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.
Boyer, SL, RM Clouse, LR Benavides, P Sharma, PJ Schwendinger, I Karunarathna, and G Giribet. 2007. “Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids..” Journal of Biogeography 34: 2070-2085.
Giribet, G, and WC Wheeler. 2007. “The case for sensitivity: a response to Grant and Kluge..” Cladistics 23: 297-296.
Baker, JM, P Funch, and G Giribet. 2007. “Cryptic speciation in the recently discovered American cycliophoran Symbion americanus; genetic structure and population expansion.” Marine Biology 151: 2183-2193.
Benavides, LR, and G Giribet. 2007. “An illustrated catalogue to the South American species of the cyphophthalmid family Neogoveidae (Arthropoda, Opiliones, Cyphophthalmi) with a report on 37 new species..” Zootaxa 1509: 1-15.
Giribet, G, CW Dunn, GD Edgecombe, and GW Rouse. 2007. “A modern look at the Animal Tree of Life..” Linnaeus Tercentenary: Progress in Invertebrate Taxonomy, 61-79. Auckland: Magnolia Press, 61-79.
Baker, JM, and G Giribet. 2007. “A molecular phylogenetic approach to the phylum Cycliophora provides further evidence for cryptic speciation in Symbion americanus..” Zoologica Scripta 36: 353-359.
Giribet, G, PP Sharma, and DB Bastawade. 2007. “A new genus and species of Cyphophthalmi (Arachnida: Opiliones) from the north-eastern states of India..” Zoological Journal of the Linnean Society 151: 663-670.
Boyer, SL, and G Giribet. 2007. “A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New Zealand..” Cladistics 23: 337-361.
Espinasa, L, C Flick, and G Giribet. 2007. “Phylogeny of the American silverfish Cubacubaninae (Hexapoda: Zygentoma: Nicoletiidae): a combined approach using morphology and five molecular loci..” Cladistics 23: 22-40.
Boyer, S.L., J. M. Baker, and G. Giribet. 2007. “Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread 'mite harvestman' defies DNA taxonomy.” Mol Ecol 16: 4999-5016.Abstract

Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi, Pettalidae), a widespread 'mite harvestman' endemic to the South Island of New Zealand, is found in leaf littler habitats throughout Nelson and Marlborough, and as far south as Arthur's Pass. We investigated the phylogeography and demographic history of A. denticulata in the first genetic population-level study within Opiliones. A total of 119 individuals from 17 localities were sequenced for 785 bp of the gene cytochrome c oxidase subunit I; 102 of these individuals were from the Aoraki subspecies A. denticulata denticulata and the remaining 17 were from the subspecies A. denticulata major. An extraordinarily high degree of genetic diversity was discovered in A. denticulata denticulata, with average uncorrected p-distances between populations as high as 19.2%. AMOVA, average numbers of pairwise differences, and pairwise F(ST) values demonstrated a significant amount of genetic diversity both within and between populations of this subspecies. Phylogenetic analysis of the data set revealed many well-supported groups within A. denticulata denticulata, generally corresponding to clusters of specimens from single populations with short internal branches, but separated by long branches from individuals from other populations. No haplotypes were shared between populations of the widespread small subspecies, A. denticulata denticulata. These results indicate a subspecies within which very little genetic exchange occurs between populations, a result consistent with the idea that Cyphophthalmi are poor dispersers. The highly structured populations and deep genetic divergences observed in A. denticulata denticulata may indicate the presence of cryptic species. However, we find a highly conserved morphology across sampling localities and large genetic divergences within populations from certain localities, equivalent to those typically found between populations from different localities. Past geological events may have contributed to the deep genetic divergences observed between sampling localities; additionally, the high divergence within populations of A. denticulata denticulata suggests that the rate of COI evolution may be accelerated in this taxon. In contrast, the larger subspecies A. denticulata major shows much less differentiation between and within sampling localities, suggesting that it may disperse more easily than its smaller counterpart. The fact that the remarkable genetic divergences within populations of A. denticulata denticulata from certain localities are equivalent to divergences between localities poses a challenge to the rapidly spreading practice of DNA taxonomy.

Giribet, G. 2007. “Efficient tree searches with available algorithms.” Evol Bioinform Online 3: 341-56.Abstract

Phylogenetic methods based on optimality criteria are highly desirable for their logic properties, but time-consuming when compared to other methods of tree construction. Traditionally, researchers have been limited to exploring tree space by using multiple replicates of Wagner addition followed by typical hill climbing algorithms such as SPR or/and TBR branch swapping but these methods have been shown to be insufficient for "large" data sets (or even for small data sets with a complex tree space). Here, I review different algorithms and search strategies used for phylogenetic analysis with the aim of clarifying certain aspects of this important part of the phylogenetic inference exercise. The techniques discussed here apply to both major families of methods based on optimality criteria-parsimony and maximum likelihood-and allow the thorough analysis of complex data sets with hundreds to thousands of terminal taxa. A new technique, called pre-processed searches is proposed for reusing phylogenetic results obtained in previous analyses, to increase the applicability of the previously proposed jumpstarting phylogenetics method. This article is aimed to serve as an educational and algorithmic reference to biologists interested in phylogenetic analysis.

Edgecombe, G.D., and G. Giribet. 2007. “Evolutionary biology of centipedes (Myriapoda: Chilopoda).” Annu Rev Entomol 52: 151-70.Abstract

New insights into the anatomy, systematics, and biogeography of centipedes have put these predatory terrestrial arthropods at the forefront of evolutionary studies. Centipedes have also played a pivotal role in understanding high-level arthropod relationships. Their deep evolutionary history, with a fossil record spanning 420 million years, explains their current worldwide distribution. Recent analyses of combined morphological and molecular data provide a stable phylogeny that underpins evolutionary interpretations of their biology. The centipede trunk, with its first pair of legs modified into a venom-delivering organ followed by 15 to 191 leg pairs, is a focus of arthropod segmentation studies. Gene expression studies and phylogenetics shed light on key questions in evolutionary developmental biology concerning the often group-specific fixed number of trunk segments, how some centipedes add segments after hatching whereas others hatch with the complete segment count, the addition of segments through evolution, and the invariably odd number of leg-bearing trunk segments.

Schulze, A., E. B. Cutler, and G. Giribet. 2007. “Phylogeny of sipunculan worms: A combined analysis of four gene regions and morphology.” Mol Phylogenet Evol 42: 171-92.Abstract

The intra-phyletic relationships of sipunculan worms were analyzed based on DNA sequence data from four gene regions and 58 morphological characters. Initially we analyzed the data under direct optimization using parsimony as optimality criterion. An implied alignment resulting from the direct optimization analysis was subsequently utilized to perform a Bayesian analysis with mixed models for the different data partitions. For this we applied a doublet model for the stem regions of the 18S rRNA. Both analyses support monophyly of Sipuncula and most of the same clades within the phylum. The analyses differ with respect to the relationships among the major groups but whereas the deep nodes in the direct optimization analysis generally show low jackknife support, they are supported by 100% posterior probability in the Bayesian analysis. Direct optimization has been useful for handling sequences of unequal length and generating conservative phylogenetic hypotheses whereas the Bayesian analysis under mixed models provided high resolution in the basal nodes of the tree.