Molecular Biology and Evolution

Seutin,, G;Lang, B, F;Mindell, D, P;Morais,, R

doi: 10.1093/oxfordjournals.molbev.a040116pmid: 8015429

Abstract In most vertebrate mitochondrial genomes, the site for initiation of light-strand replication, OL, is found within a cluster of five transfer RNA (tRNA) genes (tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), and tRNA(Tyr)). This region and part of the adjacent cytochrome c oxydase subunit I (COI) gene were sequenced for two crocodilian, two turtle, and one snake species and for Sphenodon punctatus; part of the adjacent nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2) gene was also sequenced for the crocodilian and turtle species. All had the typical vertebrate gene order. The turtles and the snake have a lengthy noncoding sequence between the tRNA(Asn) and tRNA(Cys) genes that we assumed to be homologous to the mammalian OL. The crocodilians and Sphenodon lack such a sequence, a condition they share with birds. Most proposed phylogenies for the amniotes require that OL at this position was lost at least twice during their diversification or was evolved independently more than once. Within the five tRNA genes, frequencies of substitutions are much higher in loops than in stems. Many loops vary dramatically in size among the species; in the most extreme case, the D-arm of the Sphenodon tRNA(Cys) is a "D-arm replacement" loop of seven nucleotides. Frequency of transitions in stems is relatively uniform across tRNAs, but frequency of transversions varies greatly. Mismatches in stems are infrequent, and their relative frequency in a specific tRNA is unrelated to the frequency of substitution in the corresponding gene. Several features of mammalian mitochondrial tRNAs are conserved in WANCY tRNAs throughout amniotes. The inferred initiation codon for COI is GTG in crocodilians, turtles, and the snake, a condition they share with fishes, certain amphibians, and birds. TTG appears to be the initiation codon for COI in Sphenodon; if correct, this would be a novel initiation codon for vertebrate mitochondrial DNA. Phylogenetic analyses of the inferred amino acid sequences of ND2 and COI support the sister-group relationship of birds and crocodilians and suggest that mammals are an early derived lineage within the amniotes. This content is only available as a PDF.

Slade, R, W;Moritz,, C;Heideman,, A

doi: 10.1093/oxfordjournals.molbev.a040117pmid: 8015430

Abstract Phylogenetic analyses of closely related species should use information from multiple, independent genes with relatively high rates of sequence evolution. To investigate species for which there are few prior sequence data for single-copy nuclear (scnDNA) genes, primers for gene amplification can be designed to highly conserved regions of exons in order to amplify both coding (exons) and noncoding (introns) sequences. We have explored this approach in a phylogenetic analysis of six species of pinnipeds that, together with terrestrial carnivore outgroups, encompass divergence times < or = 40-50 Mya. We sequenced one intron from each of the aldolase A (ALD-A), aldolase C (ALD-C), and histone H2AF genes; one exon from the major-histocompatibility-complex DQA gene; a H2AF processed pseudogene (psi H2AF); and, for comparison with the nuclear genes, the 5' portion of the mitochondrial DNA (mtDNA) control region. The pinniped psi H2AF genes were found to be of limited use because they were paralogous with the gene in the outgroup. The rate of silent substitution in scnDNA (primarily introns) was 5-10-fold lower than that for mtDNA control region I, and scnDNA sequence divergence increased linearly with time < or = 40-50 Mya. Alleles at three polymorphic scnDNA loci (ALD-A, H2AF, and DQA) in the southern elephant seal were paraphyletic with respect to the allele from the closely related northern elephant seal, while the more numerous mtDNA alleles were monophyletic. This we attribute to the consequences of a higher mutation rate rather than to a lower effective population size of mtDNA compared with scnDNA. Within the short (i.e., < 500-bp) sequences of individual scnDNA sequences, phylogenetically informative variation was insufficient to obtain robust phylogenies. However, the combined scnDNA sequences produced a well-supported phylogeny congruent with that derived from mtDNA. This analysis illustrates the high resolution of mtDNA sequences compared with a similar length of scnDNA sequence, but it also demonstrates the utility of combining information from multiple short scnDNA sequences obtained using broadly applicable primers. This content is only available as a PDF.

Graur,, D;Higgins, D, G

doi: 10.1093/oxfordjournals.molbev.a040118pmid: 8015431

Abstract The transition in the cetaceans from terrestrial life to a fully aquatic existence is one of the most enduring evolutionary mysteries. Resolving the phylogenetic relationships between Cetacea and the other orders of eutherian mammals may provide us with important clues to the origin of whales and may help us date the evolutionary transition to aquatic life. Previous paleontological and molecular evidence has indicated that cetaceans and artiodactyls constitute a natural clade within subclass Eutheria. Our present phylogenetic analyses of protein and mitochondrial DNA sequence data indicate that cetaceans are not only intimately related to the artiodactyls; they are in fact deeply nested within the artiodactyl phylogenetic tree; i.e., they are more closely related to the members of one suborder of artiodactyls, the Ruminantia, than either ruminants or cetaceans are to members of the other two artiodactyl suborders: Suiformes and Tylopoda. On the basis of the rate of evolution of mitochondrial DNA sequences and using paleontological reference dates for calibration, we estimate that the whale lineage has branched off a protoruminant lineage < 50 Mya. By implication, the cetacean transition to aquatic life is inferred to be a relatively recent evolutionary event. This content is only available as a PDF.

Zhang, X, H;Chinnappa, C, C

doi: 10.1093/oxfordjournals.molbev.a040119pmid: 8015432

Abstract A cDNA clone encoding cytochrome c of Stellaria longipes was isolated and characterized. The nucleotide and predicted amino acid sequences were highly similar to those from other plant, fungal, and animal species. No significant polymorphism was observed among different genotypes (ecotypes). The S. longipes genome contained a low copy number of nucleotide sequences of cytochrome c. The gene expression of cytochrome c exhibited a certain degree of tissue specificity, with more transcripts in leaf than in stem. A phylogenetic analysis of the cytochrome c amino acid sequences revealed an unusual aspect of plant cytochrome c evolution. This content is only available as a PDF.

Wingfield, B, D;Grant, W, S;Wolfaardt, J, F;Wingfield, M, J

doi: 10.1093/oxfordjournals.molbev.a040120pmid: 8015433

Abstract The genus Ceratocystis sensu stricto includes important fungal pathogens of woody and herbaceous plants. This genus is distinguished from species in Ceratocystis sensu lato by the presence of Chalara anamorphs. Ascospore shape has been used extensively in delineating Ceratocystis taxa, which show a large variety of ascospore shapes. Sequence analysis of one region of he 18S ribosomal RNA subunit and two regions of the 28S ribosomal RNA subunit showed that there was a majority of multiple substitutions at nucleotide sites and that there was a low transition/transversion ratio, T = 0.72. Both of these results suggest that these are well established, old species. Ascospore morphology, for the most part, was not congruent with the molecular phylogeny, and the use of morphological characters may be misleading in the taxonomy of these species. This content is only available as a PDF.

Zimmerman, P, A;Katholi, C, R;Wooten, M, C;Lang-Unnasch,, N;Unnasch, T, R

doi: 10.1093/oxfordjournals.molbev.a040114pmid: 7516998

Abstract Polymerase chain reaction (PCR) products were characterized for a repeated sequence family (designated "O-150") of the human filarial parasite Onchocerca volvulus. In phylogenetic inferences, the O-150 sequences clustered into closely related groups, suggesting that concerted evolution maintains sequence homology in this family. Using a novel mathematical model based on a nested application of an analysis of variance, we demonstrated that African rainforest and savannah strain parasite populations are significantly different. In contrast, parasites collected in the New World are indistinguishable from African savannah strains of O. volvulus. This finding supports the hypothesis that onchocerciasis was recently introduced into the New World, possibly as a result of the slave trade. This content is only available as a PDF.

Vogler, A, P;DeSalle,, R

doi: 10.1093/oxfordjournals.molbev.a040121pmid: 8015434

Abstract Sequence divergence in the internal transcribed spacer region 1 (ITS-1) of the ribosomal DNA locus was assessed in subspecies of the coastal North American tiger beetle, Cicindela dorsalis. The spacer region was amplified using the polymerase chain reaction and cloned for sequencing. Of a total of 50 clones obtained from 12 specimens, 42 clones were different in at least one nucleotide position. In a parsimony analysis of these sequences, the main phylogenetic distinction was found to separate sequences from the Gulf of Mexico and the Atlantic Ocean. Within these two assemblages phylogenetic resolution was low, and the variation within individuals was almost as high as the variation within the entire lineage. The pattern of sequence variation suggests the existence of two forms of the ITS-1 that are maintained on different chromosomes. Polymorphisms of limited geographical distribution could be detected, and 41 additional clones were partly sequenced, to assess the geographic distribution of these polymorphisms in more detail. In a population aggregation analysis, the geographic pattern of ITS-1 distribution was basically congruent with that obtained in earlier studies from mitochondrial DNA in the same C. dorsalis populations. This content is only available as a PDF.

Fritz, G, N;Conn,, J;Cockburn,, A;Seawright,, J

doi: 10.1093/oxfordjournals.molbev.a040122pmid: 8015435

Abstract Sequence variation of the ribosomal DNA internal transcribed spacer 2 (ITS2) was examined for populations of the malaria vector Anopheles nuneztovari collected in Colombia, Venezuela, Bolivia, Suriname, and Brazil. Mosquitoes from Colombia and Venezuela had identical ITS2 sequences and were distinguished from sequences in other populations by three insertion/deletion events (indels) and by one transversion. The length of the ITS2 was 363-369 bp, and it had a G+C content of 55.3%-55.7%. Variation in the length of the ITS2 between and within populations was due to indels in simple repeats. ITS2 consensus sequences were similar or identical for samples from the following three groups: (1) Colombia, Bolivia, and Venezuela; (2) Suriname and northern Brazil; and (3) eastern and central Brazil. The presence of two different consensus sequences from a single location near Manaus, Brazil, suggests that populations from eastern Brazil and those from Suriname converge in this region of the Amazon Basin. These data show that putative cryptic species of An. nuneztovari are distinguished by very minor differences in DNA sequence of the ITS2 region. This content is only available as a PDF.

Hughes, A, L

doi: 10.1093/oxfordjournals.molbev.a040123pmid: 8015436

Abstract A phylogenetic analysis of DNA sequences from the C3/C4/C5 complement-component family of vertebrates supported the hypothesis that the C5 gene diverged first from the common ancestor of C3 and C4 and that C3 and C4 diverged later. The close relationship of C3 and C4 was further supported by the fact that a hagfish complement-component gene showed evidence of being more closely related to both C3 and C4 than to C5. This phylogeny is most consistent with the hypothesis that the alternative complement pathway was the first to evolve, followed by the terminal pathway and then by the classical pathway. This content is only available as a PDF.

Palumbi, S, R;Baker, C, S

doi: 10.1093/oxfordjournals.molbev.a040115pmid: 7912407

Abstract Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations. This content is only available as a PDF.