The arthropods constitute the most diverse animal group, but, despite their rich fossil record and a century of study, their phylogenetic relationships remain unclear. Taxa previously proposed to be sister groups to the arthropods include Annelida, Onychophora, Tardigrada and others, but hypotheses of phylogenetic relationships have been conflicting. For example, onychophorans, like arthropods, moult periodically, have an arthropod arrangement of haemocoel, and have been related to arthropods in morphological and mitochondrial DNA sequence analyses. Like annelids, they possess segmental nephridia and muscles that are a combination of smooth and obliquely striated fibres. Our phylogenetic analysis of 18S ribosomal DNA sequences indicates a close relationship between arthropods, nematodes and all other moulting phyla. The results suggest that ecdysis (moulting) arose once and support the idea of a new clade, Ecdysozoa, containing moulting animals: arthropods, tardigrades, onychophorans, nematodes, nematomorphs, kinorhynchs and priapulids. No support is found for a clade of segmented animals, the Articulata, uniting annelids with arthropods. The hypothesis that nematodes are related to arthropods has important implications for developmental genetic studies using as model systems the nematode Caenorhabditis elegans and the arthropod Drosophila melanogaster, which are generally held to be phylogenetically distant from each other.

Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes. Extensive horizontal transfer has occurred for operational genes (those involved in housekeeping), whereas informational genes (those involved in transcription, translation, and related processes) are seldomly horizontally transferred. Through phylogenetic analysis of six complete prokaryotic genomes and the identification of 312 sets of orthologous genes present in all six genomes, we tested two theories describing the temporal f low of horizontal transfer. We show that operational genes have been horizontally transferred continuously since the divergence of the prokaryotes, rather than having been exchanged in one, or a few, massive events that occurred early in the evolution of prokaryotes. In agreement with earlier studies, we found that differences in rates of evolution between operational and informational genes are minimal, suggesting that factors other than rate of evolution are responsible for the observed differences in horizontal transfer. We propose that a major factor in the more frequent horizontal transfer of operational genes is that informational genes are typically members of large, complex systems, whereas operational genes are not, thereby making horizontal transfer of informational gene products less probable (the complexity hypothesis).

Analyses of complete genomes indicate that a massive prokaryotic gene transfer (or transfers) preceded the formation of the eukaryotic cell. In comparisons of the entire set of Methanococcus jannaschii genes with their orthologs from Escherichia coli, Synechocystis 6803, and the yeast Saccharomyces cerevisiae, it is shown that prokaryotic genomes consist of two different groups of genes. The deeper, diverging informational lineage codes for genes which function in translation, transcription, and replication, and also includes GTPases, vacuolar ATPase homologs, and most tRNA synthetases. The more recently diverging operational lineage codes for amino acid synthesis, the biosynthesis of cofactors, the cell envelope, energy metabolism, intermediary metabolism, fatty acid and phospholipid biosynthesis, nucleotide biosynthesis, and regulatory functions. In eukaryotes, the informational genes are most closely related to those of Methanococcus, whereas the majority of operational genes are most closely related to those of Escherichia, but some are closest to Methanococcus or to Synechocystis.Prokaryotic and eukaryotic evolution has long been viewed primarily through the perspective of a single molecule, rRNA. Emphasis on this perspective has led to the simplified view that prokaryotes and eukaryotes have evolved as pure lineages relatively uncorrupted by horizontal gene transfer. This view has been contradicted by some puzzling phylogenetic relationships. Recent publications demonstrate that a number of proteins such as heat shock protein HSP70, glutamate dehydrogenase, L-malate dehydrogenase, aspartate amino transferase, and others do not fit the rRNA pattern. These, and other observations, have prompted fusion, or chimeric, theories for the origin of eukaryotes (1-6). Some also indicate an intricate assortment of prokaryotic relationships (6-9). The availability of complete genomes (10-13), including the first eukaryotic genome, now provides an opportunity to reconstruct a more complete picture of eukaryotic and prokaryotic evolution through the analysis of entire functional classes.By using complete genomes from Saccharomyces cerevisiae (10), a eukaryote, Synechocystis 6803 (11), a cyanobacterium, Escherichia coli (12), a proteobacterium, and Methanococcus jannaschii (13), a methanogen, we have reconstructed the broad outlines of eukaryotic and prokaryotic evolution. Borrowing many of the comparative tools and techniques of molecular evolution (14) and having sufficiently large numbers of genes, we have followed the evolution of functional classes of genes (15) and have found two strikingly different inheritance patterns. METHODSDistances from BLASTP. Approximate distances were calculated from the ''sum probabilities'' of BLASTP (16,17) by using the distance to likelihood approximation of Kruskal (18). To assure that distances satisfied the ''symmetry'' property of distance metrics (18), P-values were symmetrized by the following procedure. If a and b are homologous genes in genomes A and B, respectively, an...

The suspension-feeding metazoan subkingdom Lophophorata exhibits characteristics of both deuterostomes and protostomes. Because the morphology and embryology of lophophorates are phylogenetically ambiguous, their origin is a major unsolved problem of metazoan phylogenetics. The complete 18S ribosomal DNA sequences of all three lophophorate phyla were obtained and analyzed to clarify the phylogenetic relationships of this subkingdom. Sequence analyses show that lophophorates are protostomes closely related to mollusks and annelids. This conclusion deviates from the commonly held view of deuterostome affinity.