Search

A phylogenetic graph search relies on a large number of highly parameterized search procedures (e.g. branch-swapping, perturbation, simulated annealing, genetic algorithm). These procedures vary in effectiveness over datasets and at alternative points in analytical pipelines. The multi-armed bandit problem is applied to phylogenetic graph searching to more effectively utilize these procedures. Thompson sampling is applied to a collection of search and optimization "bandits" to favour productive search strategies over those that are less successful. This adaptive random sampling strategy is shown to be more effective in producing heuristically optimal phylogenetic graphs and more time efficient than existing uniform probability randomized search strategies. The strategy acts as a form of unsupervised machine learning that can be applied to a diversity of phylogenetic datasets without prior knowledge of their properties., (© 2024 Willi Hennig Society.)

We present Phylogenetic Graph (PhyG), an open-source, phylogenetic search tool for diverse data types and graphs, including softwired and hardwired networks, in addition to trees. This allows for analysis of horizontal transfer and hybridization scenarios, as well as the necessary vertical inheritance of trees. PhyG is the successor to POY5 in performing combined data tree-alignment with enhancements in heuristic optimality (up to 7% in example data) and execution time (up to a factor of 200). Input data may exhibit a practically unlimited number of character states in qualitative or sequence (aligned and unaligned) types. Novel graph construction and refinement algorithms have been implemented and integrated into a variety of search procedures. Currently, PhyG implements parsimony and No-Common-Mechanism Likelihood optimization., (© 2023 Willi Hennig Society.)

An algorithm is described for the optimization of character data (e.g. qualitative, nucleic acid sequence) on softwired phylogenetic networks. The algorithm presented here is an extension of those developed for trees under the parsimony criterion and can form the basis for phylogenetic network search procedures. Although the problem is (in general) an NP-Hard optimization, the resolution-based algorithm we describe here capitalizes on the significant amount of shared structure in sub-graphs containing network edges, reducing the execution time and allowing for the analysis of empirical datasets., (© 2023 Willi Hennig Society.)

Phylogenetic graph structures used in empirical and theoretical analysis have expanded beyond trees to more general directed acyclic graphs including networks and forests. Several methods to reconcile multiple such graphs are presented and discussed here, extending existing consensus and supertree techniques to form a set of phylogenetic supergraph methods. These graphs can be used as the summary of analytical results, or as heuristic initial graphs for further phylogenetic analysis., (© 2021 Willi Hennig Society.)

The distance Wagner procedure of Farris (American Naturalist, 1972, 106, 645), in its original or random addition sequence form, is a rapid method of tree construction. The original formulation did not allow for refinement of tree hypotheses via common trajectory search operations (e.g. SPR, TBR). Here, the distance Wagner method is extended to allow for refinement of initial trees produced via the four-point condition (Mathematics and the Archeological and Historical Sciences, Edinburgh University Press, Edinburgh, 1974). The performance of the extended distance Wagner as a heuristic search procedure is evaluated with several unaligned sequences and combined source datasets within the parsimony framework. Distance Wagner both with and without refinement is shown to be a rapid and useful heuristic method to generate initial trees for further, character-based, analysis., (© 2021 Willi Hennig Society.)

The relationships of the hyline tribe Dendropsophini remain poorly studied, with most published analyses dealing with few of the species groups of Dendropsophus. In order to test the monophyly of Dendropsophini, its genera, and the species groups currently recognized in Dendropsophus, we performed a total evidence phylogenetic analysis. The molecular dataset included sequences of three mitochondrial and five nuclear genes from 210 terminals, including 12 outgroup species, the two species of Xenohyla, and 93 of the 108 recognized species of Dendropsophus. The phenomic dataset includes 46 terminals, one per species (34 Dendropsophus, one Xenohyla, and 11 outgroup species). Our results corroborate the monophyly of Dendropsophini and the reciprocal monophyly of Dendropsophus and Xenohyla. Some species groups of Dendropsophus are paraphyletic (the D. microcephalus, D. minimus, and D. parviceps groups, and the D. rubicundulus clade). On the basis of our results, we recognize nine species groups; for three of them (D. leucophyllatus, D. microcephalus, and D. parviceps groups) we recognize some nominal clades to highlight specific morphology or relationships and facilitate species taxonomy. We further discuss the evolution of oviposition site selection, where our results show multiple instances of independent evolution of terrestrial egg clutches during the evolutionary history of Dendropsophus., (© The Willi Hennig Society 2020.)

The general problem of representing collections of trees as a single graph has led to many tree summary techniques. Many consensus approaches take sets of trees (either inferred as separate gene trees or gleaned from the posterior of a Bayesian analysis) and produce a single "best" tree. In scenarios where horizontal gene transfer or hybridization are suspected, networks may be preferred, which allow for nodes to have two parents, representing the fusion of lineages. One such construct is the cluster union network (CUN), which is constructed using the union of all clusters in the input trees. The CUN has a number of mathematically desirable properties, but can also present edges not observed in the input trees. In this paper we define a new network construction, the edge union network (EUN), which displays edges if and only if they are contained in the input trees. We also demonstrate that this object can be constructed with polynomial time complexity given arbitrary phylogenetic input trees, and so can be used in conjunction with network analysis techniques for further phylogenetic hypothesis testing., (© The Willi Hennig Society 2019.)

Here, we define a sequence file format that allows for multi-character elements (FASTC). The format is derived from the FASTA format and the custom alphabet format of POY4/5. The format is more general than either of these formats and can represent a broad variety of sequence-type data. This format should be useful for analyses involving datasets encoded as linear streams such as gene synteny, comparative linguistics, temporal gene expression and development, complex animal behaviours, and general biological time-series data., (© The Willi Hennig Society 2019.)

Phylogenetic methods offer a promising advance for the historical study of language and cultural relationships. Applications to date, however, have been hampered by traditional approaches dependent on unfalsifiable authority statements: in this regard, historical linguistics remains in a similar position to evolutionary biology prior to the cladistic revolution. Influential phylogenetic studies of Bantu languages over the last two decades, which provide the foundation for multiple analyses of Bantu sociocultural histories, are a major case in point. Comparative analyses of basic lexica, instead of directly treating written words, use only numerical symbols that express non-replicable authority opinion about underlying relationships. Building on a previous study of Uto-Aztecan, here we analyse Bantu language relationships with methods deriving from DNA sequence optimization algorithms, treating basic vocabulary as sequences of sounds. This yields finer-grained results that indicate major revisions to the Bantu tree, and enables more robust inferences about the history of Bantu language expansion and/or migration throughout sub-Saharan Africa. "Early-split" versus "late-split" hypotheses for East and West Bantu are tested, and overall results are compared to trees based on numerical reductions of vocabulary data. Reconstruction of language histories is more empirically based and robust than with previous methods., (© The Willi Hennig Society 2018.)

Heteroptera, the true bugs, are part of the largest clade of non-holometabolous insects, the Hemiptera, and include > 42 000 described species in about 90 families. Despite progress in resolving phylogenetic relationships between and within infraorders since the first combined morphological and molecular analysis published in 1993 (29 taxa, 669 bp, 31 morphological characters), recent hypotheses have relied entirely on molecular data. Weakly supported nodes along the backbone of Heteroptera made these published phylogenies unsuitable for investigations into the evolution of habitats and lifestyles across true bugs. Here we present the first combined morphological and molecular analyses of Heteroptera since 1993, using 135 taxa in 60 families, 4018 aligned bp of ribosomal DNA and 81 morphological characters, and various analytical approaches. The sister-group relationship of the predominantly aquatic Nepomorpha with all remaining Heteroptera is supported in all analyses, and a clade formed by Enicocephalomorpha, Dipsocoromorpha and Gerromorpha in some. All analyses recover Leptopodomorpha + (Cimicomorpha + Pentatomomorpha), mostly with high support. Parsimony- and likelihood-based ancestral state reconstructions of habitats and lifestyles on the combined likelihood phylogeny provide new insights into the evolution of true bugs. The results indicate that aquatic and semi-aquatic true bugs invaded these habitats three times independently from terrestrial habitats in contrast to a recent hypothesis. They further suggest that the most recent common ancestor of Heteroptera was predacious, and that the two large predominantly phytophagous clades (Trichophora and Miroidea) are likely to have derived independently from predatory ancestors. We conclude that by combining morphological and molecular data and employing various analytical methods our analyses have converged on a relatively well-supported hypothesis of heteropteran infraordinal relationships that now requires further testing using phylogenomic and more extensive morphological datasets., (© The Willi Hennig Society 2018.)

We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the "ctenids" Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae., (© The Willi Hennig Society 2016.)

A new practice in systematics, "semaphoront" coding, treats developmental stages as terminals, and it derives from Hennig's concept of the same name. Semaphoront coding has been implemented recently by Lamsdell and Selden (BMC Evol. Biol., 2013, 13:98) and Wolfe and Hegna (Cladistics, 2014, 30:366) in an effort to understand the relationships of fossil taxa of unknown developmental stage. We submit that this approach is antithetical to cladistic practice and constitutes a gross misunderstanding of Hennig's original idea. Here we review the concept of the semaphoront and clarify the role of the semaphoront in phylogenetic systematics. We contend that treating ontogenetic stages as terminals both violates tenets of phylogenetic systematics and oversimplifies the complexity of developmental processes. We advocate Hennig's alternative of including data from as many semaphoronts as possible, but implemented using the superior total evidence framework. Finally, we contend that the application of semaphoront coding to any palaeontological question requires invoking multiple, unjustified assumptions, and ultimately will not yield a possible phylogenetic solution. A total evidence approach can grapple with the placement of fossil developmental stages, if only imperfectly., (© The Willi Hennig Society 2016.)

Two commonly used heuristic approaches to the generalized tree alignment problem are compared in the context of phylogenetic analysis of DNA sequence data. These approaches, multiple sequence alignment + phylogenetic tree reconstruction (MSA+TR) and direct optimization (DO), are alternative heuristic procedures used to approach the nested NP-Hard optimizations presented by the phylogenetic analysis of unaligned sequences under maximum parsimony. Multiple MSA+TR implementations and DO were compared in terms of optimality score (phylogenetic tree cost) over multiple empirical and simulated datasets with differing levels of heuristic intensity. In all cases examined, DO outperformed MSA+TR with average improvement in parsimony score of 14.78% (5.64-52.59%)., (© The Willi Hennig Society 2015.)

Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for up to 142 taxa) to tackle this problem. We assess the effects of character sampling, taxon sampling, analytical methods and assumptions in phylogenetic inference of microhylid frogs. The phylogeny of microhylids shows high susceptibility to different analytical methods and datasets used for the analyses. Clades inferred from maximum-likelihood are generally more stable across datasets than those inferred from parsimony. Parsimony trees inferred within a tree-alignment framework are generally better resolved and better supported than those inferred within a similarity-alignment framework, even under the same cost matrix (equally weighted) and same treatment of gaps (as a fifth nucleotide state). We discuss potential causes for these differences in resolution and clade stability among discovery operations. We also highlight the problem that commonly used algorithms for model-based analyses do not explicitly model insertion and deletion events (i.e. gaps are treated as missing data). Our results corroborate the monophyly of Microhylidae and most currently recognized subfamilies but fail to provide support for relationships among subfamilies. Several taxonomic updates are provided, including naming of two new subfamilies, both monotypic., (© The Willi Hennig Society 2015.)

Ants that resemble Camponotus maculatus (Fabricius, 1782) present an opportunity to test the hypothesis that the origin of the Pacific island fauna was primarily New Guinea, the Philippines, and the Indo-Malay archipelago (collectively known as Malesia). We sequenced two mitochondrial and four nuclear markers from 146 specimens from Pacific islands, Australia, and Malesia. We also added 211 specimens representing a larger worldwide sample and performed a series of phylogenetic analyses and ancestral area reconstructions. Results indicate that the Pacific members of this group comprise several robust clades that have distinctly different biogeographical histories, and they suggest an important role for Australia as a source of Pacific colonizations. Malesian areas were recovered mostly in derived positions, and one lineage appears to be Neotropical. Phylogenetic hypotheses indicate that the orange, pan-Pacific form commonly identified as C. chloroticus Emery 1897 actually consists of two distantly related lineages. Also, the lineage on Hawai'i, which has been called C. variegatus (Smith, 1858), appears to be closely related to C. tortuganus Emery, 1895 in Florida and other lineages in the New World. In Micronesia and Polynesia the C. chloroticus-like species support predictions of the taxon-cycle hypothesis and could be candidates for human-mediated dispersal., (© The Willi Hennig Society 2014.)

We present POY version 5, an open source program for the phylogenetic analysis of diverse data types including qualitative, aligned sequences, unaligned sequences, genomic data, and user-defined sequences. In addition to the maximum-parsimony optimality criterion supported by POY4, POY5 supports several types of maximum likelihood as well as posterior probability. To make these analyses feasible, new heuristic search algorithms and parallelization options have been implemented for all criteria., (© The Willi Hennig Society 2014.)

Language origins and diversification are vital for mapping human history. Traditionally, the reconstruction of language trees has been based on cognate forms among related languages, with ancestral protolanguages inferred by individual investigators. Disagreement among competing authorities is typically extensive, without empirical grounds for resolving alternative hypotheses. Here, we apply analytical methods derived from DNA sequence optimization algorithms to Uto-Aztecan languages, treating words as sequences of sounds. Our analysis yields novel relationships and suggests a resolution to current conflicts about the Proto-Uto-Aztecan homeland. The techniques used for Uto-Aztecan are applicable to written and unwritten languages, and should enable more empirically robust hypotheses of language relationships, language histories, and linguistic evolution., (© The Willi Hennig Society 2014.)

One of the most time-consuming aspects of Bayesian posterior probability analysis in the analysis of phylogenetic trees is the use of Metropolis-coupled Markov chain Monte Carlo (MC 3 ) methods to determine relative posteriors and identify maximum a posteriori (MAP) trees. Here, analytical and numerical methods are presented to determine tree likelihoods that are integrated over edge-length (and other parameter) distributions. Given topological (tree) priors (flat or otherwise), this allows for identification of the maximum posterior probability assignment (MAP-A) of character states to non-leaf tree vertices via dynamic programming. Using this form of posterior probability as an optimality criterion, tree space can be searched using standard trajectory techniques and heuristically optimal MAP-A trees can be identified with considerable time savings over MC 3 . Example cases are presented using aligned and unaligned molecular sequences as well as combined molecular and anatomical data., (© The Willi Hennig Society 2013.)

The frog clade composed of the alsodid genera Alsodes + Eupsophus is the most species-rich of the Patagonian endemic frog clades, including nearly 31 of the slightly more than 50 species of that region. The biology of this group of frogs is poorly known, its taxonomy quite complex (particularly Alsodes), and its diversity in chromosome number striking when compared with other frogs (collectively, there are species having 2n = 22, 2n = 26, 2n = 28, 2n = 30 or 2n = 34). We present a phylogenetic analysis of this Patagonian frog clade based on mitochondrial and nuclear gene sequences. We sequenced five mitochondrial genes (cytochrome b, cytochrome oxidase I, 12S, 16S, NADH dehydrogenase subunit 1) with three intervening tRNAs, and fragments of three nuclear genes (seven in absentia homolog 1, rhodopsin exon 1, RAG-1), for a maximum of 6510 bp for multiple specimens from 26 of the 31 species. We recovered Eupsophus as polyphyletic, with E. antartandicus, E. sylvaticus, and E. taeniatus in Batrachylidae, in accordance with most previous hypotheses. Based on this result, we transfer E. antartandicus and E. taeniatus back to Batrachyla, and E. sylvaticus to Hylorina (resurrected from the synonymy of Eupsophus), remediating the paraphyly of Eupsophus. Our results strongly corroborate the monophyly of Alsodes + Eupsophus (sensu stricto), the individual monophyly of these genera, and the monophyly of the species groups of Eupsophus. They also show the non-monophyly of all non-monotypic species groups of Alsodes proposed in the past. Our results expose several taxonomic problems particularly in Alsodes, and to a lesser extent in Eupsophus. This phylogenetic context suggests a rich evolutionary history of karyotypic diversification in the clade, in part corroborating previous hypotheses. In Alsodes, we predict three independent transformations of chromosome number from the plesiomorphic 2n = 26. All these, strikingly, involve increments or reductions of pairs of haploid chromosomes. Finally, the phylogenetic pattern recovered for Alsodes and Eupsophus suggests a trans-Andean origin and diversification of the group, with multiple, independent ingressions over cis-Andean regions., (© The Willi Hennig Society 2012.)

Although there has been a recent proliferation in maximum-likelihood (ML)-based tree estimation methods based on a fixed sequence alignment (MSA), little research has been done on incorporating indel information in this traditional framework. We show, using a simple model on a single character example, that a trivial alignment of a different form than that previously identified for parsimony is optimal in ML under standard assumptions treating indels as "missing" data, but that it is not optimal when indels are incorporated into the character alphabet. We show that the optimality of the trivial alignment is not an artefact of simplified theory assumptions by demonstrating that trivial alignment likelihoods of five different multiple sequence alignment datasets exhibit this phenomenon. These results demonstrate the need for use of indel information in likelihood analysis on fixed MSAs, and suggest that caution must be exercised when drawing conclusions from software implementations claiming improvements in likelihood scores under an indels-as-missing assumption. © The Willi Hennig Society 2012., (© The Willi Hennig Society 2012.)

Species of the genus Pleurodema are relatively small, plump frogs that mostly occur in strong-seasonal and dry environments. The genus currently comprises 14 species distributed from Panama to southern Patagonia. Here we present a phylogenetic analysis of Pleurodema, including all described species and several outgroups. Our goals include testing its monophyly and the monophyly of the species groups that were historically proposed, and studying the evolution of some character systems, particularly macroglands and egg-clutch structure; this last point also provided the chance for a discussion of foam nest evolution in anurans. Our dataset includes portions of the mitochondrial genes cytochromeb, 12S, 16S, and the intervening tRNA Val ; the nuclear gene sequences include portions of rhodopsin exon 1 and seven in absentia homolog I. Our results support a clade composed of Pleurodema and including the monotypic SomuncuriaLynch, 1978 nested within it. The latter genus is therefore considered a junior synonym of Pleurodema and its sole species is added to this genus. Furthermore, our results indicate the non-monophyly of several species groups proposed previously. We recognize four clades in Pleurodema: the P. bibroni clade (P. bibroni, P. cordobae and P. kriegi), the P. thaul clade (P. bufoninum, P. marmoratum, P. somuncurensis and P. thaul), the P. brachyops clade (P. alium, P. borellii, P. brachyops, P. cinereum, P. diplolister and P. tucumanum) and the P. nebulosum clade (P. guayapae and P. nebulosum). Our results further indicate the need for a taxonomic reassessment of P. borellii and P. cinereum (as did previous studies), P. guayapae and P. nebulosum, and the three species in the P. bibroni clade. Pleurodema shows a striking pattern of variation in presence/absence of lumbar glands. Our results indicate multiple losses or independent gains of this character associated with defensive displays. The reproductive modes of Pleurodema include four different egg-clutch structures. The optimization of these indicates that there are at least two independent transformations from the plesiomorphic mode of foam nests to egg-clutch structures involving gelatinous masses of different sorts (ovoid plates, masses, or strings). We hypothesize that these independent transformations could involve changes at the behavioural (the loss of foam beating behaviour by the parent) and/or structural level (transformations involving the pars convoluta dilata, the section of the oviduct where the foam-making substance is secreted). Finally, our study of foam nest evolution in Pleurodema is extended to the other groups of anurans where foam-nesting occurs, on the basis of available data and recent phylogenetic hypotheses. In the different hyloid groups where it occurs, foam-nesting evolved from clutches laid in water. However, in all ranoids in which foam-nesting occurs, it evolved from terrestrial clutches, with eggs laid hanging in vegetation, or, if the clutches are laid on a restricted volume of water, involving endotrophic development. © The Willi Hennig Society 2012., (© The Willi Hennig Society 2012.)

We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database. © The Willi Hennig Society 2012., (© The Willi Hennig Society 2012.)

The first comprehensive analysis of higher-level phylogeny of the order Hymenoptera is presented. The analysis includes representatives of all extant superfamilies, scored for 392 morphological characters, and sequence data for four loci (18S, 28S, COI and EF-1α). Including three outgroup taxa, 111 terminals were analyzed. Relationships within symphytans (sawflies) and Apocrita are mostly resolved. Well supported relationships include: Xyeloidea is monophyletic, Cephoidea is the sister group of Siricoidea + [Xiphydrioidea + (Orussoidea + Apocrita)]; Anaxyelidae is included in the Siricoidea, and together they are the sister group of Xiphydrioidea + (Orussoidea + Apocrita); Orussoidea is the sister group of Apocrita, Apocrita is monophyletic; Evanioidea is monophyletic; Aculeata is the sister group of Evanioidea; Proctotrupomorpha is monophyletic; Ichneumonoidea is the sister group of Proctotrupomorpha; Platygastroidea is sister group to Cynipoidea, and together they are sister group to the remaining Proctotrupomorpha; Proctotrupoidea s. str. is monophyletic; Mymarommatoidea is the sister group of Chalcidoidea; Mymarommatoidea + Chalcidoidea + Diaprioidea is monophyletic. Weakly supported relationships include: Stephanoidea is the sister group of the remaining Apocrita; Diaprioidea is monophyletic; Ceraphronoidea is the sister group of Megalyroidea, which together form the sister group of [Trigonaloidea (Aculeata + Evanioidea)]. Aside from paraphyly of Vespoidea within Aculeata, all currently recognized superfamilies are supported as monophyletic. The diapriid subfamily Ismarinae is raised to family status, Ismaridae stat. nov. © The Will Henning Society 2011., (© The Willi Hennig Society 2011.)

Novel pathogens have the potential to become critical issues of national security, public health and economic welfare. As demonstrated by the response to Severe Acute Respiratory Syndrome (SARS) and influenza, genomic sequencing has become an important method for diagnosing agents of infectious disease. Despite the value of genomic sequences in characterizing novel pathogens, raw data on their own do not provide the information needed by public health officials and researchers. One must integrate knowledge of the genomes of pathogens with host biology and geography to understand the etiology of epidemics. To these ends, we have created an application called Supramap (http://supramap.osu.edu) to put information on the spread of pathogens and key mutations across time, space and various hosts into a geographic information system (GIS). To build this application, we created a web service for integrated sequence alignment and phylogenetic analysis as well as methods to describe the tree, mutations, and host shifts in Keyhole Markup Language (KML). We apply the application to 239 sequences of the polymerase basic 2 (PB2) gene of recent isolates of avian influenza (H5N1). We map a mutation, glutamic acid to lysine at position 627 in the PB2 protein (E627K), in H5N1 influenza that allows for increased replication of the virus in mammals. We use a statistical test to support the hypothesis of a correlation of E627K mutations with avian-mammalian host shifts but reject the hypothesis that lineages with E627K are moving westward. Data, instructions for use, and visualizations are included as supplemental materials at: http://supramap.osu.edu/sm/supramap/publications. © The Willi Hennig Society 2010., (© The Willi Hennig Society 2010.)

The leaf or monkey frogs of the hylid subfamily Phyllomedusinae are a unique group of charismatic anurans. We present a molecular phylogenetic analysis that includes 45 of the 60 species of phyllomedusines using up to 12 genes and intervening tRNAs. The aims were to gain a better understanding of the phylogenetic position of Phrynomedusa, test the monophyly and explore the relationships among several putative lineages (Hylomantis, the H. buckleyi Group, Phasmahyla, the four species groups of Phyllomedusa, and the species of Phyllomedusa that remain unassigned to any group), and to examine the implications of our phylogeny for the evolution of several characters in phyllomedusines. The analyses resulted in a well-supported phylogenetic hypothesis that provides a historical framework for a discussion of the evolution of characters associated with reproductive biology, gliding behaviour, the physiology of waterproofing, and bioactive peptides. Implications include an earlier origin for eggless capsules than for leaf-folding behaviour during amplexus, two independent origins of gliding, and an earlier origin of reduction in evaporative water loss than uricotelism, which is a result that originally was predicted on the basis of physiology alone. Furthermore, our results support the prediction that bioactive peptides from different peptide families are to be expected in all species of Phyllomedusinae. Hylomantis (as recently redefined) is shown to be paraphyletic and the synonymy of Agalychnis is revised to remedy this problem by including both Hylomantis and Pachymedusa.  © The Willi Hennig Society 2009., (© The Willi Hennig Society 2009.)

We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data. POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance). Compared with previous versions, POY 4 provides greater flexibility, a larger number of supported parameter sets, numerous execution time improvements, a vastly improved user interface, greater quality control, and extensive documentation. We introduce POY's basic features, and present a simple example illustrating the performance improvements over previous versions of the application. © The Willi Hennig Society 2009., (© The Willi Hennig Society 2009.)

Phylogenetic relationships within the Pentatomoidea are investigated through the coding and analysis of character data derived from morphology and DNA sequences. In total, 135 terminal taxa were investigated, representing most of the major family groups; 84 ingroup taxa are coded for 57 characters in a morphological matrix. As many as 3500 bp of DNA data are adduced for each of 52 terminal taxa, including 44 ingroup taxa, comprising the 18S rRNA, 16S rRNA, 28S rRNA, and COI gene regions. Character data are analysed separately and in the form of a total evidence analysis. Major conclusions of the phylogenetic analysis include: the concept of Urostylididae is restricted to that of earlier authors; the Saileriolinae is raised to family rank and treated as the sister group of all Pentatomoidea exclusive of Urostylididae sensu stricto; a broadly conceived Cydnidae, as recognized by Dolling, 1981, is not supported; the placement of Thaumastellidae within the Pentatomoidea is affirmed and the taxon is recognized at family rank rather than as a subfamily of Cydnidae, although its exact phylogenetic position within the Pentatomoidea remains equivocal; the Parastrachiinae is treated as also including Dismegistus Amyot & Serville and placed within a broadly conceived Corimelaenidae, the latter group being treated at family rank; the family-group taxa Dinidoridae and Tessaratomidae probably represent a monophyletic group, but the recognition of monophyletic subgroups will benefit from additional representation in the sequence data set; and the Lestoniidae is treated as the sister group of the Acanthosomatidae. The Acanthosomatidae and Scutelleridae are consistently recovered as monophyletic. The monophyly of the Pentatomidae appears unequivocal, inclusive of the Aphylinae and Cyrtocorinae, on the basis of morphology, the latter two taxa not being represented in the molecular data set. © The Willi Hennig Society 2008., (© The Willi Hennig Society 2008.)

The phylogenetic relationships of branchiopod crustaceans have been in the focus of a number of recent morphological and molecular systematic studies. Although agreeing in some respects, major differences remain. We analyzed molecular sequences and morphological characters for 43 branchiopods and two outgroups. The branchiopod terminals comprise all eight "orders". The molecular data include six loci: two nuclear ribosomal genes (18S rRNA, 28S rRNA), two mitochondrial ribosomal genes (12S rRNA, 16S rRNA), one nuclear protein coding gene (elongation factor 1α), and one mitochondrial protein coding gene (cytochrome c oxidase subunit I). A total of 65 morphological characters were analyzed dealing with different aspects of branchiopod morphology, including internal anatomy and larval characters. The morphological analysis resulted in a monophyletic Phyllopoda, with Notostraca as the sister group to the remaining taxa supporting the Diplostraca concept ("Conchostraca" + Cladocera). "Conchostraca" is not supported but Cyclestheria hislopi is the sister group to Cladocera (constituting together Cladoceromorpha) and Spinicaudata is closer to Cladoceromorpha than to Laevicaudata. Cladocera is supported as monophyletic. The combined analysis under equal weighting gave results in some respects similar to the morphological analysis. Within Phyllopoda, Cladocera, Cladoceromorpha and Spinicaudata + Cladoceromorpha are monophyletic. The combined analysis is different from the morphological analysis with respect to the position of Notostraca and Laevicaudata. Here, Laevicaudata is the sister group to the remaining Phyllopoda and Notostraca is sister group to Spinicaudata and Cladoceromorpha. A sensitivity analysis using 20 different parameter sets (different insertion-deletion [indel]/substitution and transversion/transition ratios) show the monophyly of Anostraca, Notostraca, Laevicaudata, Spinicaudata, Cladoceromorpha, Cladocera, and within Cladocera, of Onychopoda and Gymnomera under all or almost all (i.e., 19 of 20) parameter sets. Analyses with an indel-to-transversion ratio up to 2 result in monophyletic Phyllopoda, with Laevicaudata as sister group to the remaining Phyllopoda and with Spinicaudata and Cladoceromorpha as sister groups. Almost all analyses (including those with higher indel weights) result in the same topology when only ingroup taxa are considered., (© The Willi Hennig Society 2007.)

Higher-level phylogenetics of Pycnogonida has been discussed for many decades but scarcely studied from a cladistic perspective. Traditional taxonomic classifications are yet to be tested and affinities among families and genera are not well understood. Pycnogonida includes more than 1300 species described, but no systematic revisions at any level are available. Previous attempts to propose a phylogeny of the sea spiders were limited in characters and taxon sampling, therefore not allowing a robust test of relationships among lineages. Herein, we present the first comprehensive phylogenetic analysis of the Pycnogonida based on a total evidence approach and Direct Optimization. Sixty-three pycnogonid species representing all families including fossil taxa were included. For most of the extant taxa more than 6 kb of nuclear and mitochondrial DNA and 78 morphological characters were scored. The most parsimonious hypotheses obtained in equally weighted total evidence analyses show the two most diverse families Ammotheidae and Callipallenidae to be non-monophyletic. Austrodecidae + Colossendeidae + Pycnogonidae are in the basal most clade, these are morphologically diverse groups of species mostly found in cold waters. The raising of the family Pallenopsidae is supported, while Eurycyde and Ascorhynchus are definitely separated from Ammotheidae. The four fossil taxa are grouped within living Pycnogonida, instead of being an early derived clade. This phylogeny represents a solid framework to work towards the understanding of pycnogonid systematics, providing a data set and a testable hypothesis that indicate those clades that need severe testing, especially some of the deep nodes of the pycnogonid tree and the relationships of ammotheid and callipallenid forms. The inclusion of more rare taxa and additional sources of evidence are necessary for a phylogenetic classification of the Pycnogonida., (© The Willi Hennig Society 2006.)

The use of likelihood as an optimality criterion is explored in the context of dynamic homology. Simple models and procedures are described to allow the analysis of large variable length sequence data sets, alone and in combination with qualitative information (such as morphology). Several approaches are discussed that have different likelihood interpretations in terms of maximum parsimony likelihood and maximum average likelihood. Implementation is discussed and an example in arthropod systematics presented. Topological congruence comparisons with parsimony are made., (© The Willi Hennig Society 2006.)

Many authors have demonstrated that the parsimony method of phylogenetic analysis can fail to estimate phylogeny accurately under certain conditions when data follow a model that stipulates homogeneity of the evolutionary process. These demonstrations further show that no matter how much data are added, parsimony will forever exhibit this statistical inconsistency if the additional data have the same distributional properties as the original data. This final component-that the additional data must follow the same distribution as the original data-is crucial to the demonstration. Recent simulations show, however, that if data evolve heterogeneously, parsimony can perform consistently. Here we show, using natural data, that parsimony can overcome inconsistency if new data from the same gene are added to an analysis already exhibiting a condition indistinguishable from inconsistency., (© The Willi Hennig Society 2005.)

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis., (c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.)

A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple-alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These "lines of correspondence" link ancestor-descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion-deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the improvement of heuristic cladogram cost calculations are discussed., (c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.)

The problem of determining the minimum-cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete. This "tree alignment" problem has motivated the considerable effort placed in multiple sequence alignment procedures. Wheeler in 1996 proposed a heuristic method, direct optimization, to calculate cladogram costs without the intervention of multiple sequence alignment. This method, though more efficient in time and more effective in cladogram length than many alignment-based procedures, greedily optimizes nodes based on descendent information only. In their proposal of an exact multiple alignment solution, Sankoff et al. in 1976 described a heuristic procedure--the iterative improvement method--to create alignments at internal nodes by solving a series of median problems. The combination of a three-sequence direct optimization with iterative improvement and a branch-length-based cladogram cost procedure, provides an algorithm that frequently results in superior (i.e., lower) cladogram costs. This iterative pass optimization is both computation and memory intensive, but economies can be made to reduce this burden. An example in arthropod systematics is discussed., (c2003 The Willi Hennig Society. Published by Elsevier Science (USA). All rights reserved.)

The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000-2700 bp for each taxon) from the nuclear genes 18S and 28S and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae +Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))).

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones., (c2002 The Willi Hennig Society.)

Morphological and molecular data are marshalled to address the question of hexapod ordinal relationships. The combination of 275 morphological variables, 1000 bases of the small subunit nuclear rDNA (18S), and 350 bases of the large subunit nuclear rDNA (28S) are subjected to a variety of analysis parameters (indel and transversion costs). Representatives of each hexapod order are included with most orders represented multiply. Those parameters that minimize character incongruence (ILD of Mickevich and Farris, 1981, Syst. Zool. 30, 351-370), among the morphological and molecular data sets are chosen to generate the best supported cladogram. A well-resolved and robust cladogram of ordinal relationships is produced with the topology (Crustacea ((Chilopoda Diplopoda) ((Collembola Protura) ((Japygina Campodeina) (Archaeognatha (Zygentoma (Ephemerida (Odonata ((((Mantodea Blattaria) Isoptera) Zoraptera) ((Plecoptera Embiidina) (((Orthoptera Phasmida) (Grylloblattaria Dermaptera)) ((((Psocoptera Phthiraptera) Thysanoptera) Hemiptera) ((Neuropteroidea Coleoptera) (((((Strepsiptera Diptera) Mecoptera) Siphonaptera) (Trichoptera Lepidoptera)) Hymenoptera)))))))))))))).

The phylogeny of the extant chelicerate orders is examined in the light of morphological and molecular evidence. Representatives from each of the chelicerate 'orders' and mandibulate and onychophoran outgroups are examined. Molecular (small and large ribosomal subunit DNA) and morphological information is combined in a total evidence regime to determine the most consistent picture of extant chelicerate relationships for these data. Multiple phylogenetic analyses are performed with variable analysis parameters yielding largely consistent results. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis with lowest character incongruence yields the scheme of relationships (Pycnogonida+ (Xiphosura+((Opiliones+((Solifugae+Pseudoscorpiones)+Scorpiones))+((Ricinulei+Acari)+(Palpigradi+ ((Thelyphonida+Schizomida=Uropygi)+(Amblypygi+ Araneae))))))). This result is fairly robust to variation in analysis parameters, with the placement of solifugids and the status of the pedipalps responsible for most disagreement.

Abstract- Ribosomal and ubiquitin protein coding sequence data are generated from 20 arthropods and five close relatives. These molecular data are combined with morphological characters derived from the literature to approach arthropod phylogenetics from the perspective of total evidence. Trilobita were included in the analysis through morphological comparison alone. The overall data strongly support arthropod monophyly. Recent molecular analyses which have yield different results are shown to have been based on few characters, few taxa or both. The most parsimonious explanation of the data is (Annelida + (Onychophora + (Trilobita + Chelicerata) + (Crustacea + (Myriapoda + Hexapoda))))). The data are largely concordant both internally among data sets and externally with previous cladistic anatomical analyses.

Abstract- When divergent taxa are used to root networks, it is assumed that the character stales in the outgroup have historical similarity to those in the ingroup. Yet, if the data are nucleic acid sequences, the character stales shared by a divergent outgroup may be based not on history but on random similarity. A simple procedure is proposed to test this possibility. In the absence of an appropriate outgroup, root position can be estimated with the use of an asymmetrical character transformation matrix. If the matrix is sufficiently biased, it can supply the polarity information usually derived from an outgroup. This outgroup test and rooting procedure are demonstrated with ADH sequences from the genus Drosophila., (© 1990 The Willi Hennig Society.)