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1.
Masato Nikaido Kuniko Kawai Yin Cao Masashi Harada Satoru Tomita Norihiro Okada Masami Hasegawa 《Journal of molecular evolution》2001,53(4-5):508-516
The complete mitochondrial genomes of two microbats, the horseshoe bat Rhinolophus pumilus, and the Japanese pipistrelle Pipistrellus abramus, and that of an insectivore, the long-clawed shrew Sorex unguiculatus, were sequenced and analyzed phylogenetically by a maximum likelihood method in an effort to enhance our understanding of
mammalian evolution. Our analysis suggested that (1) a sister relationship exists between moles and shrews, which form an
eulipotyphlan clade; (2) chiropterans have a sister-relationship with eulipotyphlans; and (3) the Eulipotyphla/Chiroptera
clade is closely related to fereuungulates (Cetartiodactyla, Perissodactyla and Carnivora). Divergence times on the mammalian
tree were estimated from consideration of a relaxed molecular clock, the amino acid sequences of 12 concatenated mitochondrial
proteins and multiple reference criteria. Moles and shrews were estimated to have diverged approximately 48 MyrBP, and bats
and eulipotyphlans to have diverged 68 MyrBP. Recent phylogenetic controversy over the polyphyly of microbats, the monophyly
of rodents, and the position of hedgehogs is also examined.
Received: 21 December 2000 / Accepted: 16 February 2001 相似文献
2.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
3.
Complete chloroplast 23S rRNA and psbA genes from five peridinin-containing dinoflagellates (Heterocapsa pygmaea, Heterocapsa niei, Heterocapsa rotun-data, Amphidinium carterae, and Protoceratium reticulatum) were amplified by PCR and sequenced; partial sequences were obtained from Thoracosphaera heimii and Scrippsiella trochoidea. Comparison with chloroplast 23S rRNA and psbA genes of other organisms shows that dinoflagellate chloroplast genes are the most divergent and rapidly evolving of all.
Quartet puzzling, maximum likelihood, maximum parsimony, neighbor joining, and LogDet trees were constructed. Intersite rate
variation and invariant sites were allowed for with quartet puzzling and neighbor joining. All psbA and 23S rRNA trees showed peridinin-containing dinoflagellate chloroplasts as monophyletic. In psbA trees they are related to those of chromists and red algae. In 23S rRNA trees, dinoflagellates are always the sisters of
Sporozoa (apicomplexans); maximum likelihood analysis of Heterocapsa triquetra 16S rRNA also groups the dinoflagellate and sporozoan sequences, but the other methods were inconsistent. Thus, dinoflagellate
chloroplasts may actually be related to sporozoan plastids, but the possibility of reproducible long-branch artifacts cannot
be strongly ruled out. The results for all three genes fit the idea that dinoflagellate chloroplasts originated from red algae
by a secondary endosymbiosis, possibly the same one as for chromists and Sporozoa. The marked disagreement between 16S rRNA
trees using different phylogenetic algorithms indicates that this is a rather poor molecule for elucidating overall chloroplast
phylogeny. We discuss possible reasons why both plastid and mitochondrial genomes of alveolates (Dinozoa, Sporozoa and Ciliophora)
have ultra-rapid substitution rates and a proneness to unique genomic rearrangements.
Received: 27 December 1999 / Accepted: 24 March 2000 相似文献
4.
Briscoe AD 《Journal of molecular evolution》2000,51(2):110-121
It has been hypothesized that the UV-, blue-, and green-sensitive visual pigments of insects were present in the common ancestor
of crustaceans and insects, whereas red-sensitive visual pigments evolved later as a result of convergent evolution. This
hypothesis is examined with respect to the placement of six opsins from the swallowtail butterfly Papilio glaucus (PglRh1–6) in relationship to 46 other insect, crustacean, and chelicerate opsin sequences. All basal relationships established
with maximum parsimony analysis except two are present in the distance and maximum likelihood analyses. In all analyses, the
six P. glaucus opsins fall into three well-supported clades, comprised, respectively, of ultraviolet (UV), blue, and long-wavelength (LW)
pigments, which appear to predate the radiation of the insects. Lepidopteran green- and red-sensitive visual pigments form
a monophyletic clade, which lends support to the hypothesis from comparative physiological studies that red-sensitive visual
pigments in insects have paralogous origins. Polymorphic amino acid sites (180, 197, 277, 285, 308), which are essential for
generating the spectral diversity among the vertebrate red- and green-sensitive pigments are notably invariant in the Papilio red- and green-sensitive pigments. Other major tuning sites must be sought to explain the spectral diversification among
these and other insect visual pigments.
Received: 6 December 1999 / Accepted: 3 April 2000 相似文献
5.
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
6.
The complete mitochondrial genome sequence of the pig, Sus scrofa, was determined. The length of the sequence presented is 16,679 nucleotides. This figure is not absolute, however, due to
pronounced heteroplasmy caused by variable numbers of the motif GTACACGTGC in the control region of different molecules. A
phylogenetic study was performed on the concatenated amino acid and nucleotide sequences of 12 protein-coding genes of the
mitochondrial genome. The analysis identified the pig (Suiformes) as a sister group of a cow/whale clade, making Artiodactyla
paraphyletic. The split between pig and cow/whale was molecularly dated at 65 million years before present.
Received: 2 December 1997 / Accepted: 20 February 1998 相似文献
7.
Quantitative analyses were carried out on a large number of proteins that contain the highly conserved basic helix–loop–helix
domain. Measures derived from information theory were used to examine the extent of conservation at amino acid sites within
the bHLH domain as well as the extent of mutual information among sites within the domain. Using the Boltzmann entropy measure,
we described the extent of amino acid conservation throughout the bHLH domain. We used position association (pa) statistics that reflect the joint probability of occurrence of events to estimate the ``mutual information content' among
distinct amino acid sites. Further, we used pa statistics to estimate the extent of association in amino acid composition at each site in the domain and between amino acid
composition and variables reflecting clade and group membership, loop length, and the presence of a leucine zipper. The pa values were also used to describe groups of amino acid sites called ``cliques' that were highly associated with each other.
Finally, a predictive motif was constructed that accurately identifies bHLH domain-containing proteins that belong to Groups
A and B.
Received: 15 December 1997 / Accepted: 1 October 1998 相似文献
8.
Fungi have evolved a unique α-aminoadipate pathway for lysine biosynthesis. The fungal-specific enzyme homoaconitate hydratase
from this pathway is moderately similar to the aconitase-family proteins from a diverse array of taxonomic groups, which have
varying modes of obtaining lysine. We have used the similarity of homoaconitate hydratase to isopropylmalate isomerase (serving
in leucine biosynthesis), aconitase (from the tricarboxylic acid cycle), and iron-responsive element binding proteins (cytosolic
aconitase) from fungi and other eukaryotes, eubacteria, and archaea to evaluate possible evolutionary scenarios for the origin
of this pathway. Refined sequence alignments show that aconitase active site residues are highly conserved in each of the
enzymes, and intervening sequence sites are quite dissimilar. This pattern suggests strong purifying selection has acted to
preserve the aconitase active site residues for a common catalytic mechanism; numerous other substitutions occur due to adaptive
evolution or simply lack of functional constraint. We hypothesize that the similarities are the remnants of an ancestral gene
duplication, which may not have occurred within the fungal lineage. Maximum likelihood, neighbor joining, and maximum parsimony
phylogenetic comparisons show that the α-aminoadipate pathway enzyme is an outgroup to all aconitase family proteins for which
sequence is currently available.
Received: 7 October 1997 相似文献
9.
The aminoacyl-tRNA synthetases are ubiquitous enzymes which catalyze a crucial step of the cell life, the specific attachment
of amino acids to their cognate tRNA. The amino acid sequences of three archaeal seryl-tRNA synthetases (SerRS) from Haloarcula marismortui and Methanococcus jannaschii, both belonging to the group of Euryarchaeota, and from Sulfolobus solfataricus, of the group of Crenarchaeota, were aligned with other eubacterial and eukaryal available SerRS sequences. In an attempt to identify some features of adaptation
to extreme environments of these organisms, amino acid composition and amino acid substitutions between mesophilic and thermophilic
SerRS were analyzed. In addition, universal phylogenetic trees of SerRS including the three known archaeal sequences, rooted
by the threonyl-tRNA synthetases were inferred. Amino acid analyses of the SerRS revealed two ways of adaptation to thermophilic
environments between the Eubacteria and the Archaea; most of the usually described amino acid substitutions were nonsignificant in the case of archaeal thermophilic SerRS and
most amino acid composition biases seemed to be linked to the genome G+C content pressure. The phylogenetic analysis of the
SerRS showed the Archaea to be paraphyletic, H. marismortui emerging with the Gram-positive Bacteria, M. jannaschii being near the root of the tree, and S. solfataricus branching with Eucarya.
Received: 30 March 1998 / Accepted: 14 July 1998 相似文献
10.
Heat Shock Protein 70 Family: Multiple Sequence Comparisons, Function, and Evolution 总被引:14,自引:0,他引:14
The heat shock protein 70 kDa sequences (HSP70) are of great importance as molecular chaperones in protein folding and transport.
They are abundant under conditions of cellular stress. They are highly conserved in all domains of life: Archaea, eubacteria,
eukaryotes, and organelles (mitochondria, chloroplasts). A multiple alignment of a large collection of these sequences was
obtained employing our symmetric-iterative ITERALIGN program (Brocchieri and Karlin 1998). Assessments of conservation are
interpreted in evolutionary terms and with respect to functional implications. Many archaeal sequences (methanogens and halophiles)
tend to align best with the Gram-positive sequences. These two groups also miss a signature segment [about 25 amino acids
(aa) long] present in all other HSP70 species (Gupta and Golding 1993). We observed a second signature sequence of about 4
aa absent from all eukaryotic homologues, significantly aligned in all prokaryotic sequences. Consensus sequences were developed
for eight groups [Archaea, Gram-positive, proteobacterial Gram-negative, singular bacteria, mitochondria, plastids, eukaryotic
endoplasmic reticulum (ER) isoforms, eukaryotic cytoplasmic isoforms]. All group consensus comparisons tend to summarize better
the alignments than do the individual sequence comparisons. The global individual consensus ``matches' 87% with the consensus
of consensuses sequence. A functional analysis of the global consensus identifies a (new) highly significant mixed charge
cluster proximal to the carboxyl terminus of the sequence highlighting the hypercharge run EEDKKRRER (one-letter aa code used).
The individual Archaea and Gram-positive sequences contain a corresponding significant mixed charge cluster in the location
of the charge cluster of the consensus sequence. In contrast, the four Gram-negative proteobacterial sequences of the alignment
do not have a charge cluster (even at the 5% significance level). All eukaryotic HSP70 sequences have the analogous charge
cluster. Strikingly, several of the eukaryotic isoforms show multiple mixed charged clusters. These clusters were interpreted
with supporting data related to HSP70 activity in facilitating chaperone, transport, and secretion function. We observed that
the consensus contains only a single tryptophan residue and a single conserved cysteine. This is interpreted with respect
to the target rule for disaggregating misfolded proteins. The mitochondrial HSP70 connections to bacterial HSP70 are analyzed,
suggesting a polyphyletic split of Trypanosoma and Leishmania protist mitochondrial (Mt) homologues separated from Mt-animal/fungal/plant homologues. Moreover, the HSP70 sequences from
the amitochondrial Entamoeba histolytica and Trichomonas vaginalis species were analyzed. The E. histolytica HSP70 is most similar to the higher eukaryotic cytoplasmic sequences, with significantly weaker alignments to ER sequences
and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences. This appears to be at variance
with the hypothesis that E. histolytica rather recently lost its mitochondrial organelle. T. vaginalis contains two HSP70 sequences, one Mt-like and the second similar to eukaryotic cytoplasmic sequences suggesting two diverse
origins.
Received: 29 January 1998 / Accepted: 14 May 1998 相似文献
11.
Molecular Evolution of Cytochrome b of Subterranean Mole Rats, Spalax ehrenbergi Superspecies, in Israel 总被引:1,自引:0,他引:1
We describe the molecular evolution of cytochrome b of blind subterranean mole rats. We examined 12 individuals for nucleotide differences in the region of 402 base pairs of
mitochondrial cytochrome b. Each individual represents a different population from the entire ecological and speciational range of the four chromosomal
species in Israel (2n= 52, 54, 58, and 60) belonging to the Spalax ehrenbergi superspecies. Our results indicate the following. (i) There are seven first-position transitional differences, compared to
34 variable third positions, with no observed second-position substitutions. (ii) A maximum of four amino acids differences
occurs across the range. (iii) Within-species diversity increases southward. Only 1 autoapomorphic substitution characterizes
either 2n= 52 or 2n= 54, but 6–11 substitutions characterize 2n= 58, and 9–13 substitutions characterize 2n= 60. (iv) Both parsimony and maximum-likelihood trees suggest two monophyletic groups: (a) 2n= 52 and 54, and (b) 2n= 58 and 60, as identified earlier by other protein and DNA markers. (v) Mitochondrial cytochrome b heterogeneity is significantly correlated with climatic factors (rainfall) and biotic factors (body size and allozymes).
We hypothesize that two selective regimes direct cytochrome b evolution in the S. ehrenbergi superspecies: (i) purifying selection in the flooded, mesic, hypoxic northern range of 2n= 52 and 54 and (ii) diversifying selection in the climatically spatiotemporal, xeric, and variable southern range of 2n= 58 and 60. Thus, the molecular evolution of mitochondrial cytochrome b in S. ehrenbergi is explicable by opposite selective stresses across the range of S. ehrenbergi in Israel, associated with the ecological adaptive radiation of the complex.
Received: 23 October 1998 / Accepted: 2 May 1999 相似文献
12.
Primary Structure and Phylogenetic Relationships of a Malate Dehydrogenase Gene from Giardia lamblia
The lactate and malate dehydrogenases comprise a complex protein superfamily with multiple enzyme homologues found in eubacteria,
archaebacteria, and eukaryotes. In this study we describe the sequence and phylogenetic relationships of a malate dehydrogenase
(MDH) gene from the amitochondriate diplomonad protist, Giardia lamblia. Parsimony, distance, and maximum-likelihood analyses of the MDH protein family solidly position G. lamblia MDH within a eukaryote cytosolic MDH clade, to the exclusion of chloroplast, mitochondrial, and peroxisomal homologues. Furthermore,
G. lamblia MDH is specifically related to a homologue from Trichomonas vaginalis. This MDH topology, together with published phylogenetic analyses of β-tubulin, chaperonin 60, valyl-tRNA synthetase, and
EF-1α, suggests a sister-group relationship between diplomonads and parabasalids. Since these amitochondriate lineages contain
genes encoding proteins which are characteristic of mitochondria and α-proteobacteria, their shared ancestry suggests that
mitochondrial properties were lost in the common ancestor of both groups.
Received: 14 September 1998 / Accepted: 29 December 1998 相似文献
13.
The genus Chrysolina consists of specialized phytophagous leaf-beetles (Coleoptera, Chrysomelidae) with feed on several plant families. There
is no explicit phylogenetic hypothesis available for this genus, which includes 65 subgenera and more than 400 species with
a wide distribution. We obtained 839-bp sequence data from the 16S rDNA and cytochrome oxidase subunit I (COI) mitochondrial
genes. Thirty Chrysolina taxa representing eight host–plant affiliations, two species of the closely related genus Oreina, and two outgroups were sampled. These data sets were used separately and combined to obtain the mitochondrial cladogram of
the group using maximum-parsimony and maximum-likelihood criteria. The results were compared to current proposals for Chrysolina systematics that are based on morphological, ecological, and karyological data. The trees obtained were in the most part
congruent with the proposed ancestral association of Chrysolina to Lamiaceae based on chromosome number in several lineages. A minimum of five host-plant switches from the ancestral state
inferred at the family level and two at the subclass level suggests the absence of parallel evolution of beetles and their
host plants. Another switch leading to oligophagy at the family level was deduced to have occurred in the lineage of the subgenus
Chrysolina s.str.
Received: 22 May 1998 / Accepted: 16 September 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.
The large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale were determined. These sequences were combined with small subunit ribosomal RNA sequences in order to carry out a phylogenetic
analysis based on neighbor-joining, maximum parsimony, and maximum likelihood methods. Our results indicate that heterokont
fungi and heterokont algae each are monophyletic, and confirm that they together form a monophyletic group called ``stramenopiles.'
Within the heterokont algae, the eustigmatophyte Nannochloropsis salina either clusters with the chrysophyte Ochromonas danica or forms a sister group to a cluster comprising the phaeophyte Scytosiphon lomentaria and the xanthophyte Tribonema aequale. The alveolates were identified as the closest relatives of the stramenopiles, but the exact order of divergence between the
eukaryotic crown taxa could not be established with confidence.
Received: 22 November 1996 / Accepted: 14 February 1997 相似文献
16.
17.
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
18.
19.
Taillades J Collet H Garrel L Beuzelin I Boiteau L Choukroun H Commeyras A 《Journal of molecular evolution》1999,48(6):638-645
α-N-Carbamoyl amino acid (CAA), whose conditions of formation in a prebiotic hydrosphere have been described previously (Taillades
et al. 1998), could have been an important intermediate in prebiotic peptide synthesis through reaction with atmospheric NO
x
. Nitrosation of solid CAA (glycine or valine derivative) by a 4/1 NO/O2 gaseous mixture (1 atm) yields N-carboxyanhydride (NCA) quantitatively in less than 1 h at room temperature. The crude solid NCA undergoes quantitative oligomerization
(from trimer to nonamer under the conditions we used) when treated with a (bi)carbonate aqueous buffer at pH 9. We therefore
suggest that part of the prebiotic amino acid activation/polymerization process may have taken place in a dry phase (``drying-lagoon'
scenario).
Received: 23 June 1998 / Accepted: 7 December 1998 相似文献
20.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献