Phylogenetic position of phylum Nemertini, inferred from 18S rRNA sequences: molecular data as a test of morphological character homology.

Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protostome coelomate clade, as suggested by more recent morphological analyses. Maximum-parsimony analysis supports the inclusion of the nemertine within a protostome-coelomate clade that falls within a more inclusive coelomate clade. Bootstrap analysis indicates strong support for a monophyletic Coelomata composed of a deuterostome and protostome-coelomate clade. Support for a monophyletic protostome Coelomata is weak. Inference by distance analysis is consistent with that of maximum parsimony. Analysis of down-weighted paired sites by maximum parsimony reveals variation in topology only within the protostome-coelomate clade. The relationships among the protostome coelomates cannot be reliably inferred from the partial sequences, suggesting that coelomate protostomes diversified rapidly. Results with evolutionary parsimony are consistent with the inclusion of the nemertine in a coelomate clade. The molecular inference corroborates recent morphological character analyses that reveal no synapomorphies of nemertines and flatworms but instead suggest that the circulatory system and rhynchocoel of nemertines are homologous to coelomic cavities of protostome coelomates, thus supporting the corresponding hypothesis that nemertines belong within a protostome-coelomate clade. The sequence data provide an independent test of morphological character homology.     

Phylogenetic systematics and biogeography of the poison frogs: evidence from mitochondrial DNA sequences

Regions of the mitochondrial genome were sequenced and analysed in representative species of poison frogs, in order to investigate phylogenetic relationships within the family Dendrobatidae. Mitochondrial DNA (mfDNA) fragments from three gene regions; cytochrome b, 16S ribosomal RNA (rRNA), and 12S rRNA, provided 1198 base pairs of DNA sequence and 589 informative sites. Phylogenetic analysis using parsimony was used to infer the evolutionary relationships among the species in the survey. Our analysis supported previous partitions of species into the genera Epipedobates, Phyllobates and Dendrobates , with two exceptions; Epipedobates (Allobates) femoralis was placed outside the clade containing the other toxic dendrobatids, and Minyobates minutus was placed within the genus Dendrobates. Genetic distances estimated between all pairs of taxa using the Kimura 2-parameter model indicated substantial genetic divergence between species, particularly those found in Amazonia. Time of divergence estimates were highly variable depending on gene region, but even the lowest estimates were inconsistent with the Pleistocene Refugia hypothesis.     

A multilocus phylogeny of archiheterodont bivalves (Mollusca,Bivalvia, Archiheterodonta)

The bivalve clade Heterodonta encompasses more than half of the extant bivalve species and is presently considered a derived group of the modern bivalves (Newell 1965 ; Waller 1998 ). Heterodonta is subdivided into two major lineages, the hyperdiverse Euheterodonta and Archiheterodonta. The latter comprises four relatively small extant families: Astartidae, Carditidae, Condylocardiidae and Crassatellidae, whose relationships and internal phylogeny are poorly understood. We assessed the phylogeny of archiheterodont bivalves using a multilocus data set comprised of molecular sequence data from six loci (18S rRNA, 28S rRNA, cytochrome c oxidase subunit I, cytochrome b, internal transcribed spacer 2 and histone H3). Resultant data sets of ~4 Kb of concatenated molecular sequence data were analysed using probabilistic approaches (maximum likelihood and Bayesian inference) and parsimony direct optimization. We recovered strong support for the monophyly of Archiheterodonta, within which Astartidae is the sister group of Crassatellidae, and these two constitute the sister clade of Carditidae, which is paraphyletic with respect to Condylocardiidae. The relationships among the constituent species groups were evaluated in the context of the archiheterodont fossil record through the estimation of divergence times. Diversification times of archiheterodont families were congruent with bounded estimates of origins based on palaeontological data: Archiheterodonta diversified during the Devonian, 373.1 Ma (95% highest posterior density interval [HPD] 325.8–428.2); Crassatelloidea around the Carboniferous, 330.1 Ma (95% HPD 291.0–372.7); Crassatellidae around the Triassic, 224.0 (95% HPD 140.6–320.2); Astartidae around the Permian, 288.2 Ma (95% HPD 269.2–307.3); and Carditoidea around the Jurassic, 178.8 Ma (95% HPD 120.9–228.3).     

RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes.     

A phylogeny of anisopterous dragonflies (Insecta,Odonata) using mtRNA genes and mixed nucleotide/doublet models

The application of mixed nucleotide/doublet substitution models has recently received attention in RNA‐based phylogenetics. Within a Bayesian approach, it was shown that mixed models outperformed analyses relying on simple nucleotide models. We analysed an mt RNA data set of dragonflies representing all major lineages of Anisoptera plus outgroups, using a mixed model in a Bayesian and parsimony (MP) approach. We used a published mt 16S rRNA secondary consensus structure model and inferred consensus models for the mt 12S rRNA and tRNA valine. Secondary structure information was used to set data partitions for paired and unpaired sites on which doublet or nucleotide models were applied, respectively. Several different doublet models are currently available of which we chose the most appropriate one by a Bayes factor test. The MP reconstructions relied on recoded data for paired sites in order to account for character covariance and an application of the ratchet strategy to find most parsimonious trees. Bayesian and parsimony reconstructions are partly differently resolved, indicating sensitivity of the reconstructions to model specification. Our analyses depict a tree in which the damselfly family Lestidae is sister group to a monophyletic clade Epiophlebia + Anisoptera, contradicting recent morphological and molecular work. In Bayesian analyses, we found a deep split between Libelluloidea and a clade ‘Aeshnoidea’ within Anisoptera largely congruent with Tillyard’s early ideas of anisopteran evolution, which had been based on evidently plesiomorphic character states. However, parsimony analysis did not support a clade ‘Aeshnoidea’, but instead, placed Gomphidae as sister taxon to Libelluloidea. Monophyly of Libelluloidea is only modestly supported, and many inter‐family relationships within Libelluloidea do not receive substantial support in Bayesian and parsimony analyses. We checked whether high Bayesian node support was inflated owing to either: (i) wrong secondary consensus structures; (ii) under‐sampling of the MCMC process, thereby missing other local maxima; or (iii) unrealistic prior assumptions on topologies or branch lengths. We found that different consensus structure models exert strong influence on the reconstruction, which demonstrates the importance of taxon‐specific realistic secondary structure models in RNA phylogenetics.     

Phylogenetic relationships and evolution of Orbiniidae (Annelida, Polychaeta) based on molecular data

The phylogenetic relationships of orbiniid taxa were reconstructed based on sequence data of the mitochondrial 16S rRNA and nuclear 18S rRNA genes. Both genes were analysed separately and in combination using maximum likelihood, Bayesian inference and maximum parsimony. Regardless of the method used, a clade consisting of the investigated Orbiniidae, Methanoaricia dendrobranchiata and Questa was strongly supported by the 18S dataset. The analysis of the combined dataset suggests inclusion of M. dendrobranchiata within the Orbiniidae with close relationships to species of Orbinia and Phylo, rather than as a sister taxon to all other orbiniids. Evidence is given for the paraphyletic status of Leitoscoloplos , Naineris , Orbinia , Phylo and Scoloplos , which represent the most species-rich genera of the Orbiniidae. It is thus reasoned that the morphological characters presently used for genus diagnosis are not informative for cladistic analysis. No support is found for the hypothesis that taxa of the Protoariciinae represent juveniles of Orbiniinae. Instead, in the case of Protoaricia oerstedi , strong support for a progenetic origin is found.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 144 , 59−73.     

The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal?

Previous studies of the phylogeny of land plants based on analysis of 18S ribosomal DNA (rDNA) sequences have generally found weak support for the relationships recovered and at least some obviously spurious relationships, resulting in equivocal inferences of land plant phylogeny. We hypothesized that greater sampling of both characters and taxa would improve inferences of land plant phylogeny based on 18S rDNA sequences. We therefore conducted a phylogenetic analysis of complete (or nearly complete) 18S rDNA sequences for 93 species of land plants and 7 green algal relatives. Parsimony analyses with equal weighting of characters and characters state changes and parsimony analyses weighting (1) stem bases half as much as loop bases and (2) transitions half as much as transversions did not produce substantially different topologies. Although the general structure of the shortest trees is consistent with most hypotheses of land plant phylogeny, several relationships, particularly among major groups of land plants, appear spurious. Increased character and taxon sampling did not substantially improve the performance of 18S rDNA in phylogenetic analyses of land plants, nor did analyses designed to accommodate variation in evolutionary rates among sites. The rate and pattern of 18S rDNA evolution across land plants may limit the usefulness of this gene for phylogeny reconstruction at deep levels of plant phylogeny. We conclude that the mosaic structure of 18S rDNA, consisting of highly conserved and highly variable regions, may contain historical signal at two levels. Rapidly evolving regions are informative for relatively recent divergences (e.g., within angiosperms, seed plants, and ferns), but homoplasy at these sites makes it difficult to resolve relationships among these groups. At deeper levels, changes in the highly conserved regions of small-subunit rDNAs provide signal across all of life. Because constraints imposed by the secondary structure of the rRNA may affect the phylogenetic information content of 18S rDNA, we suggest that 18S rDNA sequences be combined with other data and that methods of analysis be employed to accommodate these differences in evolutionary patterns, particularly across deep divergences in the tree of life.     

Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.     

Variation patterns of the mitochondrial 16S rRNA gene with secondary structure constraints and their application to phylogeny of cyprinine fishes (Teleostei: Cypriniformes)

The mitochondrial 16S ribosomal RNA (rRNA) gene sequences from 93 cyprinid fishes were examined to reconstruct the phylogenetic relationships within the diverse and economically important subfamily Cyprininae. Within the subfamily a biased nucleotide composition (A>T, C>G) was observed in the loop regions of the gene, and in stem regions apparent selective pressures of base pairing showed a bias in favor of G over C and T over A. The bias may be associated with transition-transversion bias. Rates of nucleotide substitution were lower in stems than in loops. Analysis of compensatory substitutions across these taxa demonstrates 68% covariation in the gene and a logical weighting factor to account for dependence in mutations for phylogenetic inference should be 0.66. Comparisons of varied stem-loop weighting schemes indicate that the down-weightings for stem regions could improve the phylogenetic analysis and the degree of non-independence of stem substitutions was not as important as expected. Bayesian inference under four models of nucleotide substitution indicated that likelihood-based phylogenetic analyses were more effective in improving the phylogenetic performance than was weighted parsimony analysis. In Bayesian analyses, the resolution of phylogenies under the 16-state models for paired regions, incorporating GTR + G + I models for unpaired regions was better than those under other models. The subfamily Cyprininae was resolved as a monophyletic group, as well as tribe Labein and several genera. However, the monophyly of the currently recognized tribes, such as Schizothoracin, Barbin, Cyprinion + Onychostoma lineages, and some genera was rejected. Furthermore, comparisons of the parsimony and Bayesian analyses and results of variable length bootstrap analysis indicates that the mitochondrial 16S rRNA gene should contain important character variation to recover well-supported phylogeny of cyprinid taxa whose divergences occurred within the recent 8 MY, but could not provide resolution power for deep phylogenies spanning 10-19 MYA.     

A phylogeny of Vetigastropoda and other “archaeogastropods”: re-organizing old gastropod clades

Abstract. The phylogenetic relationships among the “archaeogastropod” clades Patellogastropoda, Vetigastropoda, Neritimorpha, and Neomphalina are uncertain; the phylogenetic placement of these clades varies across different analyses, and particularly among those using morphological characteristics and those relying on molecular data. This study explores the relationships among these groups using a combined analysis with seven molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, cytochrome c oxidase subunit I [COI], myosin heavy-chain type II, and elongation factor-1α [EF-1α]) sequenced for 31 ingroup taxa and eight outgroup taxa. The deep evolutionary splits among these groups have made resolution of stable relationships difficult, and so EF-1α and myosin are used in an attempt to re-examine these ancient radiation events. Three phylogenetic analyses were performed utilizing all seven genes: a single-step direct optimization analysis using parsimony, and two-step approaches using parsimony and maximum likelihood. A single-step direct optimization parsimony analysis was also performed using only five molecular loci (18S rRNA, 28S rRNA, histone H3, 16S rRNA, and COI) in order to determine the utility of EF-1α and myosin in resolving deep relationships. In the likelihood and POY optimal phylogenetic analyses, Gastropoda, Caenogastropoda, Neritimorpha, Neomphalina, and Patellogastropoda were monophyletic. Additionally, Neomphalina and Pleurotomariidae fell outside the remaining vetigastropods, indicating the need for further investigation into the relationship of these groups with other gastropods.     

A story: unpaired adenosine bases in ribosomal RNAs

In 1985 an analysis of the Escherichia coli 16 S rRNA covariation-based structure model revealed a strong bias for unpaired adenosines. The same analysis revealed that the majority of the G, C, and U bases were paired. These biases are (now) consistent with the high percentage of unpaired adenosine nucleotides in several structure motifs.An analysis of a larger set of bacterial comparative 16 S and 23 S rRNA structure models has substantiated this initial finding and revealed new biases in the distribution of adenosine nucleotides in loop regions. The majority of the adenosine nucleotides are unpaired, while the majority of the G, C, and U bases are paired in the covariation-based structure model. The unpaired adenosine nucleotides predominate in the middle and at the 3' end of loops, and are the second most frequent nucleotide type at the 5' end of loops (G is the most common nucleotide). There are additional biases for unpaired adenosine nucleotides at the 3' end of loops and adjacent to a G at the 5' end of the helix. The most prevalent consecutive nucleotides are GG, GA, AG, and AA. A total of 70 % of the GG sequences are within helices, while more than 70 % of the AA sequences are unpaired. Nearly 50 % of the GA sequences are unpaired, and approximately one-third of the AG sequences are within helices while another third are at the 3' loop.5' helix junction. Unpaired positions with an adenosine nucleotide in more than 50 % of the sequences at the 3' end of 16 S and 23 S rRNA loops were identified and arranged into the A-motif categories XAZ, AAZ, XAG, AAG, and AAG:U, where G or Z is paired, G:U is a base-pair, and X is not an A and Z is not a G in more than 50 % of the sequences. These sequence motifs were associated with several structural motifs, such as adenosine platforms, E and E-like loops, A:A and A:G pairings at the end of helices, G:A tandem base-pairs, GNRA tetraloop hairpins, and U-turns.     

Sequencing and analysis of the internal transcribed spacers (ITSs) and coding regions in the EcoR I fragment of the ribosomal DNA of the Japanese pond frog Rana nigromaculata

The rDNA of eukaryotic organisms is transcribed as the 40S-45S rRNA precursor, and this precursor contains the following segments: 5' - ETS - 18S rRNA - ITS 1 - 5.8S rRNA - ITS 2 - 28S rRNA - 3'. In amphibians, the nucleotide sequences of the rRNA precursor have been completely determined in only two species of Xenopus. In the other amphibian species investigated so far, only the short nucleotide sequences of some rDNA fragments have been reported. We obtained a genomic clone containing the rDNA precursor from the Japanese pond frog Rana nigromaculata and analyzed its nucleotide sequence. The cloned genomic fragment was 4,806 bp long and included the 3'-terminus of 18S rRNA, ITS 1, 5.8S rRNA, ITS 2, and a long portion of 28S rRNA. A comparison of nucleotide sequences among Rana, the two species of Xenopus, and human revealed the following: (1) The 3'-terminus of 18S rRNA and the complete 5.8S rRNA were highly conserved among these four taxa. (2) The regions corresponding to the stem and loop of the secondary structure in 28S rRNA were conserved between Xenopus and Rana, but the rate of substitutions in the loop was higher than that in the stem. Many of the human loop regions had large insertions not seen in amphibians. (3) Two ITS regions had highly diverged sequences that made it difficult to compare the sequences not only between human and frogs, but also between Xenopus and Rana. (4) The short tracts in the ITS regions were strictly conserved between the two Xenopus species, and there was a corresponding sequence for Rana. Our data on the nucleotide sequence of the rRNA precursor from the Japanese pond frog Rana nigromaculata were used to examine the potential usefulness of the rRNA genes and ITS regions for evolutionary studies on frogs, because the rRNA precursor contains both highly conserved regions and rapidly evolving regions.     

18S rRNA alignments derived from different secondary structure models can produce alternative phylogenies

Molecular sequence data are often aligned on the basis of secondary and/or tertiary structure models. However, these models are regularly updated and sometimes differ depending on the way in which they were constructed. We examined whether the choice of a particular 18S rRNA secondary structure model as alignment basis influences phylogeny inference. We therefore compared 18S rRNA phylogenies derived from alignments based on different models. We used: 1. Maximum parsimony; 2. The neighbour-joining method; 3. The maximum-likelihood approach; and 4. Evolutionary parsimony. This demonstrated that the secondary structure model on which an alignment is based may influence: 1. The tree topologies found by these four methods; 2. The numbers of most parsimonious trees found; and 3. The statistical values calculated by the evolutionary parsimony method.     

基于16S rRNA和Cyt b基因序列的鰶亚科系统发育研究

对鰶亚科4属5种鱼类的线粒体基因组16S rRNA和Cyt b基因片段序列进行序列比较和系统发育关系分析。结果显示:5种鰶亚科鱼类的16S rRNA和Cy tb基因片段同源序列长度分别为525 bp和402 bp,序列联合后的序列总长度为927 bp,其中多态位点178个,简约信息位点123个。选取太平洋鲱Clupea pallasii和大西洋鲱C.harengus为外类群,采用邻接法(NJ)、最大简约法(MP)、最大似然法(ML)和贝叶斯法(BI)分别对2个基因片段序列进行了聚类分析,并联合2个基因片段利用邻接法、最大简约法和贝叶斯法进行分析。系统发育分析显示:斑鰶Konosirus punctatus与花鰶Clupanodon thriss亲缘关系最近,分布于美洲大陆的真鰶属Dorosoma鱼类与印度洋、太平洋分布的斑鰶属、花鰶属和海鰶属Nematalosa鱼类亲缘关系较远。     

Mouse rDNA: sequences and evolutionary analysis of spacer and mature RNA regions.

Two regions of mouse rDNA were sequenced. One contained the last 323 nucleotides of the external transcribed spacer and the first 595 nucleotides of 18S rRNA; the other spanned the entire internal transcribed spacer and included the 3' end of 18S rRNA, 5.8S rRNA, and the 5' end of 28S rRNA. The mature rRNA sequences are very highly conserved from yeast to mouse (unit evolutionary period, the time required for a 1% divergence of sequence, was 30 X 10(6) to 100 X 10(6) years). In 18S rRNA, at least some of the evolutionary expansion and increase in G + C content is due to a progressive accretion of discrete G + C-rich insertions. Spacer sequence comparisons between mouse and rat rRNA reveal much more extensive and frequent insertions and substitutions of G + C-rich segments. As a result, spacers conserve overall G + C richness but not sequence (UEP, 0.3 X 10(6) years) or specific base-paired stems. Although no stems analogous to those bracketing 16S and 23S rRNA in Escherichia coli pre-rRNA are evident, certain features of the spacer regions flanking eucaryotic mature rRNAs are conserved and could be involved in rRNA processing or ribosome formation. These conserved regions include some short homologous sequence patterns and closely spaced direct repeats.     

Phylogeny of the colonial green flagellates: a study of 18S and 26S rRNA sequence data.

A study of phylogenetic relationships of the colonial green algal flagellates based on nuclear 18S and 26S rRNA sequence data suggests that the colonial habit has had at least two independent origins. All colonial taxa included in the analysis, except Stephanosphaera, are allied in a clade with Chlamydomonas reinhardtii and other Chlamydomonas taxa ascribed to the Euchlamydomonas group by Ettl. In contrast, Stephanosphaera is allied with other unicellular flagellates including Haematococcus. Comparison of the 18S and 26S data shows that the two sets of data yield different results following cladistic analysis. The 18S data provide the principal signal that supports the more basal divergences, but the data do not unambiguously address relationships among taxa in the clade that includes most colonial flagellates and Chlamydomonas taxa representative of the Euchlamydomonas group (sensu Ettl). In contrast, the 26S data have fewer informative sites that support basal divergences than the 18S data, but provide much of the signal that supports resolution of taxa in the colonial flagellate clade in an analysis of the combined 18S and 26S rRNA sequence data. Additional sequence data from the 26S molecule and additional taxa may reduce the topological ambiguity inferred from the sequence data for the colonial flagellates. Alternatively, an ancient and rapid radiation of taxa in the colonial lineage could account for the topological ambiguity. Despite some unresolved questions of relationships, cladistic analysis of the combined data sets provides some robustly supported concepts of evolution in these flagellates.     

A phylogenetic analysis of the 18S ribosomal RNA sequence of the coelacanth Latimeria chalumnae

Synopsis Approximately 98% of the sequence of the 18S ribosomal RNA (rRNA) of the coelacanth Latimeria chalumnae was determined by a combination of direct RNA sequencing and sequencing of rRNA genes amplified by the polymerase chain reaction. This sequence was compared with 18S rRNA sequences of similar length from seven other vertebrate species, representing the taxa Petromyzontiformes, Holocephali, Elasmobranchii, Actinopterygii, Dipnoi, Amphibia, and Amniota, in order to determine the most likely sister group of the coelacanth. Maximum parsimony analysis of these sequences resulted in a single most parsimonious tree containing a number of anomalous relationships among these groups. A bootstrap analysis showed that none of the relationships in this tree was significantly supported at the 95% level, however. Addition of data from 15 other vertebrates (providing multiple representatives of most of the higher taxa) resulted in similar ambiguous groupings, as did a number of methods of editing the sites compared (designed to eliminate rapidly evolving positions). These results may be due to a relatively rapid radiation of the major lineages of osteichthyans, the resolution of which will require molecular information from a larger portion of the coelacanth genome.     

Sequence evolution in mitochondrial ribosomal and ND-1 genes in lepidoptera: implications for phylogenetic analyses.

A 2,256-bp sequence of the mitochondrial genome of a lepidopteran (Spodoptera frugiperda) contains tRNAs for valine and leucine, the 16S rRNA, and three-quarters of the ND-1 presumptive protein-coding gene. A 64-bp stretch of unknown function was located between the rRNA and leucine tRNA. Sequence divergence in the 16S rRNA obtained from alignment with published insect sequences is consistent with phylogenetic hypotheses, in that Diptera and Lepidoptera are more closely related to each other (24% sequence divergence) than either is to Hymenoptera (31%). Within the ND-1 gene, sequences for four additional Lepidoptera were generated for a 314-bp region and contrasted with published sequences for the locust and Drosophila. Sequence divergence in this region was consistent with accepted phylogenetic relationships, but results of parsimony analyses were not. Cladograms consistently recovered accepted higher level relationships (monophyly of Lepidoptera), despite high homoplasy, but were unable to resolve superfamily and family relationships within Lepidoptera, regardless of the outgroup or character subset analyzed. Character analysis indicated that homoplasy was decreased at higher levels when first- and second-codon sites were used exclusively. At the lowest level (families), resolution was enhanced by inclusion of third-codon sites. Inability of molecular data to recover a well-established phylogeny may be rectified by additional characters or taxa, but it is clear that homoplasy is sufficiently high to caution against the acceptance of relationships generated with this molecular region that are not extremely robust.     

Partial small subunit (18S) rRNA gene sequences from fish parasites of the families Lepocreadiidae and Fellodistomidae (Digenea) and their use in phylogenetic analyses

Digeneans of the families Lepocreadiidae and Fellodistomidae are common parasites of shallow and deep-water marine fishes. Worms recovered from these contrasting environments may be indistinguishable or very similar morphologically and little is known concerning their inter-relationships. To investigate the systematic status of these forms, partial sequences from a small subunit 18S rRNA gene were generated from four species of lepocreadiids (Lepidapedon elongatum, L. gaevskayae, L. rachion and Opechona bacillaris) and two fellodistomids (Fellodistomum fellis and Steringophorus agnotus). Approximately 1,637 bases were sequenced for L. elongatum, L. rachion and F. fellis. A comparison of these sequences identified regions which varied between the two families. As a result, two regions were identified as containing potential phylogenetically informative sites and sequenced from the remaining species. Analyses of these regions by both maximum parsimony and distance methods showed that nucleic acid sequence data can be used to resolve the two families. The results indicate that 18S rRNA sequences are likely to be more satisfactory at resolving higher levels of phylogeny, i.e. at the family level, than at the generic level due to the similarity shown between the sequences of congeners.