Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

Wägele, Johann‐Wolfgang; Mayer, Christoph

doi:10.1186/1471-2148-7-147

Cited by 123 publications

(127 citation statements)

References 116 publications

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“…While the MP analyses support a basal, paraphyletic position of Neojaera and Janira, Bayesian inference and maximum likelihood clearly give evidence for a monophyletic clade including both genera (1.00/93). The reason for this difference could be that, in the MP analyses, the long branch of Janira maculosa is attracted by the long branch of the outgroup (see Bergsten 2005;Wägele & Mayer 2007), a well-known weakness of MP analyses. In the case of the Nannoniscidae, maximum parsimony favours a more basal position of this group within the munnopsid radiation when compared with the Bayesian phylogeny.…”

Section: Discussionmentioning

confidence: 99%

Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

et al. 2008

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The Asellota are a highly variable group of Isopoda with many species in freshwater and marine shallowwater environments. However, in the deep sea, they show their most impressive radiation with a broad range of astonishing morphological adaptations and bizarre body forms. Nevertheless, the evolution and phylogeny of the deep-sea Asellota are poorly known because of difficulties in scoring morphological characters. In this study, the molecular phylogeny of the Asellota is evaluated for 15 marine shallowwater species and 101 deep-sea species, using complete 18S and partial 28S rDNA gene sequences. Our molecular data support the monophyly of most deep-sea families and give evidence for a multiple colonization of the deep sea by at least four major lineages of asellote isopods. According to our molecular data, one of these lineages indicates an impressive radiation in the deep sea. Furthermore, the present study rejects the monophyly of the family Janiridae, a group of plesiomorphic shallow-water Asellota, and several shallow-water and deep-sea genera (Acanthaspidia, Ianthopsis, Haploniscus, Echinozone, Eurycope, Munnopsurus and Syneurycope).

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Section: Discussionmentioning

confidence: 99%

Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

et al. 2008

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“…, Felsenstein 1985b;Hedges 1992;Hillis & Bull 1993 for bootstrapping;Felsenstein 1985a;Debry 2001 for the decay index; Zander 2004 for a comparison of various metrics). Even stronger cases can be made by employing state-of-the art tests that take an explicit falsification approach (Schulte et al 1998) by comparing the preferred hypothesis with alternatives (e.g., Shimodaira & Hasegawa 1999;Shimodaira 2002), and by verifying an adequate signal to noise ratio in the data set (Wägele & Mayer 2007).…”

Section: Subcriterion (I)mentioning

confidence: 99%

To name or not to name: Criteria to promote economy of change in Linnaean classification schemes

Vences¹,

Guayasamín²,

Miralles³

et al. 2013

Zootaxa

155

177

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The Linnaean classification system provides the universal reference system for communicating about the diversity of life and its hierarchic history. Several limitations that challenge the stability of this system have been identified and, as a result, alternative systems have been proposed since its early inception. The revolution caused by molecular phylogenetics has, more than ever, exemplified that Linnaean classification schemes are subject to a degree of instability that may hamper their significance and communication power. Our analysis of recent changes in the classification of several groups of organisms, with a focus on amphibians and reptiles, reveals two main sources of instability: (i) revisionary, objective (empirical) changes based on the discovery of unambiguous instances of non-monophyly and on progress in the Globe's species inventory, and (ii) subjective changes based on author preferences or on a poor analysis of the advantages and limitations of new classification schemes. To avoid subjective taxonomic instability, we review and elaborate proposals for the assignment of Linnaean rank to clades, and thereby for the naming of these clades as Linnaean taxa (Taxon Naming Criteria: TNCs). These are drafted from the perspective of practicing taxonomists and can help choosing among alternative monophyly-based classifications under a premise of economy of change. We provide a rationale for each TNC along with real and theoretical examples to illustrate their practical advantages and disadvantages. We conclude that not all TNCs lead to equally informative and stable taxonomies. Therefore, we order the various TNCs by the generality of their implications and provide a workflow scheme to guide the procedure of taxonomic decisions concerning the creation or modification of supraspecific classifications. The following criteria are considered primary when naming taxa: (i) Monophyly of the taxon in an inferred species tree; (ii) Clade Stability, i.e., the monophyly of a clade to be named as taxon should be as strongly supported as possible by various methods of tree inference, tests of clade robustness, and different data sets; and (iii) Phenotypic Diagnosability, i.e., ranked supraspecific taxa should be those that are phenotypically most conspicuous although in phenotypically cryptic groups of organisms it can be warranted to name taxa based on molecular differences alone. We consider various other criteria as secondary (i.e., the Time Banding, Biogeography, Adaptive Zone, and Hybrid Viability TNCs) and refute using them as sole arguments for the modification of established classifications or proposal of new ones. Taxonomists are encouraged to be explicit and consistent when applying TNCs for creating or modifying classifications. We emphasize that, except for monophyly, the priority TNCs are not proposed as mandatory requisites of a Linnaean taxon but as yardsticks to allow for an informed choice among various clades in a tree that could alternatively be named as Linnaean taxa. Despite a need for plurality, classifications should avoid deliberately violating any of the three primary TNCs because taxa of unstable monophyly or poor diagnosability reduce the information content and hence the utility of the Linnaean system.

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“…Causes in this category also relate to the power of natural selection or shared constraints to produce convergent evolution, and parallelisms (nonrandom non-phylogenetic signal) that may lead to the false inference of monophyletic taxa. This can be an important problem for both morphological and molecular phylogenetic analyses ( Waegele & Mayer 2007). It also captures problems caused by the evolution of random noise (undirected homoplasy), such as may arise purely by chance, e.g.…”

Section: Progress and Remaining Controversymentioning

confidence: 99%

“…It may thus be unsurprising that sessile taxa (ectoprocts, brachiopods, phoronids), very small (possibly miniaturized) taxa (tardigrades, placozoans, Lobatocerebrum) and parasitic taxa (pentastomids, myxozoans) have been particularly prominent Problematica. Another consequence is that molecular phylogenies of the Metazoa bear the typical signature of short stems and long terminal branches, providing ample opportunity for long branch attraction ( Waegele & Mayer 2007). This has been a problem for the placement of several taxa, ranging from myxozoans to acoels ).…”

Section: Extant Problematicamentioning

confidence: 99%

Problematica old and new

Jenner

Littlewood

2008

Phil. Trans. R. Soc. B

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Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.

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Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects

Cited by 123 publications

References 116 publications

Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data

To name or not to name: Criteria to promote economy of change in Linnaean classification schemes

Problematica old and new

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