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This document comprising guidelines for authors, is divided into three sections. The editor kindly requests that authors respect these guidelines. This abstract should be no longer than ten lines. An abstract in French should also be given. Both are written in Times New Roman 9pt on 11pt, italic, with a space of 3pt in between each subsection. RSUM: L'ensemble des consignes rassembles ci-dessous s'organise en trois rubriques. La rdaction remercie les auteurs pour le strict respect qu'ils accorderont ces dispositions. La taille de ce rsum ne doit pas dpasser une dizaine de lignes. Il est composer en Times corps 9 italique, interlign 11 points. Un rsum en anglais doit l'accompagner. KEY WORDS: a maximum of six significant words should be chosen in English and in French and presented as key words MOTS-CLS: un maximum de six mots significatifs, en franais et en anglais, doivent tre isols sous forme de mots-cls 122 Title of journal. Volume X -- No. X/2000 1.

Recent Nematoda includes 3 classes, 31 orders, 267 families, 2829 genera and 24,783 species, with fossil taxa represented in 2 genera by 10 species. There are 7 genera and 7 species known only as fossils. 2. Rudolphi (1808) is most often cited as the author of the accepted name of the phylum, which is Nematoda. The first holophyletic diagnosis at Phylum rank used the name "Nemates " (Cobb 1932). The latter name has never been in wide use, and the competing claims of the two names have been discussed extensively (Chitwood 1957, 1958, Dougherty 1958a, 1958b). Following the principle outlined below, Cobb (1932) is cited as authority because his use is specifically as a phylum. 3. The evolutionary affinities of Nematoda have long been controversial (see discussion in Hodda 2007). The most recent molecular evidence has favoured affinities first with Nematomorpha, then with decreasing relationships to Kinorhyncha, Priapulida and Loricifera within a superphylum Ecdysozoa (Aguinaldo et al. 1997, Dunn et al. 2008). However, significant unresolved differences between phylogenies hypothesised using different taxa, assumptions, methods and lines of evidence remain. 4. Unless indicated otherwise, the classification follows Hodda (2007). The higher classification of the phylum has been interpreted in many ways, with consequent changes in the hierarchical level of many names (Hodda 2007). Above the level of the genus nematode classification has been—and continues to be—volatile. Particularly, analyses of accumulating molecular data have produced only broadly similar phylogenies,

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Abstract. — We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relation-ships in the South American "lava lizards " (genus Microlophus) and describe a strategy for aligning noncoding sequences that accounts for differences in tempo and class of mutational events. We focus on seven nuclear introns that vary in size and frequency of multibase length mutations (i.e., indels) and present a manual alignment strategy that incorporates insertions and deletions (indels) for each intron. Our method is based on mechanistic explanations of intron evolution that does not require a guide tree. We also use a progressive alignment algorithm (Probabilistic Alignment Kit; PRANK) and distinguishes insertions from deletions and avoids the "gapcost " conundrum. We describe an approach to selecting a guide tree purged of ambiguously aligned regions and use this to refine PRANK performance. We show that although manual alignment is successful in finding repeat motifs and the most obvious indels, some regions can only be subjectively aligned, and there are limits to the size and complexity of a data matrix for which this approach can be taken. PRANK alignments identified more parsimony-informative indels while simultaneously increasing nucleotide identity in conserved sequence blocks flanking the indel regions. When comparing manual and PRANK with two widely used methods (CLUSTAL, MUSCLE) for the alignment of the most length-variable intron, only PRANK recovered a tree congruent at deeper nodes with the combined data tree inferred from all nuclear gene regions. We take this concordance as an objective function of alignment quality and present a strongly supported phylogenetic hypothesis for Microlophus relationships. From this hypothesis we show that

2 This document provides additional information for the 10kTrees Project. If you have questions or comments, feel free to contact me, Christian Arnold (carnold@fas.harvard.edu). I will be happy to answer any questions related to this project as well as questions related to the web-implementation.