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1.
Kazuhiko Takahashi Mutsumi Nishida Masahide Yuma Norihiro Okada 《Journal of molecular evolution》2001,53(4-5):496-507
Lake Malawi is home to more than 450 species of endemic cichlids, which provide a spectacular example of adaptive radiation.
To clarify the phylogenetic relationships among these fish, we examined the presence and absence of SINEs (short interspersed
repetitive elements) at orthologous loci. We identified six loci at which a SINE sequence had apparently been specifically
inserted by retroposition in the common ancestor of all the investigated species of endemic cichlids in Lake Malawi. At another
locus, unique sharing of a SINE sequence was evident among all the investigated species of endemic non-Mbuna cichlids with
the exception of Rhamphochromis sp. The relationships were in good agreement with those deduced in previous studies with various different markers, demonstrating
that the SINE method is useful for the elucidation of phylogenetic relationships among cichlids in Lake Malawi. We also characterized
a locus that exhibited transspecies polymorphism with respect to the presence or absence of the SINE sequence among non-Mbuna
species. This result suggests that incomplete lineage sorting and/or interspecific hybridization might have occurred or be
occurring among the species in this group, which might potentially cause misinterpretation of phylogenetic data, in particular
when a single-locus marker, such as a sequence in the mitochondrial DNA, is used for analysis.
Received: 15 December 2000 / Accepted: 30 January 2001 相似文献
2.
Geneviàve Pont-Kingdon Norichika A. Okada Jane L. Macfarlane C. Timothy Beagley Cristi D. Watkins-Sims Thomas Cavalier-Smith G. Desmond Clark-Walker David R. Wolstenholme 《Journal of molecular evolution》1998,46(4):419-431
The nucleotide sequences of two segments of 6,737 ntp and 258 ntp of the 18.4-kb circular mitochondrial (mt) DNA molecule
of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains
the 3′ 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome
b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5′ terminal 1,124 ntp of the gene for the large subunit rRNA (l-rRNA). These genes are arranged in the order given
and all are transcribed from the same strand of the molecule. The smaller segment contains the 3′ terminal 134 ntp of the
ND4 gene and a complete tRNAf-Met gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify
arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan
rather than termination. Also, as in M. senile the mt-tRNAf-Met gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and TψC loop sequences, and a mismatched nucleotide pair at the top of
the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity
in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast
Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of
the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an
MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.
Received: 13 January 1997 / Accepted: 23 September 1997 相似文献
3.
Singhania NA Dyer KD Zhang J Deming MS Bonville CA Domachowske JB Rosenberg HF 《Journal of molecular evolution》1999,49(6):721-728
The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase
3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs
of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of
eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine
counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have
occurred at these loci recently, sometime after the divergence of these two rodent species (∼10–15 million years ago). Nonsynonymous
substitutions per site (d
N) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated
rates, and comparisons of nonsynonymous to synonymous substitution (d
N / d
S) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures
promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain,
our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.
Received: 8 April 1999 / Accepted: 22 June 1999 相似文献
4.
Charles M. Matthews Cassandra J. Vandenberg Clive N.A. Trotman 《Journal of molecular evolution》1998,46(6):729-733
The Artemia hemoglobin is a dimer comprising two nine-domain covalent polymers in quaternary association. Each polymer is encoded by
a gene representing nine successive globin domains which have different sequences and are presumed to have been copied originally
from a single-domain gene. Two different polymers exist as the result of a complete duplication of the nine-domain gene, allowing
the formation of either homodimers or the heterodimer. The total population size of 18 domains comprising nine corresponding
pairs, coupled with the probability that they reflect several hundred million years of evolution in the same lineage, provides
a unique model in which the process of gene multiplication can be analyzed. The outcome has important implications for the
reliability of local molecular clocks.
The two polymers differ from each other at 11.7% of amino acid sites; however when corresponding individual domains are compared
between polymers, amino acid substitution fluctuates by a factor of 2.7-fold from lowest to highest. This variation is not
obvious at the DNA level: Domain pair identity values fluctuate by 1.3-fold. Identity values are, however, uncorrected for
multiple substitutions, and both silent and nonsilent changes are pooled. Therefore, to determine the variability in relative
substitution rates at the DNA level, we have used the method of Li (1993, J Mol Evol 36:96–99) to determine estimates of nonsynonymous (K
A
) and synonymous (K
S
) substitutions per site for the nine pairs of domains. As expected, the overall level of silent substitutions (K
S
of 56.9%) far exceeded nonsilent substitutions (K
A
of 6.7%); however, for corresponding domain pairs, K
A
fluctuates by 2.3-fold and K
S
by 1.7-fold. The large discrepancies reflected in the expressed protein have accrued within a single lineage and the implication
is that divergence dates of different genera based on amino acid sequences, even with well-studied proteins of reasonable
size, can be wrong by a factor well in excess of 2.
Received: 4 June 1997 / Accepted: 17 December 1997 相似文献
5.
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
6.
Phylogenetic Relationships of the Glycolytic Enzyme, Glyceraldehyde-3-Phosphate Dehydrogenase, from Parabasalid Flagellates 总被引:4,自引:0,他引:4
Over 90% of the open reading frame of gap genes for glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) was obtained with PCR from five species
of Parabasala. With gap1 from Trichomonas vaginalis obtained earlier, the data include two sequences each for three species. All sequences were colinear with T. vaginalis gap1 and shared with it as a synapomorphy a 10- to 11-residue insertion not found in any other gap and an S-loop with characteristic features of eubacterial GAPDH. All residues known to be highly conserved in this enzyme
were present. The parabasalid sequences formed a robust monophyletic group in phylogenetic reconstructions with distance-based,
maximum-parsimony, and maximum-likelihood methods. The two genes of the amphibian commensal, Trichomitus batrachorum, shared a common ancestor with the rest, which separate into two well-supported lineages. T. vaginalis and Tetratrichomonas gallinarum (both representatives of Trichomonadinae) formed one, while Monocercomonas sp. and Tritrichomonas foetus formed the other. These data agreed with and/or were close to published reconstructions based on other macromolecules. They
did not support the ancestral position of Monocercomonas sp. proposed on the basis of morphological characteristics but confirmed an early emergence of Trichomitus batrachorum. The sequence pairs obtained from three species indicated either gene duplications subsequent to the divergence of the corresponding
lineages or a strong gene conversion later in these lineages. The parabasalid clade was a robust part of the eubacterial radiation
of GAPDH and showed no relationships to the clade that contained all other eukaryotic gap genes. The data clearly reveal that the members of this lineage use in their glycolytic pathway a GAPDH species with properties
and an evolutionary history that are unique among all eukaryotes studied so far.
Received: 28 April 1997 / Accepted: 14 October 1997 相似文献
7.
To date, the small nuclear 4.5SI RNA has only been studied in the rat (Rattus norvegicus). Combining PCR and hybridization analyses, we have revealed 4.5SI RNA homologues sequences in the genomes of four myomorph rodent families (Muridae, Cricetidae, Spalicidae, and Rhizomyidae),
and not in other myomorph families (Dipodidae, Zapodidae, Geomyidae, and Heteromyidae) or sciuromorph and caviomorph rodents.
By Northern-hybridization, 4.5SI RNA has been detected in the common rat (R. norvegicus, Muridae), golden hamster (Mesocricetus auratus, Cricetidae), and Russian mole rat (Spalax microphthalmus, Spalacidae), but not in the related great jerboa (Allactaga jaculus, Dipodidae) or in four non-myomorph rodent species tested. cDNA derived from 4.5SI RNA of M. auratus and S. microphthalmus has been cloned and sequenced. The hamster RNA is found to differ from rat 4.5SI RNA by only one nucleotide substitution. For the mole rat, two variants of 4.5SI RNA are detected: short (S) and long (L) with length 101 and 108 nt, respectively. The L variant differs from the S variant
as well as from murid and cricetid 4.5SI RNAs by both a 7 nt insertion and a varying number of nucleotide substitutions. The sequence similarity between the spalacid
S-variant and murid/crecitid variants of 4.5SI RNA is 90%. Judging from species distribution, 4.5SI RNA genes emerged during the same period of time as the related short interspersed element B2 arose. This occurred after
the divergence of Dipodidae lineage but before the branching of Spalicidae/Rhizomyidae lineage from a common myomorph rodent
stem. S variant genes seemed to emerge in a common ancestor of spalacids and rhizomyds whereas L variant genes formed in spalacids
following the divergence of these two families. The low rate of evolutionary changes of 4.5SI RNA, at least, in murids and cricetids (6 × 10−4 substitutions per site per million years), suggests that this RNA is under selection constraint and have a function. This
is a remarkable fact if the recent origin and narrow species distribution range of 4.5SI RNA genes is taken into account. Genes with narrow species distribution are proposed to be referred to as stenogenes.
Received: 11 December 2000 / Accepted: 27 August 2001 相似文献
8.
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
9.
We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome
b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis
of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other
primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has
remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.
Received: 15 December 1997 / Accepted: 24 February 1998 相似文献
10.
We previously reported the sequence of a 9260-bp fragment of mitochondrial (mt) DNA of the cephalopod Loligo bleekeri [J. Sasuga et al. (1999) J. Mol. Evol. 48:692–702]. To clarify further the characteristics of Loligo mtDNA, we have sequenced an 8148-bp fragment to reveal the complete mt genome sequence. Loligo mtDNA is 17,211 bp long and possesses a standard set of metazoan mt genes. Its gene arrangement is not identical to any other
metazoan mt gene arrangement reported so far. Three of the 19 noncoding regions longer than 10 bp are 515, 507, and 509 bp
long, and their sequences are nearly identical, suggesting that multiplication of these noncoding regions occurred in an ancestral
Loligo mt genome. Comparison of the gene arrangements of Loligo, Katharina tunicata, and Littorina saxatilis mt genomes revealed that 17 tRNA genes of the Loligo mt genome are adjacent to noncoding regions. A majority (15 tRNA genes) of their counterparts is found in two tRNA gene clusters
of the Katharina mt genome. Therefore, the Loligo mt genome (17 tRNA genes) may have spread over the genome, and this may have been coupled with the multiplication of the
noncoding regions. Maximum likelihood analysis of mt protein genes supports the clade Mollusca + Annelida + Brachiopoda but
fails to infer the relationships among Katharina, Loligo, and three gastropod species.
Received: 9 May 2001 / Accepted: 3 October 2001 相似文献
11.
A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3′ end of the 16S rRNA
gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5′ portion of ATPase subunit 6. The Porifera cluster distinctly
within the eumetazoan radiation, as a sister group to the Cnidaria. Also, the mitochondrial genetic code of this sponge is
likely identical to that found in the Cnidaria. Both the full COII DNA and protein sequences and a portion of the 16S rRNA
gene were found to possess a striking similarity to published Cnidarian mtDNA sequences, allying the Porifera more closely
to the Cnidaria than to any other metazoan phylum. The gene arrangement, COII—tRNALys—ATP8—ATP6, is observed in many Eumetazoan phyla and is apparently ancestral in the metazoa.
Received: 24 November 1997 / Accepted: 14 September 1998 相似文献
12.
We have compared all available deduced protein sequences of the ErbB family of receptors and their ligands. Analysis of the
aligned sequences of the receptors indicates that there are some differences in the receptors that are specific to invertebrates.
In addition, comparison of the vertebrate ErbB receptors suggest that a gene duplication event generated two ancestral receptors,
the ErbB3/ErbB4 precursor and the ErbB1/ErbB2 precursor. Subsequent gene duplications of these precursors generated the four
receptors present in mammals. Analysis of the sequences for the known ligands of the ErbB receptors suggests that the vertebrate
ligands segregate into the ErbB1 ligands and the ErbB3/ErbB4 ligands, paralleling the evolution of the receptors; however,
it is difficult to ascertain any correlation between the invertebrate and the vertebrate ligands. Even though ErbB3 is kinase-impaired,
there is significant conservation of the kinase domain within the vertebrate lineage (human, rat, and F. rubripes), suggesting some function for this domain other than kinase activity, such as mediating protein–protein interactions that
are involved in receptor dimerization and/or activation of the kinase domain of the heterodimerization partner. To date, no
ligand for ErbB2 has been identified, and comparison of the extracellular domains of ErbB2 reveals two regions that are not
conserved across the mammalian species. These two regions of divergence align with sequences in ErbB1 that have been shown
to be proximal to the amino-terminus and to the carboxyl-terminal region, respectively, of bound EGF. Further, one of these
regions contains an insertion, relative to the other members of the mammalian ErbB family, which might affect the ligand binding
site and provide a structural basis for this receptor's apparent inability to bind ligand independently.
Received: 8 September 1999 / Accepted: 17 January 2000 相似文献
13.
Partial sequences of two mitochondrial genes, the 12S ribosomal gene (739 bp) and the cytochrome b gene (672 bp), were analyzed in hopes of reconstructing the evolutionary relationships of 11 leporid species, representative
of seven genera. However, partial cytochrome b sequences were of little phylogenetic value in this study. A suite of pairwise comparisons between taxa revealed that at
the intergeneric level, the cytochrome b gene is saturated at synonymous coding positions due to multiple substitution events. Furthermore, variation at the nonsynonymous
positions is limited, rendering the cytochrome b gene of little phylogenetic value for assessing the relationships between leporid genera. If the cytochrome b data are analyzed without accounting for these two classes of nucleotides (i.e., synonymous and nonsynonymous sites), one
may incorrectly conclude that signal exists in the cytochrome b data. The mitochondrial 12S rRNA gene, on the other hand, has not experienced excessive saturation at either stem or loop
positions. Phylogenies reconstructed from the 12S rDNA data support hypotheses based on fossil evidence that African rock
rabbits (Pronolagus) are outside of the main leporid stock and that leporids experienced a rapid radiation. However, the molecular data suggest
that this radiation event occurred in the mid-Miocene several millions of years earlier than the Pleistocene dates suggested
by paleontological evidence.
Received: 23 April 1998 / Accepted: 14 May 1998 相似文献
14.
Biglycan and decorin are two members of a family of small extracellular matrix proteoglycans characterized by the presence
of 10 leucine-rich repeats and one or two attachment sites for glucosaminoglycans. Both have thus far been described only
from tetrapod species, mainly mammals. Because the extracellular matrix has played an important part in the evolution of Metazoa,
the phylogeny of its components is of considerable interest. In this study, biglycan-like (BGL) cDNA sequences have been obtained
from two teleost (Oreochromis cichlid and zebrafish) and two lamprey species. The analysis of the sequences suggests that, like tetrapods, the lampreys
possess two types of proteoglycans, both of which are biglycan-like; decorin-like proteoglycans could not be identified in
these species. The genes specifying these two types apparently arose by duplication in the lamprey lineage after its divergence
from gnathostomes. The two teleost species possess a BGL proteoglycan and a bona fide decorin. The BGL proteoglycan is highly
divergent from the tetrapod biglycan and related to the BGL proteoglycans of the lamprey. Hence, although the duplication
generating the ancestors of biglycan and decorin genes occurred after the divergence of agnathans but before the emergence
of teleosts, only decorin acquired its characteristic properties in the bony fishes. The BGL gene presumably turned into a typical biglycan only in the tetrapod lineages. The presumed acquisitions of new functions
appear to have been accompanied by changes in the evolutionary rate.
Received: 13 April 2000 / Accepted: 4 July 2000 相似文献
15.
Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals 总被引:1,自引:0,他引:1
Relationships among families and suborders of scleractinian corals are poorly understood because of difficulties 1) in making
inferences about the evolution of the morphological characters used in coral taxonomy and 2) in interpreting their 240-million-year
fossil record. Here we describe patterns of molecular evolution in a segment of the mitochondrial (mt) 16S ribosomal gene from taxa of 14 families of corals and the use of this gene segment in a phylogenetic analysis of relationships
within the order. We show that sequences obtained from scleractinians are homologous to other metazoan 16S ribosomal sequences
and fall into two distinct clades defined by size of the amplified gene product. Comparisons of sequences from the two clades
demonstrate that both sets of sequences are evolving under similar evolutionary constraints: they do not differ in nucleotide
composition, numbers of transition and transversion substitutions, spatial patterns of substitutions, or in rates of divergence.
The characteristics and patterns observed in these sequences as well as the secondary structures, are similar to those observed
in mt 16S ribosomal DNA sequences from other taxa. Phylogenetic analysis of these sequences shows that they are useful for evaluating
relationships within the order. The hypothesis generated from this analysis differs from traditional hypotheses for evolutionary
relationships among the Scleractinia and suggests that a reevaluation of evolutionary affinities in the order is needed.
Received: 4 September 1996 / Accepted: 7 April 1997 相似文献
16.
Comparison of Substitution Rates in ZFX and ZFY Introns of Sheep and Goat Related Species Supports the Hypothesis of Male-Biased Mutation Rates 总被引:6,自引:0,他引:6
There is a growing body of evidence that males serve as the major generators of mutations, due to the larger number of cell
divisions involved in sperm compared to egg production. In mammals, this hypothesis (referred to as ``male-driven evolution')
has been tested by comparison of nucleotide substitution rates on the X and Y sex chromosomes in a limited number of taxa,
predominantly primates and rodents. This study asks whether male-driven evolution is a more general phenomenon among mammals,
by comparison of paralogous ZFX and ZFY intron sequences in sheep and goat species (the tribe Caprini). The male-to-female mutation ratio, αm, was estimated to be between 2.93 (95% CI, 1.51–8.61) and 3.94 (95% CI, 1.25–32.29) when calculated using pairwise distance
and branch length, respectively, suggesting that the Caprini are subject to weak, male-driven evolution. Comparison to published
values for primates, felids, and rodents implies that there may be some correlation with reproductive life span. However,
this is difficult to test with current data because confidence intervals are large and overlapping. Nonindependent evolution
of paralogous sequences and/or the presence of selective constraints could lead to inaccurate estimates of αm. No evidence for gene conversion between the ZFX and the ZFY introns was found, and this suggests that they have evolved independently during the radiation of the Caprini. Finally, there
was no apparent evidence that these introns are subject to selective constraints, although low levels of intraspecific polymorphism
reduce the power of neutrality tests.
Received: 13 February 2001 / Accepted: 23 May 2001 相似文献
17.
Thomas A. Gorr Barbara K. Mable Traute Kleinschmidt 《Journal of molecular evolution》1998,47(4):471-485
Phylogenetic relationships among reptiles were examined using previously published and newly determined hemoglobin sequences.
Trees reconstructed from these sequences using maximum-parsimony, neighbor-joining, and maximum-likelihood algorithms were
compared with a phylogenetic tree of Amniota, which was assembled on the basis of published morphological data. All analyses differentiated α chains into αA and αD types, which are present in all reptiles except crocodiles, where only αA chains are expressed. The occurrence of the αD chain in squamates (lizards and snakes only in this study) appears to be a general characteristic of these species. Lizards
and snakes also express two types of β chains (βI and βII), while only one type of β chain is present in birds and crocodiles.
Reconstructed hemoglobin trees for both α and β sequences did not yield the monophyletic Archosauria (i.e., crocodilians + birds) and Lepidosauria (i.e., Sphenodon+ squamates) groups defined by the morphology tree. This discrepancy, as well as some other poorly resolved nodes, might be
due to substantial heterogeneity in evolutionary rates among single hemoglobin lineages. Estimation of branch lengths based
on uncorrected amino acid substitutions and on distances corrected for multiple substitutions (PAM distances) revealed that
relative rates for squamate αA and αD chains and crocodilian β chains are at least twice as high as those of the rest of the chains considered. In contrast to
these rate inequalities between reptilian orders, little variation was found within squamates, which allowed determination
of absolute evolutionary rates for this subset of hemoglobins. Rate estimates for hemoglobins of lizards and snakes yielded
1.7 (αA) and 3.3 (β) million years/PAM when calibrated with published divergence time vs. PAM distance correlates for several speciation
events within snakes and for the squamate ↔ sphenodontid split. This suggests that hemoglobin chains of squamate reptiles
evolved ∼3.5 (αA) or ∼1.7 times (β) faster than their mammalian equivalents. These data also were used to obtain a first estimate of some
intrasquamate divergence times.
Received: 15 September 1997 / Accepted: 4 February 1998 相似文献
18.
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
19.
Ballard JW 《Journal of molecular evolution》2000,51(1):64-75
The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct
mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution
of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is
no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency
of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous
substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions
relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary
force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci.
Received: 16 September 1999 / Accepted: 14 March 2000 相似文献
20.
Yi-Hong Zhou David Hewett-Emmett Jeannette P. Ward Wen-Hsiung Li 《Journal of molecular evolution》1997,45(6):610-618
Bush babies have had a long history of nocturnal life and it would be interesting to know whether their color vision genes
have become degenerate. Therefore, we used PCR techniques to sequence the X-linked pigment gene of two of these nocturnal
prosimians: Galago senegalensis and Otolemur garnettii. Southern hybridization of genomic DNA of G. senegalensis showed a single X-linked pigment gene. Interestingly, the deduced pigment sequences of the two bush babies are identical.
By comparing the X-linked pigments of bush baby, human, squirrel monkey, and marmoset, 38 variable positions were identified.
At those positions that may cause a spectral shift, the bush baby pigment has identical or biochemically similar residues
to those of the marmoset cone pigment with a spectral peak of 543 nm. This result is consistent with the estimate of 544–545
nm for the spectral peak of the X-linked pigment of Otolemur crassicaudatus, which is closely related to Otolemur garnettii. The neighbor-joining tree of mammalian X-linked pigments showed a significantly shorter branch in the bush baby lineage than
in other primate lineages. A relative rate test showed that the nonsynonymous substitution rate of the bush baby X-linked
pigment gene is about three times slower than that of the human red pigment gene, though the synonymous substitution rates
of the two genes are similar. The slower nonsynonymous rate in the bush baby lineage suggests that the bush baby X-linked
pigment gene is under functional constraints, in spite of its nocturnal life. Two radical changes at positions in the intradiskal
surface next to the sixth transmembrane domain were observed in the X-linked cone pigment of bush babies but not in other
primates. They are changes from Ala to Ser and from Asn to His, which are similar in function to the corresponding residues
in rhodopsins. These two changes may be of importance for dim light sensitivity, which is consistent with our proposal that
the evolution of the bush baby X-linked pigment gene is under selective pressure. In addition, the 2.5% divergence in introns
2 and 5 of the X-linked pigment gene between the two bush babies supports their classification into two separate genera.
Received: 30 November 1996 / Accepted: 17 June 1997 相似文献