Branch support via resampling: an empirical study

The success of resampling approaches to branch support depends on the effectiveness of the underlying tree searches. Two primary factors are identified as key: the depth of tree search and the number of trees saved per resampling replicate. Two datasets were explored for a range of search parameters using jackknifing. Greater depth of tree search tends to increase support values because shorter trees conflict less with each other, while increasing numbers of trees saved tends to reduce support values because of conflict that reduces structure in the replicate consensus. Although a relatively small amount of branch swapping will achieve near‐accurate values for a majority of clades, some clades do not yield accurate values until more extensive searches are performed. This means that in order to maximize the accuracy of resampling analyses, one should employ as extensive a search strategy as possible, and save as many trees per replicate as possible. Strict consensus summary of resampling replicates is preferable to frequency‐within‐replicates summary because it is a more conservative approach to the reporting of replicate results. Jackknife analysis is preferable to bootstrap because of its closer relationship to the original data.© The Willi Hennig Society 2010.     

Spurious 99% bootstrap and jackknife support for unsupported clades

Quantifying branch support using the bootstrap and/or jackknife is generally considered to be an essential component of rigorous parsimony and maximum likelihood phylogenetic analyses. Previous authors have described how application of the frequency-within-replicates approach to treating multiple equally optimal trees found in a given bootstrap pseudoreplicate can provide apparent support for otherwise unsupported clades. We demonstrate how a similar problem may occur when a non-representative subset of equally optimal trees are held per pseudoreplicate, which we term the undersampling-within-replicates artifact. We illustrate the frequency-within-replicates and undersampling-within-replicates bootstrap and jackknife artifacts using both contrived and empirical examples, demonstrate that the artifacts can occur in both parsimony and likelihood analyses, and show that the artifacts occur in outputs from multiple different phylogenetic-inference programs. Based on our results, we make the following five recommendations, which are particularly relevant to supermatrix analyses, but apply to all phylogenetic analyses. First, when two or more optimal trees are found in a given pseudoreplicate they should be summarized using the strict-consensus rather than frequency-within-replicates approach. Second jackknife resampling should be used rather than bootstrap resampling. Third, multiple tree searches while holding multiple trees per search should be conducted in each pseudoreplicate rather than conducting only a single search and holding only a single tree. Fourth, branches with a minimum possible optimized length of zero should be collapsed within each tree search rather than collapsing branches only if their maximum possible optimized length is zero. Fifth, resampling values should be mapped onto the strict consensus of all optimal trees found rather than simply presenting the ≥ 50% bootstrap or jackknife tree or mapping the resampling values onto a single optimal tree.     

Phylogenetic relationships in Epidendroideae (Orchidaceae), one of the great flowering plant radiations: progressive specialization and diversification

Background and Aims The largest subfamily of orchids, Epidendroideae, represents one of the most significant diversifications among flowering plants in terms of pollination strategy, vegetative adaptation and number of species. Although many groups in the subfamily have been resolved, significant relationships in the tree remain unclear, limiting conclusions about diversification and creating uncertainty in the classification. This study brings together DNA sequences from nuclear, plastid and mitochrondrial genomes in order to clarify relationships, to test associations of key characters with diversification and to improve the classification.Methods Sequences from seven loci were concatenated in a supermatrix analysis for 312 genera representing most of epidendroid diversity. Maximum-likelihood and parsimony analyses were performed on this matrix and on subsets of the data to generate trees and to investigate the effect of missing values. Statistical character-associated diversification analyses were performed.Key Results Likelihood and parsimony analyses yielded highly resolved trees that are in strong agreement and show significant support for many key clades. Many previously proposed relationships among tribes and subtribes are supported, and some new relationships are revealed. Analyses of subsets of the data suggest that the relatively high number of missing data for the full analysis is not problematic. Diversification analyses show that epiphytism is most strongly associated with diversification among epidendroids, followed by expansion into the New World and anther characters that are involved with pollinator specificity, namely early anther inflexion, cellular pollinium stalks and the superposed pollinium arrangement.Conclusions All tested characters show significant association with speciation in Epidendroideae, suggesting that no single character accounts for the success of this group. Rather, it appears that a succession of key features appeared that have contributed to diversification, sometimes in parallel.     

The Relationship between the Number of Loci and the Statistical Support for the Topology of UPGMA Trees Obtained from Genetic Distance Data

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28: 579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35: 1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.     

Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability.     

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.      

Using jackknife methods for estimating the parameter in dilution series

Dilution assays are quantal dose-response assays that detect a positive or negative response in each individual culture within groups of replicate cultures that vary in the dose of cells/organisms tested. We propose three jackknife versions of the maximum likelihood estimator of the unknown parameter, i.e., the frequency of a well-defined cell within the context of limiting dilution assays or the density of organisms within the context of serial dilution assays. The methods have been evaluated with artificial data from extensive Monte Carlo experiments. As a result of these experiments and theoretical considerations, the jackknife version based on deleting one individual culture at a time is proposed as the statistical procedure of choice. The next best method is the jackknife version based on leaving out the same replicate from each of the culture groups at a time.     

Phylogeny of subfamily Epidendroideae (Orchidaceae) inferred from ndhF chloroplast gene sequences

This project undertakes the first molecular-based phylogenetic study of subfamily Epidendroideae (Orchidaceae). Approximately 1200 nucleotides (from the 3' half of the chloroplast gene ndhF for 34 orchid taxa and a lilioid monocot, Clivia miniata (Amaryllidaceae), were subjected to phylogenetic analysis using parsimony and maximum likelihood methods. Oryza sativa (Poaceae), a nonlilioid monocot, was designated as outgroup. Trees from both parsimony and maximum likelihood methods suggest that subfamily Epidendroideae is monophyletic, with Listera (Neottieae) as sister. Although subtribal relationships are typically well resolved and have strong branch support, intertribal relationships are generally poorly resolved. Perhaps this general lack of resolution among tribes reflects a rapid species radiation that coincided with anatomical, physiological, and anatomical adaptations that initiated large-scale epiphytism in the ancestral Epidendroideae. Six taxa in this study exhibit deletions that are not evenly divisible by three and result in extensive sequence frameshifts. For example, one deletion is 227 bp in length and is flanked by the short direct repeat sequence; TCAATAGGAATTTCTTTT. Multiple deletions and frameshifts suggest that ndhF may be a pseudogene, in at least some orchid taxa.     

The internal phylogeny of ants (Hymenoptera: Formicidae)

Abstract. The higher phylogeny of the Formicidae was analysed using 68 characters and 19 taxa: the 14 currently recognized ant subfamilies plus 5 potentially critical infrasubfamilial taxa. The results justified the recognition of 3 additional subfamilies: Aenictogitoninae Ashmead (new status), Apomyrminae Dlussky & Fedoseeva (new status), and Leptanilloidinae Bolton (new subfamily). A second analysis on these better delimited 17 subfamilies resulted in 24 equally most parsimonious trees. All trees showed a basal division of extant Formicidae into two groups, the first containing (Myrmicinae, Pseudomyrmecinae, Nothomyrmeciinae, Myrmeciinae, Formicinae, Dolichoderinae, Aneuretinae) and the second the remaining subfamilies. Clades appearing within these groups included the Cerapachyinae plus 'army ants', the Nothomyrmeciinae plus Myrmeciinae, the 'formicoid' subfamilies (Aneuretinae + Dolichoderinae + Formicinae), and the Old World army ants (Aenictinae + Aenictogitoninae + Doryline), but relationships within the last two groups were not resolved, and the relative positions of the Apomyrminae, Leptanillinae and Ponerinae remained ambiguous. Moreover, a bootstrap analysis produced a consensus tree in which all branches were represented in proportions much lower than 95%. A reconstruction of the ground plan of the Formicidae indicated that the most specialized of all recent ants are the members of the subfamily Dorylinae and the least specialized ones are the monotypic Apomyrminae.     

What does morphology tell us about orchid relationships?—a cladistic analysis

A cladistic analysis of Orchidaceae was undertaken for 98 genera using 71 morphological apomorphies based on a reconsideration of previous character analyses and newly discovered variation. The equally weighted analysis found 60 000 most parsimonious trees with low consistency (CI = 0.29) but high retention (RI = 0.83). The strict consensus reveals a significant amount of structure, and most traditionally recognized subfamilies are supported as monophyletic, including the Apostasioideae, Cypripedioideae, Spiranthoideae, and Epidendroideae. Orchidoideae in the broad sense are paraphyletic, giving rise to spiranthoids. Vanilloids are sister to epidendroids, although exhibiting several states otherwise found only in clearly basal groups, such as Apostasioideae. The nonvandoid epidendroids are poorly resolved, due to a high degree of homoplasy. The vandoids appear to be monophyletic, contrary to recent molecular evidence, possibly due to repeated parallel development of the vandoid character suite. The importance of vegetative characters as evidence putatively independent from floral features is demonstrated in the placement of Tropidia. Implied weighting analysis of these data resulted in similar patterns at high levels, although the Orchidoideae and Spiranthoideae may each be monophyletic and the nonvandoid epidendroids are more resolved. The high degree of structure implied in previous orchid classifications must be reconsidered, given the poor resolution at lower levels in the present trees.     

Phylogeny and feeding trait evolution of the mega‐diverse Gelechioidea (Lepidoptera: Obtectomera): new insight from 19 nuclear genes

The Gelechioidea (>18 000 species), one of the largest superfamilies of Lepidoptera, are a major element of terrestrial ecosystems and include important pests and biological model species. Despite much recent progress, our understanding of the classification, phylogeny and evolution of Gelechioidea remains limited. Building on recent molecular studies of this superfamily and a recently revised family/subfamily classification, we provide an independent estimate of among‐family relationships, with little overlap in gene sample. We analysed up to five nuclear genes, totalling 6633 bp, for each of 77 gelechioids, plus up to 14 additional genes, for a total of 14 826 bp, in 45 of those taxa and all 19 outgroup taxa. Our maximum‐likelihood (ML) analyses, like those of previous authors, strongly support monophyly for most multiply‐sampled families and subfamilies, but very weakly support most relationships above the family level. Our tree looks superficially divergent from that of the most recent molecular study of gelechioids, but when the previous tree is re‐rooted to accord maximally with ours, the two phylogenies agree entirely on the deepest‐level divergences in Gelechioidea, and strongly though incompletely on among‐family relationships within the major groups. This concordance between independent studies is evidence that the groupings (or at least the unrooted branching order) are probably accurate, despite the low bootstrap values. After re‐rooting, both trees divide the families into three monophyletic groups: a ‘Gelechiid Assemblage,’ consisting of Gelechiidae and Cosmopterigidae; a ‘Scythridid Assemblage,’ consisting of Stathmopodidae, Scythrididae, Blastobasidae, Elachistidae, Momphidae, Coleophoridae and Batrachedridae; and a ‘Depressariid Assemblage,’ consisting of Autostichidae, Xyloryctidae, Lecithoceridae, Oecophoridae, Depressariidae and Lypusidae. Within the largest family, Gelechiidae, our results strongly support the pairing of Anomologinae with Gelechiinae, in accordance with a recent study of this family. Relationships among the other subfamilies, however, conflict moderately to strongly between studies, leaving the intrafamily phylogeny unsettled. Within the ‘Scythridid Assemblage,’ both trees support an ‘SSB clade’ consisting of Blastobasidae + (Scythrididae + Stathmopodidae), strongly resolved only in our results. Coleophoridae + Batrachedridae is supported, albeit weakly, in both trees, and only Momphidae differ in position between studies. Within the ‘Depressariid Assemblage,’ both trees support an ‘AXLO’ clade consisting of Autostichidae, Xyloryctidae, Lecithoceridae and Oecophoridae. The monophyly of this clade and relationships therein are supported weakly in previous results but strongly in ours. The recently re‐defined family Depressariidae is paraphyletic in our tree, but the evidence against depressariid monophyly is very weak. There is moderate support for a core group of Depressariidae consisting, among the seven subfamilies we sampled, of Depressariinae, Aeolanthinae and Hypertrophinae. We show that gelechioids have a higher total number and percentage of species that are saprophagous as larvae than any other apoditrysian superfamily, that saprophagy is concentrated primarily in the ‘AXLO clade,’ and that the ancestral gelechioid condition was probably feeding on live plants. Among the living‐plant feeders, concealed external feeding was probably the ancestral state. The multiple origins of internal feeding of various kinds, including leaf mining (otherwise almost unknown in Apoditrysia), are restricted mostly to the Scythridid and Gelechiid Assemblages. The traits that predispose or permit lineages to adopt these unusual life histories are worthy of study.     

Phylogeny of snout butterflies (Lepidoptera: Nymphalidae: Libytheinae): combining evidence from the morphology of extant, fossil, and recently extinct taxa

Snout butterflies (Nymphalidae: Libytheinae) are morphologically one of the most unusual groups of Lepidoptera. Relationships among libytheines remain uncertain, especially in the placement of the recently extinct Libythea cinyras and two fossils, L. florissanti , and L. vagabunda . The aim of this study is to present the first phylogenetic hypothesis of Libytheinae utilizing all available morphological data from extant and extinct species. Forty-three parsimony-informative characters were coded, and the all-taxa analysis resulted in six most parsimonious trees (length 92 steps, CI = 0.66, RI = 0.82). The subfamily was resolved as monophyletic and was split into Old World and New World clades. Inclusion of extinct species with considerable missing data had little effect on relationships of extant taxa, although Bremer support values and jackknife frequencies generally decreased if extinct species were included. In order to preserve the monophyly of extant genera, two fossils are assigned to Libytheana for the first time ( L. florissanti comb. n. and L. vagabunda comb. n.). This study demonstrates the value of morphological data in phylogenetic analysis, and highlights the contribution that can be made by scoring extinct taxa and including them directly into the analysis.     

The ecological tale of Gonyleptidae (Arachnida,Opiliones) evolution: phylogeny of a Neotropical lineage of armoured harvestmen using ecological,behavioural and chemical characters

The large Neotropical family Gonyleptidae comprises nearly 820 species divided into 16 subfamilies. The majority of publications on harvestman ecology, behaviour and scent gland secretion chemistry have focused on this family. We used the information available in the literature and combined it with an intensive search for ecological, behavioural and chemical data to infer the phylogeny of the Gonyleptidae. We included 28 species belonging to 14 of the 16 gonyleptid subfamilies in the ingroup and four species belonging to the families Cosmetidae, Stygnidae and Manaosbiidae in the outgroup. We performed the analyses using equally weighted characters and coded 63 characters comprising 153 states, which makes this the largest non‐morphological, non‐molecular phylogenetic data matrix published to date. We obtained five most parsimonious trees, and the strict consensus resulted in six collapsed nodes. The results show that the monophyly of Gonyleptidae is equivocal because Metasarcinae is placed at a basal polytomy with the outgroups Cosmetidae and Stygnidae. Gonyleptinae, Pachylinae and Progonyleptoidellinae are polyphyletic groups, but the remaining subfamilies are monophyletic and have several synapomorphies. Based on the resulting topology, we discuss the performance of ecological, behavioural and chemical characters, and map a selected set of characters to discuss their evolutionary patterns in the family.     

Pollinium development and number in the Orchidaceae

Development of anthers in three subfamilies of Orchidaceae was studied anatomically to examine homology hypotheses for pollinium number characters and to produce a model of pollinium development for the family. Serial sections of plastic-embedded embryonic inflorescences revealed that anther primordia were either flattened or ovoid; subsequent expansion of thecae and their inward (adaxial) reorientation (“rotation”), achieved by differential cell division and elongation in the connective, result in a mature anther with strongly introrse morphology and pollinia oriented side by side (juxtaposed). Strongly introrse anthers occur in at least some members of all subfamilies and are probably the basal state for the family. All anthers examined (from Orchidoideae, Spiranthoideae, and Epidendroideae) showed a single meristematic region, which would later give rise to pollen, per theca at earliest stages; septation of each of these regions resulted in four or eight pollinia per anther, while lack of septation in some members of the Epidendroideae gave two pollinia. In contrast, the two bipartite pollinia found in many Spiranthoideae and Orchidoideae were produced by adherence of the contents of two locules at a late ontogenetic stage, and should be recognized as a distinct character state. Eight pollinia result from partitioning by two longitudinal septa or a longitudinal and a transverse septum; these two morphologies may also represent separate character states.     

Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: Braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage

The microgastroid complex of braconid wasps is a widely recognized and biologically coherent lineage of endoparasitoids of lepidopteran larvae (caterpillars). The complex has received significant phylogenetic attention in recent years due in part to the taxons' association with mutualistic polydnaviruses, with which they compromise host immune systems. A number of previous attempts using a variety of morphological and molecular approaches have not unequivocally resolved relationships amongst the main subfamilies. This work represents a more extensive attempt to resolve the microgastroid relationships, using seven genes (16S rRNA, cytochrome oxidase I (CO1), 28S rRNA, arginine kinase (ArgK), long wavelength rhodopsin (Ops), elongation factor 1 alpha (EF1a) and wingless (Wg)) and a greater taxonomic representation. Bayesian, likelihood and parsimony phylogenetic reconstructions of this improved data set has determined that the chelonines diverged first from the remainder of the microgastroids, however the relationships amongst the other subfamilies are still unclear, suggesting a greater nucleotide sample is required to resolve them. Examination of the contribution of individual gene trees to the phylogeny demonstrates why the relationships between subfamilies are still unclear, with not all groups monophyletic for all trees. Filtered supernetworks demonstrate that monophyly of all subfamilies is only recovered when splits found in only one or two genes are excluded, but this also results in little remaining structure left in the deep nodes to resolve inter-subfamily relationships. By increasing the breadth of the study we were also able to re-evaluate previous attempts at dating the lineage and, therefore the origin of the polydnavirus association. Previous attempts used a much reduced data set and fewer fossil calibrations. Thorough literature searches have revealed a substantial increase in the fossil calibrations and these, combined with more sophisticated molecular dating analysis, have substantially increased the age of the microgastroid lineage from previous estimates of approximately 73MYA to approximately 100MYA. Examination of the resultant linearized clock tree also allows an insight into the evolution of the more species rich subfamilies. The chelonines appear to have had a steady rate of evolution, whilst the microgastrines and cardiochilines appear to have undergone a more significant "burst" of evolution. It is hypothesized that the different parasitism strategies of subfamilies (Chelonines are egg parasitoids and the remainder are larval parasitioids) may have influenced the evolutionary rates of the groups.     

Chromosomal phylogeny of Robertsonian races of the house mouse on the island of Madeira: testing between alternative mutational processes

The ancestral karyotype of the house mouse (Mus musculus) consists of 40 acrocentric chromosomes, but numerous races exist within the domesticus subspecies characterized by different metacentric chromosomes formed by the joining at the centromere of two acrocentrics. An exemplary case is present on the island of Madeira where six highly divergent chromosomal races have accumulated different combinations of 20 metacentrics in 500-1000 years. Chromosomal cladistic phylogenies were performed to test the relative performance of Robertsonian (Rb) fusions, Rb fissions and whole-arm reciprocal translocations (WARTs) in resolving relationships between the chromosomal races. The different trees yielded roughly similar topologies, but varied in the number of steps and branch support. The analyses using Rb fusions/fissions as characters resulted in poorly supported trees requiring six to eight homoplasious events. Allowance for WARTs considerably increased nodal support and yielded the most parsimonious trees since homoplasy was reduced to a single event. The WART-based trees required five to nine WARTs and 12 to 16 Rb fusions. These analyses provide support for the role of WARTs in generating the extensive chromosomal diversification observed in house mice. The repeated occurrence of Rb fusions and WARTs highlights the contribution of centromere-related rearrangements to accelerated rates of chromosomal change in the house mouse.     

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.     

Phylogenetic relationships within the Eurasian cattish family Siluridae (Pisces: Siluriformes), with comments on generic validities and biogeography

A numerical cladistic analysis, based on 23 terminal groups and 63 morphological characters, was done to infer phylogenetic relationships within the Eurasian catfish family Siluridae. Nine hundred and forty-five equally most parsimonious trees (134 steps, consistency index 0.634) were found that differ in their resolutions of four polychotomies. Strict consensus of these trees includes ten internal nodes, does not support monophyly of Silurus, Ompok and Kryptopterus , as usually defined, and offers ambiguous support for monophyly of Wallago. Silurus and Kryptopterus are each composed of two non-sister group clades, and Ompok is composed of at least two such clades. Heuristic searches constrained by monophyly of Silurus, Ompok or Kryptopterus yielded trees five or six steps longer than the shortest trees free of constraints. The strict consensus also infers a basal dichotomy that separates the Siluridae into a temperate Eurasian clade with about 20 nominal species and a subtropical/tropical south and southeast Asian clade with about 75 nominal species. The distributions of these clades overlap in a relatively narrow region of east Asia. A heuristic search for trees 1 step longer than the shortest trees yielded 253890 trees. A strict consensus of these trees also infers a basal dichotomy between the above-mentioned clades. This analysis revealed four additional putative synapomorphies of the Siluridae, pending further resolution of the family's outgroup relationships.