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1.
The increasing amount of data generated in recent years has opened the way to exhaustive studies of the relationships among
different members of the Ty3/gypsy group of LTR retrotransposons, a widespread group of eukaryotic transposable elements. Former research led to the identification
of several independent lineages within this group. One of the worse represented of them is that of mdg1, integrated so far only by the Drosophila retrotransposons mdg1 and 412. Our exhaustive database searches indicate the existence of three other Drosophila members of this lineage. Two of them correspond to elements already known, namely, Stalker and blood, but the third one is a new element, which we have called Pilgrim. This element is well represented within the D. melanogaster genome, as revealed by our Southern blot analysis of different strains. The case of Stalker is particularly remarkable, since its phylogenetic relationships clearly point to the mosaic origin of its genome. Finally,
our analysis of the evolution of a small ORF preserved within the 5′ leader region of these elements indicates different evolutionary
rates, presumably as a result of distinct selective constraints.
Received: 16 October 2000 / Accepted: 6 April 2001 相似文献
2.
Karen Miller Clare Lynch Joanne Martin Elisabeth Herniou Michael Tristem 《Journal of molecular evolution》1999,49(3):358-366
Gypsy LTR-retrotransposons have been identified in the genomes of many organisms, but only a small number of vertebrate examples
have been reported to date. Here we show that members of this family are likely to be widespread in many vertebrate classes
with the possible exceptions of mammals and birds. Phylogenetic analyses demonstrate that although there are several distinct
lineages of vertebrate gypsy LTR-retrotransposons, the majority clusters into one monophyletic clade. Groups of fungal, plant, and insect elements were
also observed, suggesting horizontal transfer between phyla may be infrequent. However, in contrast to this, there was little
evidence to support sister relationships between elements derived from vertebrate and insect hosts. In fact, the majority
of the vertebrate elements appeared to be most closely related to a group of gypsy LTR-retrotransposons present within fungi. This implies either that at least one horizontal transmission between these two
phyla has occurred previously or that a gypsy LTR-retrotransposon lineage has been lost from insect taxa.
Received: 22 December 1998 / Accepted: 6 April 1999 相似文献
3.
4.
7S RNA sequences from the hagfish (Myxiniformes) and lamprey (Petromyzontiformes) were cloned and analyzed. In both species,
7S L RNA (also designated SRP RNA, since it represents the RNA constituent of the signal recognition particle) was clearly
detectable. The sequence similarity between the two species was 86%, compared with about 75% similarity between either of
these species and mammals. 7S K RNA was also cloned from the lamprey. The similarity between the 7S K RNA of the lamprey and
that of mammals was 68%. Interestingly, several interspersed elements were found with nearly 100% similarity compared with
mammals. In contrast to the lamprey, no 7S K RNA-related sequences were detectable among hagfish RNA, neither in northern
blots nor with the PCR assay. In view of the significant conservation between the 7S K RNA of lamprey and that of mammals
(human), this unexpected result clearly separates lamprey and hagfish. In addition, the lack of detectable 7S K RNA sequences
in an outgroup, such as amphioxus, indicates that these results do not reflect an autapomorphy of hagfish. Therefore, our
data provide additional support to the notion of a sister group relationship between Petromyzontiformes and gnathostomous
vertebrates to the exclusion of Myxiniformes.
Received: 24 September 1999 / Accepted: 9 February 2000 相似文献
5.
The vertebrates are traditionally classified into two distinct groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed
vertebrates). Extant agnathans are represented by hagfishes (Myxiniformes) and lampreys (Petromyzontiformes), frequently grouped
together within the Cyclostomata. Whereas the recognition of the Gnathostomata as a clade is commonly acknowledged, a consensus
has not been reached regarding whether or not Cyclostomata represents a clade. In the present study we have used newly established
sequences of the protein-coding genes of the mitochondrial DNA molecule of the hagfish to explore agnathan and gnathostome
relationships. The phylogenetic analysis of Pisces, using echinoderms as outgroup, placed the hagfish as a sister group of
Vertebrata sensu stricto, i.e., the lamprey and the gnathostomes. The phylogenetic analysis of the Gnathostomata identified
a basal divergence between gnathostome fishes and a branch leading to birds and mammals, i.e., between ``Anamnia' and Amniota.
The lungfish has a basal position among gnathostome fishes with the teleosts as the most recently evolving lineage. The findings
portray a hitherto unrecognized polarity in the evolution of bony fishes. The presently established relationships are incompatible
with previous molecular studies.
Received: 15 August 1997 / Accepted: 1 October 1997 相似文献
6.
Zelus D Robinson-Rechavi M Delacre M Auriault C Laudet V 《Journal of molecular evolution》2000,51(3):234-244
Interleukin-2 (IL-2) is a cytokine involved in induction and regulation of the immune response in mammals. There have been
numerous reports about the search for IL-2 in species other than mammals, and recently an IL-2-like gene has been isolated
in chicken. Using PCR, we searched for IL-2 gene sequences in a wide variety of mammals, including marsupials and monotremes,
as well as in birds. Although we can readily amplify IL-2 gene fragments in placental mammals, no amplification was obtained
in other species. This is best explained by very high substitution rates. This suggest that strategies to isolate IL-2 homologous
genes outside mammals should involve functional assays, as for the chicken gene, and not hybridization-based techniques. Nonsynonymous
substitution rates are especially high in ruminants, due to positive selection acting on regions important in term of structure-function.
We suggest that, although globally similar, the immune response of various mammals is not identical, mainly at the level of
cytokine-mediated regulations.
Received: 27 July 1999 / Accepted: 15 April 2000 相似文献
7.
8.
Jerzy K. Kulski Silvana Gaudieri Matthew Bellgard Lois Balmer Keith Giles Hidetoshi Inoko Roger L. Dawkins 《Journal of molecular evolution》1997,45(6):599-609
Sequence analysis of a 237 kb genomic fragment from the central region of the MHC has revealed that the HLA-B and HLA-C genes
are contained within duplicated segments peri-B (53 kb) and peri-C (48 kb), respectively, and separated by an intervening
sequence (IF) of 30 kb. The peri-B and peri-C segments share at least 90% sequence homology except when interrupted by insertions/deletions
including Alu, L1, an endogenous retrovirus, and pseudogenes. The sequences of peri-B, IF, and peri-C were searched for the
presence of Alu elements to use as markers of evolution, chromosomal rearrangements, and polymorphism. Of 29 Alu elements,
14 were identified in peri-B, 11 in peri-C, and 4 in IF. The Alu elements in peri-B and peri-C clustered phylogenetically
into two clades which were classified as ``preduplication' and ``postduplication' clades. Four Alu J elements that are shared
by peri-B and peri-C and are flanked by homologous sequences in their paralogous locations, respectively, clustered into a
``preduplication' clade. By contrast, the majority of Alu elements, which are unique to either peri-B or peri-C, clustered
into a postduplication clade together with the Alu consensus subfamily members ranging from platyrrhine-specific (Spqxcg)
to catarrhine-specific Alu sequences (Y). The insertion of platyrrhine-specific Alu elements in postduplication locations
of peri-B and peri-C implies that these two segments are the products of a duplication which occurred in primates prior to
the divergence of the New World primate from the human lineage (35–44 mya). Examination of the paralogous Alu integration
sites revealed that 9 of 14 postduplication Alu sequences have produced microsatellites of different length and sequence within
the Alu 3′-poly A tail. The present analysis supports the hypothesis that HLA-B and HLA-C genes are products of an extended
segmental duplication between 44 and 81 million years ago (mya), and that subsequent diversification of both genomic segments
occurred because of the mobility and mutation of retroelements such as Alu repeats.
Received: 21 May 1997 / Accepted: 9 July 1997 相似文献
9.
We combined widely different biochemical methods to analyze proteins of the cell surface of P. tetraurelia since so far one can isolate only a subfraction of cell membrane vesicles enriched in the GPI-anchored surface antigens (``immoblization'
or ``i-AGs'). We also found that i-AGs may undergo partial degradation by endogenous proteases. Genuine intrinsic membrane
proteins were recognized particularly with lipophilic 5-[125I]-iodonaphthalene-1-azide (INA) labeling which reportedly ``sees' integral proteins and cytoplasmic cell membrane-associated
proteins. With INA (+DTT), bands of ≤55 kDa were similar as with hydrophilic iodogen (+DTT), but instead of large size bands
including i-AGs, a group of 122, 104 and 94 kDa appeared. Several bands of the non i-AG type are compatible with integral
(possibly oligomeric) or associated proteins of the cell membrane of established molecular identity, as we discuss. In summary,
we can discriminate between i-AGs and some functionally important minor cell membrane components. Our methodical approach
might be relevant also for an analysis of some related protozoan parasites.
Received: 5 April 1999/Revised: 19 July 1999 相似文献
10.
Genomic imprinting in ruminants: allele-specific gene expression in parthenogenetic sheep 总被引:5,自引:0,他引:5
Studies in the mouse have established that both parental genomes are essential for normal embryonic development. Parthenogenetic
mouse embryos (which have two maternal genomes and no paternal genome), for example, are growth-retarded and die at early
postimplantation stages. The distinct maternal and paternal contributions are mediated by genomic imprinting, an epigenetic
mechanism by which the expression of certain genes is dependent on whether they are inherited from mother or father. Although
comparative studies have established that many imprinted mouse (and rat) genes are allele-specifically expressed in humans
as well (and vice versa), so far imprinting studies have not been performed in other mammalian species. When considering evolutionary
theories of genomic imprinting, it would be important to know how widely it is conserved among placental mammals. We have
investigated its conservation in a bovid ruminant, the domestic sheep, by comparing parthenogenetic and normal control embryos.
Our study establishes that, like in the mouse, parthenogenetic development in sheep is associated with growth-retardation
and does not proceed beyond early fetal stages. These developmental abnormalities are most likely caused by imprinted genes.
We demonstrate that, indeed, like in mice and humans, the growth-related PEG1/MEST and Insulin-like Growth Factor 2 (IGF2) genes are expressed from the paternal chromosome in sheep. These observations suggest that genomic imprinting is conserved
in a third, evolutionarily rather diverged group of placental mammals, the ruminants.
Received: 13 May 1998 / Accepted: 16 July 1998 相似文献
11.
Complete sequences of mitochondrial DNA (mtDNA) are useful for the reconstruction of phylogenetic trees of mammals and, in
particular, for inferring higher-order relationships in mammals. In this study, we determined the complete sequence (16,705
bp) of the mtDNA of a Japanese megabat, the Ryukyu flying fox (Pteropus dasymallus). We analyzed this sequence phylogenetically by comparing it with the complete sequence of mtDNAs of 35 mammals in an effort
to reevaluate the enigmatic relationship between Megachiroptera and Microchiroptera and the relationships between them and
other mammals. Maximum-likelihood analysis of 12 concatenated mitochondrial proteins from 36 mammals strongly suggested the
monophyly of the order Chiroptera and its close relationship to Fereuungulata (Carnivora + Perissodactyla + Cetartiodactyla).
We estimated that megabats and microbats diverged approximately 58 MyrBP and discussed the origin and early evolution of Chiroptera
based on our findings.
Received: 28 January 2000 / Accepted: 30 June 2000 相似文献
12.
P elements of two different subfamilies designated as M- and O-type are thought to have invaded host species in the Drosophila obscura group via horizontal transmission from external sources. Sequence comparisons with P elements isolated from other species suggested that the horizontal invasion by the O-type must have been a rather recent
event, whereas the M-type invasion should have occurred in the more distant past. To trace the phylogenetic history of O-type
elements, additional taxa were screened for the presence of O- and M-type elements using type-specific PCR primers. The phylogeny
deduced from the sequence data of a 927-bp section (14 taxa) indicate that O-type elements have undergone longer periods of
regular vertical transmission in the lineages of the saltans and willistoni groups of Drosophila. However, starting from a species of the D. willistoni group they were transmitted horizontally into other lineages. First the lineage of the D. affinis subgroup was infected, and finally, in a more recent wave of horizontal spread, species of three different genera were invaded
by O-type elements from the D. affinis lineage: Scaptomyza, Lordiphosa, and the sibling species D. bifasciata/D. imaii of the Drosophila obscura subgroup. The O-type elements isolated from these taxa are almost identical (sequence divergence <1%). In contrast, no such
striking similarities are observed among M-type elements. Nevertheless, the sequence phylogeny of M-type elements is also
not in accordance with the phylogeny of their host species, suggesting earlier horizontal transfer events. The results imply
that P elements cross species barriers more frequently than previously thought but require a particular genomic environment and
thus seem to be confined to a rather narrow spectrum of host species. Consequently, different P element types acquired by successive horizontal transmission events often coexist within the same genome.
Received: 15 May 2000 / Accepted: 19 July 2000 相似文献
13.
Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes 总被引:28,自引:0,他引:28
Zhang J 《Journal of molecular evolution》2000,50(1):56-68
To understand the process and mechanism of protein evolution, it is important to know what types of amino acid substitutions
are more likely to be under selection and what types are mostly neutral. An amino acid substitution can be classified as either
conservative or radical, depending on whether it involves a change in a certain physicochemical property of the amino acid.
Assuming Kimura's two-parameter model of nucleotide substitution, I present a method for computing the numbers of conservative
and radical nonsynonymous (amino acid altering) nucleotide substitutions per site and estimate these rates for 47 nuclear
genes from mammals. The results are as follows. (1) The average radical/conservative rate ratio is 0.81 for charge changes,
0.85 for polarity changes, and 0.49 when both polarity and volume changes are considered. (2) The radical/conservative rate
ratio is positively correlated with the nonsynonymous/synonymous rate ratio for charge changes or when both polarity and volume
changes are considered. (3) Both the conservative/synonymous rate ratio and the radical/synonymous rate ratio are lower in
the rodent lineage than in the primate or artiodactyl lineage, suggesting more intense purifying selection in the rodent lineage,
for both conservative and radical nonsynonymous substitutions. (4) Neglecting transition/transversion bias would cause an
underestimation of both radical and conservative rates and the ratio thereof. (5) Transversions induce more dramatic genetic
alternations than transitions in that transversions produce more amino acid altering changes and among which, more radical
changes.
Received: 6 April 1999 / Accepted: 16 August 1999 相似文献
14.
Alexander E. Vinogradov 《Journal of molecular evolution》1999,49(3):376-384
The intron–genome size relationship was studied across a wide evolutionary range (from slime mold and yeast to human and
maize), as well as the relationship between genome size and the ratio of intervening/coding sequence size. The average intron
size is scaled to genome size with a slope of about one-fourth for the log-transformed values; i.e., on the global scale its
increase in evolution is lower than the increase in genome size by four orders of magnitude. There are exceptions to the general
trend. In baker's yeast introns are extraordinarily long for its genome size. Tetrapods also have longer introns than expected
for their genome sizes. In teleost fish the mean intron size does not differ significantly, notwithstanding the differences
in genome size. In contrast to previous reports, avian introns were not found to be significantly shorter than introns of
mammals, although avian genomes are smaller than genomes of mammals on average by about a factor of 2.5. The extra-/intragenic
ratio of noncoding DNA can be higher in fungi than in animals, notwithstanding the smaller fungal genomes. In vertebrates
and invertebrates taken separately, this ratio is increasing as the increase in genome size. Two hypotheses are proposed to
explain the variation in the extra-/intragenic ratio of noncoding DNA in organisms with similar numbers of genes: transition
(dynamic) and equilibrium (static). According to the transition model, this variation arises with the rapid shift of genome
size because the bulk of extragenic DNA can be changed more rapidly than the finely interspersed intron sequences. The equilibrium
model assumes that this variation is a result of selective adjustment of genome size with constraints imposed on the intron
size due to its putative link to chromatin structure (and constraints of the splicing machinery).
Received: 23 October 1997 / Accepted: 14 April 1999 相似文献
15.
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
16.
17.
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
18.
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
19.
The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence
of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes
as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial
heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two
distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths
specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to
the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed
in parasitic helminths and possibly also in other anaerobically adapted eukaryotes.
Received: 18 October 1999 / Accepted: 23 June 2000 相似文献
20.
We carried out an analysis of partial sequences from expressed major histocompatibility complex (MHC) class I genes isolated
from a range of equid species and more distantly related members of the mammalian order Perissodactyla. Phylogenetic analysis
revealed a minimum of six groups, five of which contained genes and alleles that are found in equid species and one group
specific to the rhinoceros. Four of the groups contained only one, or very few sequences, indicating the presence of relatively
nonpolymorphic loci, while another group contained the majority of the equid sequences identified. These data suggest that
a diversification of MHC genes took place after the split between the Equidae and the Rhinocerotidae yet before the speciation
events within the genus Equus.
Received: 17 November 1998 / Accepted: 7 April 1999 相似文献