Alvarez-Padilla, F., Dimitrov. D, Giribet. G, and Hormiga. G. 2009. “Phylogenetic relationships of the spider family Tetragnathidae (Araneae, Araneoidea) based on morphological and DNA sequence data.” Cladistics 25: 109-146.
Alberti, G., Giribet. G, and Gutjahr. M. 2009. “Ultrastructure of spermatozoa of different species of Neogoveidae, Sironidae, and Stylocellidae (Cyphophthalmi: Opiliones).” Contributions to Natural History - Scientific papers from the Natural History Museum Bern 12: 53-69.
Wilson, NG, D Huang, MC Goldstein, H Cha, G Giribet, and GW Rouse. 2009. “Field collection of Laevipilina hyalina McLean, 1979 from southern California, the most accessible living monoplacophoran.” Journal of Molluscan Studies 75: 195-197.
Hejnol, A., M. Obst, A. Stamatakis, M. Ott, G. W. Rouse, G.D. Edgecombe, P. Martinez, et al. 2009. “Assessing the root of bilaterian animals with scalable phylogenomic methods.” Proc Biol Sci 276: 4261-70. Abstract

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.

Giribet, G. 2009. “On velvet worms and caterpillars: science, fiction, or science fiction?” Proc Natl Acad Sci U S A 106: E131; author reply E132.
Alberti, G., E Lipke, and G Giribet. 2008. “On the ultrastructure and identity of the eyes of Cyphophthalmi based on a study of Stylocellus sp. (Opiliones, Stylocellidae).” Journal of Arachnology 36: 379-387.
Giribet, G. 2008. “Assembling the lophotrochozoan (=spiralian) tree of life.” Philos Trans R Soc Lond B Biol Sci 363: 1513-22. Abstract

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.

Dunn, C. W., A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, E. Seaver, et al. 2008. “Broad phylogenomic sampling improves resolution of the animal tree of life.” Nature 452: 745-9. Abstract

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

Murienne, J., M. S. Harvey, and G. Giribet. 2008. “First molecular phylogeny of the major clades of Pseudoscorpiones (Arthropoda: Chelicerata).” Mol Phylogenet Evol 49: 170-84. Abstract

The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey--a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.

Clouse, RM, and G Giribet. 2007. “Across Lydekker's Line -- first report of mite harvestmen (Opiliones: Cyphophthalmi: Stylocellidae) from New Guinea.” Invertrabrate Systematics 21: 207-227.