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1.
Molecular Phylogeny of Metazoan Intermediate Filament Proteins 总被引:7,自引:0,他引:7
Andreas Erber Dieter Riemer Marc Bovenschulte Klaus Weber 《Journal of molecular evolution》1998,47(6):751-762
We have cloned cytoplasmic intermediate filament (IF) proteins from a large number of invertebrate phyla using cDNA probes,
the monoclonal antibody IFA, peptide sequence information, and various RT-PCR procedures. Novel IF protein sequences reported
here include the urochordata and nine protostomic phyla, i.e., Annelida, Brachiopoda, Chaetognatha, Echiura, Nematomorpha,
Nemertea, Platyhelminthes, Phoronida, and Sipuncula. Taken together with the wealth of data on IF proteins of vertebrates
and the results on IF proteins of Cephalochordata, Mollusca, Annelida, and Nematoda, two IF prototypes emerge. The L-type,
which includes 35 sequences from 11 protostomic phyla, shares with the nuclear lamins the long version of the coil 1b subdomain
and, in most cases, a homology segment of some 120 residues in the carboxyterminal tail domain. The S-type, which includes
all four subfamilies (types I to IV) of vertebrate IF proteins, lacks 42 residues in the coil 1b subdomain and the carboxyterminal
lamin homology segment. Since IF proteins from all three phyla of the chordates have the 42-residue deletion, this deletion
arose in a progenitor prior to the divergence of the chordates into the urochordate, cephalochordate, and vertebrate lineages,
possibly already at the origin of the deuterostomic branch. Four phyla recently placed into the protostomia on grounds of
their 18S rDNA sequences (Brachiopoda, Nemertea, Phoronida, and Platyhelminthes) show IF proteins of the L-type and fit by
sequence identity criteria into the lophotrochozoic branch of the protostomia.
Received: 2 April 1998 / Accepted: 19 June 1998 相似文献
2.
The aldo-keto reductase enzymes comprise a functionally diverse gene family which catalyze the NADPH-dependant reduction
of a variety of carbonyl compounds. The protein sequences of 45 members of this family were aligned and phylogenetic trees
were deduced from this alignment using the neighbor-joining and Fitch algorithms. The branching order of these trees indicates
that the vertebrate enzymes cluster in three groups, which have a monophyletic origin distinct from the bacterial, plant,
and invertebrate enzymes. A high level of conservation was observed between the vertebrate hydroxysteroid dehydrogenase enzymes,
prostaglandin F synthase, and ρ-crystallin of Xenopus laevis. We infer from the phylogenetic analysis that prostaglandin F synthase may represent a recent recruit to the eicosanoid biosynthetic
pathway from the hydroxysteroid dehydrogenase pathway and furthermore that, in the context of gene recruitment, Xenopus laevisρ-crystallin may represent a shared gene.
Received: 26 August 1996 / Accepted: 5 June 1997 相似文献
3.
Michael Kruse Vera Gamulin Helena Cetkovic Zeev Pancer Isabel M. Müller Werner E. G. Müller 《Journal of molecular evolution》1996,43(4):374-383
Protein kinases C (PKCs) comprise closely related Ser/Thr kinases, ubiquitously present in animal tissues; they respond to
second messengers, e.g., Ca2+ and/or diacylglycerol, to express their activities. Two PKCs have been sequenced from Geodia cydonium, a member of the lowest multicellular animals, the sponges (Porifera). One sponge G. cydonium PKC, GCPKC1, belongs to the ``novel' (Ca2+-independent) PKC (nPKC) subfamily while the second one, GCPKC2, has the hallmarks of the ``conventional' (Ca2+-dependent) PKC (cPKC) subfamily. The alignment of the Ser/Thr catalytic kinase domains, of the predicted aa sequences for
these cDNAs with respective segments from previously reported sequences, revealed highest homology to PKCs from animals but
also distant relationships to Ser/Thr kinases from protozoa, plants, and bacteria. However, a comparison of the complete structures
of the sponge PKCs, which are—already—identical to those of nPKCs and cPKCs from higher metazoa, with the structures of protozoan,
plant, and bacterial Ser/Thr kinases indicates that the metazoan PKCs have to be distinguished from the nonmetazoan enzymes.
These data indicate that metazoan PKCs have a universal common ancestor which they share with the nonmetazoan Ser/Thr kinases
with respect to the kinase domain, but they differ from them in overall structural composition.
Received: 10 January 1996 / Accepted: 12 March 1996 相似文献
4.
The complete nucleotide sequence of the 18S subunit of ribosomal DNA (rDNA) was determined for the venerid clams Callista chione (Pitarinae) and Venus verrucosa (Venerinae). Comparison of the new sequences with the published sequences of 1 annelid, 2 gastropods, 2 polyplacophorans,
and 19 bivalves showed that when the annelids are used as outgroup the gastropods diverge from the bivalves, which form a
cluster including the polyplacophorans. When the gastropods alone were compared with the bivalves, the latter split in two
groups corresponding to the two subclasses of Heterodonta and Pteriomorpha. The former include two taxa that diverged early,
Galeomma and Tridacna, while the Veneridae and Mactridae form two sister groups. In contrast to previous reports and in line with morphological
data, the Ostreidae are included in the Pteriomorphia and form a monophyletic group.
Received: 16 May 1998 / Accepted: 11 August 1998 相似文献
5.
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
6.
Michael S.Y. Lee 《Journal of molecular evolution》1999,49(3):385-391
It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear
genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two ``internal' calibration points were used.
However, only one fossil divergence date (the mammal–bird split) was directly used to calibrate the molecular clock. The second
calibration point (the primate–rodent split) was based on molecular estimates that were ultimately also calibrated by the
same mammal–bird split. However, the first tetrapods that can be assigned with confidence to either the mammal (synapsid)
lineage or the bird (diapsid) lineage are approximately 288 million years old, while the first mammals that can be assigned
with confidence to either the primate or the rodent lineages are 65 million years old, or 85 million years old if ferungulates
are part of the primate lineage and zhelestids are accepted as ferungulate relatives. Recalibration of the protein data using
these fossil dates indicates that metazoans diverged between 791 and 528 million years ago, a result broadly consistent with
the palaeontological documentation of the ``Cambrian explosion.' The third, ``external' calibration point (the metazoan–fungal
divergence) was similarly problematic, since it was based on a controversial molecular study (which in turn used fossil dates
including the mammal–bird split); direct use of fossils for this calibration point gives the absurd dating of 455 million
years for metazoan divergences. Similar calibration problems affect another recent study (Wang et al. 1999), which proposes
divergences for metazoans of 1000 million years or more: recalibrations of their clock again yields much more recent dates,
some consistent with a ``Cambrian explosion' scenario. Molecular clock studies have persuasively argued for the imperfection
of the fossil record but have rarely acknowledged that their inferences are also directly based on this same record.
Received: 26 January 1999 / Accepted: 14 April 1999 相似文献
7.
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
8.
We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the
neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included
species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles,
and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials
from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree
structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually
as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information
from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird
neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore,
the results confirmed the present classification of four Australasian marsupial orders based on morphological characters,
and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia
and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals
and that neurotrophins can resolve basal relationships in the evolutionary tree.
Received: 27 January 1997 / Accepted: 20 March 1997 相似文献
9.
Phylogenetic relationships among the Japanese papilionid butterflies were analyzed by comparing 783 nucleotide sequences
of the mitochondrial gene encoding NADH dehydrogenase subunit 5 (ND5). Phylogenetic trees of the representative species from each family in the superfamily Papilionoidea revealed that the species
of the family Papilionidae and those of all other families formed distinct clusters, with a few species of the family Hesperiidae
(Hesperioidea) as an outgroup. In the phylogenetic trees of most Japanese species of the family Papilionidae with Nymphalis xanthomelas (Nymphalidae) as an outgroup, the tribe Parnassiini (Parnassiinae) formed a cluster, and the rest formed the other cluster
in which the tribe Zerynthiini (Parnassiinae) and the subfamily Papilioninae formed different subclusters. In the Papilioninae
cluster, the tribes Troidini and Graphiini formed a subcluster, and the tribe Papilionini formed the other subcluster. These
results generally agree with the traditional classification of the papilionid butterflies based on their morphological characteristics
and support the proposed evolutionary genealogy of the butterflies based on their morphology, behavior, and larval host plants,
except that the tribes Parnasiini and Zerynthiini (both Parnassiinae) are not in the same cluster.
Received: 16 March 1998 / Accepted: 28 April 1998 相似文献
10.
When divergence between viral species is large, the analysis and comparison of nucleotide or protein sequences are dependent
on mutation biases and multiple substitutions per site leading, among other things, to the underestimation of branch lengths
in phylogenetic trees. To avoid the problem of multiply substituted sites, a method not directly based on the nucleic or protein
sequences has been applied to retroviruses. It consisted of asking questions about genome structure or organization, and gene
function, the series of answers creating coded sequences analyzed by phylogenic software. This method recovered the principal
retroviral groups such as the lentiviruses and spumaviruses and highlighted questions and answers characteristic of each group
of retroviruses. In general, there was reasonable concordance between the coded genome methodology and that based on conventional
phylogeny of the integrase protein sequence, indicating that integrase was fixing mutations slowly enough to marginalize the
problem of multiple substitutions at sites. To a first approximation, this suggests that the acquisition of novel genetic
features generally parallels the fixation of amino acid substitutions.
Received: 18 May 2001 / Accepted: 7 September 2001 相似文献
11.
12.
Molecular Data from the 16S rRNA Gene for the Phylogeny of Pectinidae (Mollusca: Bivalvia) 总被引:17,自引:0,他引:17
The phylogenetic relationships among the species belonging to the family Pectinidae are still an issue of debate. The mitochondrial
DNA sequences from the large ribosomal RNA gene may be of great value for systematic and phylogenetic studies within families.
Partial sequences of the 16S rRNA gene were obtained for the scallop species Adamussium colbecki, Aequipecten opercularis, Chlamys glabra, C. islandica, C. varia, and Pecten jacobeus and compared with the published sequence of Pecten maximus. The present molecular data show that Chlamys are polyphyletic and do not support the assignment of these species to the two subfamilies Chlamydinae and Pectininae. Moreover,
the minimal genetic distance between P. maximus and P. jacobeus suggests that they could belong to the same species.
Received: 24 May 1999 / Accepted: 1 September 1999 相似文献
13.
14.
G.J. Mitchison 《Journal of molecular evolution》1999,49(1):11-22
Carrying out simultaneous tree-building and alignment of sequence data is a difficult computational task, and the methods
currently available are either limited to a few sequences or restricted to highly simplified models of alignment and phylogeny.
A method is given here for overcoming these limitations by Bayesian sampling of trees and alignments simultaneously. The method
uses a standard substitution matrix model for residues together with a hidden Markov model structure that allows affine gap
penalties. It escapes the heavy computational burdens of other models by using an approximation called the ``*' rule, which
replaces missing data by a sum over all possible values of variables. The behavior of the model is demonstrated on test sets
of globins.
Received: 25 May 1998 / Accepted: 8 December 1998 相似文献
15.
Of Worms and Men: An Evolutionary Perspective on the Fibroblast Growth Factor (FGF) and FGF Receptor Families 总被引:6,自引:0,他引:6
François Coulier Pierre Pontarotti Régine Roubin Helge Hartung Mitchell Goldfarb Daniel Birnbaum 《Journal of molecular evolution》1997,44(1):43-56
FGFs (fibroblast growth factors) play major roles in a number of developmental processes. Recent studies of several human
disorders, and concurrent analysis of gene knock-out and properties of the corresponding recombinant proteins have shown that
FGFs and their receptors are prominently involved in the development of the skeletal system in mammals. We have compared the
sequences of the nine known mammalian FGFs, FGFs from other vertebrates, and three additional sequences that we extracted
from existing databases: two human FGF sequences that we tentatively designated FGF10 and FGF11, and an FGF sequence from
C?norhabditis elegans. Similarly, we have compared the sequences of the four FGF receptor paralogs found in chordates with four non-chordate FGF
receptors, including one recently identified in C. elegans. The comparison of FGF and FGF receptor sequences in vertebrates and nonvertebrates shows that the FGF and FGF receptor families
have evolved through phases of gene duplications, one of which may have coincided with the emergence of vertebrates, in relation
with their new system of body scaffold.
Received: 6 April 1996 / Accepted: 5 July 1996 相似文献
16.
In this paper we have analyzed 49 vertebrate gene families that were generated in the early stage of vertebrates and/or shortly
before the origin of vertebrates, each of which consists of three or four member genes. We have dated the first (T1) and second (T2) gene duplications of 26 gene families with 3 member genes. The means of T1 (594 mya) and T2 (488 mya) are largely consistent to a well-cited version of two-round (2R) genome duplication theory. Moreover, in most cases,
the time interval between two successive gene duplications is large enough that the fate of duplicate genes generated by the
first gene duplication was likely to be determined before the second one took place. However, the phylogenetic pattern of
23 gene families with 4 members is complicated; only 5 of them are predicted by 2R model, but 11 families require an additional
gene (or genome) duplication. For the rest (7 families), at least one gene duplication event had occurred before the divergence
between vertebrate and Drosophila, indicating a possible misleading of the 4:1 rule (member gene ratio between vertebrates and invertebrates). Our results show
that Ohno's 2R conjecture is valid as a working hypothesis for providing a most parsimonious explanation. Although for some
gene families, additional gene duplication is needed, the credibility of the third genome duplication (3R) remains to be investigated.
Received: 13 December 1999 / Accepted: 7 April 2000 相似文献
17.
The Molecular Evolution of the Vertebrate Trypsinogens 总被引:1,自引:0,他引:1
We expand the already large number of known trypsinogen nucleotide and amino acid sequences by presenting additional trypsinogen
sequences from the tunicate (Boltenia villosa), the lamprey (Petromyzon marinus), the pufferfish (Fugu rubripes), and the frog (Xenopus laevis). The current array of known trypsinogen sequences now spans the entire vertebrate phylogeny. Phylogenetic analysis is made
difficult by the presence of multiple isozymes within species and rates of evolution that vary highly between both species
and isozymes. We nevertheless present a Fitch-Margoliash phylogeny constructed from pairwise distances. We employ this phylogeny
as a vehicle for speculation on the evolution of the trypsinogen gene family as well as the general modes of evolution of
multigene families. Unique attributes of the lamprey and tunicate trypsinogens are noted.
Received: 12 July 1997 相似文献
18.
Cristian Cañestro Ricard Albalat Lars Hjelmqvist Laura Godoy Hans Jörnvall Roser Gonzàlez-Duarte 《Journal of molecular evolution》2002,54(1):81-89
The alcohol dehydrogenase (ADH) family has evolved into at least eight ADH classes during vertebrate evolution. We have characterized
three prevertebrate forms of the parent enzyme of this family, including one from an urochordate (Ciona intestinalis) and two from cephalochordates (Branchiostoma floridae and Branchiostoma lanceolatum). An evolutionary analysis of the family was performed gathering data from protein and gene structures, exon–intron distribution,
and functional features through chordate lines. Our data strongly support that the ADH family expansion occurred 500 million
years ago, after the cephalochordate/vertebrate split, probably in the gnathostome subphylum line of the vertebrates. Evolutionary
rates differ between the ancestral, ADH3 (glutathione-dependent formaldehyde dehydrogenase), and the emerging forms, including
the classical alcohol dehydrogenase, ADH1, which has an evolutionary rate 3.6-fold that of the ADH3 form. Phylogenetic analysis
and chromosomal mapping of the vertebrate Adh gene cluster suggest that family expansion took place by tandem duplications, probably concurrent with the extensive isoform
burst observed before the fish/tetrapode split, rather than through the large-scale genome duplications also postulated in
early vertebrate evolution. The absence of multifunctionality in lower chordate ADHs and the structures compared argue in
favor of the acquisition of new functions in vertebrate ADH classes. Finally, comparison between B. floridae and B. lanceolatum Adhs provides the first estimate for a cephalochordate speciation, 190 million years ago, probably concomitant with the beginning
of the drifting of major land masses from the Pangea.
Received: 10 April 2001 / Accepted: 23 May 2001 相似文献
19.
Abdelaziz Heddi Hubert Charles Chaqué Khatchadourian Guy Bonnot Paul Nardon 《Journal of molecular evolution》1998,47(1):52-61
The principal intracellular symbiotic bacteria of the cereal weevil Sitophilus oryzae were characterized using the sequence of the 16S rDNA gene (rrs gene) and G + C content analysis. Polymerase chain reaction amplification with universal eubacterial primers of the rrs gene showed a single expected sequence of 1,501 bp. Comparison of this sequence with the available database sequences placed
the intracellular bacteria of S. oryzae as members of the Enterobacteriaceae family, closely related to the free-living bacteria, Erwinia herbicola and Escherichia coli, and the endocytobiotic bacteria of the tsetse fly and aphids. Moreover, by high-performance liquid chromatography, we measured
the genomic G + C content of the S. oryzae principal endocytobiotes (SOPE) as 54%, while the known genomic G + C content of most intracellular bacteria is about 39.5%.
Furthermore, based on the third codon position G + C content and the rrs gene G + C content, we demonstrated that most intracellular bacteria except SOPE are A + T biased irrespective of their phylogenetic
position. Finally, using the hsp60 gene sequence, the codon usage of SOPE was compared with that of two phylogenetically closely related bacteria: E. coli, a free-living bacterium, and Buchnera aphidicola, the intracellular symbiotic bacteria of aphids. Taken together, these results show a peculiar and distinctly different DNA
composition of SOPE with respect to the other obligate intracellular bacteria, and, combined with biological and biochemical
data, they elucidate the evolution of symbiosis in S. oryzae.
Received: 8 September 1997 / Accepted: 24 October 1997 相似文献
20.
Margaret J. Beaton Andrew J. Roger Thomas Cavalier-Smith 《Journal of molecular evolution》1998,47(6):697-708
The nucleotide sequence for an 11,715-bp segment of the mitochondrial genome of the octocoral Sarcophyton glaucum is presented, completing the analysis of the entire genome for this anthozoan member of the phylum Cnidaria. The genome contained
the same 13 protein-coding and 2 ribosomal RNA genes as in other animals. However, it also included an unusual mismatch repair
gene homologue reported previously and codes for only a single tRNA gene. Intermediate in length compared to two other cnidarians
(17,443 and 18,911 bp), this organellar genome contained the smallest amount of noncoding DNA (428, compared to 1283 and 781
nt, respectively), making it the most compact one found for the phylum to date. The mitochondrial genes of S. glaucum exhibited an identical arrangement to that found in another octocoral, Renilla kolikeri, with five protein-coding genes in the same order as has been found in insect and vertebrate mitochondrial genomes. Although
gene order appears to be highly conserved among octocorals, compared to the hexacoral, Metridium senile, few similarities were found. Like other metazoan mitochondrial genomes, the A + T composition was elevated and a general
bias against codons ending in G or C was observed. However, an exception to this was the infrequent use of TGA compared to
TGG to code for tryptophan. This divergent codon bias is unusual but appears to be a conserved feature among two rather distantly
related anthozoans.
Received: 27 January 1998 / Accepted: 25 May 1998 相似文献