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1.
2.
Francine Hamel Rodolphe Boivin Colette Tremblay Guy Bellemare 《Journal of molecular evolution》1997,44(6):614-624
The analysis of nuclear-encoded chitinase sequences from various angiosperms has allowed the categorization of the chitinases
into discrete classes. Nucleotide sequences of their catalytic domains were compared in this study to investigate the evolutionary
relationships between chitinase classes. The functionally distinct class III chitinases appear to be more closely related
to fungal enzymes involved in morphogenesis than to other plant chitinases. The ordering of other plant chitinases into additional
classes mainly relied on the presence of auxiliary domains—namely, a chitin-binding domain and a carboxy-terminal extension—flanking
the main catalytic domain. The results of our phylogenetic analyses showed that classes I and IV form discrete and well-supported
monophyletic groups derived from a common ancestral sequence that predates the divergence of dicots and monocots. In contrast,
other sequences included in classes I* and II, lacking one or both types of auxiliary domains, were nested within class I
sequences, indicating that they have a polyphyletic origin. According to phylogenetic analyses and the calculation of evolutionary
rates, these chitinases probably arose from different class I lineages by relatively recent deletion events. The occurrence
of such evolutionary trends in cultivated plants and their potential involvement in host–pathogen interactions are discussed.
Received: 5 July 1996 / Accepted: 9 January 1997 相似文献
3.
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
4.
This paper reports an intraorder study on the D-loop-containing region of the mitochondrial DNA in rodents. A complete multialignment
of this region is not feasible with the exception of some conserved regions. The comparative analysis of 25 complete rodent
sequences from 23 species plus one lagomorph has revealed that only the central domain (CD), a conserved region of about 80
bp in the extended termination-associated sequences (ETAS) domain, adjacent to the CD, the ETAS1, and conserved sequence block
(CSB) 1 blocks are present in all rodent species, whereas the presence of CSB2 and CSB3 is erratic within the order. We have
also found a conserved region of 90 bp located between tRNAPro and ETAS1 present in fat dormouse, squirrel, guinea pig, and
rabbit. Repeated sequences are present in both the ETAS and the CSB domain, but the repeats differ in length, copy number,
and base composition in different species. The potential use of the D-loop for evolutionary studies has been investigated;
the presence/absence of conserved blocks and/or repeated sequences cannot be used as a reliable phylogenetic marker, since
in some cases they may be shared by distantly related organisms but not by close ones, while in other ones a relationship
between tree topology and presence/absence of such motifs is observed. Better results can be obtained by the use of the CD,
which, however, due to its reduced size, when used for tracing a phylogenetic tree, shows some nodes with low statistical
support.
Received: 26 February 2001 / Accepted: 6 June 2001 相似文献
5.
We examined the evolution of the repeat regions of three noncoding microsatellite loci in 58 species of the Polistinae, a
subfamily of wasps that diverged over 140 million years ago. A phylogenetic approach allows two new kinds of approaches to
studying microsatellite evolution: character mapping and comparative analysis. The basic repeat structure of the loci was
highly conserved, but was often punctuated with imperfections that appear to be phylogenetically informative. Repeat numbers
evolved more rapidly than other changes in the repeat region. Changes in number of repeats among species seem consistent with
the stepwise mutation model, which is based on slippage during replication as the main source of mutations. Changes in repeat
numbers can occur even when there are very few tandem repeats but longer repeats, especially perfect repeats led to greater
rates of evolutionary change. Species phylogenetically closer to the one from which we identified the loci had longer stretches
of uninterrupted repeats and more different motifs, but not longer total repeat regions. The number of perfect repeats increased
more often than it decreased. However, there was no evidence that some species have consistently greater numbers of repeats
across loci than other species have, once ascertainment bias is eliminated. We also found no evidence for a population size
effect posited by one form of the directionality hypothesis. Overall, phylogenetic variation in repeat regions can be explained
by adding neutral evolution to what is already known about the mutation process. The life cycle of microsatellites appears
to reflect a balance between growth by slippage and degradation by an essentially irreversible accumulation of imperfections.
Received: 13 April 1999 / Accepted: 8 September 1999 相似文献
6.
To study the evolution of mtDNA and the intergeneric relationships of New World Jays (Aves: Corvidae), we sequenced the entire
mitochondrial DNA control region (CR) from 21 species representing all genera of New World jays, an Old World jay, crows,
and a magpie. Using maximum likelihood methods, we found that both the transition/transversion ratio (κ) and among site rate
variation (α) were higher in flanking domains I and II than in the conserved central domain and that the frequency of indels
was highest in domain II. Estimates of κ and α were much more influenced by the density of taxon sampling than by alternative
optimal tree topologies. We implemented a successive approximation method incorporating these parameters into phylogenetic
analysis. In addition we compared our study in detail to a previous study using cytochrome b and morphology to examine the effect of taxon sampling, evolutionary rates of genes, and combined data on tree resolution.
We found that the particular weighting scheme used had no effect on tree topology and little effect on tree robustness. Taxon
sampling had a significant effect on tree robustness but little effect on the topology of the best tree. The CR data set differed
nonsignificantly from the tree derived from the cytochrome b/morphological data set primarily in the placement of the genus Gymnorhinus, which is near the base of the CR tree. However, contrary to conventional taxonomy, the CR data set suggested that blue and
black jays (Cyanocorax sensu lato) might be paraphyletic and that the brown jay Psilorhinus (=Cyanocorax) morio is the sister group to magpie jays (Calocitta), a phylogenetic hypothesis that is likely as parsimonious with regard to nonmolecular characters as monophyly of Cyanocorax. The CR tree also suggests that the common ancestor of NWJs was likely a cooperative breeder. Consistent with recent systematic
theory, our data suggest that DNA sequences with high substitution rates such as the CR may nonetheless be useful in reconstructing
relatively deep phylogenetic nodes in avian groups.
Received: 10 November 1999 / Accepted: 16 March 2000 相似文献
7.
The members of the PKA regulatory subunit family (PKA-R family) were analyzed by multiple sequence alignment and clustering
based on phylogenetic tree construction. According to the phylogenetic trees generated from multiple sequence alignment of
the complete sequences, the PKA-R family was divided into four subfamilies (types I to IV). Members of each subfamily were
exclusively from animals (types I and II), fungi (type III), and alveolates (type IV). Application of the same methodology
to the cAMP-binding domains, and subsequently to the region delimited by β-strands 6 and 7 of the crystal structures of bovine
RIα and rat RIIβ (the phosphate-binding cassette; PBC), proved that this highly conserved region was enough to classify unequivocally
the members of the PKA-R family. A single signature sequence, F–G–E–[LIV]–A–L–[LIMV]–x(3)–[PV]–R–[ANQV]–A, corresponding to
the PBC was identified which is characteristic of the PKA-R family and is sufficient to distinguish it from other members
of the cyclic nucleotide-binding protein superfamily. Specific determinants for the A and B domains of each R-subunit type
were also identified. Conserved residues defining the signature motif are important for interaction with cAMP or for positioning
the residues that directly interact with cAMP. Conversely, residues that define subfamilies or domain types are not conserved
and are mostly located on the loop that connects α-helix B′ and β strand 7.
Received: 2 November 2000/Accepted: 14 June 2001 相似文献
8.
We present here the sequence and characterization of various minisatellite-like tandem repeat loci isolated from the genome
of Atlantic salmon (Salmo salar). Their diversity of sequence and lack of core motifs common to minisatellites of other species suggest the presence of numerous
and previously unidentified simple sequence repeat families in this salmonid. Evidence for their ubiquity was provided by
screening of a salmon genomic library. Southern blot analysis of the phylogenetic distribution of a subset of the minisatellites
found one sequence to be pervasive among vertebrates, others present only in Salmoninae or Salmonidae species, and one amplified
only in Atlantic salmon. There is evidence for the positioning of microsatellite and minisatellite arrays in close proximity
at many loci. Furthermore, one tandem repeat appears to have been inserted into the transposase coding region of a copy of
the Tc1 transposon-like element recently identified in salmonids.
Received: 9 October 1996 / Accepted: 20 May 1997 相似文献
9.
Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes 总被引:36,自引:0,他引:36
The majority of plant disease resistance genes are members of very large multigene families. They encode structurally related
proteins containing nucleotide binding site domains (NBS) and C-terminal leucine rich repeats (LRR). The N-terminal region
of some resistance genes contain a short sequence called TIR with homology to the animal innate immunity factors, Toll and interleukin receptor-like genes. Only a few plant resistance genes have been functionally analyzed and the origin and
evolution of plant resistance genes remain obscure. We have reconstructed gene phylogeny by exhaustive analysis of available
genome and amplified NBS domain sequences. Our study shows that NBS domains faithfully predict whole gene structure and can
be divided into two major groups. Group I NBS domains contain group-specific motifs that are always linked with the TIR sequence
in the N terminus. Significantly, Group I NBS domains and their associated TIR domains are widely distributed in dicot species
but were not detected in cereal databases. Furthermore, Group I specific NBS sequences were readily amplified from dicot genomic
DNA but could not be amplified from cereal genomic DNA. In contrast, Group II NBS domains are always associated with putative
coiled-coil domains in their N terminus and appear to be present throughout the angiosperms. These results suggest that the
two main groups of resistance genes underwent divergent evolution in cereal and dicot genomes and imply that their cognate
signaling pathways have diverged as well.
Received: 17 May 1999 / Accepted: 25 September 1999 相似文献
10.
Christiane Delarbre Ann-Sofie Rasmussen Ulfur Arnason Gabriel Gachelin 《Journal of molecular evolution》2001,53(6):634-641
The complete sequence of the mitochondrial DNA of the hagfish Myxine glutinosa has been determined. The hagfish mtDNA (18,909 bp) is the longest vertebrate mtDNA determined so far. The gene arrangement
conforms to the consensus vertebrate type and differs from that of lampreys. The exceptionally long (3628-bp) control region
of the hagfish contains the typical conserved elements found in other vertebrate mtDNAs but is characterized by a large number
of putative hairpins, which can potentially fold into a highly compact secondary structure that appears to be unique to hagfish.
The comparison of the mtDNAs of two M. glutinosa specimens, excluding the control region, shows a 0.6% divergence at the nucleotide level as a sample of intraspecies polymorphism.
Received: 21 August 2000 / Accepted: 2 March 2001 相似文献
11.
Francesco Frati Chris Simon Jack Sullivan David L. Swofford 《Journal of molecular evolution》1997,44(2):145-158
The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic
levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic
relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all
insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the
basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions
appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in
some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels
observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or
exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity
of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information
was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical
support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well
supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from
an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.
Received: 12 January 1996 / Accepted: 10 August 1996 相似文献
12.
A new, model-based method was devised to locate nucleotide changes in a given phylogenetic tree. For each site, the posterior
probability of any possible change in each branch of the tree is computed. This probabilistic method is a valuable alternative
to the maximum parsimony method when base composition is skewed (i.e., different from 25% A, 25% C, 25% G, 25% T): computer
simulations showed that parsimony misses more rare → common than common → rare changes, resulting in biased inferred change
matrices, whereas the new method appeared unbiased. The probabilistic method was applied to the analysis of the mutation and
substitution processes in the mitochondrial control region of mouse. Distinct change patterns were found at the polymorphism
(within species) and divergence (between species) levels, rejecting the hypothesis of a neutral evolution of base composition
in mitochondrial DNA.
Received: 15 March 1999 / Accepted: 7 October 1999 相似文献
13.
Stefan Hiendleder Heidrun Lewalski Rudolph Wassmuth Axel Janke 《Journal of molecular evolution》1998,47(4):441-448
The complete mitochondrial DNA (mtDNA) molecule of the domestic sheep, Ovis aries, was sequenced, together with part of the mtDNA of a specimen representing the other major O. aries haplotype group. The length of the complete ovine mtDNA presented is 16,616 nucleotides (nt). This length is not absolute,
however, due to heteroplasmy caused by the occurrence of different numbers of a 75-nt-long tandem repeat in the control region.
The sequence data were included in analyses of intraspecific ovine molecular differences, molecular comparisons with bovine
mtDNAs, and phylogenetic analyses based on complete mtDNAs. The comparisons with bovine mtDNAs were based on the central domains
of the ovine control regions, representing both major ovine haplotype groups, and the corresponding domains of Bos taurus and B. indicus. The comparisons showed that the difference between the bovids was 1.4 times greater than the intraspecific ovine difference.
These findings suggest that the strains of wild sheep from which domestic sheep originated were more closely related than
were the B. primigenius subspecies which gave rise to B. indicus and B. taurus cattle. Datings based on complete mtDNAs suggest that the bovine and ovine lineages diverged about 30 million years before
present. This dating is considerably earlier than that proposed previously.
Received: 5 September 1997 / Accepted: 5 May 1998 相似文献
14.
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
15.
16.
This study investigated the evolution of a transition metal ion-binding cluster ([H–X–X–X–H]
n
; Tx) in the alternatively spliced NH2-terminal variable region of avian pectoral muscle troponin T (TnT). Encoded by avian fast skeletal muscle TnT-specific P
exons, Tx-like structures were expressed in the breast muscle TnT's of almost all birds examined. Their presence results in
the developmentally up-regulated high molecular weight pectoral muscle TnT. Sequence analysis and metal affinity chromatography
revealed that in Galliformes and Craciformes, the Tx structure evolved into multiple H–X–X–X–H pairs with a high-affinity
metal-binding capacity. Turkey, chicken, quail, and curassow breast muscle TnT's contain nine, seven, four, and three consecutive
or closely located metal-binding sites, respectively, in the NH2-terminal region. The metal-binding affinity of the Tx element increased as the number of His pairs increased due to the duplication
of P exons and the conversion of other exon sequences. The data show two related components of avian pectoral muscle TnT evolution:
a larger, more acidic NH2-terminal segment and a cluster of transition metal-binding sites, both of which may have functional significance for their
selection value. The evolution of the Tx segment in the NH2-terminal variable region of avian pectoral muscle TnT demonstrates a functional divergence on the basis of tolerance to structural
drifting.
Received: 2 May 2000 / Accepted: 5 September 2000 相似文献
17.
The vertebrates are traditionally classified into two distinct groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed
vertebrates). Extant agnathans are represented by hagfishes (Myxiniformes) and lampreys (Petromyzontiformes), frequently grouped
together within the Cyclostomata. Whereas the recognition of the Gnathostomata as a clade is commonly acknowledged, a consensus
has not been reached regarding whether or not Cyclostomata represents a clade. In the present study we have used newly established
sequences of the protein-coding genes of the mitochondrial DNA molecule of the hagfish to explore agnathan and gnathostome
relationships. The phylogenetic analysis of Pisces, using echinoderms as outgroup, placed the hagfish as a sister group of
Vertebrata sensu stricto, i.e., the lamprey and the gnathostomes. The phylogenetic analysis of the Gnathostomata identified
a basal divergence between gnathostome fishes and a branch leading to birds and mammals, i.e., between ``Anamnia' and Amniota.
The lungfish has a basal position among gnathostome fishes with the teleosts as the most recently evolving lineage. The findings
portray a hitherto unrecognized polarity in the evolution of bony fishes. The presently established relationships are incompatible
with previous molecular studies.
Received: 15 August 1997 / Accepted: 1 October 1997 相似文献
18.
19.
Eduardo Eizirik Sandro L. Bonatto Warren E. Johnson Peter G. Crawshaw Jr. Jean Cristophe Vié Dulce M. Brousset Stephen J. O'Brien Francisco M. Salzano 《Journal of molecular evolution》1998,47(5):613-624
The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation
of the Panamanian land bridge 3–5 million years ago. Patterns of population genetic divergence of each species were studied
by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution
of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed,
identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography,
population genetic structure, and demographic history were used to formulate conservation recommendations for these species.
In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region
in closely related felids.
Received: 26 January 1998 / Accepted: 14 May 1998 相似文献
20.
Molecular evolution of calmodulin-like domain protein kinases (CDPKs) in plants and protists 总被引:1,自引:0,他引:1
Many genes for calmodulin-like domain protein kinases (CDPKs) have been identified in plants and Alveolate protists. To study
the molecular evolution of the CDPK gene family, we performed a phylogenetic analysis of CDPK genomic sequences. Analysis
of introns supports the phylogenetic analysis; CDPK genes with similar intron/exon structure are grouped together on the phylogenetic
tree. Conserved introns support a monophyletic origin for plant CDPKs, CDPK-related kinases, and phosphoenolpyruvate carboxylase
kinases. Plant CDPKs divide into two major branches. Plant CDPK genes on one branch share common intron positions with protist
CDPK genes. The introns shared between protist and plant CDPKs presumably originated before the divergence of plants from
Alveolates. Additionally, the calmodulin-like domains of protist CDPKs have intron positions in common with animal and fungal
calmodulin genes. These results, together with the presence of a highly conserved phase zero intron located precisely at the
beginning of the calmodulin-like domain, suggest that the ancestral CDPK gene could have originated from the fusion of protein
kinase and calmodulin genes facilitated by recombination of ancient introns.
Received: 11 July 2000 / Accepted: 18 April 2001 相似文献