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1.
Axel Janke Ola Magnell Georg Wieczorek Michael Westerman Ulfur Arnason 《Journal of molecular evolution》2002,54(1):71-80
The monotremes, the duck-billed platypus and the echidnas, are characterized by a number of unique morphological characteristics,
which have led to the common belief that they represent the living survivors of an ancestral stock of mammals. Analysis of
new data from the complete mitochondrial (mt) genomes of a second monotreme, the spiny anteater, and another marsupial, the
wombat, yielded clear support for the Marsupionta hypothesis. According to this hypothesis marsupials are more closely related
to monotremes than to eutherians, consistent with a basal split between eutherians and marsupials/monotremes among extant
mammals. This finding was also supported by analysis of new sequences from a nuclear gene—18S rRNA. The mt genome of the wombat
shares some unique features with previously described marsupial mtDNAs (tRNA rearrangement, a missing tRNALys, and evidence for RNA editing of the tRNAAsp). Molecular estimates of genetic divergence suggest that the divergence between the platypus and the spiny anteater took
place ≈34 million years before present (MYBP), and that between South American and Australian marsupials ≈72 MYBP.
Received: 28 October 2000 / Accepted: 23 March 2001 相似文献
2.
Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative
of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at
the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous
positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one
may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop
positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock
rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest
that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested
by paleontological evidence.
Received: 23 April 1998 / Accepted: 14 May 1998 相似文献
3.
Conflict Among Individual Mitochondrial Proteins in Resolving the Phylogeny of Eutherian Orders 总被引:19,自引:0,他引:19
Ying Cao Axel Janke Peter J. Waddell Michael Westerman Osamu Takenaka Shigenori Murata Norihiro Okada Svante Pääbo Masami Hasegawa 《Journal of molecular evolution》1998,47(3):307-322
The phylogenetic relationship among primates, ferungulates (artiodactyls + cetaceans + perissodactyls + carnivores), and
rodents was examined using proteins encoded by the H strand of mtDNA, with marsupials and monotremes as the outgroup. Trees
estimated from individual proteins were compared in detail with the tree estimated from all 12 proteins (either concatenated
or summing up log-likelihood scores for each gene). Although the overall evidence strongly suggests ((primates, ferungulates),
rodents), the ND1 data clearly support another tree, ((primates, rodents), ferungulates). To clarify whether this contradiction
is due to (1) a stochastic (sampling) error; (2) minor model-based errors (e.g., ignoring site rate variability), or (3) convergent
and parallel evolution (specifically between either primates and rodents or ferungulates and the outgroup), the ND1 genes
from many additional species of primates, rodents, other eutherian orders, and the outgroup (marsupials + monotremes) were
sequenced. The phylogenetic analyses were extensive and aimed to eliminate the following artifacts as possible causes of the
aberrant result: base composition biases, unequal site substitution rates, or the cumulative effects of both. Neither more
sophisticated evolutionary analyses nor the addition of species changed the previous conclusion. That is, the statistical
support for grouping rodents and primates to the exclusion of all other taxa fluctuates upward or downward in quite a tight
range centered near 95% confidence. These results and a site-by-site examination of the sequences clearly suggest that convergent
or parallel evolution has occurred in ND1 between primates and rodents and/or between ferungulates and the outgroup. While
the primate/rodent grouping is strange, ND1 also throws some interesting light on the relationships of some eutherian orders,
marsupials, and montremes. In these parts of the tree, ND1 shows no apparent tendency for unexplained convergences.
Received: 5 December 1997 / Accepted: 24 February 1998 相似文献
4.
Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria 总被引:11,自引:0,他引:11
Kenji V. P. Nagashima Akira Hiraishi Keizo Shimada Katsumi Matsuura 《Journal of molecular evolution》1997,45(2):131-136
Phylogenetic trees were drawn and analyzed based on the nucleotide sequences of the 1.5-kb gene fragment coding for the L
and M subunits of the photochemical reaction center of various purple photosynthetic bacteria. These trees are mostly consistent
with phylogenetic trees based on 16S rRNA and soluble cytochrome c, but differ in some significant details. This inconsistency implies horizontal transfer of the genes that code for the photosynthetic
apparatus in purple bacteria. Possibilities of similar transfers of photosynthesis genes during the evolution of photosynthesis
are discussed especially for the establishment of oxygenic photosynthesis.
Received: 8 July 1996 / Accepted: 12 March 1997 相似文献
5.
Miyuki Noro Ryuichi Masuda Irena A. Dubrovo Michihiro C. Yoshida Makoto Kato 《Journal of molecular evolution》1998,46(3):314-326
Complete sequences of cytochrome b (1,137 bases) and 12S ribosomal RNA (961 bases) genes in mitochondrial DNA were successfully determined from the woolly mammoth
(Mammuthus primigenius), African elephant (Loxodonta africana), and Asian elephant (Elephas maximus). From these sequence data, phylogenetic relationships among three genera were examined. Molecular phylogenetic trees reconstructed
by the neighbor-joining and the maximum parsimony methods provided an identical topology both for cytochrome b and 12S rRNA genes. These results support the ``Mammuthus-Loxodonta' clade, which is contrary to some previous morphological reports that Mammuthus is more closely related to Elephas than to Loxodonta.
Received: 8 April 1997 / Accepted: 23 July 1997 相似文献
6.
The complete nucleotide sequence of the mitochondrial genome was determined for a conger eel, Conger myriaster (Elopomorpha: Anguilliformes), using a PCR-based approach that employs a long PCR technique and many fish-versatile primers.
Although the genome [18,705 base pairs (bp)] contained the same set of 37 mitochondrial genes [two ribosomal RNA (rRNA), 22
transfer RNA (tRNA), and 13 protein-coding genes] as found in other vertebrates, the gene order differed from that recorded
for any other vertebrates. In typical vertebrates, the ND6, tRNAGlu, and tRNAPro genes are located between the ND5 gene and the control region, whereas the former three genes, in C. myriaster, have been translocated to a position between the control region and the tRNAPhe gene that are contiguously located at the 5′ end of the 12S rRNA gene in typical vertebrates. This gene order is similar
to the recently reported gene order in four lineages of birds in that the latter lack the ND6, tRNAGlu, and tRNAPro genes between the ND5 gene and the control region; however, the relative position of the tRNAPro to the ND6–tRNAGlu genes in C. myriaster was different from that in the four birds, which presumably resulted from different patterns of tandem duplication of gene
regions followed by gene deletions in two distantly related groups of organisms. Sequencing of the ND5–cyt b region in 11 other anguilliform species, representing 11 families, plus one outgroup species, revealed that the same gene
order as C. myriaster was shared by another 4 families, belonging to the suborder Congroidei. Although the novel gene orders of four lineages of
birds were indicated to have multiple independent origins, phylogenetic analyses using nucleotide sequences from the mitochondrial
12S rRNA and cyt b genes suggested that the novel gene orders of the five anguilliform families had originated in a single ancestral species.
Received: 13 July 2000 / Accepted: 30 November 2000 相似文献
7.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
8.
A 314-bp fragment of the mitochondrial 12S rRNA gene from 21 cestodes species of eight families was synthesized by PCR with
specially designed primers. These allowed amplification of parasite DNA without concomitant synthesis of host DNA. Phylogenetic
trees were inferred from the sequence data using three methods (maximum parsimony, maximum likelihood, and Fitch–Margoliash).
At the major nodes all three trees were similar. For the first time the genus Mesocestoides could be arranged into the Cyclophyllidea and a narrow relationship between the Mesocestoididae, Taeniidae, Hymenolepididae,
Anoplocephalidae, and Dipylidiidae was shown. Members of the families Catenotaeniidae and a cluster of two families (Hymenolepididae
and Dilepididae) form two monophyletic groups which derive prior to the remaining families of this phylogenetic study. A third
and a fourth clear monophyletic group were formed by the Taeniidae and by the Mesocestoididae. A high degree of variation
within the examined 304-bp fragment was observed between two isolates of Taenia taeniaeformis, supporting often discussed genetic heterogeneity within this species. In contrast, only one nucleotide exchange was found
in 23 isolates of Echinococcus multilocularis of various geographic origin, indicating that this species is genetically homogenous.
Received: 1 October 1997 / Accepted: 4 December 1997 相似文献
9.
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
10.
Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules 总被引:10,自引:0,他引:10
Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials,
37 placentals), including 11 new sequences, were employed to establish a ``core' secondary structure model for mammalian
12S rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence
for base-pairing in the form of compensatory mutations. In cases where compensatory evidence was not available among mammalian
sequences, we evaluated evidence among other vertebrate 12S rRNAs. Our results suggest a core model for secondary structure
in mammalian 12S rRNAs with deletions as well as additions to the Gutell (1994: Nucleic Acids Res. 22) models for Bos and Homo. In all, we recognize 40 stems, 34 of which are supported by at least some compensatory evidence within Mammalia. We also
investigated the occurrence and conservation in mammalian 12S rRNAs of nucleotide positions that are known to participate
in the decoding site in E. coli. Twenty-four nucleotide positions known to participate in the decoding site in E. coli also occur among mammalian 12S rRNAs and 17 are invariant for the same base as in E. coli. Patterns of nucleotide substitution were assessed based on our secondary structure model. Transitions in loops become saturated
by approximately 10–20 million years. Transitions in stems, in turn, show partial saturation at 20 million years but divergence
continues to increase beyond 100 million years. Transversions accumulate linearly beyond 100 million years in both stems and
loops although the rate of accumulation of transversions is three- to fourfold higher in loops. Presumably, this difference
results from constraints to maintain pairing in stems.
Received: 21 June 1995 / Accepted: 25 March 1996 相似文献
11.
Sequence differences in the tRNA-proline (tRNApro) end of the mitochondrial control-region of three species of Pacific butterflyfishes accumulated 33–43 times more rapidly
than did changes within the mitochondrial cytochrome b gene (cytb). Rapid evolution in this region was accompanied by strong
transition/transversion bias and large variation in the probability of a DNA substitution among sites. These substitution
constraints placed an absolute ceiling on the magnitude of sequence divergence that could be detected between individuals.
This divergence ``ceiling' was reached rapidly and led to a decay in the relative rate of control-region/cytb b evolution.
A high rate of evolution in this section of the control-region of butterflyfishes stands in marked contrast to the patterns
reported in some other fish lineages. Although the mechanism underlying rate variation remains unclear, all taxa with rapid
evolution in the 5′-end of the control-region showed extreme transition biases. By contrast, in taxa with slower control-region
evolution, transitions accumulated at nearly the same rate as transversions. More information is needed to understand the
relationship between nucleotide bias and the rate of evolution in the 5′-end of the control-region.
Despite strong constraints on sequence change, phylogenetic information was preserved in the group of recently differentiated
species and supported the clustering of sequences into three major mtDNA groupings. Within these groups, very similar control-region
sequences were widely distributed across the Pacific Ocean and were shared between recognized species, indicating a lack of
mitochondrial sequence monophyly among species.
Received: 30 June 1996 / Accepted: 15 May 1997 相似文献
12.
Phylogenetics of Perissodactyla and Tests of the Molecular Clock 总被引:3,自引:0,他引:3
Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian
order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for
calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points.
Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the
results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all
three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species
of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly
different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find
significant rate differences among taxa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither
calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl
radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional
views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support
for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict
for tapir relationships.
Received: 6 January 1999 / Accepted: 2 August 1999 相似文献
13.
In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging
to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of
the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin:
The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles
and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor
BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont
algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded
by the well-supported successive divergence of labyrinthulomycetes and bicosoecids.
On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching
order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae,
and several smaller groups of organisms remains largely unresolved.
When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution
rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving
sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic
grouping in most distance trees.
Received: 11 June 1997 / Accepted: 21 July 1997 相似文献
14.
Geneviàve Pont-Kingdon Norichika A. Okada Jane L. Macfarlane C. Timothy Beagley Cristi D. Watkins-Sims Thomas Cavalier-Smith G. Desmond Clark-Walker David R. Wolstenholme 《Journal of molecular evolution》1998,46(4):419-431
The nucleotide sequences of two segments of 6,737 ntp and 258 ntp of the 18.4-kb circular mitochondrial (mt) DNA molecule
of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains
the 3′ 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome
b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5′ terminal 1,124 ntp of the gene for the large subunit rRNA (l-rRNA). These genes are arranged in the order given
and all are transcribed from the same strand of the molecule. The smaller segment contains the 3′ terminal 134 ntp of the
ND4 gene and a complete tRNAf-Met gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify
arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan
rather than termination. Also, as in M. senile the mt-tRNAf-Met gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and TψC loop sequences, and a mismatched nucleotide pair at the top of
the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity
in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast
Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of
the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an
MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.
Received: 13 January 1997 / Accepted: 23 September 1997 相似文献
15.
Yuji Inagaki Yasuko Hayashi-Ishimaru Megumi Ehara Ikuo Igarashi Takeshi Ohama 《Journal of molecular evolution》1997,45(3):295-300
The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired
during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have
been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase
subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan
protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and
algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The
COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes,
but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes
and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host
cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts
are remnants of endosymbiotic algae.
Received: 24 March 1997 / Accepted: 21 April 1997 相似文献
16.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all.
Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate
variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of
Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate
chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot
be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae
by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA
trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast
phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora)
have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Received: 27 December 1999 / Accepted: 24 March 2000 相似文献
17.
Liao D 《Journal of molecular evolution》2000,51(4):305-317
Multiple copies of a given ribosomal RNA gene family undergo concerted evolution such that sequences of all gene copies are
virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal
crossing over are the proposed mechanisms for concerted evolution of tandemly repeated sequences, whereas dispersed genes
are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic
rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12
prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were
found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events
convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly,
the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization
do not affect rRNA gene homogenization. Thus, gene conversion underlies concerted evolution of bacterial rRNA genes, which
normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic
sequence.
Received: 31 March 2000 / Accepted: 15 June 2000 相似文献
18.
Mitochondrial small-subunit (19S) rDNA sequences were obtained from 10 angiosperms to further characterize sequence divergence
levels and structural variation in this molecule. These sequences were derived from seven holoparasitic (nonphotosynthetic)
angiosperms as well as three photosynthetic plants. 19S rRNA is composed of a conservative core region (ca. 1450 nucleotides)
as well as two variable regions (V1 and V7). In pairwise comparisons of photosynthetic angiosperms to Glycine, the core 19S rDNA sequences differed by less than 1.4%, thus supporting the observation that variation in mitochondrial rDNA
is 3–4 times lower than seen in protein coding and rDNA genes of other subcellular organelles. Sequences representing four
distinct lineages of nonasterid holoparasites showed significantly increased numbers of substitutions in their core 19S rDNA
sequences (2.3–7.6%), thus paralleling previous findings that showed accelerated rates in nuclear (18S) and plastid (16S)
rDNA from the same plants. Relative rate tests confirmed the accelerated nucleotide substitution rates in the holoparasites
whereas rates in nonparasitic plants were not significantly increased. Among comparisons of both parasitic and nonparasitic
plants, transversions outnumbered transitions, in many cases more than two to one. The core 19S rRNA is conserved in sequence
and structure among all nonparasitic angiosperms whereas 19S rRNA from members of holoparasitic Balanophoraceae have unique
extensions to the V5 and V6 variable domains. Substitution and insertion/deletion mutations characterized the V1 and V7 regions
of the nonasterid holoparasites. The V7 sequence of one holoparasite (Scybalium) contained repeat motifs. The cause of substitution rate increases in the holoparasites does not appear to be a result of
RNA editing, hence the underlying molecular mechanism remains to be fully documented.
Received: 18 May 1997 / Accepted: 11 July 1997 相似文献
19.
Peek AS Gaut BS Feldman RA Barry JP Kochevar RE Lutz RA Vrijenhoek RC 《Journal of molecular evolution》2000,50(2):141-153
Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae)
were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit
I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism.
Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene,
the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species.
Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships
between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns
of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific
nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend
hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular
methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.
Received: 10 March 1999 / Accepted: 13 September 1999 相似文献
20.
Romeu Cardoso Guimarães Edward N. Trifonov Jaime Lagunez-Otero 《Journal of molecular evolution》1997,45(3):271-277
Linguistic similarities and dissimilarities between 5 S rRNA sequences allowed taxonomical separation of species and classes.
Comparisons with the molecule from mammals distinguished fungi and plants from protists and animals. Similarities to mammalians
progressively increased from protists to invertebrates and to somatic-type molecules of the vertebrates lineage. In this,
deviations were detected in avian, oocyte type, and pseudogene sequences. Among bacteria, actinobacteria were most similar
to the mammalians, which could be related to the high frequency of associations among members of these groups. Some archaebacterial
species most similar to the mammalians belonged to the Thermoproteales and Halobacteria groups. Comparisons with the soybean
mitochondrial molecule revealed high internal homogeneity among plant mitochondria. The eubacterial groups most similar to
it were Thermus and Rhodobacteria γ-1 and α-2. Other procedures have already indicated similarities of Rhodobacteria α to
mitochondria but the linguistic similarities were on the average higher with the first two groups.
Received: 5 August 1996 / Accepted: 9 April 1997 相似文献