Giribet, G. 2002. “Current advances in the phylogenetic reconstruction of metazoan evolution. A new paradigm for the Cambrian explosion?.” Mol Phylogenet Evol 24: 345-57.Abstract

The study of metazoan evolution has fascinated biologists for centuries, and it will certainly keep doing so. Recent interest on the origin of metazoan body plans, early metazoan evolution, genetic mechanisms generating disparity and diversity, molecular clock information, paleontology, and biogeochemistry is contributing to a better understanding of the current phyletic diversity. Unfortunately, the pattern of the metazoan tree of life still shows some important gaps in knowledge. It is the aim of this article to review some of the most important issues related to the inference of the metazoan tree, and point towards possible ways of solving certain obscure aspects in the history of animal evolution. A new hypothesis of the metazoan diversification during the Cambrian explosion is proposed by synthesizing ideas from phylogenetics, molecular evolution, paleontology, and developmental biology.

Giribet, G., W.C. Wheeler, and J. Muona. 2002. “DNA multiple sequence alignments.” EXS, 107-14.Abstract

In this chapter we examine the procedure of multiple sequence alignment. We first examine the heuristic procedures commonly used in multiple sequence alignment. Next we examine sources of ambiguity involved in the alignment procedure. We suggest that several alignment parameters be employed to examine alignment sensitivity. We end by presenting an experiment with humans showing the ambiguity involved in manual alignment.

Giribet, G., G.D. Edgecombe, W.C. Wheeler, and C. Babbitt. 2002. “Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data.” Cladistics 18: 5-70.Abstract

The ordinal level phylogeny of the Arachnida and the suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morphological characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for the morphological data matrix and via direct optimization for the molecular and combined data matrices. A sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelicerate relationships (except for Tetrapulmonata, Pedipalpi, and Camarostomata), and the sister group of the Opiliones is not clearly established, although the monophyly of Dromopoda is supported under many parameter sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi (Eupnoi (Dyspnoi + Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opiliones.

Giribet, G., R. DeSalle, and W.C. Wheeler. 2002. “'Pluralism' and the aims of phylogenetic research.” EXS, 141-6.Abstract

In science, and particularly in the field of phylogenetic systematics, investigators may choose among different methods to analyze their data. These methods include neighbor-joining (or other genetic distance approaches), maximum-likelihood, and cladistic parsimony, among others. These distinct methods of analysis differ considerably in how they process information from the observed data. However, many published molecular analyses utilize trees generated under more than one of these methods, which we will call a 'pluralistic' approach. Here, we explore the statistical, philosophical and operational aspects of the pluralistic approach. We suggest that the pluralistic approach is misguided from all three perspectives and we propose an alternative, logically consistent, strategy as an aim of phylogenetic research.

Giribet, G. 2002. “Relationships among metazoan phyla as inferred from 18S rRNA sequence data: a methodological approach.” EXS, 85-101.Abstract

The relationships among the phyla of Metazoa have been investigated by several authors. Different genes have been applied to this problem, but only the ribosomal gene 18S rRNA has been investigated for enough phyla so as to attempt an answer to the question of how the current living forms are related to each other (only one phylum, the Loricifera, is missing). In this chapter, I propose an alternative way to analyze the data obtained from ribosomal genes, or other non-coding genes that show sequence length variation.

Giribet, G, and WC Wheeler. 2001. “Some unusual small-subunit ribosomal RNA sequences of metazoans..” American Museum Novitates 3337: 1-14.
Giribet, G., G.D. Edgecombe, and W.C. Wheeler. 2001. “Arthropod phylogeny based on eight molecular loci and morphology.” Nature 413: 157-61.Abstract

The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

Giribet, G. 2001. “Exploring the behavior of POY, a program for direct optimization of molecular data.” Cladistics 17: S60-70.Abstract

The performance of the computer program for phylogenetic analysis, POY, and its two implemented methods, "optimization alignment" and "fixed-states optimization," are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are undertaken according to gap cost, number of fragments in which the sequences are divided, tree length, character congruence, topological congruence, primary homology statements, and computation time.

Giribet, G. 2000. “Catalogue of the Cyphophthalmi of the World (Arachnida, Opiliones).” Revista Iberica de Aracnologia 2: 49-76.
Giribet, G, and C Ribera. 2000. “A review of arthropod phylogeny: new data based on ribosomal DNA sequences and direct character optimization..” Cladistics 16: 204-231.
Giribet, G., D. L. Distel, M. Polz, W. Sterrer, and W.C. Wheeler. 2000. “Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology.” Syst Biol 49: 539-62.Abstract

Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, which seems to happen because of the extreme distance that separates diploblastic from triploblastic taxa according to the 18S rDNA data. Multiple phylogenetic analyses performed with variable analysis parameters yield largely inconsistent results for certain groups such as Chaetognatha, Acoela, and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis having the least character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha) (Nematoda + Nematomorpha)) ((Onychophora + Tardigrada) Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda) (Entoprocta (Nemertea (Sipuncula (Mollusca (Pogonophora (Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida (Cycliophora + Syndermata)) (Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time, a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, Biol. Rev. 73:203-266, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (= Gnathifera), which is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata.

Baguna, J., S. Carranza, M Pala, C Ribera, G Giribet, MA Arnedo, M Ribas, and M Riutort. 1999. “From morphology and karyology to molecules. New methods for taxonomical identification of asexual populations of freshwater planarians. A tribute to Professor Mario Benazzi..” Italian Journal of Zoology 66: 207-214.
Giribet, G, and WC Wheeler. 1999. “On gaps..” Molecular Phylogenetics and Evolution 13: 132-143.
Giribet, G, M Rambla, S Carranza, J Baguna, M Riutort, and C Ribera. 1999. “Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S and partial 28S ribosomal DNA sequences and morphology..” Molecular Phylogenetics and Evolution 11: 296-307.
Giribet, G, and A Penas. 1999. “Revision of the genus Goodallia (Bivalvia: Astartidae) with the description of two new species..” Journal of Molluscan Studies 65: 251-265.
Giribet, G, and WC Wheeler. 1999. “On gaps.” Mol Phylogenet Evol 13: 132-43.Abstract

Gaps result from the alignment of sequences of unequal length during primary homology assessment. Viewed as character states originating from particular biological events (mutation), gaps contain historical information suitable for phylogenetic analysis. The effect of gaps as a source of phylogenetic data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitrary (although they must be explicit) and thus data exploration is a necessity of molecular analyses, while character congruence is necessary as an external criterion for hypothesis decision.

Giribet, G., S. Carranza, M. Riutort, J. Baguna, and C. Ribera. 1999. “Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences.” Philos Trans R Soc Lond B Biol Sci 354: 215-22.Abstract

The internal phylogeny of the 'myriapod' class Chilopoda is evaluated for 12 species belonging to the five extant centipede orders, using 18S rDNA complete gene sequence and 28S rDNA partial gene sequence data. Equally and differentially weighted parsimony, neighbour-joining and maximum-likelihood were used for phylogenetic reconstruction, and bootstrapping and branch support analyses were performed to evaluate tree topology stability. The results show that the Chilopoda constitute a monophyletic group that is divided into two lines, Notostigmophora (= Scutigeromorpha) and Pleurostigmophora, as found in previous morphological analyses. The Notostigmophora are markedly modified for their epigenic mode of life. The first offshoot of the Pleurostigmophora are the Lithobiomorpha, followed by the Craterostigmomorpha and by the Epimorpha s. str. (= Scolopendromorpha + Geophilomorpha), although strong support for the monophyly of the Epimorpha s. lat. (= Craterostigmomorpha + Epimorpha s. str.) is only found in the differentially weighted parsimony analysis.

Giribet, G, M Rambla, S Carranza, J Baguna, M Riutort, and C Ribera. 1999. “Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S and partial 28S ribosomal DNA sequences and morphology.” Mol Phylogenet Evol 11: 296-307.Abstract

The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones were investigated by means of molecular (complete 18S rDNA and the D3 region of the 28S rDNA genes) and morphological data sets. Equally and differentially weighted parsimony analyses of independent and combined data sets provide evidence for the monophyly of the Opiliones. In all the analyses, the internal relationships of the group coincide in the monophyly of the following main groups: Cyphophthalmi, Eupnoi Palpatores, Dyspnoi Palpatores, and Laniatores. The Cyphophthalmi are monophyletic and sister to a clade that includes all the remaining opilionid taxa (=Phalangida). Within the Phalangida the most supported hypothesis suggests that Palpatores are paraphyletic, as follows: (Eupnoi (Dyspnoi + Laniatores)), but the alternative hypothesis (Laniatores (Eupnoi + Dyspnoi)) is more parsimonious in some molecular data analyses. Relationships within the four main clades are also addressed. Evolution of some morphological characters is discussed, and plesiomorphic states of these characters are evaluated using molecular data outgroup polarization. Finally, Martens' hypothesis of opilionid evolution is assessed in relation to our results.

Giribet, G., and W.C. Wheeler. 1999. “The position of arthropods in the animal kingdom: Ecdysozoa, islands, trees, and the "Parsimony ratchet".” Mol Phylogenet Evol 13: 619-23.
Giribet, G., and S. Carranza. 1999. “What can 18S rDNA do for bivalve phylogeny?.” J Mol Evol 48: 256-61.