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1.
We analyzed nucleotide variation in the hsp70 genes of Drosophila melanogaster (five genes) and D. simulans (four genes) to characterize the homogenizing and diversifying roles of gene conversion in their evolution. Gene conversion
within and between the 87A7 and 87C1 gene clusters homogenize the hsp70 coding regions; in both D. melanogaster and D. simulans, same-cluster paralogues are virtually identical, and large intercluster conversion tracts diminish 87A7/87C1 divergence.
Same-cluster paralogues share many polymorphisms, consistent with frequent intracluster conversion. Shared polymorphism is
highly biased toward silent variation; homogenizing conversion interacts with purifying selection. In contrast to the coding
regions, some hsp70 flanking regions show conversion-mediated diversification. Strong reductions of nucleotide variability and linkage disequilibria
among conversion-mediated sites in hsp70Ab and hsp70Bb alleles sampled from a single natural population are consistent with a selective sweep. Comparison of the D. melanogaster and D. simulans hsp70 genes reveals whole-family fixed differences, consistent with rapid propagation of novel mutations among duplicate genes.
These results suggest that the homogenizing and diversifying roles of conversion interact to drive dynamic concerted evolution
of the hsp70 genes.
Received: 25 June 2001 / Accepted: 10 October 2001 相似文献
2.
The extracellular hemoglobins of cladocerans derive from the aggregation of 12 two-domain globin subunits that are apparently
encoded by four genes. This study establishes that at least some of these genes occur as a tandem array in both Daphnia magna and Daphnia exilis. The genes share a uniform structure; a bridge intron separates two globin domains which each include three exons and two
introns. Introns are small, averaging just 77 bp, but a longer sequence (2.2–3.2 kb) separates adjacent globin genes. A survey
of structural diversity in globin genes from other daphniids revealed three independent cases of intron loss, but exon lengths
were identical, excepting a 3-bp insertion in exon 5 of Simocephalus. Heterogeneity in the extent of nucleotide divergence was marked among exons, largely as a result of the pronounced diversification
of the terminal exon. This variation reflected, in part, varying exposure to concerted evolution. Conversion events were frequent
in exons 1–4 but were absent from exons 5 and 6. Because of this difference, the results of phylogenetic analyses were strongly
affected by the sequences employed in this construction. Phylogenies based on total nucleotide divergence in exons 1–4 revealed
affinities among all genes isolated from a single species, reflecting the impact of gene conversion events. In contrast, phylogenies
based on total nucleotide divergence in exons 5 and 6 revealed affinities among orthologous genes from different taxa.
Received: 8 March 1999 / Accepted: 14 July 1999 相似文献
3.
The polyubiquitin gene, encoding tandemly repeated multiple ubiquitins, constitutes a uniquitin gene subfamily. It has been
demonstrated that polyubiquitin genes are subject to concerted evolution; namely, the individual ubiquitin coding units contained
within a polyubiquitin gene are more similar to one another than they are to the ubiquitin coding units in the orthologous
gene from other species. However there has been no comprehensive study on the concerted evolution of polyubiquitin genes in
a wide range of species, because the relationships (orthologous or paralogous) among multiple polyubiquitin genes from different
species have not been extensively analyzed yet. In this report, we present the results of analyzing the nucleotide sequence
of polyubiquitin genes of mammals, available in the DDBJ/EMBL/GenBank nucleotide sequence databases, in which we found that
there are two groups of polyubiquitin genes in an orthologous relationship. Based on this result, we analyzed the concerted
evolution of the polyubiquitin gene in various species and compared the frequency of concerted evolutionary events interspecifically
by taking into consideration that the rate of synonymous substitution at the polyubiquitin gene locus may vary depending on
species. We found that the concerted evolutionary events in polyubiquitin genes have been more frequent in rats and Chinese
hamsters than those in humans, cows, and sheep. The guinea pig polyubiquitin gene was an intermediate example. The frequency
of concerted evolution in the mouse gene was unexpectedly low compared to that of other rodent genes.
Received: 18 January 2000 / Accepted: 26 April 2000 相似文献
4.
Phylogenetic Relationships of Acanthocephala Based on Analysis of 18S Ribosomal RNA Gene Sequences 总被引:3,自引:0,他引:3
García-Varela M Pérez-Ponce de León G de la Torre P Cummings MP Sarma SS Laclette JP 《Journal of molecular evolution》2000,50(6):532-540
Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most
phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala,
and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence
of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy,
and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera,
we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species
of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses
of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a
clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the
nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the
monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea
and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala.
Received: 12 October 1999 / Accepted: 8 February 2000 相似文献
5.
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
6.
Sequences of the α1, α2 and θ globin genes from six equid species have been determined to investigate relationships within
the genus Equus. Analyses using standard phylogenetic methods, or an approach designed to account for the effects of gene conversion between
the α genes, gave broadly similar results and show that the horses diverged from the zebra/ass ancestor ∼2.4 million years
ago and that the zebra and ass species arose in a rapid radiation ∼0.9 million years ago. These results from the α genes are
corroborated by θ gene data and are in contrast to mitochondrial DNA studies of the phylogeny of this genus, which suggest
a more gradual set of speciation events.
Received: 22 April 1997 / Accepted: 20 July 1998 相似文献
7.
Tandemly duplicated actin genes have been isolated from a Helicoverpa armigera genomic library. Sequence comparisons with actin genes from other species suggest they encode cytoplasmic actins, being most
closely related to the Bombyx mori A3 actin gene. The duplicated H. armigera actin genes, termed A3a and A3b, share 98.3% nucleotide sequence identity over their entire putative coding region. Analysis
of the distribution of nucleotide differences shows the first 763 bp are identical between the two coding regions, with the
18 nucleotide changes occurring in the remaining 366 bp. This observation suggests a gene conversion event has taken place
between the duplicated H. armigera A3a and A3b actin genes. Translation of the open-reading frames indicates the products of these genes are identical, apart
from a single amino acid difference at codon 273. Polymerase chain reaction and northern blot analysis have shown both H. armigera A3a and A3b genes are expressed during pupal development and in the brain of newly eclosed adults. A region 5′ of the H. armigera A3a actin gene start codon has been identified which contains regulatory sequences commonly found in the promoter region
of actin genes, including TATA, CAAT, and CArG motifs.
Received: 10 January 1996 / Accepted: 12 March 1996 相似文献
8.
Takehiro Kusakabe Isato Araki Noriyuki Satoh William R. Jeffery 《Journal of molecular evolution》1997,44(3):289-298
The origin and evolutionary relationship of actin isoforms was investigated in chordates by isolating and characterizing
two new ascidian cytoplasmic and muscle actin genes. The exon–intron organization and sequences of these genes were compared
with those of other invertebrate and vertebrate actin genes. The gene HrCA1 encodes a cytoplasmic (nonmuscle)-type actin, whereas the MocuMA2 gene encodes an adult muscle-type actin. Our analysis of these genes showed that intron positions are conserved among the
deuterostome actin genes. This suggests that actin gene families evolved from a single actin gene in the ancestral deuterostome.
Sequence comparisons and molecular phylogenetic analyses also suggested a close relationship between the ascidian and vertebrate
actin isoforms. It was also found that there are two distinct lineages of muscle actin isoforms in ascidians: the larval muscle
and adult body-wall isoforms. The four muscle isoforms in vertebrates show a closer relationship to each other than to the
ascidian muscle isoforms. Similarly, the two cytoplasmic isoforms in vertebrates show a closer relationship to each other
than to the ascidian and echinoderm cytoplasmic isoforms. In contrast, the two types of ascidian muscle actin diverge from
each other. The close relationship between the ascidian larval muscle actin and the vertebrate muscle isoforms was supported
by both neighbor-joining and maximum parsimony analyses. These results suggest that the chordate ancestor had at least two
muscle actin isoforms and that the vertebrate actin isoforms evolved after the separation of the vertebrates and urochordates.
Received: 20 June 1996 / Accepted: 16 October 1996 相似文献
9.
While globin genes ctt-2β and ctt-9.1 in Chironomus thummi thummi each have a single intron, all of the other insect globin genes reported so far are intronless. We analyzed four globin genes
linked to the two intron-bearing genes in C. th. thummi. Three have a single intron at the same position as ctt-2β and ctt-9.1; the fourth is intronless and lies between intron bearing genes. Finally, in addition to its intron, one gene (ctt-13RT) was recently interrupted by retrotransposition. Phylogenetic analyses show that the six genes in C. th. thummi share common ancestry with five globin genes in the distantly related species C. tentans, and that a 5-gene ancestral cluster predates the divergence of the two species. One gene in the ancestral cluster gave rise
to ctn-ORFB in C. tentans, and duplicated in C. th. thummi to create ctt-11 and ctt-12. From parsimonious calculations of evolutionary distances since speciation, ctt-11, ctt-12, and ctn-ORFB evolved rapidly, while ctn-ORFE in C. tentans evolved slowly compared to other globin genes in the clusters. While these four globins are under selective pressure, we
suggest that most chironomid globin genes were not selected for their unique function. Instead, we propose that high gene
copy number itself was selected because conditions favored organisms that could synthesize more hemoglobin. High gene copy
number selection to produce more of a useful product may be the basis of forming multigene families, all of whose members
initially accumulate neutral substitutions while retaining essential function. Maintenance of a large family of globin genes
not only ensured high levels of hemoglobin production, but may have facilitated the extensive divergence of chironomids into
as many as 5000 species.
Received: 31 December 1996 / Accepted: 16 May 1997 相似文献
10.
Julius Lukeš Milan Jirků David Doležel Ivica Kral'ová Laura Hollar Dmitri A. Maslov 《Journal of molecular evolution》1997,44(5):521-527
To further investigate the phylogeny of protozoa from the order Kinetoplastida we have sequenced the small subunit (SSU)
and a portion of the large subunit (LSU) nuclear rRNA genes. The SSU and LSU sequences were determined from a lizard trypanosome,
Trypanosoma scelopori and a bodonid, Rhynchobodo sp., and the LSU sequences were determined from an insect trypanosomatid, Crithidia oncopelti, and a bodonid, Dimastigella trypaniformis. Contrary to previous results, in which trypanosomes were found to be paraphyletic, with Trypanosoma brucei representing the earliest-diverging lineage, we have now found evidence for the monophyly of trypanosomes. Addition of new
taxa which subdivide long branches (such as that of T. brucei) have helped to identify homoplasies responsible for the paraphyletic trees in previous studies. Although the monophyly of
the trypanosome clade is supported in the bootstrap analyses for maximum likelihood at 97% and maximum parsimony at 92%, there
is only a small difference in ln-likelihood value or tree length between the most optimal monophyletic tree and the best suboptimal
paraphyletic tree. Within the trypanosomatid subtree, the clade of trypanosomes is a sister group to the monophyletic clade
of the nontrypanosome genera. Different groups of trypanosomes group on the tree according to their mode of transmission.
This suggests that the adaptation to invertebrate vectors plays a more important role in the trypanosome evolution than the
adaptation to vertebrate hosts.
Received: 5 July 1996 / Accepted: 26 September 1996 相似文献
11.
12.
A comprehensive analysis of duplication and gene conversion for 7394 Caenorhabditis elegans genes (about half the expected total for the genome) is presented. Of the genes examined, 40% are involved in duplicated
gene pairs. Intrachromosomal or cis gene duplications occur approximately two times more often than expected. In general the closer the members of duplicated
gene pairs are, the more likely it is that gene orientation is conserved. Gene conversion events are detectable between only
2% of the duplicated pairs. Even given the excesses of cis duplications, there is an excess of gene conversion events between cis duplicated pairs on every chromosome except the X chromosome. The relative rates of cis and trans gene conversion and the negative correlation between conversion frequency and DNA sequence divergence for unconverted regions
of converted pairs are consistent with previous experimental studies in yeast. Three recent, regional duplications, each spanning
three genes are described. All three have already undergone substantial deletions spanning hundreds of base pairs. The relative
rates of duplication and deletion may contribute to the compactness of the C. elegans genome.
Received: 30 July 1998 / Accepted: 12 October 1998 相似文献
13.
Ronald W. DeBry 《Journal of molecular evolution》1998,46(3):355-360
Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published sequence from M. musculus shows that this gene has likely been a pseudogene throughout the evolution of the genus Mus, while the gene from Rattus norvegicus is likely functional. Three large (>20 bp) deletions were found among the Mus pseudogenes, a feature that is very unusual compared to surveys of processed pseudogenes. In addition, there are two single-base
deletions and one 4-bp insertion among the Mus pseudogenes. The species distributions of one of the large deletions and the 4-bp insertion require either independent insertions
of an identical sequence, independent deletions with identical boundaries, or a deletion followed by precise reintegration
of the original sequence. The evidence favors the hypothesis of multiple deletions with identical boundaries. The ``coding'
regions of the Mus pseudogenes show a much reduced level of among-species variability in the 3′ half of the pseudogene, compared both to the
5′ half and to flanking sequences. This supports a hypothesis that the 3′ end of the pseudogene is the target of frequent
gene conversion by functional H2a genes.
Received: 1 April 1997 / Accepted: 12 June 1997 相似文献
14.
Glutamine synthetase type I (GSI) genes have previously been described only in prokaryotes except that the fungus Emericella nidulans contains a gene (fluG) which encodes a protein with a large N-terminal domain linked to a C-terminal GSI-like domain. Eukaryotes generally contain
the type II (GSII) genes which have been shown to occur also in some prokaryotes. The question of whether GSI and GSII genes
are orthologues or paralogues remains a point of controversy. In this article we show that GSI-like genes are widespread in
higher plants and have characterized one of the genes from the legume Medicago truncatula. This gene is part of a small gene family and is expressed in many organs of the plant. It encodes a protein similar in size
and with between 36 and 46% amino acid sequence similarity to prokaryotic GS proteins used in the analyses, whereas it is
larger and with less than 25% similarity to GSII proteins, including those from the same plant species. Phylogenetic analyses
suggest that this protein is most similar to putative proteins encoded by expressed sequence tags of other higher plant species
(including dicots and a monocot) and forms a cluster with FluG as the most divergent of the GSI sequences. The discovery of
GSI-like genes in higher plants supports the paralogous evolution of GSI and GSII genes, which has implications for the use
of GS in molecular studies on evolution.
Received: 4 May 1999 / Accepted: 17 September 1999 相似文献
15.
Diversity, Distribution, and Ancient Taxonomic Relationships Within the TIR and Non-TIR NBS-LRR Resistance Gene Subfamilies 总被引:1,自引:0,他引:1
Cannon SB Zhu H Baumgarten AM Spangler R May G Cook DR Young ND 《Journal of molecular evolution》2002,54(4):548-562
Phylogenetic relationships among the NBS-LRR (nucleotide binding site–leucine-rich repeat) resistance gene homologues (RGHs)
from 30 genera and nine families were evaluated relative to phylogenies for these taxa. More than 800 NBS-LRR RGHs were analyzed,
primarily from Fabaceae, Brassicaceae, Poaceae, and Solanaceae species, but also from representatives of other angiosperm
and gymnosperm families. Parsimony, maximum likelihood, and distance methods were used to classify these RGHs relative to
previously observed gene subfamilies as well as within more closely related sequence clades. Grouping sequences using a distance
cutoff of 250 PAM units (point accepted mutations per 100 residues) identified at least five ancient sequence clades with
representatives from several plant families: the previously observed TIR gene subfamily and a minimum of four deep splits
within the non-TIR gene subfamily. The deep splits in the non-TIR subfamily are also reflected in comparisons of amino acid
substitution rates in various species and in ratios of nonsynonymous-to-synonymous nucleotide substitution rates (K
A/K
S values) in Arabidopsis thaliana. Lower K
A/K
S values in the TIR than the non-TIR sequences suggest greater functional constraints in the TIR subfamily. At least three
of the five identified ancient clades appear to predate the angiosperm–gymnosperm radiation. Monocot sequences are absent
from the TIR subfamily, as observed in previous studies. In both subfamilies, clades with sequences separated by approximately
150 PAM units are family but not genus specific, providing a rough measure of minimum dates for the first diversification
event within these clades. Within any one clade, particular taxa may be dramatically over- or underrepresented, suggesting
preferential expansions or losses of certain RGH types within particular taxa and suggesting that no one species will provide
models for all major sequence types in other taxa.
Received: 13 June 2001 / Accepted: 22 October 2001 相似文献
16.
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
17.
Graziano Pesole Luigi R. Ceci Carmela Gissi Cecilia Saccone Carla Quagliariello 《Journal of molecular evolution》1996,43(5):447-452
We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic
reconstruction. The two coding regions, containing from 25 to 35 editing sites in the various plants, have been concatenated
in order to increase the significance of the analysis. Differing from the corresponding chloroplast sequences, unedited mitochondrial
DNA sequences seem to evolve under a quasi-neutral substitution process which undifferentiates the nucleotide substitution
rates for the three codon positions. By using complete gene sequences (all codon positions) we found that genomic sequences
provide a classical angiosperm phylogenetic tree with a clear-cut grouping of monocotyledons and dicotyledons with Magnoliidae
at the basal branch of the tree. Conversely, owing to their low nucleotide substitution rates, edited mRNA sequences were
found not to be suitable for studying phylogenetic relationships among angiosperms.
Received: 24 January 1996 / Accepted: 5 June 1996 相似文献
18.
The chaetognaths are an extraordinarily homogeneous phylum of animals at the morphological level, with a bauplan that can
be traced back to the Cambrian. Despite the attention of zoologists for over two centuries, there is little agreement on classification
within the phylum. We have used a molecular biological approach to investigate the phylogeny of extant chaetognaths. A rapidly
evolving expansion segment toward the 5′ end of 28S ribosomal DNA (rDNA) was amplified using the polymerase chain reaction
(PCR), cloned, and sequenced from 26 chaetognath samples representing 18 species. An unusual finding was the presence of two
distinct classes of 28S rDNA gene in chaetognaths; our analyses suggest these arose by a gene (or gene cluster) duplication
in a common ancestor of extant chaetognaths. The two classes of chaetognath 28S rDNA have been subject to different rates
of molecular evolution; we present evidence that both are expressed and functional. In phylogenetic reconstructions, the two
classes of 28S rDNA yield trees that root each other; these clearly demonstrate that the Aphragmophora and Phragmophora are
natural groups. Within the Aphragmophora, we find good support for the groupings denoted Solidosagitta, Parasagitta, and Pseudosagitta. The relationships between several well-supported groups within the Aphragmophora are uncertain; we suggest this reflects
rapid, recent radiation during chaetognath evolution.
Received: 19 March 1996 / Accepted: 5 August 1996 相似文献
19.
Analysis of the 18S rDNA sequences of five species of the family Dugesiidae (phylum Platyhelminthes, suborder Tricladida,
infraorder Paludicola) and eight species belonging to families Dendrocoelidae and Planaridae and to the infraorder Maricola
showed that members of the family Dugesiidae have two types of 18S rDNA genes, while the rest of the species have only one.
The duplication event also affected the ITS-1, 5.8S, ITS-2 region and probably the 28S gene. The mean divergence value between
the type I and the type II sequences is 9% and type II 18S rDNA genes are evolving 2.3 times more rapidly than type I. The
evolutionary rates of type I and type II genes were calibrated from biogeographical data, and an approximate date for the
duplication event of 80–120 million years ago was calculated. The type II gene was shown, by RT-PCR, to be transcribed in
adult individuals of Schmidtea polychroa, though at very low levels. This result, together with the fact that most of the functionally important positions for small-subunit
rRNA in prokaryotes have been conserved, indicates that the type II gene is probably functional.
Received: 24 March 1998 / Accepted: 17 March 1999 相似文献
20.
Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due
to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should
provide insights into the origin of genetic complexity in eukaryotes. We have previously isolated and characterized a calmodulin
gene from the early-diverging chordate Branchiostoma lanceolatum (CaM1). In this paper, we report the existence of a second calmodulin gene (CaM2) as well as two CaM-like genomic fragments (CaML-2, CaML-3) in B. lanceolatum and a CaM2 and three CaM-like genes (CaML-1, CaML-2, CaML-3) in B. floridae. The CaM-like genes were isolated using low-stringency PCR. Surprisingly, the nucleotide sequences of the B. lanceolatum CaM1 and CaM2 cDNAs differ by 19.3%. Moreover, the CaM2 protein differs at two positions from the amino acid sequence of CaM1; the latter
is identical to calmodulins in Drosophila melanogaster, the mollusc Aplysia californica, and the tunicate Halocynthia roretzi. The two B. lanceolatum CaM-like genes are more closely related to the CaM2 than to the CaM1 gene. This relationship is supported by the phylogenetic analyses and the identical exon/intron organization of these three
genes, a relationship unique among animal CaM sequences. These data demonstrate the existence of a CaM multigene family in the cephalochordate Branchiostoma, which may have evolved independently from the multigene family in vertebrates.
Received: 2 November 1999 / Accepted: 25 April 2000 相似文献