Molecular phylogeny of the major arthropod groups indicates polyphyly of crustaceans and a new hypothesis for the origin of hexapods.

A phylogeny of the arthropods was inferred from analyses of amino acid sequences derived from the nuclear genes encoding elongation factor-1 alpha and the largest subunit of RNA polymerase II using maximum-parsimony, neighbor-joining, and maximum-likelihood methods. Analyses of elongation factor-1 alpha from 17 arthropods and 4 outgroup taxa recovered many arthropod clades supported by previous morphological studies, including Diplopoda, Myriapoda, Insecta, Hexapoda, Branchiopoda (Crustacea), Araneae, Tetrapulmonata, Arachnida, Chelicerata, and Malacostraca (Crustacea). However, counter to previous studies, elongation factor-1 alpha placed Malacostraca as sister group to the other arthropods. Branchiopod crustaceans were found to be more closely related to hexapods and myriapods than to malacostracan crustaceans. Sequences for RNA polymerase II were obtained from 11 arthropod taxa and were analyzed separately and in combination with elongation factor-1 alpha. Results from these analyses were concordant with those derived from elongation factor-1 alpha alone and provided support for a Hexapoda/Branchiopoda clade, thus arguing against the monophyly of the traditionally defined Atelocerata (Hexapoda + Myriapoda).

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title: Disparity as an evolutionary index; a comparison of Cambrian and Recent arthropods
abstract: Disparity is a measure of the range or significance of morphology in a given sample of organisms, as opposed to diversity, which is expressed in terms of the number (and sometimes ranking) of taxa. At present there is no agreed definition of disparity, much less any consensus on how to measure it. Two possible categories of metric are considered here, one independent of any hypothesis of relationship (phenetics), the other constrained within an evolutionary framework (cladistics). The Early Cambrian radiation was clearly a period of significant morphologic and taxonomic diversification. However, we question the interpretation of its first generation products as numerous body plans at the highest level. Four phenetic and two cladistic measures have been used to compare disparity among Cambrian arthropods with that in the living fauna. Phenetic methods assessing character-state variability and the amount of morphological attribute space occupied yield similar results for Cambrian and Recent arthropods. Assessments of disparity within a taxonomic framework rely on the identification of particular characters that delineate higher level body plans. This requires a phylogenetic interpretation, a cladistic investigation of hierarchical structure in the data. Both sets of arthropods fall within the same major clades, and within this cladistic framework the amount of character-state evolution in the two groups is comparable. None of these methods identifies markedly greater disparity among the Cambrian compared with the Recent taxa. Although measures of disparity are applied here to a consideration of the Cambrian radiation, the metrics clearly have a much wider potential for estimating macroevolutionary trends independently from existing taxonomic frameworks. Geometric morphometry is ideal for measuring morphological variety at lower taxonomic levels, but it requires the recognition of homologous landmarks in all the forms under comparison, or the identification of entire homologous structures. Conventional phenetics has much wider application as it can operate on data coded as discrete homologous character states (this facility is also a requirement of cladistics), which are a more appropriate basis for comparing disparity in markedly dissimilar forms.

title: Insect-Crustacean Relationships: Insights from Comparative Developmental and Molecular Studies
abstract: The phylogenetic relationships between the major arthropod groups are still far from being resolved. Phylogenetic analyses have usually relied on detailed morphological comparisons which are confounded by the extensive occurrence of convergence. We examine the available morphological evidence in the light of recent comparative developmental and molecular studies and suggest ways in which genetic-developmental information could help assess homology and overcome the problem of convergence. On the basis of such considerations we support the common origin of crustaceans and insects from a crustacean-like mandibulate ancestor. Focusing on the specific relationships between crustaceans, myriapods and insects, we suggest that insects could emerge from this crustacean-like ancestor independently from myriapods, and after the major crustacean radiations.

title: The Development of Crustacean Limbs and the Evolution of Arthropods
abstract: Arthropods exhibit great diversity in the position, number, morphology, and function of their limbs. The evolutionary relations among limb types and among the arthropod groups that bear them (insects, crustaceans, myriapods, and chelicerates) are controversial. Here, the use of molecular probes, including an antibody to proteins encoded by arthropod and vertebrate Distal-less (Dll and Dlx) genes, provided evidence that common genetic mechanisms underlie the development of all arthropod limbs and their branches and that all arthropods derive from a common ancestor. However, differences between crustacean and insect body plans were found to correlate with differences in the deployment of particular homeotic genes and in the ways that these genes regulate limb development.

title: Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain
abstract: SummaryPhylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the “eocyte tree” (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletia-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.

title: Phylogenetic Information Content of Five Nuclear Gene Sequences in Animals: Initial Assessment of Character Sets from Concordance and Divergence Studies
abstract: The phylogenetic information content of five nuclear genes encoding amino acid sequences was assessed on the basis of their character support of well-established "test" phy? logenies and their ability to recover these phylogenies using parsimony methods. The five genes encode dopa decarboxylase, phosphoenolpyruvate carboxykinase, RNA polymerase ll (largest subunit), elongation factor-2, and elongation factor-la. The analyses employ the unambiguously alignable portions of all available animal sequences for these genes, representing a range of divergence times from about 10 to >550 million years ago. Separate analyses, including character mappings on the test phylogenies and, when different, on the most-parsimonious trees, were performed with nucleotides separated by codon position and with amino acids. Pairwise sequence divergences were calculated for all comparisons and are related to character information content. Amino acid and most nucleotide character sets recovered the test phylogenies, although with varying degrees of support, homoplasy, and resolution, confirming that these genes contain substantial phylogenetic information. An estimate is provided of the time span over which each character set in each gene will prove phylogenetically most informative. These genes should prove widely useful for systematics. (Nuclear genes; animals; character sets; sequence diver? gences; concordance studies.

title: Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data
abstract: SummaryPhylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1α by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.

title: The "Uniramia" do not exist: the ground plan of the Pterygota as revealed by Permian Diaphanopterodea from Russia (Insecta: Paleodictyopteroidea)
abstract: The paleomorphology of extinct Paleozoic Diaphanopterodea (Paleodictyopteroidea: Paleoptera) in exceptionally well-preserved Lower Permian Uralia (Parelmoidea) and Paruralia (Paruraliidae) from Tsh...

title: ARTHROPOD PHYLOGENY: A COMBINED APPROACH
abstract: Ribosomal and ubiquitin protein coding sequence data are generated from 20 arthropods and five close relatives. These molecular data are combined with morphological characters derived from the literature to approach arthropod phylogenetics from the perspective of total evidence. Trilobita were included in the analysis through morphological comparison alone. The overall data strongly support arthropod monophyly. Recent molecular analyses which have yield different results are shown to have been based on few characters, few taxa or both. The most parsimonious explanation of the data is (Annelida + (Onychophora + (Trilobita + Chelicerata) + (Crustacea + (Myriapoda + Hexapoda))))). The data are largely concordant both internally among data sets and externally with previous cladistic anatomical analyses.

title: Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods.
abstract: The evolutionary relationships of the onychophorans (velvet worms) and the monophyly of the arthropods have generated considerable debate. Cladistic analyses of 12S ribosomal RNA sequences indicate that arthropods are monophyletic and include the onychophorans. Maximum parsimony analyses and monophyly testing within arthropods indicate that myriapods (millipedes and centipedes) form a sister group to all other assemblages, whereas crustaceans (shrimps and lobsters) plus hexapods (insects and allied groups) form a well-supported monophyletic group. Parsimony analysis further suggests that onychophorans form a sister group to chelicerates (spiders and scorpions) and crustaceans plus hexapods, but this relationship is not well supported by monophyly testing. These relationships conflict with current hypotheses of evolutionary pathways within arthropods.

title: Homologies in Cambrian Onychophora
abstract: Marine animals related to Recent onychophorans form a significant component in Cambrian faunas. Twelve characters are analysed for homologies in the seven best known Cambrian onychophorans. New morphological evidence and homology analyses for several characters indicate an anteroposterior reversal of Hallucigenia and Microdictyon. Proposed expansion of the trunk in Microdietyon during compaction is rejected. A jaw is tentatively identified in Onychodictyon. The shape of the annulations and the disposition of the tenth leg pair in Aysheaia are reinterpreted, and the suggestion of two somites to the first appendage pair is rejected. A suggested morphocline may mirror the phylogeny of the group. The taxonomic confusion surrounding the supposed radiolarian family Eoconchariidae is cleared

title: Ribosomal DNA phylogeny of the major extant arthropod classes and the evolution of myriapods
abstract: THE evolutionary relationships among arthropods are of particular interest because the best-studied model system for ontogenetic pattern formation, the insect Drosophila, is a member of this phylum. Evolutionary inferences about the developmental mechanisms that have led to the various designs of the arthropod body plan depend on a knowledge of the phylogenetic framework of arthropod evolution. Based on morphological evidence13, but also on palaeonto-logical considerations4, the sister group of the insects is believed to be found among the myriapods. Using nuclear ribosomal gene sequences for constructing a molecular phylogeny, we provide strong evidence that the crustaceans and not the myriapods should be considered to be the sister group of the insects. Moreover, the degree of sequence divergence suggests that the diversification of the myriapods occurred during the Cambrian, Our findings have general implications for the course of land colonization by the different arthropod groups, as well as for the interpretation of primitive and derived features of arthropod morphology.

title: Arthropod evolution: great brains, beautiful bodies.
abstract: While arthropod phylogeny remains controversial, comparative studies of the genetic control of segmentation and of the nervous system have begun to throw light on how mandibulate arthropods (myriapods, crustaceans and insects) reached their current level of morphological and behavioural complexity. Insects and crustaceans show remarkable similarities in the construction of their brains, suggesting that their common ancestor had typically arthropod behaviour, while developmental genetic studies are consistent with this ancestor having had distinct head, trunk and tail regions. This conclusion contrasts with the influential view, drawn from comparative embryology and functional anatomy, that insects and crustaceans evolved independently from a simple worm-like organism, perhaps resembling an annelid.

title: Molecular phylogeny of the animal kingdom.
abstract: A rapid sequencing method for ribosomal RNA was applied to the resolution of evolutionary relationships among Metazoa. Representatives of 22 classes in 10 animal phyla were used to infer phylogenetic relationships, based on evolutionary distances determined from pairwise comparisons of the 18S ribosomal RNA sequences. The classical Eumetazoa are divided into two groups. Cnidarians arose from a protist ancestry different from the second group, the Bilateria. Within the Bilateria, an early split gave rise to Platyhelminthes (flatworms) and the coelomate lineage. Coelomates are thus monophyletic, and they radiated rapidly into four groups: chordates, echinoderms, arthropods, and eucoelomate protostomes.

title: Cladistic permutation tests for monophyly and nonmonophyly
abstract: Recent work on randomization or permutation tests for cladistic structure (Archie, 1989a, 1989b; Faith, 1990; Faith and Cranston, 1991) has revealed some dramatic cases in which apparently phylogenetically informative data in fact have structure that could easily be matched by chance alone. In these tests a particular null model is used in which each character's states are reassigned randomly to the taxa, so that the resulting randomized data set represents random covariation among the characters. The corresponding null hypothesis is that the observed hierarchical structure could be found for such randomized data. A necessary companion to the randomcharacter-covariation null model is some criterion for evaluating and quantifying hierarchical structure. This measure of structure represents a criterion model that prescribes the manner in which the data are expected to relate to the underlying pattern (Faith and Cranston, 1991). In the examples referred to above, hierarchical structure is measured by the length of the corresponding minimum-length tree (other measures of hierarchical structure have been used in a general version of this test; see Faith [1991]). The choice of the parsimony criterion of cladistics implies that the null hypothesis is evaluated by comparing the observed minimum length to that achieved for many randomized data sets. The proportion of all sets (observed and random) having lengths as short as or shorter than the observed length yields the "cladistic permutation tail probability," or PTP (Faith and Cranston, 1991; the same test was independentlyl proposed by Archie [1989a]). The null hypothesis may be rejected, for example at the usual 0.05 level, if 5% or fewer of the data sets have a length equal to or less than that of the original (PTP < 0.05). One of the initial applications of this test (Faith, 1990) and the reply to it (Thomas et al., 1990) have raised some important points of controversy that will be addressed in this paper. In an earlier paper, Thomas et al. (1989) used 12S ribosomal RNA gene sequence data to explore the relationships among South American and Australian marsupials, addressing longstanding controversies about the relationship of the presumed-extinct thylacine (Thylacinus) to these other taxa. Based on their cladistic analysis of these data, they argued that the thylacine is not an outgroup to the Australian marsupials, and is the sister of the Dasyuridae. However, application of the PTP test showed that this data set, which consisted of only seven phylogenetically informative characters (Table la), did not have significant cladistic structure. Thus, the 12S ribosomal RNA gene sequence data constituted insufficient evidence for the inference of the phylogenetic relationship of the thylacine to these other taxa (Faith, 1990). In their reply, Thomas et al. (1990) argued that although the data set as a whole did not have significant hierarchical structure, this was not directly relevant to their hypothesis of interest, which was represented in their reply as the specific question of the monophyly of thylacines and dasyurids. They claimed that, for the evaluation of such hypotheses of monophyly, the bootstrap (Felsenstein, 1985) was a more powerful test (see also Archie, 1989a). Application of the bootstrap test revealed significant support for their hypothesis of

title: COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE?: ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE
abstract: Absolute criteria for evaluating cladistic analyses are useful, not only because cladistic algorithms impose structure, but also because applications of cladistic results demand some assessment of the degree of corroboration of the cladogram. Here, a means of quantitative evaluation is presented based on tree length. The length of the most‐parsimonious tree reflects the degree to which the observed characters co‐vary such that a single tree topology can explain shared character states among the taxa. This “cladistic covariation” can be quantified by comparing the length of the most parsimonious tree for the observed data set to that found for data sets with random covariation of characters. A random data set is defined as one in which the original number of characters and their character states are maintained, but for each character, the states are randomly reassigned to the taxa. The cladistic permutation tail probability, PTP, is defined as the estimate of the proportion of times that a tree can be found as short or shorter than the original tree. Significant cladistic covariation exists if the PTP is less than a prescribed value, for example, 0.05. In case studies based on molecular and morphological data sets, application of the PTP shows that:

title: Ribosomal RNA in Vertebrates: Evolution and Phylogenetic Applications
abstract: Many evolutionary biologists seek to learn about genealogy among life forms. Toward this end, researchers have sought out informative systems or characters from fields as disparate as behavior, morphology, physiology, biogeography, and molecular genetics. DNA sequences in particular appear promising for resolving evolutionary questions, due in part to the fact that they constitute the physical material of inheritance in its most particulate form. However, the promise of DNA rests on the assumption that historical change in nucleotide sequences can be inferred unambiguously from sequences of extant (or recently extinct) forms, and this task remains as a challenge. It is important to recognize that the pursuits of molecular systematics (history of descent among organisms) and molecular evolution (history of change among and within molecules) are mutually informing. Molecular systematic studies have been instrumental in studies of molecular evolution because patterns of sequence change over thousands and millions of years can be inferred only by comparing sequences among taxa whose divergences span

title: Ubiquitins revisited: further examples of within- and between-locus concerted evolution.
abstract: Ubiquitin genes provide a model for studying the effects of concerted evolution on the evolution of a family of short repeated sequences. Previous work has demonstrated the occurrence of within-locus concerted evolution and raised the question of the effectiveness of between-locus concerted evolution for ubiquitin repeats. In this study comparative analysis of additional nucleotide sequences of ubiquitin tandem repeats provides further details of within-locus concerted evolution. Moreover, the availability of multiple polyubiquitin loci and ubiquitin fusion loci within a species makes possible the detection of between-locus concerted evolution. These data indicate that concerted evolution is an effective force for homogenizing repeats between, as well as within, loci.

title: A Concern for Evidence and a Phylogenetic Hypothesis of Relationships among Epicrates (Boidae, Serpentes)
abstract: -Character congruence, the principle of using all the relevant data, and character independence are important concepts in phylogenetic inference, because they relate directly to the evidence on which hypotheses are based. Taxonomic congruence, which is agreement among patterns of taxonomic relationships, is less important, because its connection to the underlying character evidence is indirect and often imperfect. Also, taxonomic congruence is difficult to justify, because of the arbitrariness involved in choosing a consensus method and index with which to estimate agreement. High levels of character congruence were observed among 89 biochemical and morphological synapomorphies scored on 10 species of Epicrates. Such agreement is consistent with the phylogenetic interpretation attached to the resulting hypothesis, which is a consensus of two equally parsimonious cladograms: (cenchria (angulifer (striatus ((chrysogaster, exsul) (inornatus, subflavus) (gracilis (fordii, monensis)))))). Relatively little (11.4%) of the character incongruence was due to the disparity between the biochemical and morphological data sets. Each of the clades in the consensus cladogram was confirmed by two or more unique and unreversed novelties, and six of the eight clades were corroborated by biochemical and morphological evidence. Such combinations of characters add confidence to the phylogenetic hypothesis, assuming the qualitatively different kinds of data are more likely to count as independent than are observations drawn from the same character system. Most of the incongruence occurred in the skeletal subset of characters, and much of that independent evolution seemed to be the result of paedomorphosis.  The goals of cladistics and phenetics are different. The former estimates phylogeny (Hennig, 1966), the latter seeks stability and convenience in classification (Sokal, 1986:424). Unfortunately, these objectives have become confused, especially where stability is concerned. For example, Hillis (1987:35) stated that "[c]lassifications are best based on information in common among multiple data sets (i.e., consensus trees), whereas the best estimate of phylogeny and best estimate of character evolution are represented in the analysis of the combined data sets." The importance of a conservative information storage-retrieval system is undeniable (e.g., International Code of Zoological Nomenclature, 1985:3), and pheneticists sought justification for their methods in this simple truth (Sokal and Sneath, 1963). Even cladists attributed some significance to stability per se, because the lack of it confounds attempts to discover the single historical pattern (Schuh and Farris, 1981). Not unexpectedly, cladists responded (e.g., Farris, 1971) to the proposition that phenetic methods produce more stable classifications (e.g., Sokal and Sneath, 1963: 264). Analytical precision was demanded by the contestants, and an incredible array of consensus methods and indexes were developed (see lists below). It is important to bear in mind that only information on taxonomic grouping can be used to evaluate the pheneticists' claims, because character congruence is difficult to judge in phenetic analyses. Eventually, the controversy over stability became a relative issue, with cladists arguing greater stability for classifications produced by their methods, as if stability was a goal of phylogenetic systematics. Further, Nelson and Platnick (1981:219; see also Nelson, 1979) attempted to justify cla-

title: High and low annealing temperatures increase both specificity and yield in touchdown and stepdown PCR.
abstract: Touchdown (TD) PCR represents a versatile one-step procedure for optimizing PCRs even if the degree of primer-template complementarity is not fully known. The protocol relies on incremental annealing temperature decreases in progressive cycles designed to bracket the melting temperature (Tm) of the reaction. Here we investigate the characteristics of TD PCR that serve to minimize the need to optimize annealing temperature or buffer conditions and yet produce single strong target amplicons. We demonstrate that priming initiates above the optimum annealing temperature; this helps to ensure a competitive advantage for the target amplicon. On the other hand, as the cycling program progresses, annealing temperatures well below the Tm can serve to significantly increase yields in reactions that would otherwise be marginal due to suboptimal buffer composition and yet do not promote spurious amplification. Modified forms of TD PCR, termed stepdown PCR, consisting of fewer but steeper incremental declines in annealing temperature, are also shown to be effective and can simplify thermal cycler programming.

title: A highly conserved nuclear gene for low-level phylogenetics: elongation factor-1 alpha recovers morphology-based tree for heliothine moths.
abstract: Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain a wealth of information about lower-level taxonomic relationships as well, with the advantage that amino acid conservatism makes both alignment and primer definition straightforward. We tested this postulate for the elongation factor-1 alpha (EF-1 alpha) gene in the noctuid moth subfamily Heliothinae, which has probably diversified since the middle Tertiary. We sequenced 1,240 bp in 18 taxa representing heliothine groupings strongly supported by previous morphological and allozyme studies. The single most parsimonious gene tree and the neighbor-joining tree for all nucleotides show almost complete concordance with the morphological tree. Homoplasy and pairwise divergence levels are low, transition/transversion ratios are high, and phylogenetic information is spread evenly across gene regions. The EF-1 alpha gene and presumably other highly conserved genes hold much promise for phylogenetics of Tertiary age eukaryote groups.

title: The genetic data environment an expandable GUI for multiple sequence analysis
abstract: An X-Windows-based graphic user interface is presented which allows the seamless integration of numerous existing biomolecular programs into a single analysis environment. This environment is based on a core multiple sequence editor that is linked to external programs by a user-expandable menu system and is supported on Sun and DEC workstations. There is no limitation to the number of external functions that can be linked to the interface. The length and number of sequences that can be handled are limited only by the size of virtual memory present on the workstation. The sequence data itself is used as the reference point from which analysis is done, and scalable graphic views are supported. It is suggested that future software development utilizing this expandable, user-defined menu system and the I/O linkage of external programs will allow biologists to easily integrate expertise from disparate fields into a single environment.

title: THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION
abstract: Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.

title: Phylogenetic relationships of Dipsacales based on rbcl sequences
abstract: Nucleotide sequences of the chloroplast gene rbcL were obtained from Lonicera, Sambucus, Adoxa, and Cornus. Phylogenetic analyses of these sequences, along with previously sequenced Dipsacales and placeholders for other Asteridae and Rosidae, lead to the following conclusions: (1) the genera of Caprifoliaceae (in any traditional sense) do not form a monophyletic group; (2) Symphoricarpos and Lonicera (representing Caprifoliaceae sens. str.) are related and are united with Valerianaceae and Dipsacaceae; and (3) Adoxa and Sambucus are directly linked and are possibly related to Viburnum

title: The rapid generation of mutation data matrices from protein sequences
abstract: An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.

title: First molecular evidence for the existence of a Tardigrada + Arthropoda clade.
abstract: The complete 18S rDNA gene sequence of Macrobiotus group hufelandi (Tardigrada) was obtained and aligned with 18S rDNA and rRNA gene sequences of 24 metazoans (mainly protostomes). Discrete character (maximum-parsimony) and distance (neighbor-joining) methods were used to infer their phylogeny. The evolution of bootstrap proportions with sequence length (pattern of resolved nodes, PRN) was studied to test the resolution of the nodes in neighbor-joining trees. The results show that arthropods are monophyletic. Tardigrades represent the sister group of arthropods (in parsimony analyses) or they are related with crustaceans (distance analysis and PRN). Arthropoda are divided into two main evolutionary lines, the Hexapoda + Crustacea line (weakly supported), and the Myriapoda + Chelicerata line. The Hexapoda + Crustacea line includes Pentastomida, but the internal resolution is far from clear. The Insecta (Ectognatha) are monophyletic, but no evidence for the monophyly of Hexapoda is found. The Chelicerata are a monophyletic group and the Myriapoda cluster close to Arachnida. Overall, the results obtained represent the first molecular evidence for a Tardigrada + Arthropoda clade. In addition, the congruence between molecular phylogenies of the Arthropoda from other authors and this obtained here indicates the need to review those obtained solely on morphological characters.

title: Deducing the pattern of arthropod phytogeny from mitochondrial DNA rearrangements
abstract: THE origins of arthropods and the phylogenetic relationships among their three major living groups (atelocerates, crustaceans and chelicerates) are vigorously contended. To help resolve this, we determined mitochondrial gene arrangements for a chelicerate, a myriapod, two crustaceans, an onychophoran, a mollusc and an annelid, and compared them with published gene orders of other species. The result strongly supports the monophyly of Arthropoda and of Mandibulata (atelocerates plus crustaceans) and refutes the Uniramia (atelocerates plus onychophorans). Gene arrangement comparisons are emerging as a powerful new tool for resolving ancient phylogenetic relationships.

title: Evolutionary origin of insect wings from ancestral gills
abstract: Two hypotheses have been proposed for the origin of insect wings. One holds that wings evolved by modification of limb branches that were already present in multibranched ancestral appendages and probably functioned as gills1–5. The second proposes that wings arose as novel outgrowths of the body wall, not directly related to any pre-existing limbs6. If wings derive from dorsal structures of multibranched appendages, we expect that some of their distinctive features will have been built on genetic functions that were already present in the structural progenitors of insect wings, and in homologous structures of other arthropod limbs. We have isolated crustacean homologues of two genes that have wing-specific functions in insects, pdm (nubbin) and apterous. Their expression patterns support the hypothesis that insect wings evolved from gill-like appendages that were already present in the aquatic ancestors of both crustaceans and insects.

title: The Terrestrial Invasion: An Ecophysiological Approach to the Origins of Land Animals
abstract: Preface Part I.  1. Perspective 2. Problems: terrestrial versus aquatic habitats 3. The evidence Part II. Routes on to Land: 4. The origins of terrestrial animals in relation to salt and water balance 5. Muddy and sandy shores: interstitial fauna and the burrowers 6. Saltmarshes and mangrove swamps as routes on to land 7. Rocky and shingle shores as routes on to land 8. The freshwater route to land Part III. Life on Land: 9. Terrestrial adaptations 10. Terrestrial ecosystems.

title: Ubiquitin genes as a paradigm of concerted evolution of tandem repeats
abstract: SummaryUbiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.

title: The ecology of Paleozoic terrestrial arthropods: the fossil evidence
abstract: The available fossil evidence for the ecology of terrestrial arthropods in the Paleozoic is reviewed and reinterpreted. Some original data are provided, derived mainly from the detailed morphology of mouthparts, genitalia, cuticular vestiture, and body form. Paleozoic chelicerates were more diverse than their modern descendants and were probably dominant ground-level and arboreal predators. Web-building spiders and highly diversified mites appear to have been absent. Paleozoic myriapods include possibly the earliest land animals, and as abundant detritivores, provided a major conduit for primary productivity into higher trophic levels. Paleozoic insects present many difficulties of interpretation, but appear to have been extraordinarily diverse and may have played quite different ecological roles from today's insects, viewed as a whole. It is postulated that herbivory, defined as predation on living plants, may have been rare in early Paleozoic terrestrial ecosystems, and that most primary productivity wa...

title: Land animals in the silurian: arachnids and myriapods from shropshire, England.
abstract: A new assemblage of arthropod cuticles from Upper Silurian rocks in Shropshire, England, includes at least two centipedes and a trigonotarbid arachnid. This unequivocal terrestrial fauna from the Silurian constitutes the earliest direct record of land animals. The presence of predatory arthropods suggests that complex terrestrial ecosystems were in place by the late Silurian (414 x 10(6) years before present) and that the animal invasion of the land occurred earlier than was previously thought.

title: Reflections on the Phylogenetic Position of the Cephalocarida
abstract: This essay re-evaluates the phylogenetic position of the Cephalocarida in the light of the recently discovered Orsten (Upper Cambrian) crustaceans, the living Remipedia, and new interpretation of the Paleozoic ‘trilobitomorphs’. The Orsten crustaceans reinforce the belief that cephalocarid external morphology is primitive, except to show that the early crustacean trunk limb was almost surely biramous. The epipod appears to be a synapomorphy of the Cephalocarida, Branchiopoda and Malacostraca, thus justifying the existence of the Thoracopoda, which is coequal to the Maxillopoda and Remipedia. External morphology of the Remipedia is too specialized to support the hypothesis that it approximates that of the urcrustacean. Crustaceans and chelicerates are still best regarded as subgroups of the Schizoramia.

title: Phylogenies from molecular sequences: inference and reliability.
abstract: Article de synthese sur les methodes d'obtention de phylogenese a partir de sequences moleculaires, tests statistiques des phylogeneses et simulations sur ordinateur