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)      

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data

DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.     

A phylogenetic analysis of the Arecoid Line of palms based on plastid DNA sequence data

A phylogenetic analysis of the Arecoid Line (sensu Moore) of palms was conducted using 7 kb of coding and noncoding plastid DNA sequence data. Recovered maximum-parsimony and maximum-likelihood phylogenies support monophyly for the Arecoid Line relative to the rest of the family but paraphyly for subfamily Arecoideae and polyphyly for subfamily Ceroxyloideae (sensu Dransfield and Uhl). Tribes Cocoeae, Geonomeae, Hyophorbeae, and Iriarteae and subfamily Phytelephantoideae were identified as monophyletic as were subfamily Phytelephantoideae + Ravenea (tribe Ceroxyleae of Ceroxyloideae), Podococcus (tribe Podococceae of Arecoideae) + Pseudophoenix (tribe Cyclospatheae of Ceroxyloideae), Reinhardtia (tribe Malortieinae) + tribe Cocoeae (both of Arecoideae), and a clade containing all IndoPacific pseudomonomerous genera of tribe Areceae (Arecoideae). A few taxa show spurious resolution with noncoding plastid DNA data but noncoding data are generally congruent with protein-coding data. Biogeographic interpretation suggests a Gondwanan origin for the Arecoid Line with several lineages found on more than one fragment of the former supercontinent and primary diversification in these groups possibly due to continental breakup vicariance. Three groups involving Cocos, Orania, and the IndoPacific clade demonstrate independent dispersals into the IndoPacific region from a Gondwanan origin.     

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.     

Exploration of phylogenetic data using a global sequence analysis method

Background  

Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.     

The phylogenetic relationships of the extant pelicans inferred from DNA sequence data

The pelicans are a charismatic group of large water birds, whose evolutionary relationships have been long debated. Here we use DNA sequence data from both mitochondrial and nuclear genes to derive a robust phylogeny of all the extant species. Our data rejects the widespread notion that pelicans can be divided into white- and brown-plumaged groups. Instead, we find that, in contrast to all previous evolutionary hypotheses, the species fall into three well-supported clades: an Old World clade of the Dalmatian, Spot-billed, Pink-backed and Australian Pelicans, a New World clade of the American White, Brown and Peruvian Pelicans, and monospecific clade consisting solely of the Great White Pelican, weakly grouped with the Old World clade. We discuss possible evolutionary scenarios giving rise to this diversity.     

Complimentary DNA sequence data analysis of prokaryotic systems

Complimentary DNA sequence data of Φ × 174, fd, f1, G4, Ml3, MS2, λ and T7 phages ofEscherichia coli are analysed at mono-, di-, tri- and tetranucleotide levels. Our analysis shows that, (i) mononucleotides have certain preferences to occur at specific positions X₁, X₂, X₃ of codon, (ii) These nucleotides interact nonlinearly to form dinucleotide and this dinucleotide also interacts nonlinearely with a third nucleotide to form codon, (iii) However, nonlinear interactions are negligible at tetranucleotide level suggesting that, coding regions of complimentary DNA are Markov chains of order two. Trinucleotide potential values in three frames have suggested that, at least thirteen different trinucleotides can be used as a marker to locate coding regions in DNA of prokaryotes. (iv) Parallel paired codons are expressed in such a way that one of the codons in the pair expresses with high frequency while the other with low frequency. On the other hand the complimentary codon pairs express with small frequency difference, (v) In the synonymous codon groups, codon ending with T are found to express with more frequency     

Multiple sequence alignment in phylogenetic analysis

Multiple sequence alignment is discussed in light of homology assessments in phylogenetic research. Pairwise and multiple alignment methods are reviewed as exact and heuristic procedures. Since the object of alignment is to create the most efficient statement of initial homology, methods that minimize nonhomology are to be favored. Therefore, among all possible alignments, the one that satisfies the phylogenetic optimality criterion the best should be considered the best alignment. Since all homology statements are subject to testing and explanation this way, consistency of optimality criteria is desirable. This consistency is based on the treatment of alignment gaps as character information and the consistent use of a cost function (e.g., insertion-deletion, transversion, and transition) through analysis from alignment to phylogeny reconstruction. Cost functions are not subject to testing via inspection; hence the assumptions they make should be examined by varying the assumed values in a sensitivity analysis context to test for the robustness of results. Agreement among data may be used to choose an optimal solution set from all of those examined through parameter variation. This idea of consistency between assumption and analysis through alignment and cladogram reconstruction is not limited to parsimony analysis and could and should be applied to other forms of analysis such as maximum likelihood.     

A phylogenetic hypothesis for passerine birds: taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data

Passerine birds comprise over half of avian diversity, but have proved difficult to classify. Despite a long history of work on this group, no comprehensive hypothesis of passerine family-level relationships was available until recent analyses of DNA-DNA hybridization data. Unfortunately, given the value of such a hypothesis in comparative studies of passerine ecology and behaviour, the DNA-hybridization results have not been well tested using independent data and analytical approaches. Therefore, we analysed nucleotide sequence variation at the nuclear RAG-1 and c-mos genes from 69 passerine taxa, including representatives of most currently recognized families. In contradiction to previous DNA-hybridization studies, our analyses suggest paraphyly of suboscine passerines because the suboscine New Zealand wren Acanthisitta was found to be sister to all other passerines. Additionally, we reconstructed the parvorder Corvida as a basal paraphyletic grade within the oscine passerines. Finally, we found strong evidence that several family-level taxa are misplaced in the hybridization results, including the Alaudidae, Irenidae, and Melanocharitidae. The hypothesis of relationships we present here suggests that the oscine passerines arose on the Australian continental plate while it was isolated by oceanic barriers and that a major northern radiation of oscines (i.e. the parvorder Passerida) originated subsequent to dispersal from the south.     

Combining data in phylogenetic analysis

Systematists have access to multiple sources of character information in phylogenetic analysis. For example, it is not unusual to have nucleotide sequences from several different genes, or to have molecular and morphological data. How should diverse data be analyzed in phylogenetic analysis? Several methods have been proposed for the treatment of partitioned data: the total evidence, separate analysis, and conditional combination approaches. Here, we review some of the advantages and disadvantages of the different approaches, with special concentration on which methods help us to discern the evolutionary process and provide the most accurate estimates of phylogeny.     

Origin and phylogenetic analysis of Tibetan Mastiff based on the mitochondrial DNA sequence

At present, the Tibetan Mastiff is the oldest and most ferocious dog in the world. However, the origin of the Tibetan Mastiff and its Phylogenetic relationship with other large breed dogs such as Saint Bernard are unclear. In this study, the primers were designed according to the mitochondrial genome sequence of the domestic dog, and the 2,525 bp mitochondrial sequence, containing the whole sequence of Cytochrome b, tRNA-Thr, tRNA-Pro, and control region of the Tibetan Mastiff, was obtained. Using grey wolves and coyotes as outgroups, the Tibetan Mastiff and 12 breeds of domestic dogs were analyzed in phylogenesis. Tibetan Mastiff, domestic dog breeds, and grey wolves were clustered into a group and coyotes were clustered in a group separately. This indicated that the Tibetan Mastiff and the other domestic dogs originated from the grey wolf, and the Tibetan Mastiff belonged to Carnivora, Canidae, Canis, Canis lupus, Canis lupus familiaris on the animal taxonomy. In domestic dogs, the middle and small breed dogs were clustered at first; German Sheepdog, Swedish Elkhound, and Black Russian Terrier were clustered into one group, and the Tibetan Mastiff, Old English Sheepdog, Leonberger, and Saint Bernard were clustered in another group. This confirmed the viewpoint that many of the famous large breed dogs worldwide Such as Saint Bernard possibly had the blood lineage of the Tibetan Mastiff, based on the molecular data. According to the substitution rate, we concluded that the approximate divergence time between Tibetan Mastiff and grey wolf was 58,000 years before the present (YBP), and the approximate divergence time between other domestic dogs and grey wolf was 42,000 YBP, demonstrating that the time of origin of the Tibetan Mastiff was earlier than that of the other domestic dogs.     

A phylogenetic analysis of Primulaceae s.l. based on internal transcribed spacer (ITS) DNA sequence data

 Phylogenetic relationships in Primulaceae were investigated by analysis of nuclear rDNA ITS sequences. Thirty-four species of Primulaceae, two of Myrsinaceae and four outgroup taxa were analyzed. In accordance to the results of recently published papers on the phylogeny of Primulaceae we found the family to be paraphyletic and resolved the positions of some genera. Our results show (a) the rather basal position of Centunculus within Lysimachieae, the genus thus being rather distantly related to Anagallis, (b) the close relationship between Lysimachia sect. Lerouxia, Anagallis, Asterolinon, and Pelletiera, (c) the well-supported monophyly of a group consisting of the four genera Hottonia, Omphalogramma, Bryocarpum, and Soldanella, and (d) the affinity of Stimpsonia to the Myrsinaceae-Lysimachieae-Ardisiandra clade. The ITS sequence data do not provide sufficient information to resolve basal relationships within the Primulaceae s.l. There is evidence against the monophyly of the large genera Primula, Androsace, and Lysimachia. In contrast to the phylogenetic reconstructions based on plastid gene sequences, Cyclamen does not appear as a member of the Myrsinaceae-Lysimachieae clade, but its position remains unclear. Revised July 10, 2002; accepted November 21, 2002 Published online: March 20, 2003     

Hierarchical phylogenetic models for analyzing multipartite sequence data

Debate exists over how to incorporate information from multipartite sequence data in phylogenetic analyses. Strict combined-data approaches argue for concatenation of all partitions and estimation of one evolutionary history, maximizing the explanatory power of the data. Consensus/independence approaches endorse a two-step procedure where partitions are analyzed independently and then a consensus is determined from the multiple results. Mixtures across the model space of a strict combined-data approach and a priori independent parameters are popular methods to integrate these methods. We propose an alternative middle ground by constructing a Bayesian hierarchical phylogenetic model. Our hierarchical framework enables researchers to pool information across data partitions to improve estimate precision in individual partitions while permitting estimation and testing of tendencies in across-partition quantities. Such across-partition quantities include the distribution from which individual topologies relating the sequences within a partition are drawn. We propose standard hierarchical priors on continuous evolutionary parameters across partitions, while the structure on topologies varies depending on the research problem. We illustrate our model with three examples. We first explore the evolutionary history of the guinea pig (Cavia porcellus) using alignments of 13 mitochondrial genes. The hierarchical model returns substantially more precise continuous parameter estimates than an independent parameter approach without losing the salient features of the data. Second, we analyze the frequency of horizontal gene transfer using 50 prokaryotic genes. We assume an unknown species-level topology and allow individual gene topologies to differ from this with a small estimable probability. Simultaneously inferring the species and individual gene topologies returns a transfer frequency of 17%. We also examine HIV sequences longitudinally sampled from HIV+ patients. We ask whether posttreatment development of CCR5 coreceptor virus represents concerted evolution from middisease CXCR4 virus or reemergence of initial infecting CCR5 virus. The hierarchical model pools partitions from multiple unrelated patients by assuming that the topology for each patient is drawn from a multinomial distribution with unknown probabilities. Preliminary results suggest evolution and not reemergence.     

The analysis of population survey data on DNA sequence variation

A technique is presented for the partitioning of nucleotide diversity into within- and between-population components for the case in which multiple populations have been surveyed for restriction-site variation. This allows the estimation of an analogue of FST at the DNA level. Approximate expressions are given for the variance of these estimates resulting from nucleotide, individual, and population sampling. Application of the technique to existing studies on mitochondrial DNA in several animal species and on several nuclear genes in Drosophila indicates that the standard errors of genetic diversity estimates are usually quite large. Thus, comparative studies of nucleotide diversity need to be substantially larger than the current standards. Normally, only a very small fraction of the sampling variance is caused by sampling of individuals. Even when 20 or so restriction enzymes are employed, nucleotide sampling is a major source of error, and population sampling is often quite important. Generally, the degree of population subdivision at the nucleotide level is comparable with that at the haplotype level, but significant differences do arise as a result of inequalities in the genetic distances between haplotypes.     

Plastid DNA sequence data help to clarify phylogenetic relationships and reticulate evolution in Lycoris (Amaryllidaceae)

The temperate East Asian genus Lycoris is a well known lineage of ornamental geophytes consisting of at least 20 species, some of which are thought to be of natural hybrid origin. Previous genetic studies have supported this hypothesis, but these have relied solely on the use of karyology and/or nuclear ribosomal ITS sequences. No plastid DNA data have been available to address interspecific relationships within Lycoris until now. In this study, 500 individuals from 29 populations representing 16 of the 20 published Lycoris spp. were sampled, and DNA sequences were generated for two plastid markers (trnS‐trnfM and trnC‐ycf6). From these data we inferred phylogenetic relationships among the sampled taxa at the species and population levels using concatenated phylogenetic methods. A well resolved and strongly supported phylogenetic reconstruction for Lycoris was obtained. Although the plastid DNA topology differs from that derived previously using ITS, both genomes produce trees that cluster Lycoris spp. into three clades. One of these, containing polyploid taxa such as L. albiflora, L. caldwellii, L. straminea and L. houdyshelii, shows strong evidence of reticulation, and we discuss the identity of potential parents of these allopolyploids. In contrast, we offer evidence that challenges the hypothesis that triploid individuals of L. radiata are the result of hybridization. Instead, they appear to be autotriploids that have arisen in more than one location. By comparing the phylogenetic results obtained using nuclear genomic data to those from the plastid genome, a much clearer picture of the role that hybridization and reticulation have played in the evolution of Lycoris is emerging. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 115–126.     

Bayesian phylogenetic analysis of combined data

The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.