Wiley InterScience : Cladisticshttp://dx.doi.org/10.1111%2F07483007John Wiley & Sons, Incen© 2010 The Willi Hennig Society2010-02-100748-30071096-0031http://dx.doi.org/10.1111%2Fj.1096-0031.2010.00304.xJohn V. Freudenstein, Jerrold I. Davis2010-02-05T05:00:00Z10.1111/j.1096-0031.2010.00304.x© 2010 The Willi Hennig SocietyJohn Wiley & Sons, Inc.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.http://dx.doi.org/10.1111%2Fj.1096-0031.2010.00302.xSantiago A. Catalano, Pablo A. Goloboff, Norberto P. Giannini2010-01-28T05:01:00Z10.1111/j.1096-0031.2010.00302.x© 2010 The Willi Hennig SocietyJohn Wiley & Sons, Inc.A method for the direct use of aligned landmark data (2D or 3D coordinates of comparable points) in phylogenetic analysis is described. The approach is based on finding, for each of the landmark points, the ancestral positions that minimize the distance between the ancestor/descendant points along the tree. Doing so amounts to maximizing the degree to which similar positions of the landmarks in different taxa can be accounted for by common ancestry, i.e. parsimony. This method requires no transformation of the aligned data or the results: the data themselves are the x, y, z coordinates of the landmarks, and the output of mapping a character onto a given tree is the x, y, z coordinates for the hypothetical ancestors. In the special case of collinear points, the results are identical to those of optimization of (continuous) additive characters.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00303.xKevin M. Pitz, Petra Sierwald2010-01-21T04:01:00Z10.1111/j.1096-0031.2009.00303.x© 2010 The Willi Hennig SocietyJohn Wiley & Sons, Inc.This study examines relationships within the millipede order Spirobolida using an exemplar approach, sampling within families to maximize geographical and morphological diversity; due to lack of available material, Allopocockiidae and Hoffmanobolidae were not included in analyses. The focus of this study was to test monophyly of the order, the suborders, and the families of Spirobolida and to propose interfamilial relationships using morphological and molecular data in a total-evidence approach. Both maximum-parsimony analyses and Bayesian inference were employed to analyse two datasets consisting of combined morphological and molecular data, one aligned using progressive alignment methods and the second aligned by secondary structure models. Rhinocricidae was recovered sister to all remaining spirobolidan millipedes and is elevated to suborder status as suborder Rhinocricidea. Trigoniulidea was recovered as monophyletic as was Spirobolidea excluding Rhinocricidae; Spirobolidea is redefined to reflect this change. All previously recognized families were recovered, with the exception of Spirobolidae; in all instances, this family was paraphyletic or part of a polytomy that lacked sufficient resolution to assess its monophyly. The results reaffirm much of the existing taxonomic foundation within Spirobolida. This study provides the first phylogenetic test of higher-level relationships within Spirobolida and will serve as a foundation for future work in this group at finer levels. © The Willi Hennig Society 2010.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00301.xChristopher P. Randle, Kurt M. Pickett2010-01-04T15:13:00Z10.1111/j.1096-0031.2009.00301.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The objective Bayesian approach relies on the construction of prior distributions that reflect ignorance. When topologies are considered equally probable a priori, clades cannot be. Shifting justifications have been offered for the use of uniform topological priors in Bayesian inference. These include: (i) topological priors do not inappropriately influence Bayesian inference when they are uniform; (ii) although clade priors are not uniform, their undesirable influence is negated by the likelihood function, even when data sets are small; and (iii) the influence of nonuniform clade priors is an appropriate reflection of knowledge. The first two justifications have been addressed previously: the first is false, and the second was found to be questionable. The third and most recent justification is inconsistent with the first two, and with the objective Bayesian philosophy itself. Thus, there has been no coherent justification for the use of nonflat clade priors in Bayesian phylogenetics. We discuss several solutions: (i) Bayesian inference can be abandoned in favour of other methods of phylogenetic inference; (ii) the objective Bayesian philosophy can be abandoned in favour of a subjective interpretation; (iii) the topology with the greatest posterior probability, which is also the tree of greatest marginal likelihood, can be accepted as optimal, with clade support estimated using other means; or (iv) a Bayes factor, which accounts for differences in priors among competing hypotheses, can be used to assess the weight of evidence in support of clades.©The Willi Hennig Society 2009http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00300.xBen H. Warren, Dominique Strasberg, J. Henrich Bruggemann, Robert P. Prys-Jones, Christophe Thébaud2009-12-15T04:23:00Z10.1111/j.1096-0031.2009.00300.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.A corollary of island biogeographical theory is that islands are largely colonized from their nearest mainland source. Despite Madagascar's extreme isolation from India and proximity to Africa, a high proportion of the biota of the Madagascar region has Asian affinities. This pattern has rarely been viewed as surprising, as it is consistent with Gondwanan vicariance. Molecular phylogenetic data provide strong support for such Asian affinities, but often not for their vicariant origin; most divergences between lineages in Asia and the Madagascar region post-date the separation of India and Madagascar considerably (up to 87 Myr), implying a high frequency of dispersal that mirrors colonization of the Hawaiian archipelago in distance. Indian Ocean bathymetry and the magnitude of recent sea-level lowstands support the repeated existence of sizeable islands across the western Indian Ocean, greatly reducing the isolation of Madagascar from Asia. We put forward predictions to test the role of this historical factor in the assembly of the regional biota. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00299.xJosé G. Palacios Vargas, Enrique García-Barros, José C. Simón Benito2009-12-01T11:52:00Z10.1111/j.1096-0031.2009.00299.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.In order to assess the phylogenetic structure of the springtail genus Palmanura, as well as to test the monophyly of the tribe Sensillanurini (Neanuridae: Neanurinae), a data matrix of morphological (chaetotactic and other) characters of members of this group was assembled and analysed in the light of Wagner parsimony. The data matrix included all the known members of the Neotropical genus Palmanura, plus representatives of Sensillanura and Americanura. Although not all the clades obtained were highly supported by bootstrap resampling, some structures were relatively constant under different approaches. Alternative analyses (unordered and ordered character states, rescaled weighting procedure) were applied. While alternative solutions were obtained, a number of structures were shared by the results irrespective of the method used. On this basis, the results suggest that some further reassessment is required to confirm formally the monophyly of the tribe Sensillanurini. The genera Palmanura and Americanura are mutually poly/paraphyletic; we thus suggest that Palmanura should be considered as a synonym of Americanura, although some character reassessment and more varied outgroup species may be necessary before a formal generic redefinition can be proposed. Finally, a comparison of the performance of the characters under Wagner parsimony analysis indicated that differences in the characters' retention indexes are due not to the topological (tagmal) position of the traits involved, but to character coding: the characters describing quantitative features (generally numbers of setae) generally performed worse than other types of characters under parsimony. An updated list of the known members of the Sensillanurini (Collembola: Neanuridae: Neanurinae) is presented.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00298.xFrancisco J. Prevosti2009-12-01T11:44:00Z10.1111/j.1096-0031.2009.00298.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.South America currently possesses a high diversity of canids, comprising mainly small to medium-sized omnivorous species, but in the Pleistocene there were large hypercarnivorous taxa that were assigned to Protocyon spp., Theriodictis spp., Canis gezi, Canis nehringi and Canis dirus. These fossils have never been included in phylogenies based on quantitative cladistics, but hand-constructed cladograms published in the 1980s included some of them in the South American canine clade and others in the Canis clade. In this work, the phylogenetic position of the large extinct South American canids was studied using a large sample of living and extinct canids, as well as different sources of characters (e.g. DNA and 133 osteological characters). The phylogenetic analysis corroborates the inclusion of Theriodictis and Protocyon in the "South American clade", where C. gezi is also included. In addition, the position of C. dirus as a highly derived Canis species is confirmed. The simultaneous analysis supports hypercarnivory having arisen at least three times in Caninae and once in the "South American clade". The combination of the phylogenetic analyses, the fossil record and divergence dates estimated in previous works suggests that at least three or four independent lineages of the "South American clade" invaded South America after the establishment of the Panama bridge around 3 million years ago, plus other events corresponding to the immigration of Urocyon and Canis dirus.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00295.xMark E. Siddall2009-11-24T04:28:00Z10.1111/j.1096-0031.2009.00295.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Several large phylogenomic analyses have recently cast doubt on long-held beliefs about early metazoan phylogenetic patterns. Those data sets, and the relative bootstrap support for various controversial clades, are reanalysed in the context of parsimony, yielding results that are at considerable odds with the original likelihood or Bayesian findings. Discrepancies are considered in light of the tendency of RAxML to overestimate support values by virtue (sic) of its lazy search algorithm and its autocorrelated pseudoreplication as well as the extraordinary ability for Bayesian analyses to be led astray by missing data. In addition to standard nonparametric bootstrapping as a measure of support, a new strategy involving resampling loci as units, partition bootstrap support, is introduced as a more defensible alternative to resampling nonindependent sites.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00278.xChristian S. Wirkner, Stefan Richter2009-10-09T03:45:00Z10.1111/j.1096-0031.2009.00278.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.We demonstrate that by formulating guidelines for evolutionary morphology the transparency, reproducibility, and intersubject testability of evolutionary hypotheses based on morphological data can be enhanced. The five main steps in our concept of evolutionary morphology are (i) taxon sampling, (ii) structural analysis, (iii) character conceptualization, (iv) phylogenetic analysis, and (v) evolutionary interpretation. We illustrate this concept on the example of the morphology of the circulatory organs in peracarid Malacostraca. The analysis is based on recently published accounts in which detailed structural analyses were carried out, and on the older literature. Detailed conceptualizations of 22 characters of the circulatory system are given for 28 terminals. In a further step these characters are included in a recently revised matrix, resulting in 110 characters. The resulting parsimony analysis yielded a single most parsimonious tree with a length of 309 steps. The most significant results are that Peracarida is monophyletic, Amphipoda is the sister taxon to the Mancoida sensu stricto, the relict cave-dwelling taxa Thermosbaenacea, Spelaeogriphacea, and Mictocarididae form a monophylum and Tanaidacea is the sister group to a monophylum comprising Cumacea and Isopoda. The evolutionary analysis shows that the ground pattern features of the circulatory organs in Peracarida are a tubular heart extending through the whole thorax, a posterior aorta with lateral arteries, and a ventral vessel system. Important features within the Peracarida are the backward shift of the anterior border of the heart, the reduction of the ventral vessel system, and two patterns of cardiac arteries, one common to the amphipod and tanaidacean terminals, and one to the cumacean and isopod terminals. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00296.xGonzalo Giribet, Lars Vogt, Abel Pérez González, Prashant Sharma, Adriano B. Kury2009-11-16T13:45:00Z10.1111/j.1096-0031.2009.00296.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers for ca. 140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well-supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoi + Dyspnoi). Maximum-likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoi + Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum-likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi: Hesperonemastoma is transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family for Zuma acuta.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00292.xMichael J. Wise2009-11-11T04:03:00Z10.1111/j.1096-0031.2009.00292.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Most phylogenetic-tree building applications use multiple sequence alignments as a starting point. A recent meta-level methodology, called Heads or Tails, aims to reveal the quality of multiple sequence alignments by comparing alignments taken in the forward direction with the alignments of the same sequences when the sequences are reversed. Through an examination of a special case for multiple sequence alignment [ndash] pair-wise alignments, where an optimal algorithm exists [ndash] and the use of a modified global-alignment application, it is shown that the forward and reverse alignments, even when they are the same, do not capture all the possible variations in the alignments and when the forward and reverse alignments differ there may be other alignments that remain unaccounted for. The implication is that comparing just the forward and (biologically irrelevant) reverse alignments is not sufficient to capture the variability in multiple sequence alignments, and the Heads or Tails methodology is therefore not suitable as a method for investigating multiple sequence alignment accuracy. Part of the reason is the inability of individual multiple sequence alignment applications to adequately sample the space of possible alignments. A further implication is that the Hall [Hall, B.G., 2008. Mol. Biol. Evol. 25, 1576[ndash]1580] methodology may create optimal synthetic multiple sequence alignments that extant aligners will be unable to completely recover ab initio due to alternative alignments being possible at particular sites. In general, it is shown that more divergent sequences will give rise to an increased number of alternative alignments, so sequence sets with a higher degree of similarity are preferable to sets with lower similarity as the starting point for phylogenetic tree building. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00293.xPaola Pedraza-Peñalosa2009-11-02T08:16:00Z10.1111/j.1096-0031.2009.00293.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Disterigma sensu lato (s.l.) is a polyphyletic genus of neotropical blueberries that comprises 37 species found in Central and South America, mostly in Andean cloud forests and páramos. The present phylogenetic analysis, based on molecular and morphological data for 84% of the species of Disterigma s.l., addressed the monophyly of the genus and identified the putative morphological synapomorphies of the main clades. The sensitivity of the phylogenetic hypotheses to the choice of analytical parameters was addressed in detail, by varying all possible parameters and applying different treatments for indel coding. A total of 29 transformation cost matrices were investigated and all these analyses were performed in POY 4, using direct optimization. A diagnosable Disterigma sensu stricto (s.s.) clade was recovered in all analyses, despite changes in the transformation costs. Additionally, none of the analyses refuted the segregation of D. trimerum, D. ulei, D. pentandrum, D. rimbachii, and D. bracteatum from Disterigma s.s. Although measurements of congruence are used to choose among alternative analytical parameter sets, the behaviour of the RILD index (rescaled incongruence length difference) in this study suggested that it may not be a good measure of congruence and that further studies are necessary to better understand its performance.© The Willi Hennig Society 2009http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00291.xAstrid Cruaud, Roula Jabbour-Zahab, Gwenaëlle Genson, Corinne Cruaud, Arnaud Couloux, Finn Kjellberg, Simon van Noort, Jean-Yves Rasplus2009-11-02T08:16:00Z10.1111/j.1096-0031.2009.00291.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.A phylogeny of the Agaonidae (Chalcidoidea) in their restricted sense, pollinators of Ficus species (Moraceae), is estimated using 4182 nucleotides from six genes, obtained from 101 species representing 19 of the 20 recognized genera, and four outgroups. Data analysed by parsimony and Bayesian inference methods demonstrate that Agaonidae are monophyletic and that the previous classification is not supported. Agaonidae are partitioned into four groups: (i) Tetrapus, (ii) Ceratosolen + Kradibia, (iii) some Blastophaga + Wiebesia species, and (iv) all genera associated with monoecious figs and a few Blastophaga and Wiebesia. The latter group is subdivided into subgroups: (i) Pleistodontes, (ii) Blastophaga psenes and neocaledonian Dolichoris, (iii) some Blastophaga and Wiebesia species, and (iv) Platyscapa, all afrotropical genera and all genera associated with section Conosycea. Eleven genera were recovered as monophyletic, six were para- or polyphyletic, and two cannot be tested with our data set. Based on our phylogeny we propose a new classification for the Agaonidae. Two new subfamilies are proposed: Tetrapusiinae for the genus Tetrapus, and Kradibiinae for Ceratosolen + Kradibia. Liporrhopalum is synonymized with Kradibia and the subgenus Valisia of Blastophaga is elevated to generic rank. These changes resulted in 36 new combinations. Finally, we discuss the hypothesis of co-speciation between the pollinators and their host species by comparing the two phylogenies.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00294.xOlivier Rieppel2009-10-27T06:08:00Z10.1111/j.1096-0031.2009.00294.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00290.xKee-Jeong Ahn, Mi-Jeong Jeon, Marc A. Branham2009-10-23T03:30:00Z10.1111/j.1096-0031.2009.00290.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.A phylogenetic analysis of the tribe Liparocephalini Fenyes is presented based on morphological and molecular characters. The data set comprised 50 adult morphological characters, partial COI (907 bp), COII (366 bp) and 12S rDNA (325[ndash]355 bp), and nearly complete sequences of 18S rDNA (1768[ndash]1902 bp) for 21 species. Eighteen species of liparocephaline beetles from all eight genera and three outgroups, are included. The sequences were analysed separately and simultaneously with morphological characters by direct optimization in the program POY4 and by partitioned Bayesian analysis for the combined data. The direct optimization (DO) tree for the combined data under equal weighting, which also shows a minimum incongruence length difference value, resulted in a monophyletic Liparocephalini with the following patterns of phylogenetic relationships (outgroup ((Baeostethus, Ianmoorea) (Paramblopusa ((Amblopusa, Halorhadinus) (Liparocephalus, Diaulota))))). A sensitivity analysis using 16 different parameter sets for the combined data shows the monophyly of the liparocephalines and all its genera under all parameter sets. Bayesian analysis resulted in topological differences in comparison with the DO tree under equal weighting only in the position of the genus Paramblopusa and clade (Amblopusa + Halorhadinus), which were reversed. Historical biogeography and the stepwise evolutionary colonization of intertidal habitat in the Liparocephalini are discussed. Based on the biogeographical analyses, we hypothesize that the ancestor of the Liparocephalini occurred along the Panthallassan Ocean, the direct antecedent of the Pacific Ocean, followed by repeated dispersals to the Nearctic from the Palearctic. We also hypothesize that ancestors of the Liparocephalini appear to have arisen in the littoral zone of beaches and then colonized rocky reef areas in the low tidal zone later through high- to mid-tide zones.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00285.xClaudia Szumik, Pablo Goloboff2009-10-23T03:30:00Z10.1111/j.1096-0031.2009.00285.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The 27th meeting of the Willi Hennig Society was held at the Sierras de San Javier, Tucumán (27[ndash]31 October 2008), jointly with the VIII Reunión Argentina de Cladística y Biogeografía. This was the second Hennig meeting held in South America and the third in Latin America. The event was attended by 129 participants from 16 countries, with the strongest presence from Argentina, USA and Brazil. As pointed out in the minutes of previous meetings, student participation is a good measure of the health of a society, and by this measure, the Hennig society is doing very well. For this meeting, 64 of the participants (50%) were students, 40 of which had authored or co-authored a talk or poster. The schedule was intense, with 98 presentations (67 talks and 31 posters). The sessions consisted of contributed papers, and five symposia on diverse topics: Large Scale Analyses of Large Chunks of Life, Molecular Systematics, Latin American Biogeography in the 21st Century, Methodology, and Botanical Phylogenetics (each of the symposia, except the "green" one, had two or three student speakers). As is usual at these meetings, the atmosphere was informal and relaxed, with much discussion and debate (although the biogeographic symposium took first place for the heat of its exchanges). The Student Award Committee (Lone Aagesen, Dan Janies and Gitte Petersen) selected Santiago Catalano for the Hennig Award ('The optimization of landmark data: a three-dimensional approach'), Prashant Sharma for the Brundin Award ('Phylogenetic analysis of Sandokanidae (Arachnida, Opiliones, Laniatores): Evaluating the independence of associated gene regions'), and Sebastian Barrionuevo for the Rosen Award ('Continuous characters in a phylogenetic analysis of the frog genus Telmatobius'). In addition to the logistics and funding provided by the Willi Hennig Society, the event was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas, Fundación Miguel Lillo, Instituto Superior de Entomología 'Dr Abraham Willink', and the Agencia Nacional de Promoción Científica y Tecnológica.© The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00289.xFrancisco J. Prevosti, María A. Chemisquy2009-10-19T05:10:00Z10.1111/j.1096-0031.2009.00289.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Here we explore the effect of missing data in phylogenetic analyses using a large number of real morphological matrices. Different percentages and patterns of missing entries were added to each matrix, and their influence was evaluated by comparing the accuracy and error of most parsimonious trees. The relationships between accuracy and error and different parameters (e.g. the number of taxa and characters, homoplasy, support) were also evaluated. Our findings, based on real matrices, agree with the simulation studies, i.e. the negative effect increases with the percentage of missing entries, and decreases with the addition of more characters. This indicates that the main problem is the lack of information, not just the presence of missing data per se. Accuracy varies with different distribution patterns of missing entries; the worst case is when missing data are concentrated in a few taxa, while the best is when the missing entries are restricted to just a few characters. The results expand our knowledge of the missing data problem, corroborate many of the findings previously published using simulations, and could be useful for empirical or theoretical studies. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00288.xE.K. Lienau, R. DeSalle2009-10-14T10:51:00Z10.1111/j.1096-0031.2009.00288.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The field of microbial phylogenetics has questioned the feasibility of using a tree-like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree-like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree-like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00287.xJulián Faivovich, Célio F. B. Haddad, Délio Baêta, Karl-Heinz Jungfer, Guilherme F. R. Álvares, Reuber A. Brandão, Christopher Sheil, Lucas S. Barrientos, César L. Barrio-Amorós, Carlos A. G. Cruz, Ward C. Wheeler2009-10-14T10:51:00Z10.1111/j.1096-0031.2009.00287.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.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.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00286.xLars Vogt, Thomas Bartolomaeus, Gonzalo Giribet2009-10-07T05:00:00Z10.1111/j.1096-0031.2009.00286.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The present article discusses the need for standardization in morphology in order to increase comparability and communicability of morphological data. We analyse why only morphological descriptions and not character matrices represent morphological data and why morphological terminology must be free of homology assumptions. We discuss why images only support and substantiate data but are not data themselves. By comparing morphological traits and DNA sequence data we reveal fundamental conceptual shortcomings of the former that result from their high average degree of individuality. We argue that the delimitation of morphological units, of datum units, and of evidence units must be distinguished, each of which involves its own specific problems. We conclude that morphology suffers from the linguistic problem of morphology that results from the lack of (i) a commonly accepted standardized morphological terminology, (ii) a commonly accepted standardized and formalized method of description, and (iii) a rationale for the delimitation of morphological traits. Although this is not problematic for standardizing metadata, it hinders standardizing morphological data. We provide the foundation for a solution to the linguistic problem of morphology, which is based on a morphological structure concept. We argue that this structure concept can be represented with knowledge representation languages such as the resource description framework (RDF) and that it can be applied for morphological descriptions. We conclude with a discussion of how online databases can improve morphological data documentation and how a controlled and formalized morphological vocabulary, i.e. a morphological RDF ontology, if it is based on a structure concept, can provide a possible solution to the linguistic problem of morphology. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00283.xGerasimos Cassis, Randall T. Schuh2009-09-28T04:31:00Z10.1111/j.1096-0031.2009.00283.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Three recent papers dealing with phylogenetic relationships within the Heteroptera are discussed and analysed. A character set representing 43 taxa and 78 characters is used to test theories presented in those papers. The conclusions of Grimaldi and Engel concerning the placement of the Cretaceous fossil taxon Cretopiesma in the Piesmatidae are rejected in favour of placement in the Aradidae. The placement by Nel et al. of Protodoris from Eocene amber of the Paris Basin in the Thaumastocoridae is considered ambiguous because it has none of the diagnostic characters of that family group and is therefore regarded as incertae sedis. The arguments of Sweet concerning the elevation of the Aradoidea to infraordinal status on the basis of autapomorphies are also treated as invalid. General arguments against the use of phenetic methods in palaeontology, and ad hoc approaches under the guise of cladistics, are offered, with the conclusion that rigorous cladistic analyses are a prerequisite to testable conclusions concerning the placement of fossil and Recent taxa. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00284.xSoili Stenroos, Tomi Laukka, Seppo Huhtinen, Peter Döbbeler, Leena Myllys, Kimmo Syrjänen, Jaakko Hyvönen2009-09-24T10:49:00Z10.1111/j.1096-0031.2009.00284.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit-bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00277.xLorenzo Prendini, Oscar F. Francke, Valerio Vignoli2009-09-10T05:29:00Z10.1111/j.1096-0031.2009.00277.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.The scorpion family Typhlochactidae Mitchell, 1971 is endemic to eastern Mexico and exclusively troglomorphic. Six of the nine species in the family are hypogean (troglobitic), morphologically specialized for life in the cave environment, whereas three are endogean (humicolous) and comparably less specialized. The family therefore provides a model for testing the hypotheses that ecological specialists (stenotopes) evolve from generalist ancestors (eurytopes) and that specialization (in this case to the cavernicolous habitat) is an irreversible, evolutionary dead-end that ultimately leads to extinction. Due to their cryptic ecology, inaccessible habitat, and apparently low population density, Typhlochactidae are very poorly known. The monophyly of these troglomorphic scorpions has never been rigorously tested, nor has their phylogeny been investigated in a quantitative analysis. We test and confirm their monophyly with a cladistic analysis of 195 morphological characters (142 phylogenetically informative), the first for a group of scorpions in which primary homology of pedipalp trichobothria was determined strictly according to topographical identity (the "placeholder approach"). The phylogeny of Typhlochactidae challenges the conventional wisdom that ecological specialization (stenotopy) is unidirectional and irreversible, falsifying Cope's Law of the unspecialized and Dollo's Law of evolutionary irreversibility. Troglobitism is not an evolutionary dead-end: endogean scorpions evolved from hypogean ancestors on more than one occasion. © The Willi Hennig Society 2009.http://dx.doi.org/10.1111%2Fj.1096-0031.2009.00281.xMieczyslaw Wolsan, Jun J. Sato2009-09-01T05:33:00Z10.1111/j.1096-0031.2009.00281.x© 2009 The Willi Hennig SocietyJohn Wiley & Sons, Inc.Missing data are commonly thought to impede a resolved or accurate reconstruction of phylogenetic relationships, and probabilistic analysis techniques are increasingly viewed as less vulnerable to the negative effects of data incompleteness than parsimony analyses. We test both assumptions empirically by conducting parsimony and Bayesian analyses on an approximately 1.5 × 106-cell (27 965 characters × 52 species) mustelid[ndash]procyonid molecular supermatrix with 62.7% missing entries. Contrary to the first assumption, phylogenetic relationships inferred from our analyses are fully (Bayesian) or almost fully (parsimony) resolved topologically with mostly strong support and also largely in accord with prior molecular estimations of mustelid and procyonid phylogeny derived with parsimony, Bayesian, and other probabilistic analysis techniques from smaller but complete or nearly complete data sets. Contrary to the second assumption, we found no compelling evidence in support of a relationship between the inferior performance of parsimony and taxon incompleteness (i.e. the proportion of missing character data for a taxon), although we found evidence for a connection between the inferior performance of parsimony and character incompleteness (i.e. no overlap in character data between some taxa). The relatively good performance of our analyses may be related to the large number of sampled characters, so that most taxa (even highly incomplete ones) are represented by a sufficient number of characters allowing both approaches to resolve their relationships. © The Willi Hennig Society 2009.