To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

BackgroundComparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields.ResultsWe have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems.ConclusionsThis online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.

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Knowledge of the rate of point mutation is of fundamental importance, because mutations are a vital source of genetic novelty and a significant cause of human diseases. Currently, mutation rate is thought to vary many fold among genes within a genome and among lineages in mammals. We have conducted a computational analysis of 5,669 genes (17,208 sequences) from species representing major groups of placental mammals to characterize the extent of mutation rate differences among genes in a genome and among diverse mammalian lineages. We find that mutation rate is approximately constant per year and largely similar among genes. Similarity of mutation rates among lineages with vastly different generation lengths and physiological attributes points to a much greater contribution of replication-independent mutational processes to the overall mutation rate. Our results suggest that the average mammalian genome mutation rate is 2.2 ؋ 10 ؊9 per base pair per year, which provides further opportunities for estimating species and population divergence times by using molecular clocks. neutral evolution ͉ substitution pattern ͉ disparity index ͉ generation length ͉ molecular clock R ates of point mutation can be determined indirectly by estimating the rate at which the neutral substitutions accumulate in protein-coding genes (1). Synonymous substitutions in protein-coding genes generally are free from natural selection and are used frequently for inferring neutral substitution rates (1, 2). In particular, the fourfold-degenerate sites are expected to harbor only the neutral substitutions, because all mutations at these sites are synonymous at the amino acid sequence level. By using estimates of evolutionary distances based on neutral substitutions, many studies have examined the null hypotheses of uniformity of neutral mutation rates among genes within a genome and among mammalian lineages and have come to conflicting conclusions (2-9). For example, significant differences in mutation rates among mammalian lineages reported over the last two decades led to the proposal of the generationtime effect hypothesis (10-13). However, Easteal et al. (14) have argued that previous results of substantial differences among lineages observed may have been caused by the use of incorrect fossil dates or inappropriate outgroups. Similarly, there is significant controversy regarding differences in mutation rate among genes within a genome (8, 9, 15) and over 10-fold differences in the estimates of the mutation rates among studies (1.1-12.4 ϫ 10 Ϫ9 substitutions per site per year; refs. 3, 11, 12, and 16-19).One common feature of many of these studies is that they have either analyzed a small number of genes or only a few species. Analysis of a large sample of genes from a genome and diverse phylogenetic lineages is the key to testing the null hypothesis of equal mutation rates within and among genomes. A large number of genes is necessary, because only a fraction (Ϸ15%) of codon positions in a sequence are fourfold-degenerate (see Fig. 1 le...