Parsimony overcomes statistical inconsistency with the addition of more data from the same gene

Comparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)

The recognized potential of using mitogenomics in phylogenetics and the more accessible use of high-throughput sequencing (HTS) offer an opportunity to investigate groups of neglected organisms. Here, we leveraged HTS to execute the most comprehensive documentation of mitogenomes for cestodes based on the number of terminals sequenced. We adopted modern approaches to obtain the complete mitogenome sequences of 86 specimens representing five orders of cestodes (three reported for the first time: Phyllobothriidea, “Tetraphyllidea” and Trypanorhyncha). These complete mitogenomes represent an increase of 41% of the mitogenomes available for cestodes (61–147) and an addition of 33% in the representativeness of the cestode orders. The complete mitochondrial genomes are conserved, circular, encoded in the same strand, and transcribed in the same direction, following the pattern observed previously for tapeworms. Their length varies from 13,369 to 13,795 bp, containing 36 genes in total. Except for the Trypanorhyncha specimen, the gene order of the other four cestode orders sequenced here suggests that it could be a synapomorphy for the acetabulate group (with a reversion for taenids). Our results also suggest that no single gene can tell all the evolutionary history contained in the mitogenome. Therefore, cestodes phylogenies based on a single mitochondrial marker may fail to capture their evolutionary history. We predict that such phylogenies would be improved if conducted under a total evidence framework. The characterization of the new mitochondrial genomes is the first step to provide a valuable resource for future studies on the evolutionary relationships of these groups of parasites.

Grebes and flamingos: standards of evidence, adjudication of disputes, and societal politics in avian systematics

The recent proposal of a sister-group relationship between the Neoavian grebes (Podicipedidae) and flamingos (Phoenicopteridae) is chronicled, and morphological evidence claimed to be supportive of the grouping is examined. The hypothesis arose from an exiguous amalgam of molecular inferences, advanced in part by a pervasive, unsupported superiority conferred upon sequence data, and adopted by several societal committees on avian classification. Morphological characters marshalled specifically to support the hypothesis were found to be erroneous, and associated phylogenetic analyses, where given, were ambiguous. A combined analysis of large data sets for morphology and RAG-1 sequences found flamingos and storks to be sister groups but with reduced support. This example illustrates problems attending the synthesis of contradictory evidence and evaluation of unprecedented hypotheses, and reveals the informality by which revisions are adopted. Procedures for rational synthesis of evidence are needed for progress during this challenging but promising period of diversified phylogenetics, without which disputes will be dominated increasingly by polarized, intransigent prejudice regarding methods and data.© The Willi Hennig Society 2010.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

To be named or not to be named-Heteropodarke pleijeli sp. n. (Annelida, Polychaeta)

Heteropodarke pleijeli n. sp. (Annelida, Polychaeta, Hesionidae) is described from Papua New Guinea. This taxon was characterized in a PhyloCode context by Pleijel in 1999 and again in 2000. The valid name for this annelid will be decided by the zoological community in the future, but the description provided here is regarded as the only available and thus valid one.

Challenges of phylogenetic analyses of aDNA sequences

One of the crucial steps of authentication of aDNA sequences is phylogenetic consistency. Amplified sequences should fit into the phylogenetic framework of their supposed origin. An inherent property of aDNA sequences however, is their short sequence length. Additionally, genes for aDNA studies are often chosen by their preservation potential rather than by phylogenetically informative content. This poses potential challenges regarding their analyses, and might result in an inaccurate reflection of the supposed phylogenetic history of the sequence or organism under study. In this paper some fundamental problems of phylogenetic analysis and interpretation of aDNA datasets are discussed. Suggestions for character sampling and treatment of missing data are made. The publication is the result of a talk from the 1st PAMINSA Meeting in Rio de Janeiro, July 2005.

A new test of phylogenetic model fitness addresses the issue of the basal angiosperm phylogeny

We readdress the issue of phylogeny of the basal extant angiosperms employing a source previously not systematically investigated, specifically, the non-coding sequences of cpDNA. Comparison of trees with and without grasses or the outgroup (Pinus) in our analyses revealed no rearrangements in tree topology that might be expected if LBA were distorting the position of the magnoliids. For each model applied, irrespective of whether monocots or ANITA members appeared basally divergent, the orchid Phalaenopsis assumed the same position on the trees with the reduced taxon set as did the branch bearing the orchid plus the grasses in the full alignment. However, our new test of model fitness revealed a different flaw influencing the placement of monocots, which is related to model mis-specification. This flaw similarly affects the full alignment and the alignment with grasses removed. In both cases the models favouring a relatively derived position for the monocots and basal placement of the branch of Amborella plus Nymphaea provide better overall prediction of the observed data structure. In the view of apparent unsuitability of the bootstrap method for large data sets, our novel test provides a new means of exploring conflicts caused by systematic errors in phylogenetic analyses.