The remarkable antiquity, diversity and ecological significance of arthropods have inspired numerous attempts to resolve their deep phylogenetic history, but the results of two decades of intensive molecular phylogenetics have been mixed. The discovery that terrestrial insects (Hexapoda) are more closely related to aquatic Crustacea than to the terrestrial centipedes and millipedes (Myriapoda) was an early, if exceptional, success. More typically, analyses based on limited samples of taxa and genes have generated results that are inconsistent, weakly supported and highly sensitive to analytical conditions. Here we present strongly supported results from likelihood, Bayesian and parsimony analyses of over 41 kilobases of aligned DNA sequence from 62 single-copy nuclear protein-coding genes from 75 arthropod species. These species represent every major arthropod lineage, plus five species of tardigrades and onychophorans as outgroups. Our results strongly support Pancrustacea (Hexapoda plus Crustacea) but also strongly favour the traditional morphology-based Mandibulata (Myriapoda plus Pancrustacea) over the molecule-based Paradoxopoda (Myriapoda plus Chelicerata). In addition to Hexapoda, Pancrustacea includes three major extant lineages of 'crustaceans', each spanning a significant range of morphological disparity. These are Oligostraca (ostracods, mystacocarids, branchiurans and pentastomids), Vericrustacea (malacostracans, thecostracans, copepods and branchiopods) and Xenocarida (cephalocarids and remipedes). Finally, within Pancrustacea we identify Xenocarida as the long-sought sister group to the Hexapoda, a result confirming that 'crustaceans' are not monophyletic. These results provide a statistically well-supported phylogenetic framework for the largest animal phylum and represent a step towards ending the often-heated, century-long debate on arthropod relationships.

Morphological evidence for resolving relationships among arachnid orders was surveyed and assembled in a matrix comprising 59 euchelicerate genera (41 extant, 18 fossil) and 202 binary and unordered multistate characters. Parsimony analysis of extant genera recovered a monophyletic Arachnida with the topology (Palpigradi (Acaromorpha (Tetrapulmonata (Haplocnemata, Stomothecata nom. nov. )))), with Acaromorpha containing Ricinulei and Acari, Tetrapulmonata containing Araneae and Pedipalpi (Amblypygi, Uropygi), Haplocnemata (Pseudoscorpiones, Solifugae) and Stomothecata (Scorpiones, Opiliones). However, nodal support and results from exploratory implied weights analysis indicated that relationships among the five clades were effectively unresolved. Analysis of extant and fossil genera recovered a clade, Pantetrapulmonata nom nov. , with the topology (Trigonotarbida (Araneae (Haptopoda (Pedipalpi)))). Arachnida was recovered as monophyletic with the internal relationships (Stomothecata (Palpigradi, Acaromorpha (Haplocnemata, Pantetrapulmonata))). Nodal support and exploratory implied weights indicated that relationships among these five clades were effectively unresolved. Thus, some interordinal relationships were strongly and/or consistently supported by morphology, but arachnid phylogeny is unresolved at its deepest levels. Alternative hypotheses proposed in the recent literature were evaluated by constraining analyses to recover hypothesized clades, an exercise that often resulted in the collapse of otherwise well-supported clades. These results suggest that attempts to resolve specific nodes based on individual characters, lists of similarities, evolutionary scenarios, etc., are problematic, as they ignore broader impacts on homoplasy and analytical effects on non-target nodes.

Abstract— This paper reports results from a cladistic analysis of the 11 Recent arachnid orders. The polarities of 64 newly discovered and traditional characters were determined through outgroup comparisons that included Eurypterida, Xiphosura, Trilobita and Crustacea. A branch‐and‐bound algorithm was used to discover a single tree (consistency index 0–59). The relationships suggested by this analysis differ substantially from previous interpretations of arachnid phylogeny, and a new taxonomic system is introduced to accommodate these results. This analysis suggests that Arachnida is monophyletic and composed of two principal lineages, Micrura and Dromopoda. Possible synapomorphies of Micrura include a pygidmm, tntosternum, six principal lateral eyes, poorly sclerotized postgenital appendages, coxal gland orifices near leg 1, an array of micxotubules associated with the spermatozoan nucleus, and absence of coxal endites on the walking legs. The micruran orders appear to have the following relationships: (Palpigradi (Araneae (Amblypygi (I helyphonida, Schizomida)))) (Ricinulei, Acari). Possible synapomorphies of Dromopoda include transverse carapaeal furrows, greatly reduced prosomal sternum, prosomal endosternite with two segmental components, stomotheca, bicondylar femoropatellar and patellotibial joints and extensor muscles. The dromopodan orders appear to have the following relationships: Opiliones (Scorpioncs (Pscudo‐scorpiones, Solifugae)).

Recent molecular analyses indicate that crustaceans and hexapods form a clade (Pancrustacea or Tetraconata), but relationships among its constituent lineages, including monophyly of crustaceans, are controversial. Our phylogenetic analysis of three protein-coding nuclear genes from 62 arthropods and lobopods (Onychophora and Tardigrada) demonstrates that Hexapoda is most closely related to the crustaceans Branchiopoda (fairy shrimp, water fleas, etc.) and Cephalocarida + Remipedia, thereby making hexapods terrestrial crustaceans and the traditionally defined Crustacea paraphyletic. Additional findings are that Malacostraca (crabs, isopods, etc.) unites with Cirripedia (barnacles, etc.) and they, in turn, with Copepoda, making the traditional crustacean class Maxillopoda paraphyletic. Ostracoda (seed shrimp)--either all or a subgroup--is associated with Branchiura (fish lice) and likely to be basal to all other pancrustaceans. A Bayesian statistical (non-clock) estimate of divergence times suggests a Precambrian origin for Pancrustacea (600 Myr ago or more), which precedes the first unambiguous arthropod fossils by over 60 Myr.

This study attempts to resolve relationships among and within the four basal arthropod lineages (Pancrustacea, Myriapoda, Euchelicerata, Pycnogonida) and to assess the widespread expectation that remaining phylogenetic problems will yield to increasing amounts of sequence data. Sixty-eight regions of 62 protein-coding nuclear genes (approximately 41 kilobases (kb)/taxon) were sequenced for 12 taxonomically diverse arthropod taxa and a tardigrade outgroup. Parsimony, likelihood, and Bayesian analyses of total nucleotide data generally strongly supported the monophyly of each of the basal lineages represented by more than one species. Other relationships within the Arthropoda were also supported, with support levels depending on method of analysis and inclusion/exclusion of synonymous changes. Removing third codon positions, where the assumption of base compositional homogeneity was rejected, altered the results. Removing the final class of synonymous mutations--first codon positions encoding leucine and arginine, which were also compositionally heterogeneous--yielded a data set that was consistent with a hypothesis of base compositional homogeneity. Furthermore, under such a data-exclusion regime, all 68 gene regions individually were consistent with base compositional homogeneity. Restricting likelihood analyses to nonsynonymous change recovered trees with strong support for the basal lineages but not for other groups that were variably supported with more inclusive data sets. In a further effort to increase phylogenetic signal, three types of data exploration were undertaken. (1) Individual genes were ranked by their average rate of nonsynonymous change, and three rate categories were assigned--fast, intermediate, and slow. Then, bootstrap analysis of each gene was performed separately to see which taxonomic groups received strong support. Five taxonomic groups were strongly supported independently by two or more genes, and these genes mostly belonged to the slow or intermediate categories, whereas groups supported only by a single gene region tended to be from genes of the fast category, arguing that fast genes provide a less consistent signal. (2) A sensitivity analysis was performed in which increasing numbers of genes were excluded, beginning with the fastest. The number of strongly supported nodes increased up to a point and then decreased slightly. Recovery of Hexapoda required removal of fast genes. Support for Mandibulata (Pancrustacea + Myriapoda) also increased, at times to "strong" levels, with removal of the fastest genes. (3) Concordance selection was evaluated by clustering genes according to their ability to recover Pancrustacea, Euchelicerata, or Myriapoda and analyzing the three clusters separately. All clusters of genes recovered the three concordance clades but were at times inconsistent in the relationships recovered among and within these clades, a result that indicates that the a priori concordance criteria may bias phylogenetic signal in unexpected ways. In a further attempt to increase su...

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7.5 Neil Arwmr, Columbu \ , Ohio 4. 3' 21 0, 1 -. S. ~ 1. 'Ihe nioiqhoIoy( ' 11 diversit! of locomotor appendages in hrachnida i\ \uin r)rd t(i IWC o i i \ t i uct phylogrnctir. iwlritiu~isllips .ind discover e\ olutionar) trends in h r m and function. 'l'hc appcntiic u1;11-Skrlctoii and mujculatiirr d' rrpresentati\ r s from the ten li\ irla arachnid ordcr, 'it r described. . i n d a system of Iiornoloqv is proposed. Character polarities arc cstablishrd through c(impariso~r u it11 d u outgroup. Iirriuicir ~O~@ / Z P V I U J Xiphosural. Cladistic analysis suggrsts t h a t Ar,rchnitlci is mcinopIi>h~tic .itid that ahsrnce of cxtcnsor muscles is a primiti\ e condition. Extrnsol-\ are primiti\ rI? Iiliw~it i n Aranc;ic. .Amblypypi. Crop!gi. I'alpigradi, Kicitlulei and Acari. .\loat similarities i i i t l i r appendages of these orders are symplcsiomorphic SO that pliylogcnrti( rclationsliip~ 'iinotig thr 'rxtcnsorlrss' groups cannot be rraolved ~k l y on tlic I i r i s i y appcndic ulaI charactcry. tutrrisor rnusrlcs ;rppc;ir i o h a \ ? rvol\ed onrr, ;ind their prcsmcc i s considci-rd a synapomoi-plii(. ti,;rturc of Opiliones. Scorpionrs, Pseudoarorpiones and Solifugac. SolifilgCic 1.1ck rxtrnson. h u t ' I I)arsinloniorr\ interprctation of other characters indicatrs that this is a sccondni-) , dcrivrd condition. 'Ilie ph)-logrnetic rrlationships among these four orden arc claritird I ] ! -modification\ of tlic patrllotibial joint. Cladistic analysis indicates thai 0piliont.s may br thv \ i m r qroup of thr otlivr thrrc ordcrs arid that Scorpiones is thr sister group (if Pscudr)sc(~rpio~~r\ 'inti Solifugae. Conrlusions concerning phylogrnetir relationships and r\olutionary morpholoq presrntcd hrrc dlfrer subtantiall!-from those of carlier studies on the Iocomritor appcnddg's of Arach nitla.

Recent phylogenetic analyses using molecular data suggest that hexapods are more closely related to crustaceans than to myriapods, a result that conflicts with long-held morphology-based hypotheses. Here we contribute additional information to this debate by conducting phylogenetic analyses on two nuclear protein-encoding genes, elongation factor-1 alpha (EF-1 alpha) and the largest subunit of RNA polymerase II (Pol II), from an extensive sample of arthropod taxa. Results were obtained from two data sets. One data set comprised 1092 nucleotides (364 amino acids) of EF-1 alpha and 372 nucleotides (124 amino acids) of Pol II from 30 arthropods and three lobopods. The other data set contained the same EF-1 alpha fragment and an expanded 1038-nucleotide (346-amino-acid) sample of Pol II from 17 arthropod taxa. Results from maximum-parsimony and maximum-likelihood analyses strongly supported the existence of a Crustacea + Hexapoda clade (Pancrustacea) over a Myriapoda + Hexapoda clade (Atelocerata). The apparent incompatibility between the molecule-based Pancrustacea hypothesis and morphology-based Atelocerata hypothesis is discussed.