Journal Articles: 2010-2006

A well-corroborated morphological scheme of interrelationships for centipedes, once broadly accepted, has been in conflict with molecular data with respect to deep branching events. Expanded taxonomic coverage compared to previous analyses adds longer fragments for 28S rRNA and a structural alignment as part of a sample of four genes (two nuclear ribosomal and two mitochondrial) for 111 extant species; these sequence data are combined with morphology under parsimony and maximum likelihood, exploring both traditional multiple sequence alignment and direct optimization approaches. Novel automated procedures to incorporate secondary structure information are also explored. The molecular data in combination yield trees that are highly congruent with morphology as regards the monophyly of all centipede orders as well as the major groups within each of the large orders. Regardless of the optimality criterion or alignment strategy, the Tasmanian/New Zealand Craterostigmomorpha is resolved in a different position by the molecular data than by morphology. Addition of morphology overturns the placement of Craterostigmomorpha in favour of the traditional morphological resolution and eliminates the need to posit major character reversals with respect to developmental mode and maternal care. Calibration of the tree with Palaeozoic and Mesozoic fossils for a relaxed clock analysis corroborates the palaeontological signal that divergences between centipede orders date to the Silurian and earliest Devonian, and familial divergences are likewise almost wholly Palaeozoic.

A clear picture of animal relationships is a prerequisite to understand how the morphological and ecological diversity of animals evolved over time. Among others, the placement of the acoelomorph flatworms, Acoela and Nemertodermatida, has fundamental implications for the origin and evolution of various animal organ systems. Their position, however, has been inconsistent in phylogenetic studies using one or several genes. Furthermore, Acoela has been among the least stable taxa in recent animal phylogenomic analyses, which simultaneously examine many genes from many species, while Nemertodermatida has not been sampled in any phylogenomic study. New sequence data are presented here from organisms targeted for their instability or lack of representation in prior analyses, and are analysed in combination with other publicly available data. We also designed new automated explicit methods for identifying and selecting common genes across different species, and developed highly optimized supercomputing tools to reconstruct relationships from gene sequences. The results of the work corroborate several recently established findings about animal relationships and provide new support for the placement of other groups. These new data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and Ectoprocta. The work highlights the implications that these arrangements have for metazoan evolution and permits a clearer picture of ancestral morphologies and life histories in the deep past.

Little is known about the familial and generic level phylogeny of Laniatores, the most diverse suborder of Opiliones. We investigated the internal phylogeny of the family Sandokanidae (formerly Oncopodidae), the putative sister group of the other families of the highly diverse infraorder Grassatores (Opiliones: Laniatores), on the basis of sequence data from eight molecular loci: 18S rRNA, 28S rRNA, 12S rRNA, 16S rRNA, cytochrome c oxidase subunit I (COI), histones H3, H4, and U2 snRNA. Exemplars of all recognized sandokanid genera, as well as a putative new genus from Thailand, were included. Data analyses were based on a direct optimization approach using parsimony, as well as maximum likelihood and Bayesian approaches on static alignments. The results obtained include the monophyly of Sandokanidae and its stability under a variety of parameter sets and methods. The internal phylogeny is relatively robust to parameter choice and demonstrates the monophyly of nearly all described genera, corroborating previous morphological observations. However, conflict among data sets exists with respect to the monophyly of the largest genus Gnomulus. Morphological character evolution, particularly of characters used to define genera, such as tarsal count and male genitalia, is reexamined and the performance of the eight molecular markers in phylogenetic estimation is evaluated.