Cladistics

Faivovich, Julián; Haddad, Célio F. B.; Baêta, Délio; Jungfer, Karl‐Heinz; Álvares, Guilherme F. R.; Brandão, Reuber A.; Sheil, Christopher; Barrientos, Lucas S.; Barrio‐Amorós, César L.; Cruz, Carlos A. G.; Wheeler, Ward C.

doi: 10.1111/j.1096-0031.2009.00287.xpmid: 34875782

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.

Cassis, Gerasimos; Schuh, Randall T.

doi: 10.1111/j.1096-0031.2009.00283.xpmid: 34875785

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.

Stenroos, Soili; Laukka, Tomi; Huhtinen, Seppo; Döbbeler, Peter; Myllys, Leena; Syrjänen, Kimmo; Hyvönen, Jaakko

doi: 10.1111/j.1096-0031.2009.00284.xpmid: 34875784

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.

Vogt, Lars; Bartolomaeus, Thomas; Giribet, Gonzalo

doi: 10.1111/j.1096-0031.2009.00286.xpmid: 34875783

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.

Prevosti, Francisco J.; Chemisquy, María A.

doi: 10.1111/j.1096-0031.2009.00289.xpmid: 34875786

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.