Morphological evidence for sister group relationship between flamingos (Aves: Phoenicopteridae) and grebes (Podicipedidae)

A recent molecular analysis strongly supported sister group relationship between flamingos (Phoenicopteridae) and grebes (Podicipedidae), a hypothesis which has not been suggested before. Flamingos are long-legged filter-feeders whereas grebes are morphologically quite divergent foot-propelled diving birds, and sister group relationship between these two taxa would thus provide an interesting example of evolution of different feeding strategies in birds. To test monophyly of a clade including grebes and flamingos, I performed a cladistic analysis of 70 morphological characters which were scored for 17 taxa. Parsimony analysis of these data supported monophyly of the taxon (Podicipedidae + Phoenicopteridae) and the clade received high bootstrap support. Previously overlooked morphological, oological and parasitological evidence is recorded which supports this hypothesis, and which makes the taxon (Podicipedidae + Phoenicopteridae) one of the best supported higher-level clades within modern birds. The phylogenetic significance of some fossil flamingo-like birds is discussed. The Middle Eocene taxon Juncitarsus is most likely the sister taxon of the clade (Podicipedidae + (Palaelodidae + Phoenicopteridae)) although resolution of its exact systematic position awaits revision of the fossil material. Contrary to previous assumptions, it is more parsimonious to assume that flamingos evolved from a highly aquatic ancestor than from a shorebird-like ancestor.  © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society , 2004, 140 , 157–169.     

Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone

While there has been strong support for Amborella and Nymphaeales (water lilies) as branching from basal-most nodes in the angiosperm phylogeny, this hypothesis has recently been challenged by phylogenetic analyses of 61 protein-coding genes extracted from the chloroplast genome sequences of Amborella, Nymphaea, and 12 other available land plant chloroplast genomes. These character-rich analyses placed the monocots, represented by three grasses (Poaceae), as sister to all other extant angiosperm lineages. We have extracted protein-coding regions from draft sequences for six additional chloroplast genomes to test whether this surprising result could be an artifact of long-branch attraction due to limited taxon sampling. The added taxa include three monocots (Acorus, Yucca, and Typha), a water lily (Nuphar), a ranunculid (Ranunculus), and a gymnosperm (Ginkgo). Phylogenetic analyses of the expanded DNA and protein data sets together with microstructural characters (indels) provided unambiguous support for Amborella and the Nymphaeales as branching from the basal-most nodes in the angiosperm phylogeny. However, their relative positions proved to be dependent on the method of analysis, with parsimony favoring Amborella as sister to all other angiosperms and maximum likelihood (ML) and neighbor-joining methods favoring an Amborella + Nymphaeales clade as sister. The ML phylogeny supported the later hypothesis, but the likelihood for the former hypothesis was not significantly different. Parametric bootstrap analysis, single-gene phylogenies, estimated divergence dates, and conflicting indel characters all help to illuminate the nature of the conflict in resolution of the most basal nodes in the angiosperm phylogeny. Molecular dating analyses provided median age estimates of 161 MYA for the most recent common ancestor (MRCA) of all extant angiosperms and 145 MYA for the MRCA of monocots, magnoliids, and eudicots. Whereas long sequences reduce variance in branch lengths and molecular dating estimates, the impact of improved taxon sampling on the rooting of the angiosperm phylogeny together with the results of parametric bootstrap analyses demonstrate how long-branch attraction might mislead genome-scale phylogenetic analyses.     

Inferring complex phylogenies using parsimony: an empirical approach using three large DNA data sets for angiosperms

To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbcL (1,428 bp), and atpB (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA + rbcL + atpB data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of > or = 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.     

类群取样与系统发育分析精确度之探索

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phylogenetic analyses is improved significantly by thorough taxon sampling efforts. Many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incorrect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applications of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computational power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.     

Relationships within Cornales and circumscription of Cornaceae-matK and rbcL sequence data and effects of outgroups and long branches

Phylogenetic relationships in Cornales were assessed using sequences rbcL and matK. Various combinations of outgroups were assessed for their suitability and the effects of long branches and outgroups on tree topology were examined using RASA 2.4 prior to conducting phylogenetic analyses. RASA identified several potentially problematic taxa having long branches in individual data sets that may have obscured phylogenetic signal, but when data sets were combined RASA no longer detected long branch problems. t(RASA) provides a more conservative measurement for phylogenetic signal than the PTP and skewness tests. The separate matK and rbcL sequence data sets were measured as not containing phylogenetic signal by RASA, but PTP and skewness tests suggested the reverse [corrected]. Nonetheless, the matK and rbcL sequence data sets suggested relationships within Cornales largely congruent with those suggested by the combined matK-rbcL sequence data set that contains significant phylogenetic signal as measured by t(RASA), PTP, and skewness tests. Our analyses also showed that a taxon having a long branch on the tree may not be identified as a "long-branched" taxon by RASA. The long branches identified by RASA had little effect on the arrangement of other taxa in the tree, but the placements of the long-branched taxa themselves were often problematic. Removing the long-branched taxa from analyses generally increased bootstrap support, often substantially. Use of non-optimal outgroups (as identified by RASA) decreased phylogenetic resolution in parsimony analyses and suggested different relationships in maximum likelihood analyses, although usually weakly supported clades (less than 50% support) were impacted. Our results do not recommend using t(RASA) as a sole criterion to discard data or taxa in phylogenetic analyses, but t(RASA) and the taxon variance ratio obtained from RASA may be useful as a guide for improved phylogenetic analyses. Results of parsimony and ML analyses of the sequence data using optimal outgroups suggested by RASA revealed four major clades within Cornales: (1) Curtisia-Grubbia, (2) Cornus-Alangium, (3) Nyssa-Camptotheca-Davidia-Mastixia-Diplopanax, and (4) Hydrangeaceae-Loasaceae, with clades (2) and (3) forming a monophyletic group sister to clade (4) and clade (1) sister to the remainder of Cornales. However, there was not strong bootstrap support for relationships among the major clades. The placement of Hydrostachys could not be reliably determined, although most analyses place the genus within Hydrangeaceae; ML analyses, for example, placed the genus as the sister of Hydrangeeae. Our results supported a Cornales including the systematically problematic Hydrostachys, a Cornaceae consisting of Cornus and Alangium, a Nyssaceae consisting of Nyssa and Camptotheca, a monogeneric Davidiaceae, a Mastixiaceae consisting of Mastixia and Diplopanax, and an expanded Grubbiaceae consisting of Grubbia and Curtisia, and two larger families, Hydrangeaceae and Loasaceae.     

Monophyletic groups within 'higher land birds'– comparison of morphological and molecular data

The relationships within the ‘higher land birds’ and putatively related taxa are analysed in a study using 89 morphological characters and DNA sequences of three nuclear, protein‐coding genes, c‐myc, RAG‐1, and myoglobin intron II. Separate analyses of the different data sets and a ‘total evidence’ analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological synapomorphies of this clade are presented. All analyses further resulted in monophyly of the taxon [Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)]. Analysis of the morphological data and of the combined data set also supported monophyly of the taxon [Strigiformes + (Falconidae + Accipitridae)]. The morphological data further support monophyly of the taxon (Upupidae + Bucerotidae). Other placements in the three analyses received either no or only weak bootstrap support.     

Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?

This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia ( > 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa×26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.     

New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.     

A Large-Scale,Higher-Level,Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

Background

Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.

Methodology / Principal Findings

483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.

Conclusions / Significance

Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.     

Strange bayes indeed: uniform topological priors imply non-uniform clade priors

While Bayesian analysis has become common in phylogenetics, the effects of topological prior probabilities on tree inference have not been investigated. In Bayesian analyses, the prior probability of topologies is almost always considered equal for all possible trees, and clade support is calculated from the majority rule consensus of the approximated posterior distribution of topologies. These uniform priors on tree topologies imply non-uniform prior probabilities of clades, which are dependent on the number of taxa in a clade as well as the number of taxa in the analysis. As such, uniform topological priors do not model ignorance with respect to clades. Here, we demonstrate that Bayesian clade support, bootstrap support, and jackknife support from 17 empirical studies are significantly and positively correlated with non-uniform clade priors resulting from uniform topological priors. Further, we demonstrate that this effect disappears for bootstrap and jackknife when data sets are free from character conflict, but remains pronounced for Bayesian clade supports, regardless of tree shape. Finally, we propose the use of a Bayes factor to account for the fact that uniform topological priors do not model ignorance with respect to clade probability.     

15 Phylogeny of the chlorophyta: inferences from 18S and 26S rDNA

Recent studies of the Chlorophyceae using 18S and 26S rDNA data in meta‐analysis have demonstrated the power of combining these two sets of rDNA data. Furthermore, the 26S rDNA data complement the more conserved 18S gene for many chlorophycean lineages. Consequently, this data approach was pursued in an expanded taxon‐sampling scheme for the Chlorophyta, with special reference to the classes Chlorophyceae and Trebouxiophyceae. Results of these new phylogenetic analyses identify Microspora sp. (UTEX LB 472) and Radiofilum transversale (UTEX LB 1252) as sister taxa which, in turn, form a basal clade in the Cylindrocapsa alliance (Treubaria, Trochiscia, Elakatothrix). The relative position of the “Cylindrocapsa” clade within the Chlorophyceae remains uncertain. The enhanced taxon‐sampling has not resolved the relative positions of the Oedogoniales, Chaetophorales or Chaetopeltidales. Furthermore, the Sphaeropleaceae are supported as members of the Sphaeropleales in only some analyses, raising concerns about the status of the order. Although based on a limited set of taxa (currently <10), a combined data approach reveals support for a monophyletic Trebouxiophyceae that includes the distinctive organisms, Geminella and Eremosphaera. The goal of a well‐resolved phylogeny for the Chlorophyta remains just that, a goal. Achieving that goal obviously will require additional taxon sampling in the Prasinophyceae and Ulvophyceae, as well as, the Trebouxiophyceae. Moreover, it is clear that other genes (e.g., cp‐atpB, cp‐rbcL, cp‐16S, mt‐nad5) will be needed to help address problems of resolution based on the rDNA data alone. Supported by NSF DEB 9726588 and DEB 0129030.     

A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data

Phylogeny reconstruction is a difficult computational problem, because the number of possible solutions increases with the number of included taxa. For example, for only 14 taxa, there are more than seven trillion possible unrooted phylogenetic trees. For this reason, phylogenetic inference methods commonly use clustering algorithms (e.g., the neighbor-joining method) or heuristic search strategies to minimize the amount of time spent evaluating nonoptimal trees. Even heuristic searches can be painfully slow, especially when computationally intensive optimality criteria such as maximum likelihood are used. I describe here a different approach to heuristic searching (using a genetic algorithm) that can tremendously reduce the time required for maximum-likelihood phylogenetic inference, especially for data sets involving large numbers of taxa. Genetic algorithms are simulations of natural selection in which individuals are encoded solutions to the problem of interest. Here, labeled phylogenetic trees are the individuals, and differential reproduction is effected by allowing the number of offspring produced by each individual to be proportional to that individual's rank likelihood score. Natural selection increases the average likelihood in the evolving population of phylogenetic trees, and the genetic algorithm is allowed to proceed until the likelihood of the best individual ceases to improve over time. An example is presented involving rbcL sequence data for 55 taxa of green plants. The genetic algorithm described here required only 6% of the computational effort required by a conventional heuristic search using tree bisection/reconnection (TBR) branch swapping to obtain the same maximum-likelihood topology.      

The platypus is in its place: nuclear genes and indels confirm the sister group relation of monotremes and Therians

Morphological data supports monotremes as the sister group of Theria (extant marsupials + eutherians), but phylogenetic analyses of 12 mitochondrial protein-coding genes have strongly supported the grouping of monotremes with marsupials: the Marsupionta hypothesis. Various nuclear genes tend to support Theria, but a comprehensive study of long concatenated sequences and broad taxon sampling is lacking. We therefore determined sequences from six nuclear genes and obtained additional sequences from the databases to create two large and independent nuclear data sets. One (data set I) emphasized taxon sampling and comprised five genes, with a concatenated length of 2,793 bp, from 21 species (two monotremes, six marsupials, nine placentals, and four outgroups). The other (data set II) emphasized gene sampling and comprised eight genes and three proteins, with a concatenated length of 10,773 bp or 3,669 amino acids, from five taxa (a monotreme, a marsupial, a rodent, human, and chicken). Both data sets were analyzed by parsimony, minimum evolution, maximum likelihood, and Bayesian methods using various models and data partitions. Data set I gave bootstrap support values for Theria between 55% and 100%, while support for Marsupionta was at most 12.3%. Taking base compositional bias into account generally increased the support for Theria. Data set II exclusively supported Theria, with the highest possible values and significantly rejected Marsupionta. Independent phylogenetic evidence in support of Theria was obtained from two single amino acid deletions and one insertion, while no supporting insertions and deletions were found for Marsupionta. On the basis of our data sets, the time of divergence between Monotremata and Theria was estimated at 231-217 MYA and between Marsupialia and Eutheria at 193-186 MYA. The morphological evidence for a basal position of Monotremata, well separated from Theria, is thus fully supported by the available molecular data from nuclear genes.     

More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)

A central question concerning data collection strategy for molecular phylogenies has been, is it better to increase the number of characters or the number of taxa sampled to improve the robustness of a phylogeny estimate? A recent simulation study concluded that increasing the number of taxa sampled is preferable to increasing the number of nucleotide characters, if taxa are chosen specifically to break up long branches. We explore this hypothesis by using empirical data from noctuoid moths, one of the largest superfamilies of insects. Separate studies of two nuclear genes, elongation factor-1 alpha (EF-1 alpha) and dopa decarboxylase (DDC), have yielded similar gene trees and high concordance with morphological groupings for 49 exemplar species. However, support levels were quite low for nodes deeper than the subfamily level. We tested the effects on phylogenetic signal of (1) increasing the taxon sampling by nearly 60%, to 77 species, and (2) combining data from the two genes in a single analysis. Surprisingly, the increased taxon sampling, although designed to break up long branches, generated greater disagreement between the two gene data sets and decreased support levels for deeper nodes. We appear to have inadvertently introduced new long branches, and breaking these up may require a yet larger taxon sample. Sampling additional characters (combining data) greatly increased the phylogenetic signal. To contrast the potential effect of combining data from independent genes with collection of the same total number of characters from a single gene, we simulated the latter by bootstrap augmentation of the single-gene data sets. Support levels for combined data were at least as high as those for the bootstrap-augmented data set for DDC and were much higher than those for the augmented EF-1 alpha data set. This supports the view that in obtaining additional sequence data to solve a refractory systematic problem, it is prudent to take them from an independent gene.     

The deep divergences of neornithine birds: a phylogenetic analysis of morphological characters

Consensus is elusive regarding the phylogenetic relationships among neornithine (crown clade) birds. The ongoing debate over their deep divergences is despite recent increases in available molecular sequence data and the publication of several larger morphological data sets. In the present study, the phylogenetic relationships among 43 neornithine higher taxa are addressed using a data set of 148 osteological and soft tissue characters, which is one of the largest to date. The Mesozoic non‐neornithine birds Apsaravis, Hesperornis, and Ichthyornis are used as outgroup taxa for this analysis. Thus, for the first time, a broad array of morphological characters (including both cranial and postcranial characters) are analyzed for an ingroup densely sampling Neornithes, with crown clade outgroups used to polarize these characters. The strict consensus cladogram of two most parsimonious trees resultant from 1000 replicate heuristic searches (random stepwise addition, tree‐bisection‐reconnection) recovered several previously identified clades; the at‐one‐time contentious clades Galloanseres (waterfowl, fowl, and allies) and Palaeognathae were supported. Most notably, our analysis recovered monophyly of Neoaves, i.e., all neognathous birds to the exclusion of the Galloanseres, although this clade was weakly supported. The recently proposed sister taxon relationship between Steatornithidae (oilbird) and Trogonidae (trogons) was recovered. The traditional taxon “Falconiformes” (Cathartidae, Sagittariidae, Accipitridae, and Falconidae) was not found to be monophyletic, as Strigiformes (owls) are placed as the sister taxon of (Falconidae + Accipitridae). Monophyly of the traditional “Gruiformes” (cranes and allies) and ”Ciconiiformes” (storks and allies) was also not recovered. The primary analysis resulted in support for a sister group relationship between Gaviidae (loons) and Podicipedidae (grebes)—foot‐propelled diving birds that share many features of the pelvis and hind limb. Exclusion of Gaviidae and reanalysis of the data set, however, recovered the sister group relationship between Phoenicopteridae (flamingos) and grebes recently proposed from molecular sequence data.     

Resolving an ancient, rapid radiation in Saxifragales

Despite the prior use of approximately 9000 bp, deep-level relationships within the angiosperm clade, Saxifragales remain enigmatic, due to an ancient, rapid radiation (89.5 to 110 Ma based on the fossil record). To resolve these deep relationships, we constructed several new data sets: (1) 16 genes representing the three genomic compartments within plant cells (2 nuclear, 10 plastid, 4 mitochondrial; aligned, analyzed length = 21,460 bp) for 28 taxa; (2) the entire plastid inverted repeat (IR; 26,625 bp) for 17 taxa; (3) "total evidence" (50,845 bp) for both 17 and 28 taxa (the latter missing the IR). Bayesian and ML methods yielded identical topologies across partitions with most clades receiving high posterior probability (pp = 1.0) and bootstrap (95% to 100%) values, suggesting that with sufficient data, rapid radiations can be resolved. In contrast, parsimony analyses of different partitions yielded conflicting topologies, particularly with respect to the placement of Paeoniaceae, a clade characterized by a long branch. In agreement with published simulations, the addition of characters increased bootstrap support for the putatively erroneous placement of Paeoniaceae. Although having far fewer parsimony-informative sites, slowly evolving plastid genes provided higher resolution and support for deep-level relationships than rapidly evolving plastid genes, yielding a topology close to the Bayesian and ML total evidence tree. The plastid IR region may be an ideal source of slowly evolving genes for resolution of deep-level angiosperm divergences that date to 90 My or more. Rapidly evolving genes provided support for tip relationships not recovered with slowly evolving genes, indicating some complementarity. Age estimates using penalized likelihood with and without age constraints for the 28-taxon, total evidence data set are comparable to fossil dates, whereas estimates based on the 17-taxon data are much older than implied by the fossil record. Hence, sufficient taxon density, and not simply numerous base pairs, is important in reliably estimating ages. Age estimates indicate that the early diversification of Saxifragales occurred rapidly, over a time span as short as 6 million years. Between 25,000 and 50,000 bp were needed to resolve this radiation with high support values. Extrapolating from Saxifragales, a similar number of base pairs may be needed to resolve the many other deep-level radiations of comparable age in angiosperms.     

Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur

DNA sequences from three mitochondrial genes and one nuclear gene were analyzed to determine the phylogeny of the Malagasy primate family Lemuridae. Whether analyzed separately or in combination, the data consistently indicate that Eulemur species comprise a clade that is sister to a Lemur catta plus Hapalemur clade. The genus Varecia is basal to both. Resolution of cladogenic events within Eulemur was found to be extremely problematic with a total of six alternative arrangements offered by various data sets and weighting regimes. We attempt to determine the best arrangement of Eulemur taxa through a variety of character and taxon sampling strategies. Because our study includes all but one Eulemur species, increased taxon sampling is probably not an option for enhancing phylogenetic accuracy. We find, however, that the combined genetic data set is more robust to changes in taxon sample than are any of the individual data sets, suggesting that increased character sampling stabilizes phylogenetic resolution. Nonetheless, due to the difficult nature of the problem, we may have to accept certain aspects of Eulemur interrelationships as uncertain.     

Flatworm phylogeny from partial 18S rDNA sequences

Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved. This revised version was published online in July 2006 with corrections to the Cover Date.     

ANOTHER MONOPHYLY INDEX: REVISITING THE JACKKNIFE

Abstract — Randomization routines have quickly gained wide usage in phylogenetic systematies. Introduced a decade ago, the jackknife has rarely been applied in cladistic methodology. This data resampling technique was re-investigated here as a means to discover the effect that taxon removal may have on the stability of the results obtained from parsimony analyses. This study shows that the removal of even a single taxon in an analysis can cause a solution of relatively few multiple equally parsimonious trees in an inclusive matrix to result in hundreds of equally parsimonious trees with the single removal of a taxon. On the other hand, removal of other taxa can stabilize the results to fewer trees. An index of clade stability, the Jackknife Monophyly Index (JMI) is developed which, like the bootstrap, applies a value to each clade according to its frequency of occurrence in jackknife pseudoreplicates. Unlike the bootstrap and earlier application of the jackknife, alternative suboptimal hypotheses are not forwarded by this method. Only those clades in the most parsimonious tree(s) are given JMI values. The behaviour of this index is investigated both in relation to a hypothetical and a real data set, as well as how it performs in comparison to the bootstrap. The JMI is found to not be influenced by uninformative characters or relative synapomorphy number, unlike the bootstrap.     

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach

Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). These data were analyzed in a complete 66-taxon matrix and 91-taxon supermatrix that included some missing data. Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e., Clavicipitaceae clade A, B, and C), whereas the tree obtained from mtATP6 is in strong conflict with the monophyly of Clavicipitaceae clade B and the sister-group relationship of Hypocreaceae and Clavicipitaceae clade C. The distribution of relative contribution of nodal support for each gene partition was assessed using both partitioned Bremer support (PBS) values and combinational bootstrap (CB) analyses, the latter of which analyzed bootstrap proportions from all possible combinations of the seven gene partitions. These results suggest that CB analyses provide a more consistent estimate of nodal support than PBS and that combining heterogeneous gene partitions, which individually support a limited number of nodes, results in increased support for overall tree topology. Analyses of the 91-taxa supermatrix data sets revealed that some nodes were more strongly supported by increased taxon sampling. Identifying the localized incongruence of mtATP6 and analyses of complete and supermatrix data sets strengthen the evidence for rejecting the monophyly of Clavicipitaceae and much of the current subfamilial classification of the family. Although the monophyly of the grass-associated subfamily Clavicipitoideae (e.g., Claviceps, Balansia, and Epichlo?) is strongly supported, the subfamily Cordycipitoideae (e.g., Cordyceps and Torrubiella) is not monophyletic. In particular, species of the genus Cordyceps, which are pathogens of arthropods and truffles, are found in all three clavicipitaceous clades. These results imply that most characters used in the current familial classification of Clavicipitaceae are not diagnostic of monophyly.