Time and biosequences

PHYLOGENETIC ANALYSIS OF BREEDING SITE USE AND α-AMANITIN TOLERANCE WITHIN THE DROSOPHILA QUINARIA SPECIES GROUP

The Drosophila quinaria group is unusual within the genus in that it comprises both mycophagous and nonmycophagous species. DNA sequence data from three regions of the mitochondrial genome were used to infer relationships among four mycophagous species and three that breed on decaying water plants. Phylogenetic analysis of these species show that breeding in mushrooms and tolerance of high levels of α-amanitin were the ancestral states within the group. Thus, breeding in decaying water plants and intolerance of α-amanitin are derived conditions. We also found that the D. quinaria species group does not comprise separate mycophagous and nonmycophagous clades, but rather that (1) the shift from mushrooms to decaying plants occurred on at least two occasions; or (2) mycophagy reevolved within a lineage that had previously shifted to breeding on plants. The correlation between mycophagy and α-amanitin tolerance is perfect across the species we have examined, indicating that there is no detectable time lag between an ecological shift to a new breeding site and correlated changes in biochemical adaptation. The genetic distance between the mycophagous D. recens and the nonmycophagous D. quinaria indicates that these species split only about 1 M.Y.B.P. In terms of α-amanitin tolerance, D. recens and D. quinaria are typical of other ecologically similar species within the group. Thus, evolutionary changes in α-amanitin tolerance can evidently occur on the order of about 1 million yr. Our data also indicate that, in comparison to other groups of Drosophila, the quinaria species group may be undergoing an adaptive radiation.

Phylogenetic utility of mitochondrial COI and nuclear Gpdh genes in Drosophila

Phylogenetic utility of the mitochondrial COI (cytochrome oxidase subunit I) and nuclear Gpdh (glycerol-3-phosphate dehydrogenase) genes was studied in the Drosophila melanogaster species group. The rate of substitution was higher in the COI gene than in the Gpdh gene. In addition, multiple substitutions, not only for transitional but also for transversional substitutions, occurred faster in the COI gene. None of the trees obtained using the COI gene supported the well-established monophyly of the ananassae subgroup. In addition, the incongruence length difference test, Templeton test, and partitioned Bremer support revealed that the trees based on the COI data are considerably different from those based on the Gpdh and the combined data set. Thus, the COI gene did not show good phylogenetic performance in the melanogaster group. The present analyses based on the Gpdh gene and the combined data set revealed that the ananassae subgroup branched off first in the melanogaster group followed by the montium subgroup and further by the melanogaster subgroup in contrast to the most recent phylogenetic hypothesis based on Amy multigenes.

Molecular phylogeny of the families Campulidae and Nasitrematidae (Trematoda) based on mtDNA sequence comparison

Historically, the systematic arrangement of the genera within the family Campulidae, and its relationship with its allied family Nasitrematidae have been rather confused, particularly because only adult morphology has been available to classical taxonomic analysis. In this paper we provide a partial phylogeny of the genera of these families based on mtDNA from five campulid species: Campula oblonga, Zalophotrema atlanticum, Hadwenius tursionis, Oschmarinella rochebruni and Orthosplanchnus fraterculus; and one nasitrematid, Nasitrema globicephalae. Fasciola hepatica and Dicrocoelium dendriticum were used as outgroups. Maximum parsimony and neighbour-joining methods were applied. Both methods produced similar trees where H. tursionis appeared as the basal campulid, with a sequential divergence of Z. atlanticum, N. globicephalae, C. oblonga, O. rochebruni and O. fraterculus. Results suggest that Nasitrematidae as defined should loose its familial status and the current subfamilial division of the family Campulidae is at least partly artificial and should not be maintained.

Impact of changes in GC content on the silent molecular clock in murids

Murid nuclear genomes are more homogeneous in GC content than those of most mammals, which leads to the question of how such important compositional changes have accumulated. This paper reports on relationships between frequencies of synonymous differences and GC change, in the lineages leading to human and murids. For this, we used the four-species approach: GC changes between human and murids were compared to the frequencies of synonymous differences, measured between two independent species without GC change (bovine and pig), by using orthologous genes common to all four species. We report three conclusions: (1) Among genes with little GC change, 60% of the variability of synonymous substitution frequencies is explained by the gene-specific rate component. (2) GC changes in murid genomes are independent of the gene-specific rate component. Slowly evolving genes in pig bovine comparison can show strong GC change in murids. (3) By using a GC-independent estimate of the substitution rate, we show that GC changes in murid genomes increase synonymous substitution frequencies. The GC homogenization considerably weakens the gene-specific conservation of substitution rates in murids, and could explain part of the increase of evolutionary rates observed in this group. We present a mechanism that can account for the evolution of the GC homogenization in murids.

Molecular phylogenetics of a protein repair methyltransferase

Protein-L-isoaspartyl (D-aspartyl) O-methyltransferase (E.C. 2.1.1.77) is a well-conserved and widely distributed protein repair enzyme that methylates isomerized or racemized aspartyl residues in age-damaged proteins. We exploited the availability of protein sequences from 10 diverse animal, plant and bacterial taxa to construct a phylogenetic tree and determine the rates of amino acid substitution for this enzyme. We used a likelihood ratio test to show that this enzyme fulfills the conditions for a molecular clock. We found that the rate of substitution is 0.39 amino acid substitutions per site per 10(9) years and remains relatively constant from bacteria to humans. We argue that this degree of sequence conservation may result from the functional constraints necessitated by the requirement to specifically recognize altered aspartyl but not normal aspartyl residues in proteins. Relative rate analysis of the Caenorhabditis elegans sequence suggests that the amino acid substitution rate in the nematode lineage may be higher than that in other lineages and that the divergence of nematodes may have been a more recent event than suggested by previous analysis.

Evolutionary dynamics of cucumber mosaic virus satellite RNA during natural epidemics in Italy

The evolutionary dynamics of 22 variants of cucumber mosaic virus satellite RNA (CMV satRNA) isolated in Italy during virus epidemics from 1988 to 1993 were investigated on the basis of their primary structure and biological properties. Most of the variants were amplified from total nucleic acid preparations extracted from field-infected plants, thus representing wild isolates of CMV satRNA. Eleven variants were associated with subgroup II CMV strains, 10 with subgroup I and 1 with a mixed infection by both strains. When inoculated onto tomato seedlings, the variants induced the phenotype (necrogenic or ameliorative) predicted by their nucleotide sequence. Phylogenetic relationships between the satRNA variants were determined using the stationary Markov model, a stochastic model for evolution. For each satRNA, the Markov analysis gave a good correlation between position in the phylogenetic tree and biological properties. The variants with ameliorative and necrogenic phenotypes in tomato followed two different evolutionary dynamics in nature. Tfn-satRNA, a 390-nt-long molecule, followed a third type of evolutionary dynamic far apart from that of the shorter satRNA molecules (i.e., those in the 334- to 340-nt-length class). Average values of the mean constant rate of nucleotide substitutions/site (Ksubs/site) indicated that in nature the variants tend to keep their heterogeneity unchanged from one epidemic episode to the other, even if the outbreaks occur in places very far from each other. This seems to be in agreement with the proposed maintenance of a functional molecular structure as a constraint to CMV satRNA evolution.

Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals

To obtain information relative to the phylogenesis and microevolutionary rate of fish mitochondrial DNA, the nucleotide sequence of cytochrome b gene in seven fish species belonging to the order of Perciformes was determined. Sequence analysis showed that fish mitochondrial DNA has a nucleotide compositional bias similar to that of sharks but lower compared to mammals and birds. Quantitative evolutionary analysis, carried out by using a markovian stochastic model, clarifies some phylogenetic relationships within the Perciformes order, particularly in the Scombridae family, and between Perciformes, Gadiformes, Cypriniformes, and Acipenseriformes. The molecular clock of mitochondrial DNA was calibrated with the nucleotide substitution rate of cytochrome b gene in five shark species having divergence times inferred from paleontological estimates. The results of such analysis showed that Acipenseriformes diverged from Perciformes by about 200 MY, that the Perciformes common ancestor dates back to 150 MY, and that fish mitochondrial DNA has a nucleotide substitution rate three to five times lower than that of mammals.

Phylogeny of the Drosophila obscura species group deduced from mitochondrial DNA sequences

Approximately 2 kb corresponding to different regions of the mtDNA of 14 different species of the obscura group of Drosophila have been sequenced. In spite of the uncertainties arising in the phylogenetic reconstruction due to a restrictive selection toward a high mtDNA A+T content, all the phylogenetic analysis carried out clearly indicate that the obscura group is formed by, at least, four well-defined lineages that would have appeared as the consequence of a rapid phyletic radiation. Two of the lineages correspond to monophyletic subgroups (i.e., affinis and pseudoobscura), whereas the obscura subgroup remains heterogeneous assemblage that could be reasonably subdivided into at least two complexes (i.e., subobscura and obscura).