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1.
Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity 总被引:5,自引:0,他引:5
The plastid-bearing members of the Cryptophyta contain two functional eukaryotic genomes of different phylogenetic origin,
residing in the nucleus and in the nucleomorph, respectively. These widespread and diverse protists thus offer a unique opportunity
to study the coevolution of two different eukaryotic genomes within one group of organisms. In this study, the SSU rRNA genes
of both genomes were PCR-amplified with specific primers and phylogenetic analyses were performed on different data sets using
different evolutionary models. The results show that the composition of the principal clades obtained from the phylogenetic
analyses of both genes was largely congruent, but striking differences in evolutionary rates were observed. These affected
the topologies of the nuclear and nucleomorph phylogenies differently, resulting in long-branch attraction artifacts when
simple evolutionary models were applied. Deletion of long-branch taxa stabilized the internal branching order in both phylogenies
and resulted in a completely resolved topology in the nucleomorph phylogeny. A comparison of the tree topologies derived from
SSU rDNA sequences with characters previously used in cryptophyte systematics revealed that the biliprotein type was congruent,
but the type of inner periplast component incongruent, with the molecular trees. The latter is indicative of a hidden cellular
dimorphism (cells with two periplast types present in a single clonal strain) of presumably widespread occurrence throughout
cryptophyte diversity, which, in consequence, has far-reaching implications for cryptophyte systematics as it is practiced
today. 相似文献
2.
We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of
among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to
clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether
18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of
among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary
structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic
information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both
within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly,
excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution
of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation)
reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for
reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S
rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion.
Received: 9 December 1997 / Accepted: 23 March 1998 相似文献
3.
We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization
and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including
both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both
paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that
paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events
between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential
paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding
than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas
coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result
in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences,
comparative mapping, and population genetic studies.
Received: 11 October 2000 / Accepted: 18 September 2001 相似文献
4.
5.
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
6.
Thorsten Burmester Holman C. Massey Jr. Stanislav O. Zakharkin Helen Benes 《Journal of molecular evolution》1998,47(1):93-108
The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment
of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny.
Although hexamerins and hemocyanins belong to a highly divergent protein superfamily and only 18 amino acid positions are
identical in all the sequences, the core structures of the three protein domains are well conserved. Under the assumption
of maximum parsimony, a phylogenetic tree was obtained that matches perfectly the assumed phylogeny of the insect orders.
An interesting common clade of the hymenopteran and coleopteran hexamerins was observed. In most insect orders, several paralogous
hexamerin subclasses were identified that diversified after the splitting of the major insect orders. The dipteran arylphorin/LSP-1-like
hexamerins were subject to closer examination, demonstrating hexamerin gene amplification and gene loss in the brachyceran
Diptera. The hexamerin receptors, which belong to the hexamerin/hemocyanin superfamily, diverged early in insect evolution,
before the radiation of the winged insects. After the elimination of some rapidly or slowly evolving sequences, a linearized
phylogenetic tree of the hexamerins was constructed under the assumption of a molecular clock. The inferred time scale of
hexamerin evolution, which dates back to the Carboniferous, agrees with the available paleontological data and reveals some
previously unknown divergence times among and within the insect orders.
Received: 4 August 1997 / Accepted: 29 October 1997 相似文献
7.
The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular
clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio
test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately
inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood
method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were
also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important
insights on HCV origin and evolution.
Received: 13 January 2001 / Accepted: 21 June 2001 相似文献
8.
Syvanen M 《Journal of molecular evolution》2002,54(2):258-266
The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gram− bacteria,
Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four
groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal
tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea,
Eukaryota) (Gram+, Gram−) topology, two genes supported the one where Gram− and Eukaryota form a clade, and one gene supported
the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing
the two central nodes into a single node. These are referred to as star phylogenies.
I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger
than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star
phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that
the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely
related species. This implies that the genes under comparison experience comparable functional constraint. However, when the
genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint
this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is
that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one
another. They presumably spread through life by horizontal gene transfer.
Received: 12 July 2001 / Accepted: 27 July 2001 相似文献
9.
Piero Cammarano Roberta Creti Anna M. Sanangelantoni Peter Palm 《Journal of molecular evolution》1999,49(4):524-537
A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible
for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence
segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the
global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and
protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain
IV), the alignment of the bacterial sequences with those of Archaea–Eucarya was not retrieved by database probing with EF-G(2)
sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in
BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly
due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea–Eucarya. Phylogenetic trees
have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned
regions, as well as positions arising from misalignment of the G′ and G″ subdomain insertion segments flanking the ``fifth'
consensus motif of the G domain (?varsson, 1995). The results show inconsistencies between trees inferred by alternative methods
and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood
and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred
substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or
terminal accretions) supporting a crenarchaeal–eucaryal clade are detectable in the new EF-G(2) sequence alignment. 相似文献
10.
Olivier Verneau François Catzeflis Anthony V. Furano 《Journal of molecular evolution》1997,45(4):424-436
We determined ∼215 bp of DNA sequence from the 3′-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from
22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them
were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred
the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique
phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The
lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study
of mammalian evolution.
Received: 8 November 1996 / Accepted: 11 April 1997 相似文献
11.
The neighbor-joining (NJ) method is widely used in reconstructing large phylogenies because of its computational speed and
the high accuracy in phylogenetic inference as revealed in computer simulation studies. However, most computer simulation
studies have quantified the overall performance of the NJ method in terms of the percentage of branches inferred correctly
or the percentage of replications in which the correct tree is recovered. We have examined other aspects of its performance,
such as the relative efficiency in correctly reconstructing shallow (close to the external branches of the tree) and deep
branches in large phylogenies; the contribution of zero-length branches to topological errors in the inferred trees; and the
influence of increasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency of the
NJ method. Results show that the correct reconstruction of deep branches is no more difficult than that of shallower branches.
The presence of zero-length branches in realized trees contributes significantly to the overall error observed in the NJ tree,
especially in large phylogenies or slowly evolving genes. Furthermore, the tree size does not influence the efficiency of
NJ in reconstructing shallow and deep branches in our simulation study, in which the evolutionary process is assumed to be
homogeneous in all lineages.
Received: 7 March 2000 / Accepted: 2 August 2000 相似文献
12.
Recombination is well known as a complicating factor in the interpretation of molecular phylogenies. Here we describe a maximum
likelihood sliding window method based on a likelihood ratio test for scanning DNA sequence alignments for regions of incongruent
phylogenetic signals, such as those influenced by recombination. Using this method, we identify several instances of gene
conversion between paralogous chaperonin genes in euryarchaeote Archaea, many of which are not detected by two other widely
used methods. In the Thermococcus/Pyrococcus lineage, where a gene duplication producing a and b paralogues predates the divergence of Thermococcus strains KS-1 and KS-8, gene conversion has homogenized portions of the a and b genes in KS-8 since the divergence of these two strains. A region near the 3′ end of the a and b paralogues in the methanogen Methanobacterium thermoautotrophicum also appears to have undergone gene conversion. We apply the method to two additional test data sets, the argF gene of Neisseria and a set of actin paralogues in maize, and show that it successfully identifies all the recombinant regions that were previously
detected with other methods. Our approach is relatively insensitive to the presence of divergent sequences in the alignment,
making it ideal for detecting recombination between both closely and distantly related genes. 相似文献
13.
Combining data sets with different phylogenetic histories 总被引:1,自引:0,他引:1
Wiens JJ 《Systematic biology》1998,47(4):568-581
The possibility that two data sets may have different underlying phylogenetic histories (such as gene trees that deviate from species trees) has become an important argument against combining data in phylogenetic analysis. However, two data sets sampled for a large number of taxa may differ in only part of their histories. This is a realistic scenario and one in which the relative advantages of combined, separate, and consensus analysis become much less clear. I propose a simple methodology for dealing with this situation that involves (1) partitioning the available data to maximize detection of different histories, (2) performing separate analyses of the data sets, and (3) combining the data but considering questionable or unresolved those parts of the combined tree that are strongly contested in the separate analyses (and which therefore may have different histories) until a majority of unlinked data sets support one resolution over another. In support of this methodology, computer simulations suggest that (1) the accuracy of combined analysis for recovering the true species phylogeny may exceed that of either of two separately analyzed data sets under some conditions, particularly when the mismatch between phylogenetic histories is small and the estimates of the underlying histories are imperfect (few characters, high homoplasy, or both) and (2) combined analysis provides a poor estimate of the species tree in areas of the phylogenies with different histories but gives an improved estimate in regions that share the same history. Thus, when there is a localized mismatch between the histories of two data sets, the separate, consensus, and combined analyses may all give unsatisfactory results in certain parts of the phylogeny. Similarly, approaches that allow data combination only after a global test of heterogeneity will suffer from the potential failings of either separate or combined analysis, depending on the outcome of the test. Excision of conflicting taxa is also problematic, in that doing so may obfuscate the position of conflicting taxa within a larger tree, even when their placement is congruent between data sets. Application of the proposed methodology to molecular and morphological data sets for Sceloporus lizards is discussed. 相似文献
14.
A mitochondrial DNA (mtDNA) phylogeny of cichlid fish is presented for the most taxonomically inclusive data set compiled
to date (64 taxa). 16S rDNA data establish with confidence relationships among major lineages of cichlids, with a general
pattern congruent with previous morphological studies and less inclusive molecular phylogenies based on nuclear genes. Cichlids
from Madagascar and India are the most basal groups of the family Cichlidae and sister to African–Neotropical cichlids. The
cichlid phylogeny suggests drift-vicariance events, consistent with the fragmentation of Gondwana, to explain current biogeographic
distributions. Important phylogenetic findings include the placement of the controversial genus Heterochromis basal among African cichlids, the South American genus Retroculus as the most basal taxon of the Neotropical cichlid assemblage, and the close relationship of the Neotropical genera Cichla with Astronotus rather than with the crenicichlines. Based on a large number of South American genera, the Neotropical cichlids are defined
as a monophyletic assemblage and shown to harbor significantly higher levels of genetic variation than their African counterparts.
Relative rate tests suggest that Neotropical cichlids have experienced accelerated rates of molecular evolution. But these
high evolutionary rates were significantly higher among geophagine cichlids.
Received: 18 September 1998 / Accepted: 16 December 1998 相似文献
15.
Wagner PJ 《Systematic biology》2000,49(1):65-86
Because phylogenies can be estimated without stratigraphic data and because estimated phylogenies also infer gaps in sampling, some workers have used phylogeny estimates as templates for evaluating sampling from the fossil record and for "correcting" historical diversity patterns. However, it is not known how sampling intensity (the probability of sampling taxa per unit time) and completeness (the proportion of taxa sampled) affect the accuracy of phylogenetic inferences, nor how phylogenetically inferred estimates of sampling and diversity respond to inaccurate estimates of phylogeny. Both issues are addressed with a series of simulations using simple models of character evolution, varying speciation patterns, and various rates of speciation, extinction, character change, and preservation. Parsimony estimates of simulated phylogenies become less accurate as sampling decreases, and inaccurate trees chronically underestimate sampling. Biotic factors such as rates of morphologic change and extinction both affect the accuracy of phylogenetic estimates and thus affect estimated gaps in sampling, indicating that differences in implied sampling need not reflect actual differences in sampling. Errors in inferred diversity are concentrated early in the history of a clade. This, coupled with failure to account for true extinction times (i.e., the Signor-Lipps effect), inflates relative diversity levels early in clade histories. Because factors other than differences in sampling predict differences in the numbers of gaps implied by phylogeny estimates, inferred phylogenies can be misleading templates for evaluating sampling or historical diversity patterns. 相似文献
16.
The Rooting of the Universal Tree of Life Is Not Reliable 总被引:19,自引:0,他引:19
Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of
life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative
sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been
shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of
evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable
phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal
tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition
particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant
groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various
ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota
sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies
inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to
root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch
was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch
of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides,
for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome
analysis. 相似文献
17.
18.
James R. Brown Frank T. Robb Robert Weiss W. Ford Doolittle 《Journal of molecular evolution》1997,45(1):9-16
Each amino acid is attached to its cognate tRNA by a distinct aminoacyl-tRNA synthetase (aaRS). The conventional evolutionary
view is that the modern complement of synthetases existed prior to the divergence of eubacteria and eukaryotes. Thus comparisons
of prokaryotic and eukaryotic aminoacyl-tRNA synthetases of the same type (charging specificity) should show greater sequence
similarities than comparisons between synthetases of different types—and this is almost always so. However, a recent study
[Ribas de Pouplana L, Furgier M, Quinn CL, Schimmel P (1996) Proc Natl Acad Sci USA 93:166–170] suggested that tryptophanyl- (TrpRS) and tyrosyl-tRNA (TyrRS) synthetases of the Eucarya (eukaryotes) are more
similar to each other than either is to counterparts in the Bacteria (eubacteria). Here, we reexamine the evolutionary relationships
of TyrRS and TrpRS using a broader range of taxa, including new sequence data from the Archaea (archaebacteria) as well as
species of Eucarya and Bacteria. Our results differ from those of Ribas de Pouplana et al.: All phylogenetic methods support
the separate monophyly of TrpRS and TyrRS. We attribute this result to the inclusion of the archaeal data which might serve
to reduce long branch effects possibly associated with eukaryotic TrpRS and TyrRS sequences. Furthermore, reciprocally rooted
phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing
the root of the universal tree in the Bacteria.
Received: 7 December 1996 / Accepted: 11 February 1997 相似文献
19.
Michael W. Hart Sheri L. Johnson Jason A. Addison Maria Byrne 《Invertebrate Biology》2004,123(4):343-356
Abstract. Historically, characters from early animal development have been a potentially rich source of phylogenetic information, but many traits associated with the gametes and larval stages of animals with complex life cycles are widely suspected to have evolved frequent convergent similarities. Such convergences will confound true phylogenetic relationships. We compared phylogenetic inferences based on early life history traits with those from mitochondrial DNA sequences for sea stars in the genera Asterina, Cryptasterina , and Patiriella (Valvatida: Asterinidae). Analysis of these two character sets produced phylogenies that shared few clades. We quantified the degree of homoplasy in each character set when mapped onto the phylogeny inferred from the alternative characters. The incongruence between early life history and nucleotide characters implies more homoplasy in the life history character set. We suggest that the early life history traits in this case are most likely to be misleading as phylogenetic characters because simple adaptive models predict convergence in early life histories. We show that adding early life history characters may slightly improve a phylogeny based on nucleotide sequences, but adding nucleotide characters may be critically important to improving inferences from phylogenies based on early life history characters. 相似文献
20.
Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa 总被引:13,自引:5,他引:8
The reconstruction of phylogenetic history is predicated on being able to
accurately establish hypotheses of character homology, which involves
sequence alignment for studies based on molecular sequence data. In an
empirical study investigating nucleotide sequence alignment, we inferred
phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based
on complete small-subunit rDNA sequences, using six different
multiple-alignment procedures: manual alignment based on the secondary
structure of the 18S rRNA molecule, and automated similarity-based
alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM
computer programs. Trees were constructed using neighboring-joining,
weighted-parsimony, and maximum- likelihood methods. All of the multiple
sequence alignment procedures yielded the same basic structure for the
estimate of the phylogenetic relationship among the taxa, which presumably
represents the underlying phylogenetic signal. However, the placement of
many of the taxa was sensitive to the alignment procedure used; and the
different alignments produced trees that were on average more dissimilar
from each other than did the different tree-building methods used. The
multiple alignments from the different procedures varied greatly in length,
but aligned sequence length was not a good predictor of the similarity of
the resulting phylogenetic trees. We also systematically varied the gap
weights (the relative cost of inserting a new gap into a sequence or
extending an already-existing gap) for the ClustalW program, and this
produced alignments that were at least as different from each other as
those produced by the different alignment algorithms. Furthermore, there
was no combination of gap weights that produced the same tree as that from
the structure alignment, in spite of the fact that many of the alignments
were similar in length to the structure alignment. We also investigated the
phylogenetic information content of the helical and nonhelical regions of
the rDNA, and conclude that the helical regions are the most informative.
We therefore conclude that many of the literature disagreements concerning
the phylogeny of the Apicomplexa are probably based on differences in
sequence alignment strategies rather than differences in data or
tree-building methods.
相似文献