Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

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Ectoparasites of 13 species of molossid, mormoopid, and vespertilionid bats from the Trans-Pecos region of Texas were studied, as follows: Antrozous pallidus (LeConte), Corynorhinus townsendii (Cooper), Eptesicus fuscus (Palisot de Beauvois), Lasiurus cinereus (Palisot de Beauvois), Mormoops megalophylla (Peters), Myotis thysanodes G. S. Miller, Myotis velifer (J. A. Allen), Myotis volans (H. Allen), Myotis yumanensis (H. Allen), Nyctinomops femorosaccus (Merriam), Nyctinomops macrotis (Gray), Pipistrellus hesperus (H. Allen), and Tadarida brasiliensis (I. Geof. St.-Hilaire). The bats were netted, examined for ectoparasites and released. Ectoparasites recovered included three species of flea, three species of streblid, three species of nycteribiid, two species of cimicid, two species of tick, and 17 species of mite. New ectoparasite records are given for hosts in seven instances and for the Trans-Pecos region of Texas in three instances.

Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected vertebrates, we investigated the effects that constraints imposed by secondary structure have on the phylogenetic analysis of rRNA sequence data. Our analysis indicates that characters from both base-pairing regions (stems) and non-base-pairing regions (loops) contain phylogenetic information, as judged by the level of support of the phylogenetic results compared with a well-established tree based on both morphological and molecular data. The best results (the greatest level of support of well-accepted nodes) were obtained when the complete data set was used. However, some previously supported nodes were resolved using either the stem or loop bases alone. Stem bases sustain a greater number of compensatory mutations than would be expected at random, but the number is < 40% of that expected under a hypothesis of perfect compensation to maintain secondary structure. Therefore, we suggest that in phylogenetic analyses, the weighting of stem characters be reduced by no more than 20%, relative to that of loop characters. In contrast to previous suggestions, we do not recommend weighting of stem positions by one-half, compared with that of loop positions, because this overcompensates for the constraints that selection imposes on the secondary structure of rRNA.

SynopsisA subgenomic library created from genomic DNA of Latimeria chalumnae was screened for 2% ribosomal RNA (rRNA) clones. The resulting clone was subcloned into a plasmid vector, and over 2 kb of the 2% rRNA region was sequenced. Sequences of 28s rRNA genes were also obtained for Rhineura floridana (Squamata), Cyprinella lutrensis (Actinopterygii), and Lampetra aepyptera (Petromyzontiformes) by cloning and/or amplification by the polymerase chain reaction. The 28s rDNA sequences were aligned for all the above species as well as for the previously published 28s rDNA sequences of the genera Mus, Rattus, and Homo (Mammalia), Xenopus (Amphibia), and Drosophila (Insecta). Phylogenetic analysis of these species (using both the insect and lamprey sequences for outgroup comparison, or using only the lamprey sequence in the outgroup) produced a single optimal solution: (Outgroup(Cyprinella(Latimeria(Xenopus(Rhineura-(Homo(Rattus(Mus)))))))).Bootstrap analysis indicated that the placement of L. chalumnae on this tree was significant at p < 0.01. Previously published alternative hypotheses of relationships of Latimeria require at least 19 additional steps compared to the optimal solution; the rDNA data are sufficient to reject the hypotheses that place Latimeria in groups other than the sarcopterygians.

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