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1.
Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology 总被引:1,自引:0,他引:1
Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony. 相似文献
2.
We analyzed the higher level phylogeny of the bee family Halictidae based on the coding regions of three single-copy nuclear genes (long-wavelength [LW] opsin, wingless, and elongation factor 1-alpha [EF-1 alpha]). Our combined data set consisted of 2,234 aligned nucleotide sites (702 base pairs [bp] for LW opsin, 405 bp for wingless, and 1,127 bp for EF-1 alpha) and 779 parsimony-informative sites. We included 58 species of halictid bees from 33 genera, representing all subfamilies and tribes, and rooted the trees using seven outgroups from other bee families: Colletidae, Andrenidae, Melittidae, and Apidae. We analyzed the separate and combined data sets by a variety of methods, including equal weights parsimony, maximum likelihood, and Bayesian methods. Analysis of the combined data set produced a strong phylogenetic signal with high bootstrap and Bremer support and high posterior probability well into the base of the tree. The phylogeny recovered the monophyly of the Halictidae and of all four subfamilies and both tribes, recovered relationships among the subfamilies and tribes congruent with morphology, and provided robust support for the relationships among the numerous genera in the tribe Halictini, sensu Michener (2000). Using our combined nucleotide data set, several recently described halictid fossils from the Oligocene and Eocene, and recently developed Bayesian methods, we estimated the antiquity of major clades within the family. Our results indicate that each of the four subfamilies arose well before the Cretaceous-Tertiary boundary and suggest that the early radiation of halictid bees involved substantial African-South American interchange roughly coincident with the separation of these two continents in the late Cretaceous. This combination of single-copy nuclear genes is capable of recovering Cretaceous-age divergences in bees with high levels of support. We propose that LW opsin, wingless, and EF-1 alpha(F2 copy) may be useful in resolving relationships among bee families and other Cretaceous-age insect lineages. 相似文献
3.
We attempted a phylogenetic reconstruction for the carabid subgenus Ohomopterus (genus Carabus), a notable case of radiation with mitochondrial introgression across species. Sequence data from five nuclear single copy loci were used, including wingless (Wg), phosphoenolpyruvate carboxykinase (PepCK), cytochrome c (Cytc), elongation factor-1alpha (EF-1alpha), and an anonymous single copy locus (Carab1). Sequences of Cytc, EF-1alpha, and Carab1 included intron or intron-like parts with length variation. The analysis of individual loci resulted in low resolution of the phylogenetic relationships, and the monophyly of several morphologically recognized species for which multiple specimens were analyzed was not revealed. Several specimens were heterozygous, with non-monophyletic alleles observed in three of the five loci at which alleles in heterozygotes were separated. In a simultaneous analysis of the five loci with ambiguously aligned parts eliminated and heterozygotic sites treated as missing, the resulting tree was well resolved, but the branch support was generally weak because of conflicting phylogenetic signals from different loci. We also attempted to incorporate allelic sequence data plus the ambiguously aligned parts in the analysis, by using all possible combinations of alleles from different loci in heterozygotic individuals, but the resultant tree was not supported more strongly. Nonetheless, these simultaneous analyses provided support for the monophyly of several species and species groups, and revealed the basic evolutionary trend of OHOMOPTERUS: initial widespread groups with simpler genitalia and the origination of exaggerated genitalia in a derived clade. This study exemplifies problems inherent in the phylogenetic reconstruction of closely related organisms where low levels of variation limit the information content from each locus, while heterozygosity, different phylogenetic history of multiple loci, and alignment ambiguity further hamper phylogenetic reconstruction unless several loci converge on a uniform signal. 相似文献
4.
Elongation factor 1 alpha (EF-1 alpha) is a highly conserved ubiquitous protein involved in translation that has been suggested to have desirable properties for phylogenetic inference. To examine the utility of EF-1 alpha as a phylogenetic marker for eukaryotes, we studied three properties of EF-1 alpha trees: congruency with other phyogenetic markers, the impact of species sampling, and the degree of substitutional saturation occurring between taxa. Our analyses indicate that the EF-1 alpha tree is congruent with some other molecular phylogenies in identifying both the deepest branches and some recent relationships in the eukaryotic line of descent. However, the topology of the intermediate portion of the EF-1 alpha tree, occupied by most of the protist lineages, differs for different phylogenetic methods, and bootstrap values for branches are low. Most problematic in this region is the failure of all phylogenetic methods to resolve the monophyly of two higher-order protistan taxa, the Ciliophora and the Alveolata. JACKMONO analyses indicated that the impact of species sampling on bootstrap support for most internal nodes of the eukaryotic EF-1 alpha tree is extreme. Furthermore, a comparison of observed versus inferred numbers of substitutions indicates that multiple overlapping substitutions have occurred, especially on the branch separating the Eukaryota from the Archaebacteria, suggesting that the rooting of the eukaryotic tree on the diplomonad lineage should be treated with caution. Overall, these results suggest that the phylogenies obtained from EF-1 alpha are congruent with other molecular phylogenies in recovering the monophyly of groups such as the Metazoa, Fungi, Magnoliophyta, and Euglenozoa. However, the interrelationships between these and other protist lineages are not well resolved. This lack of resolution may result from the combined effects of poor taxonomic sampling, relatively few informative positions, large numbers of overlapping substitutions that obscure phylogenetic signal, and lineage-specific rate increases in the EF-1 alpha data set. It is also consistent with the nearly simultaneous diversification of major eukaryotic lineages implied by the "big-bang" hypothesis of eukaryote evolution. 相似文献
5.
Elongation factor-1 alpha occurs as two copies in bees: implications for phylogenetic analysis of EF-1 alpha sequences in insects 总被引:5,自引:1,他引:4
We report the complete sequence of a paralogous copy of elongation factor-1
alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae).
This copy differs from a previously described copy in the positions of five
introns and in 25% of the nucleotide sites in the coding regions. The
existence of two paralogous copies of EF-1 alpha in Drosophila and Apis
suggests that two copies of EF-1 alpha may be widespread in the
holometabolous insect orders. To distinguish between a single, ancient gene
duplication and parallel, independent fly and bee gene duplications, we
performed a phylogenetic analysis of hexapod EF-1 alpha sequences.
Unweighted parsimony analysis of nucleotide sequences suggests an ancient
gene duplication event, whereas weighted parsimony analysis of nucleotides
and unweighted parsimony analysis of amino acids suggests the contrary:
that EF-1 alpha underwent parallel gene duplications in the Diptera and the
Hymenoptera. The hypothesis of parallel gene duplication is supported both
by congruence among nucleotide and amino acid data sets and by
topology-dependent permutation tail probability (T-PTP) tests. The
resulting tree topologies are also congruent with current views on the
relationships among the holometabolous orders included in this study
(Diptera, Hymenoptera, and Lepidoptera). More sequences, from diverse
orders of holometabolous insects, will be needed to more accurately assess
the historical patterns of gene duplication in EF-1 alpha.
相似文献
6.
Müller K 《Molecular phylogenetics and evolution》2006,38(3):667-676
With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. A new method, modified complex indel coding is described that aims at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. An algorithm is described that allows application of the method to all theoretically possible gap-nucleotide patterns. A platform-independent computer program is introduced that automates the new method as well as several previously published coding schemes. Differences to previously published indel coding approaches as well as to the integration of ambiguously aligned regions into phylogenetic analysis are discussed. 相似文献
7.
Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2 总被引:4,自引:1,他引:3
Hashimoto T; Nakamura Y; Kamaishi T; Nakamura F; Adachi J; Okamoto K; Hasegawa M 《Molecular biology and evolution》1995,12(5):782-793
Partial regions of the mRNA encoding a major part of translation elongation
factor 2 (EF-2) from a mitochondrion-lacking protozoan, Giardia lamblia,
were amplified by polymerase chain reaction, and their primary structures
were analyzed. The deduced amino acid sequence was aligned with other
eukaryotic and archaebacterial EF-2's, and the phylogenetic relationships
among eukaryotes were inferred by the maximum likelihood (ML) and the
maximum parsimony (MP) methods. The ML analyses using six different models
of amino acid substitutions and the MP analysis consistently suggest that
among eukaryotic species being analyzed, G. lamblia is likely to have
diverged from other higher eukaryotes on the early phase of eukaryotic
evolution.
相似文献
8.
The major opsin in bees (Insecta: Hymenoptera): A promising nuclear gene for higher level phylogenetics. 总被引:6,自引:0,他引:6
We report the phylogenetic utility of the nuclear gene encoding the long-wavelength opsin (LW Rh) for tribes of bees. Aligned nucleotide sequences were examined in multiple taxa from the four tribes comprising the corbiculate bees within the subfamily Apinae. Phylogenetic analyses of sequence variation in a 502-bp fragment (approx 40% of the coding region) strongly supported the monophyly of each of the four tribes, which are well established from previous studies of morphology and DNA. Trees estimated from parsimony and maximum likelihood analyses of LW Rh sequences show a strongly supported relationship between the tribes Meliponini and Bombini, a relationship that has been found uniformly in studies of other genes (28S, 16S, and cytochrome b). All of the tribal clades as well as relationships among the tribes are supported by high bootstrap values, suggesting the utility of LW Rh in estimating tribal and subfamily rank for these bees. The sequences exhibit minimal base composition bias. Both 1st + 2nd and 3rd position sites provide information for estimating a reliable tree topology. These results suggest that LW Rh, which has not been reported previously in studies of organismal phylogenetics, could provide important new data from the nuclear genome for phylogeny reconstruction. 相似文献
9.
Phylogenetic analyses that incorporate the most character information also provide the most explanatory power. Here I demonstrate the value of such an approach through a direct optimization sensitivity analysis of apid bee phylogeny. Whereas prior studies have relied solely on one class of data or the other, this analysis combines previously published molecular, morphological, and behavioural characters into a single supermatrix. The final dataset includes 191 ingroup and 30 outgroup taxa, and includes data from seven unaligned gene sequences (18S, 28S, wingless, EF1‐α, polII, Nak, LW rhodopsin), 209 adult and larval morphological characters, and two behavioural characters. Nine different sets of transformation cost parameters are evaluated, along with their relative degrees of character incongruence. The preferred parameter set returns a strict consensus tree somewhat similar to, but more resolved than, a previous parsimony tree based on molecules alone. I also describe the effects of including EF1‐α and LW rhodopsin intron sequences on the outcome of the direct optimization analysis. By accounting for more evidence, this study provides the most comprehensive treatment yet of apid phylogenetic relationships. 相似文献
10.
We use a multigene data set (the mitochondrial locus and nine nuclear gene regions) to test phylogenetic relationships in the South American "lava lizards" (genus Microlophus) and describe a strategy for aligning noncoding sequences that accounts for differences in tempo and class of mutational events. We focus on seven nuclear introns that vary in size and frequency of multibase length mutations (i.e., indels) and present a manual alignment strategy that incorporates insertions and deletions (indels) for each intron. Our method is based on mechanistic explanations of intron evolution that does not require a guide tree. We also use a progressive alignment algorithm (Probabilistic Alignment Kit; PRANK) and distinguishes insertions from deletions and avoids the "gapcost" conundrum. We describe an approach to selecting a guide tree purged of ambiguously aligned regions and use this to refine PRANK performance. We show that although manual alignment is successful in finding repeat motifs and the most obvious indels, some regions can only be subjectively aligned, and there are limits to the size and complexity of a data matrix for which this approach can be taken. PRANK alignments identified more parsimony-informative indels while simultaneously increasing nucleotide identity in conserved sequence blocks flanking the indel regions. When comparing manual and PRANK with two widely used methods (CLUSTAL, MUSCLE) for the alignment of the most length-variable intron, only PRANK recovered a tree congruent at deeper nodes with the combined data tree inferred from all nuclear gene regions. We take this concordance as an objective function of alignment quality and present a strongly supported phylogenetic hypothesis for Microlophus relationships. From this hypothesis we show that (1) a coded indel data partition derived from the PRANK alignment contributed significantly to nodal support and (2) the indel data set permitted detection of significant conflict between mitochondrial and nuclear data partitions, which we hypothesize arose from secondary contact of distantly related taxa, followed by hybridization and mtDNA introgression. 相似文献
11.
The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis. 相似文献
12.
A highly conserved nuclear gene for low-level phylogenetics: elongation factor-1 alpha recovers morphology-based tree for heliothine moths 总被引:8,自引:2,他引:6
Cho S; Mitchell A; Regier JC; Mitter C; Poole RW; Friedlander TP; Zhao S 《Molecular biology and evolution》1995,12(4):650-656
Molecular systematists need increased access to nuclear genes. Highly
conserved, low copy number protein-encoding nuclear genes have attractive
features for phylogenetic inference but have heretofore been applied mostly
to very ancient divergences. By virtue of their synonymous substitutions,
such genes should contain a wealth of information about lower-level
taxonomic relationships as well, with the advantage that amino acid
conservatism makes both alignment and primer definition straightforward. We
tested this postulate for the elongation factor-1 alpha (EF-1 alpha) gene
in the noctuid moth subfamily Heliothinae, which has probably diversified
since the middle Tertiary. We sequenced 1,240 bp in 18 taxa representing
heliothine groupings strongly supported by previous morphological and
allozyme studies. The single most parsimonious gene tree and the
neighbor-joining tree for all nucleotides show almost complete concordance
with the morphological tree. Homoplasy and pairwise divergence levels are
low, transition/transversion ratios are high, and phylogenetic information
is spread evenly across gene regions. The EF-1 alpha gene and presumably
other highly conserved genes hold much promise for phylogenetics of
Tertiary age eukaryote groups.
相似文献
13.
Hiroshi Wada Mari Kobayashi Riki Sato Nori Satoh Hitoshi Miyasaka Yoshihisa Shirayama 《Journal of molecular evolution》2002,54(1):118-128
To test the validity of intron–exon structure as a phylogenetic marker, the intron–exon structure of EF-1α genes was investigated
for starfish, acornworms, ascidians, larvaceans, and amphioxus and compared with that of vertebrates. Of the 11 distinct intron
insertion sites found within the coding regions of the deuterostome EF-1α genes, 7 are shared by several taxa, while the remainder
are unique to certain taxa. Examination of the shared introns of the deuterostome EF-1α gene revealed that independent intron
loss or intron insertion must have occurred in separate lineages of the deuterostome taxa. Maximum parsimony analysis of the
intron–exon data matrix recovered five parsimonious trees (consistency index = 0.867). From this result, we concluded that
the intron–exon structure of deuterostome EF-1α has evolved more dynamically than previously thought, rendering it unsuitable
as a phylogenetic marker. We also reconstructed an evolutionary history of intron insertion–deletion events on the deuterostome
phylogeny, based on several molecular phylogenetic studies. These analyses revealed that the deuterostome EF-1α gene has lost
individual introns more frequently than all introns simultaneously. 相似文献
14.
In the continuing quest for informative genes for use in molecular systematics, the protein-coding gene Elongation factor-1alpha (EF-1alpha) has rapidly become one of the most prevalent "single-copy" nuclear genes utilized, particularly in arthropods. This paper explores the molecular evolutionary dynamics and phylogenetic utility of EF-1alpha in the salticid spider genus Habronattus. As has been reported for other arthropod lineages, our studies indicate that multiple (two) copies of EF-1alpha exist in Habronattus. These copies differ in intron structure and thus in size, making it possible to easily separate PCR amplification products. We present data for an intronless EF-1alpha copy for three Habronattus species. The presence of nonsense mutations and generally elevated rates of amino acid change suggest that this copy is evolving under relaxed functional constraints in Habronattus. A larger taxon sample (50 species plus outgroups) is presented for an EF-1alpha copy that includes both intron and exon regions. Characteristics of both regions suggest that this is a functional, orthologous copy in the species sampled. Maximum-likelihood relative-rate comparisons show that exon third codon sites are evolving more than 100 times as fast as second codon sites in these sequences and that intron sites are evolving about twice as fast as exon third sites. In combination, the EF-1alpha data provide robust, species-level phylogenetic signal that is largely congruent with morphologically well supported areas of Habronattus phylogeny. The recovery of some novel clades, and the unexpected fragmentation of others, suggests areas requiring further phylogenetic attention. 相似文献
15.
Trichoptera are holometabolous insects with aquatic larvae that, together with the Lepidoptera, make up the Amphiesmenoptera. Despite extensive previous morphological work, little phylogenetic agreement has been reached about the relationship among the three suborders--Annulipalpia, Spicipalpia, and Integripalpia--or about the monophyly of Spicipalpia. In an effort to resolve this conflict, we sequenced fragments of the large and small subunit nuclear ribosomal RNAs (1078 nt; D1, D3, V4-5), the nuclear elongation factor 1 alpha gene (EF-1 alpha; 1098 nt), and a fragment of mitochondrial cytochrome oxidase I (COI; 411 nt). Seventy adult and larval morphological characters were reanalyzed and added to molecular data in a combined analysis. We evaluated signal and homoplasy in each of the molecular datasets and attempted to rank the particular datasets according to how appropriate they were for inferring relationships among suborders. This evaluation included testing for conflict among datasets, comparing tree lengths among alternative hypotheses, measuring the left-skew of tree-length distributions from maximally divergent sets of taxa, evaluating the recovery of expected clades, visualizing whether or not substitutions were accumulating with time, and estimating nucleotide compositional bias. Although all these measures cast doubt on the reliability of the deep-level signal coming from the nucleotides of the COI and EF-1 alpha genes, these data could still be included in combined analyses without overturning the results from the most conservative marker, the rRNA. The different datasets were found to be evolving under extremely different rates. A site-specific likelihood method for dealing with combined data with nonoverlapping parameters was proposed, and a similar weighting scheme under parsimony was evaluated. Among our phylogenetic conclusions, we found Annulipalpia to be the most basal of the three suborders, with Spicipalpia and Integripalpia forming a clade. Monophyly of Annulipalpia and Integripalpia was confirmed, but the relationships among spicipalpians remain equivocal. 相似文献
16.
Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no difference in topological accuracy for the different methods of gap coding. However, in cases where a difference was present, coding gaps as a fifth state character or as separate presence/absence characters outperformed treating gaps as unknown/missing data nearly 90% of the time. For the hypothesized alignments, on average, all gap treatment approaches performed equally well. Data sets with higher sequence divergence and more pectinate tree shapes with variable branch lengths are more affected by gap coding than datasets associated with shallower non-pectinate tree shapes. 相似文献
17.
Synergistic effects of combining morphological and molecular data in resolving the phylogeny of butterflies and skippers 总被引:13,自引:0,他引:13
Wahlberg N Braby MF Brower AV de Jong R Lee MM Nylin S Pierce NE Sperling FA Vila R Warren AD Zakharov E 《Proceedings. Biological sciences / The Royal Society》2005,272(1572):1577-1586
Phylogenetic relationships among major clades of butterflies and skippers have long been controversial, with no general consensus even today. Such lack of resolution is a substantial impediment to using the otherwise well studied butterflies as a model group in biology. Here we report the results of a combined analysis of DNA sequences from three genes and a morphological data matrix for 57 taxa (3258 characters, 1290 parsimony informative) representing all major lineages from the three putative butterfly super-families (Hedyloidea, Hesperioidea and Papilionoidea), plus out-groups representing other ditrysian Lepidoptera families. Recently, the utility of morphological data as a source of phylogenetic evidence has been debated. We present the first well supported phylogenetic hypothesis for the butterflies and skippers based on a total-evidence analysis of both traditional morphological characters and new molecular characters from three gene regions (COI, EF-1alpha and wingless). All four data partitions show substantial hidden support for the deeper nodes, which emerges only in a combined analysis in which the addition of morphological data plays a crucial role. With the exception of Nymphalidae, the traditionally recognized families are found to be strongly supported monophyletic clades with the following relationships: (Hesperiidae+(Papilionidae+(Pieridae+(Nymphalidae+(Lycaenidae+Riodinidae))))). Nymphalidae is recovered as a monophyletic clade but this clade does not have strong support. Lycaenidae and Riodinidae are sister groups with strong support and we suggest that the latter be given family rank. The position of Pieridae as the sister taxon to nymphalids, lycaenids and riodinids is supported by morphology and the EF-1alpha data but conflicted by the COI and wingless data. Hedylidae are more likely to be related to butterflies and skippers than geometrid moths and appear to be the sister group to Papilionoidea+Hesperioidea. 相似文献
18.
We discovered the presence of a unique spliceosomal intron in the F1 copy of elongation factor-1alpha (EF-1alpha) restricted to the bee family Colletidae (Hymenoptera: Apoidae). The intron ranges in size from 101 to 1044 bp and shows no positional sliding. Our data also demonstrate the complete absence of this intron from exemplars representing all other bee families, as well as from close hymenopteran relatives. A review of the literature finds that this intron is likewise absent from all other arthropods for which data are available. This provides unambiguous evidence for a relatively recent intron insertion event in the colletid common ancestor and, at least in this specific instance, lends support to the introns-late hypothesis. The comparative distribution of this novel intron also supports the monophyly of Colletidae and the exclusion of the Stenotritidae from this family, providing an example of the potential of some introns to act as robust markers of shared descent. 相似文献
19.
Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and three gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions, we studied patterns of molecular evolution and their contribution to phylogenetic signal. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 18% of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand and coding sequences on the other. 相似文献
20.
Nagahama T Hamamoto M Nakase T Shimamura S Horikoshi K 《The Journal of General and Applied Microbiology》2006,52(1):37-45
Phylogenetic relationships within the Erythrobasidium clade as a lineage of the urediniomycetous yeasts were examined using partial regions of 18S rDNA, 5.8S rDNA, 26S rDNA, internal transcribed spacers (ITSs), and elongation factor (EF)-1alpha. Combined data analysis of all segments successfully yielded a reliable phylogeny and confirmed the cohesion of species characterized by Q-10(H2) as a major ubiquinone. Differences in secondary structure predicted for a variable region in 26S rDNA corresponded to major divergences in the phylogenetic tree based on the primary sequence. The common presence of a shortened helix in this region was considered to be evidence of monophyly for species with Q-10(H2), Sakaguchia dacryoides, Rhodotorula lactosa, and Rhodotorula lamellibrachiae, although it was not as strongly supported by the combined data tree. The information on intron positions in the EF-1alpha gene had potential usefulness in the phylogenetic inference between closely related species. 相似文献