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1.
Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record 总被引:5,自引:0,他引:5
Colomban de Vargas Louisette Zaninetti Heinz Hilbrecht Jan Pawlowski 《Journal of molecular evolution》1997,45(3):285-294
Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic
and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny
inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic
families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing
the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera.
The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently,
at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution
rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10−9 substitutions/site/year in the Globigerinidae to less than 1.0 × 10−9 substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the
planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological
data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates
their effect on phylogenetic reconstructions.
Received: 21 January 1997 / Accepted: 17 April 1997 相似文献
2.
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
3.
A Molecular Phylogeny of Lilium in the Internal Transcribed Spacer Region of Nuclear Ribosomal DNA 总被引:4,自引:0,他引:4
Tomotaro Nishikawa Keiichi Okazaki Tae Uchino Katsuro Arakawa Tsukasa Nagamine 《Journal of molecular evolution》1999,49(2):238-249
Phylogenetic relationships among 55 species of Lilium, Cardiocrinum giganteum, and Nomocharis saluenensis were inferred from nucleotide sequence variations in the internal transcribed spacer (ITS) regions of 18S–25S nuclear ribosomal
DNA. The phylogeny derived from ITS sequences estimated using maximum-likelihood methods indicated that (1) most of the species
construct their own clade according to the classification based on morphological features at the section level; (2) section
Daurolirion is not independent of Sinomartagon, and it is appropriate to integrate two sections as Sinomartagon; (3) it is appropriate that L. henryi and L. bulbiferum are classified into subsection 6a and Sinomartagon–Daurolirion, respectively; (4) subsection 6b is much closer to Sinomartagon than subsection 6a and Archelirion, and it arose directly from Sinomartagon; and (5) Lilium is much closer to Nomocharis than Cardiocrinum. Phylogenetic estimation using sequences of the ITS region is suitable at the levels of genus, section, and most of subsection.
Received: 18 December 1998 / Accepted: 14 March 1999 相似文献
4.
Abstract: Members of the Clusiaceae genus Clusia (tropical trees and shrubs) belong to the small group of dicotyledonous trees which are able to perform crassulacean acid metabolism (CAM). Most of the species are able to switch between C3 and CAM modes of photosynthesis and only a few are restricted to either C3 or CAM. In order to discover possible phylogenetic relationships with regard to the mode of photosynthesis, we investigated 17 species of the genus Clusia, and one species each of the Clusiaceae genera Oedematopus and Hypericum on the basis of internal transcribed spacer (ITS) sequences between the 18S and 26S coding regions of nuclear ribosomal DNA. Little length variation was detected in the ITS region of Clusia species. ITS1 sequences ranged from 255 to 260 bp and ITS2 sequences from 208 to 210 bp. Neighbour-joining and parsimony analyses of these sequences resulted in considerable differences in cluster formation when compared to a classification based on morphological characteristics. The molecular data also give no indication of a group-specific evolution of modes of photosynthesis, i.e., C3 and CAM. We thus conclude that CAM has evolved independently several times within the genus Clusia. 相似文献
5.
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
6.
7.
The morphologically uniform species Gonium pectorale is a colonial green flagellate of worldwide distribution. The affinities of 25 isolates from 18 sites on five continents
were assessed by both DNA sequence comparisons and sexual compatibility. Complete sequences were obtained (i) for the internal
transcribed spacer ITS-1 and ITS-2 regions of ribosomal DNA and (ii) for each of three single-copy spliceosomal introns, two
in a small G protein and one in the actin gene. ITS sequences appeared to homogenize sufficiently rapidly to behave as a single
copy gene. Intron sequence differences between isolates in this species reached nucleotide substitution saturation, while
ITS sequences did not. Parsimony and evolutionary distance analysis of the two types of DNA data gave essentially the same
tree conformation. By all these criteria, the group of G. pectorale isolates fell into two main clades, A and B. Clade A, with isolates from four continents, was comprised of four subclades
of quite closely related isolates, plus one strain of ambiguous affinity. Clade B was comprised of two subclades represented
by South African and South American isolates, respectively; thus, only subclades of clade B showed geographical localization.
With respect to mating, all isolates except one homothallic strain and one apparently sterile strain fell into either one
or the other of two mating types. Pairings in all possible combinations revealed that isolates from the same site formed abundant
zygotes, which germinated to produce new, sexually active organisms. Zygotes were also formed in many pairings of other combinations,
including crosses of clade A with clade B organisms, but none of the latter produced viable germlings. The ability to mate
and produce viable progeny that were themselves capable of sexual reproduction was restricted to members of subclades established
on the basis of DNA sequence similarities. Thus, the grades of difference in both nuclear intron sequences and rDNA ITS sequences
paralleled those observed in the sexual analysis.
Received: 9 March 1998 / Accepted: 1 June 1998 相似文献
8.
Tagir Kh. Samigullin William F. Martin Aleksey V. Troitsky Andrey S. Antonov 《Journal of molecular evolution》1999,49(3):310-315
Partial sequences of the rpoC1 gene from two species of angiosperms and three species of gymnosperms (8330 base pairs) were determined and compared. The
data obtained support the hypothesis that angiosperms and gymnosperms are monophyletic and none of the recent groups of the
latter is sister to angiosperms.
Received: 20 November 1998 / Accepted: 26 April 1999 相似文献
9.
Evolutionary geneticists have increasingly used sequence variation in mitochondrial DNA (mtDNA) as a source of historical
information. However, conclusions based on these data remain tentative because a sufficiently clear understanding of the evolutionary
dynamics of mtDNA has yet to be developed. In this paper we present the results of computer simulations designed to illustrate
the effects of social structure, geographical structure, and population size on the rate of nucleotide substitution and lineage
sorting of mtDNA. The model is based in part on the social structure of macaque monkeys. Simulated populations of females
were divided into 25 social groups; the animals in each were distributed in a hierarchy of four dominance rank categories.
The probabilities for offspring survivorship were varied among dominance ranks to reflect the fitness consequences of social
structure. Population size was varied across runs from 100 to 300 females. The pattern of female migration was also varied
to mimic either the island model or the stepping-stone model. All these variables are shown to affect the lineage sorting
period (LSP), and certain combinations of parameter values can cause the retention of mtDNA polymorphisms for a very long
time. In addition, the simulations exhibited a negative relationship between the LSP and substitution rate over a modest and
realistic range of LSP values. An important implication of these results is that estimates of time since isolation based on
the assumption of a constant molecular clock may be biased and unreliable. 相似文献
10.
A DNA fragment containing short tandem repeat sequences (approximately 86-bp repeat) was isolated from a Xenopus laevis cDNA library. Southern blot and in situ hybridization analyses revealed that the repeat was highly dispersed in the genome and was present at approximately 1 million
copies per haploid genome. We named this element Xstir (Xenopus short tandemly and invertedly repeating element) after its arrangement in the genome. The majority of the genomic Xstir sequences
were digested to monomer and dimer sizes with several restriction enzymes. Their sequences were found to be highly homogeneous
and organized into tandem arrays in the genome. Alignment analyses of several known sequences showed that some of the Xstir-like
sequences were also organized into interspersed inverted repeats. The inverted repeats consisted of an inverted pair of two
differently modified Xstirs separated by a short insert. In addition, these were framed by another novel inverted repeat (Xstir-TIR).
The Xstir-TIR sequence was also found at the ends of tandem Xstir arrays. Furthermore, we found that Xstir-TIR was linked
to a motif characterizing the T2 family which belonged to a vertebrate MITE (miniature inverted-repeat transposable element)
family, suggesting the importance of Xstir-TIR for their amplification and transposition. The present study of 11 anuran and
2 urodele species revealed that Xstir or Xstir-like sequences were extensively amplified in the three Xenopus species. Genomic Xstir populations of X. borealis and X. laevis were mutually indistinguishable but significantly different from that of X. tropicalis.
Received: 5 April 2000 / Accepted: 3 August 2000 相似文献
11.
Short Retroposons of the B2 Superfamily: Evolution and Application for the Study of Rodent Phylogeny
Short retroposons can be used as natural phylogenetic markers. By means of hybridization and PCR analysis, we demonstrate
that B2 retroposon copies are present only in the three rodent families: Muridae, Cricetidae, and Spalacidae. This observation
highlights the close phylogenetic relation between these families. Two novel B2-related retroposon families, named DIP and
MEN elements, are described. DIP elements are found only in the genomes of jerboas (family Dipodidae) and birch mice (family
Zapodidae), demonstrating the close relationship between these rodents. MEN element copies were isolated from the squirrel,
Menetes berdmorei, but were not detected in three other species from the family Sciuridae. The MEN element has an unusual dimeric structure:
the left and right monomers are B2- and B1-related sequences, respectively. Comparison of the B2, DIP, MEN, and 4.5S1 RNA elements revealed an 80-bp core sequence located at the beginning of the B2 superfamily retroposons. This observation
suggests that these retroposon families descended from a common progenitor. A likely candidate for this direct progenitor
could be the ID retroposon.
Received: 20 December 1996 / Accepted: 17 June 1997 相似文献
12.
E. Rosato A. A. Peixoto A. Gallippi C. P. Kyriacou R. Costa 《Journal of molecular evolution》1996,42(4):392-408
The D. melanogaster clock gene period (per) is an internally repetitive gene encoding a tandem array of Thr-Gly codons that are highly polymorphic in length in European
natural populations. The two major length variants, (Thr-Gly)20 and (Thr-Gly)17, show a highly significant latitudinal cline. In this study we present the complete sequence of the Thr-Gly region of 91
individuals from 6 natural populations of D. melanogaster, 5 from Europe and 1 from North Africa. We further characterized these 91 individuals for polymorphic sites in two other regions,
one upstream and one downstream of the Thr-Gly repeat. We used the haplotypic combinations of Thr-Gly allele with flanking
markers in an attempt to identify the mechanisms involved in the evolution of the D. melanogaster Thr-Gly region and to infer the phylogenetic relationship existing among the Thr-Gly alleles. We observe evidence for both
intra- and interallelic mutational mechanisms, including replication slippage, unequal crossing-over, and gene conversion.
Received: 22 August 1995 / Accepted: 17 October 1995 相似文献
13.
Retrovirus-like sequences and their solitary (solo) long terminal repeats (LTRs) are common repetitive elements in eukaryotic
genomes. We reported previously that the tandemly arrayed genes encoding U2 snRNA (the RNU2 locus) in humans and apes contain a solo LTR (U2-LTR) which was presumably generated by homologous recombination between
the two LTRs of an ancestral provirus that is retained in the orthologous baboon RNU2 locus. We have now sequenced the orthologous U2-LTRs in human, chimpanzee, gorilla, orangutan, and baboon and examined numerous
homologs of the U2-LTR that are dispersed throughout the human genome. Although these U2-LTR homologs have been collectively
referred to as LTR13 in the literature, they do not display sequence similarity to any known retroviral LTRs; however, the
structure of LTR13 closely resembles that of other retroviral LTRs with a putative promoter, polyadenylation signal, and a
tandemly repeated 53-bp enhancer-like element. Genomic blotting indicates that LTR13 is primate-specific; based on sequence
analysis, we estimate there are about 2,500 LTR13 elements in the human genome. Comparison of the primate U2-LTR sequences
suggests that the homologous recombination event that gave rise to the solo U2-LTR occurred soon after insertion of the ancestral
provirus into the ancestral U2 tandem array. Phylogenetic analysis of the LTR13 family confirms that it is diverse, but the
orthologous U2-LTRs form a coherent group in which chimpanzee is closest to the humans; orangutan is a clear outgroup of human,
chimpanzee, and gorilla; and baboon is a distant relative of human, chimpanzee, gorilla, and orangutan. We compare the LTR13
family with other known LTRs and consider whether these LTRs might play a role in concerted evolution of the primate RNU2 locus.
Received: 29 September 1997 / Accepted: 16 January 1998 相似文献
14.
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
15.
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
16.
Manfred Steinemann Sigrid Steinemann Wilhelm Pinsker 《Journal of molecular evolution》1996,43(4):413-417
The larval cuticle proteins (LCPs) are encoded by a multigene family, Lcp1–4, located at the right arm of the metacentric autosome 2 (2R) in Drosophila melanogaster. Due to a chromosome fusion the Lcp locus of Drosophila miranda is situated on a pair of secondary sex chromosomes, the X2 and neo-Y chromosomes. Comparing the deduced amino acid sequences of the autosomal D. melanogaster loci with the sex-chromosomal loci of D. miranda, we were able to trace the evolution of the Lcp loci with respect to their different chromosomal inheritance. The length of the signal peptide is conserved in all four LCPs,
while the size of the mature LCPs varies. Conserved protein motifs became obvious from the alignment, indicating regions of
structural and functional importance. Analyzing intra- and interspecific sequence similarities of the Lcp gene families allowed us to reconstruct the phylogeny of the gene cluster. Alignment with cuticle amino acid sequences originating
from divergent insect species reveals motifs already present in the primordial insect LCPs. These motifs indicate different
levels of constraint acting during the evolution of the LCPs.
Received: 27 December 1995 / Accepted: 30 April 1996 相似文献
17.
18.
In this paper we report the identification and characterization of a DNA region containing putative mcpA-like gene coding for a Methyl Accepting Chemotaxis Protein (MCP) and belonging to a Burkholderia endosymbiont of the arbuscular mycorrhizal fungus Gigaspora margarita. A genomic library of total DNA extracted from the fungal spores, representative of the bacterial genome, was used to investigate
the prokaryotic genome. PCR experiments with primers designed on the Burkholderia mcpA-like gene and Southern blot analysis demonstrate that they actually belong to the genome of G. margarita endosymbiont. The expression of the mcpA-like gene in the fungal spores was demonstrated by RT-PCR experiments. The detailed comparative analysis of the bacterial
MCPs available in databases allowed to draw a possible evolutionary pathway leading to the present-day mcpA genes. Accordingly, the ancestor of the mcpA-like genes was the result of a domain shuffling event involving two ancestral mini-genes encoding a PAS-PAC and a MA domains,
respectively, followed by the elongation of the PAS-PAC moiety. The following evolutionary divergence involved not only point
mutations, but also larger rearrangements (insertions and deletions) at the 3′ end of the gene. 相似文献
19.
Jittra Kanchanaprayudh Zhihua Zhou Sunadda Yomyart Prakitsin Sihanonth Taizo Hogetsu 《Mycoscience》2003,44(4):287-294
The phylogenetic relationships among 135 Pisolithus basidiomes and two isolates collected from three pine forests, a pine-dipterocarp forest, two dipterocarp forests, and 29 eucalyptus plantations in Thailand were investigated. Internal transcribed spacer (ITS) polymorphism analyses, including terminal RFLP, divided them into 26 groups. The ITS in a representative basidiome of each group was sequenced, and a phylogenetic analysis was performed. The dendrogram suggested that at least three Pisolithus species are present in Thailand. Pisolithus basidiomes collected in the pine forests and under some Shorea roxburghii trees in a pine-dipterocarp forest corresponded to species 5 as previously described by Martin et al. in 2002. Those collected under S. roxburghii and Dipterocarp alatus trees in the dipterocarp forests did not match any previously reported species. Basidiomes collected from the eucalyptus plantations were all identified as Pisolithus albus. 相似文献
20.
The cycad genus Encephalartos is restricted to Africa and is threatened with extinction in most of its range. Total DNA was extracted from 51, i.e., 78 %, of the described species of Encephalartos. The accessions were sampled from the furthest western occurrence of the genus in Nigeria, via Sudan and Uganda, to southern South Africa. The sequences of nuclear ribosomal internal transcribed spacer regions 1 and 2 (ITS 1&2), the chloroplast encoded rbcL gene, and ISSR genomic fingerprinting were employed to resolve the molecular history and the relationships within the genus. Sequence alignment, as well as ISSR fingerprinting, data show low genetic variation among all analysed accessions, indicating diversification within the Pliocene/Pleistocene. ITS 1&2 data agree well with morphological and geographical characters and resolved three major genetic clusters with overlapping distribution ranges in eastern South Africa. This area, that contains the largest diversity of genotypes of Encephalartos, may have served as a Pliocene/Pleistocene refugium. 相似文献