We have rigorously defined 2,820 orthologous mRNA and protein sequence pairs from rats, mice, and humans. Evolutionary rate analyses indicate that mammalian genes are evolving 17–30% more slowly than previous textbook values. Data are presented on the average properties of mRNA and protein sequences, on variations in sequence conservation in coding and noncoding regions, and on the absolute and relative frequencies of repetitive elements and splice sites in untranslated regions of mRNAs. Our data set contains 1,880 unique human/rodent sequence pairs that represent about 2–4% of all mammalian genes. Of the 1,880 human orthologs, 70% are present on a new gene map of the human genome, thus providing a valuable resource for cross-referencing human and rodent genomes. In addition to comparative mapping, these results have practical applications in the interpretation of noncoding sequence conservation between syntenic regions of human and mouse genomic sequence, and in the design and calibration of gene expression arrays.

Evolutionary parameters of the transcribed mammalian genome: An analysis of 2,820 orthologous rodent and human sequences

Non-concerted ITS evolution, early origin and phylogenetic utility of ITS pseudogenes in Pyrus

We cloned and sequenced the rDNA internal transcribed spacer 2 (ITS2) of 4 species belonging to the neotropical Anopheles (Nyssorhynchus) albitarsis complex, that is, A. albitarsis; A. albitarsis B; Anopheles marajoara, a proven malaria vector; and Anopheles deaneorum, a suspected vector. Even though the ITS2 sequences of these species were very similar (� 1.17% divergence), we found differences suitable for species identification and intragenomic variation of possible consequence in phylogenetic reconstruction. Variation came from 2 microsatellite regions and a number of indels and base substitutions. The existence of partially correlated subsets of clones in A. albitarsis is hypothesized either to be separate rDNA loci or to be semiindependently evolving portions of a single rDNA locus. No differences were found between males and females, suggesting that similar rDNA arrays exist on both the X and Y chromosomes. In addition, highly variant clones, possibly pseudogenes, were found in A. marajoara from Venezuela.

Intragenomic rDNA ITS2 Variation in the Neotropical Anopheles (Nyssorhynchus) albitarsis Complex (Diptera: Culicidae)

I have analyzed a collection of published human Alu sequences. The compiled sequences show several unexpected features, including a uniform pattern of divergence from their consensus sequence, a mutual divergence that is not correlated with their age, and common features in the genomic DNA flanking the 5′ ends of the elements. I suggest that the Alu family of sequences derives from a large pool of precursors and not from a single precursor similar to the family consensus sequence, and that new elements integrate into the genome selectively at oligo-A-rich sites.

The multiple origins of human Alu sequences.

Large-subunit ribosomal DNA (LSU rDNA) gene sequences are frequently used to infer the phylogeny and species identity of organisms. The many copies of the LSU rDNA found in the genome are thought to be kept homogeneous by concerted evolution. In this study, we found high intraindividual, intraspecific and interspecific diversity in the D1-D6 region of the LSU rDNA in eight species of thecate, heterotrophic dinoflagellates using single-cell PCR, cloning, and sequencing of many clones. For each species, the clone library was usually comprised of one highly represented copy and many unique sequences. Sequence differences were primarily characterized by single base pair substitutions, single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all sequence clones gave strong support for monophyly of the polymorphic copies of each species and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU rDNA expression in three spe...

High intraindividual, intraspecific, and interspecific variability in large-subunit ribosomal DNA in the heterotrophic dinoflagellates Protoperidinium, Diplopsalis, and Preperidinium (Dinophyceae)

We discuss the evolutionary significance of four aberrant 18S rDNA clones that were obtained from human, chimpanzee, and gorilla DNA libraries. We show that these clones carry representatives of a small 18S rDNA pseudogene family that arose in a common ancestor of these species. Aspects of their structure and phylogenetic distribution suggest that the 18S pseudogenes no longer interact genetically with normal ribosomal genes and therefore may not be linked to nucleolus organizer regions.

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N Arnheim

Papers

Structure and evolution of human and African ape rDNA pseudogenes.