚属与羚羊亚科其它属分歧时间大约在5．7～8百万年。     

Interior-branch and bootstrap tests of phylogenetic trees

We have compared statistical properties of the interior-branch and bootstrap tests of phylogenetic trees when the neighbor-joining tree- building method is used. For each interior branch of a predetermined topology, the interior-branch and bootstrap tests provide the confidence values, PC and PB, respectively, that indicate the extent of statistical support of the sequence cluster generated by the branch. In phylogenetic analysis these two values are often interpreted in the same way, and if PC and PB are high (say, > or = 0.95), the sequence cluster is regarded as reliable. We have shown that PC is in fact the complement of the P-value used in the standard statistical test, but PB is not. Actually, the bootstrap test usually underestimates the extent of statistical support of species clusters. The relationship between the confidence values obtained by the two tests varies with both the topology and expected branch lengths of the true (model) tree. The most conspicuous difference between PC and PB is observed when the true tree is starlike, and there is a tendency for the difference to increase as the number of sequences in the tree increases. The reason for this is that the bootstrap test tends to become progressively more conservative as the number of sequences in the tree increases. Unlike the bootstrap, the interior-branch test has the same statistical properties irrespective of the number of sequences used when a predetermined tree is considered. Therefore, the interior-branch test appears to be preferable to the bootstrap test as long as unbiased estimators of evolutionary distances are used. However, when the interior-branch is applied to a tree estimated from a given data set, PC may give an overestimate of statistical confidence. For this case, we developed a method for computing a modified version (P'C) of the PC value and showed that this P'C tends to give a conservative estimate of statistical confidence, though it is not as conservative as PB. In this paper we have introduced a model in which evolutionary distances between sequences follow a multivariate normal distribution. This model allowed us to study the relationships between the two tests analytically.      

A heuristic approach of maximum likelihood method for inferring phylogenetic tree and an application to the mammalian SOX-3 origin of the testis-determining gene SRY

Applying the tree bisection and reconnection (TBR) algorithm, we have developed a heuristic method (maximum likelihood (ML)-TBR) for inferring the ML tree based on tree topology search. For initial trees from which iterative processes start in ML-TBR, two cases were considered: one is 100 neighbor-joining (NJ) trees based on the bootstrap resampling and the other is 100 randomly generated trees. The same ML tree was obtained in both cases. All different iterative processes started from 100 independent initial trees ultimately converged on one optimum tree with the largest log-likelihood value, suggesting that a limited number of initial trees will be quite enough in ML-TBR. This also suggests that the optimum tree corresponds to the global optimum in tree topology space and thus probably coincides with the ML tree inferred by intact ML analysis. This method has been applied to the inference of phylogenetic tree of the SOX family members. The mammalian testis-determining gene SRY is believed to have evolved from SOX-3, a member of the SOX family, based on several lines of evidence, including their sequence similarity, the location of SOX-3 on the X chromosome and some aspects of their expression. This model should be supported directly from the phylogenetic tree of the SOX family, but no evidence has been provided to date. A recently published NJ tree shows implausibly remote origin of SRY, suggesting that a more sophisticated method is required for understanding this problem. The ML tree inferred by the present method showed that the SRYs of marsupial and placental mammals form a monophyletic cluster which had diverged from the mammalian SOX-3 in the early evolution of mammals.     

Phylogenetic analysis of the non-pathogenic genusSpiromastix (Onygenaceae) and related onygenalean taxa based on large subunit ribosomal DNA sequences

The phylogenetic positioning of the non-pathogenic genusSpiromastix in the Onygenales was studied based on large subunit rDNA (LSU rDNA) partial sequences (ca. 570 bp.). FourSpiromastix species and 28 representative taxa of the Onygenales were newly sequenced. Phylogenetic trees were constructed by the neighbor-joining (NJ) method and evaluated by the maximum parsimony (MP) method with the data of 13 taxa retrieved from DNA databases.Spiromastix and dimorphic systemic pathogens,Ajellomyces andParacoccidioides, appear to be a monophyletic group with 74% bootstrap probability (BP) in the NJ tree constructed with the representative taxa of the Onygenales. The tree topology was concordant with the NJ tree based on SSU rDNA sequences of our previous work and corresponded to the classification system of the Onygenales by Currah (1985) and its minor modification by Udagawa (1997) with the exception of the classification of the Onygenaceae. The Onygeneceae sensu Udagawa may still be polyphyletic, since three independent lineages were recognized. The taxa forming helicoid peridial appendages were localized to two clades on the tree. The topology of the NJ tree constructed withSpiromastix and its close relatives suggested that the helicoid peridial appendages were apomorphic and acquired independently in the two clades of the Onygenales.     

Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.     

分子系统进化关系分析的一种新方法--贝叶斯法在硬蜱属中的应用

距离矩阵邻接法、最大简约法和最大似然法是重建生物系统关系的3种主要方法。普遍认为最大似然法在原理上优于前二种方法，但其计算复杂费时。由于现行计算机的能力尚达不到其要求而实用性差，特别是在处理大数据集样本(即大于25个分类单元)时，用此方法几乎不可能。新近提出的贝叶斯法(Bayesianmethod)既保留了最大似然法的基本原理，又引进了马尔科夫链的蒙特卡洛方法，并使计算时间大大缩短。本文用贝叶斯法对硬蜱属(Ixodes)19个种的线粒体16S rDNA片段进行了系统进化分析。从总体上看，分析结果与现有的基于形态学的分类体系基本吻合。但与现存的假说相反，莱姆病的主要宿主蓖籽硬蜱复合种组并非单系。通过比较贝叶斯法与其它三种方法的结果，我们认为贝叶斯法是一种系统进化分析的好方法，它既能根据分子进化的现有理论和各种模型用概率重建系统进化关系，又克服了最大似然法计算速度慢、不适用于大数据集样本的缺陷。贝叶斯法根据后验概率直观地表示系统进化关系的分析结果，不需要用自引导法进行检验。可以预料，贝叶斯法将会被广泛地应用到系统进化分析上[动物学报49(3)：380—388，2003]。     

REEXAMINATION OF PHYLOGENETIC RELATIONSHIPS WITHIN THE COLONIAL VOLVOCALES (CHLOROPHYTA): AN ANALYSIS OF atpB AND rbcL GENE SEQUENCES

The chloroplast-encoded atp B gene was sequenced from 33 strains representing 28 species of the colonial Volvocales (the Volvocaceae and its relatives) to reexamine phylogenetic relationships as previously deduced by morphological data and rbc L gene sequence data.1128 base pairs in the coding regions of the atp B gene were analyzed by MP, NJ, and ML analyses. Although supported with relatively low bootstrap values (75% and 65% in the NJ and ML analyses, respectively), three anisogamous/oogamous volvocacean genera— Eudorina, Pleodorina, and Volvox, excluding the section Volvox (= Euvolvox, illegitimate name), constituted a large monophyletic group (Eudorina group). Outside the Eudorina group, a robust lineage composed of three species of Volvox sect. Volvox was resolved as in the rbc L gene trees, rejecting the hypothesis of the previous cladistic analysis based on morphological data that the genus Volvox is monophyletic. In addition, the NJ and ML trees suggested that Eudorina is a nonmonophyletic genus as inferred from the morphological data and rbc L gene sequences. Although phylogenetic status of the genus Gonium is ambiguous in the rbc L gene trees and the paraphyly of this genus is resolved in the cladistic analysis based on morphological data, the atp B gene sequence data suggest monophyly of Gonium with relatively low bootstrap values (56–61%) in the NJ and ML trees. On the basis of the combined sequence data (2256 base pairs) from atp B and rbc L genes, Gonium was resolved as a robust monophyletic genus in the NJ and ML trees (with 68–86% bootstrap values), and Eudorina elegans Ehrenberg represented a paraphyletic species positioned most basally within the Eudorina group. However, phylogenetic status and relationships of the families of the colonial Volvocales were still almost ambiguous even in the combined analysis.     

The consistency of several phylogeny-inference methods under varying evolutionary rates.

A phylogenetic method is a consistent estimator of phylogeny if and only if it is guaranteed to give the correct tree, given that sufficient (possibly infinite) independent data are examined. The following methods are examined for consistency: UPGMA (unweighted pair-group method, averages), NJ (neighbor joining), MF (modified Farris), and P (parsimony). A two-parameter model of nucleotide sequence substitution is used, and the expected distribution of character states is calculated. Without perfect correction for superimposed substitutions, all four methods may be inconsistent if there is but one branch evolving at a faster rate than the other branches. Partial correction of observed distances improves the robustness of the NJ method to rate variation, and perfect correction makes the NJ method a consistent estimator for all combinations of rates that were examined. The sensitivity of all the methods to unequal rates varies over a wide range, so relative-rate tests are unlikely to be a reliable guide for accepting or rejecting phylogenies based on parsimony analysis.