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1.
Ingrid Felger Vikki M. Marshal John C. Reeder John A. Hunt Charles S. Mgone Hans-Peter Beck 《Journal of molecular evolution》1997,45(2):154-160
Eleven new alleles of the Plasmodium falciparum merozoite surface antigen 2 (MSA2) from Papua New Guinea were analyzed by direct sequencing of polymerase chain reaction (PCR) products. We have used the sequence
information to trace the molecular evolution of MSA2. The repeats of ten alleles belonging to the 3D7 allelic family differed considerably in size, nucleotide sequence, and repeat copy number. In the repeat region of these
new alleles, codon usage was extremely biased with an exclusive use of NNT codons. Another new allele sequenced belonged to
the FC27 family and confirmed the family-specific conserved structure of 96 and 36 bp repeats. In order to assess sequence microheterogeneity
within samples defined as the same genotype by restriction fragment length polymorphism (RFLP), we have analyzed single-strand
conformation polymorphism (SSCP) of different samples of the most frequent allele (D10 of the FC27 family) in the study population. No sequence heterogeneity could be detected within the repeat region. Based on analysis
of the repeat regions in both allelic families, we discuss the hypothesis of a different evolutionary strategy being represented
by each of the allelic families.
Received: 8 February 1995 / Accepted: 24 March 1997 相似文献
2.
Microsatellite length variation was investigated at a highly variable microsatellite locus in four species of Apodemus. Information obtained from microsatellite allele sequences was contrasted with allele sizes, which included 18 electromorphs.
Additional analysis of a 400-bp unique sequence in the flanking region identified 26 different haplotype sequences or ``true'
alleles in the sample. Three molecular mechanisms, namely, (1) addition/deletion of repeats, (2) substitutions and indels
in the flanking region, and (3) mutations interrupting the repeat, contributed to the generation of allelic variation. Size
homoplasy can be inferred for alleles within populations, from different populations of the same species, and from different
species. We propose that microsatellite flanking sequences may be informative markers for investigating mutation processes
in microsatellite repeats as well as phylogenetic relationships among alleles, populations, and species.
Received: 3 November 1999 / Accepted: 2 May 2000 相似文献
3.
Like humans, non-human primates express the antigens A and B of the ABO histoblood group system. In chimpanzees, only A and
O types are found, while the types A, B, AB, and O are found in macaques. The sequences of exons 6 and 7 of two chimpanzee
O alleles (O
del
and O
x
), two macaque species O alleles (rhesus monkey and crab-eating macaque), and sequences of exon 7 of two major chimpanzee A alleles (A
1ch
and A
2ch
) were established. The sequences of cDNAs corresponding to the chimpanzee and rhesus monkey O alleles were characterized from exon 1 to 7 and from exon 4 to 7, respectively. A comparison of our results with ABO gene sequences already published by others demonstrates that human and non-human primate O alleles are species-specific and result from independent silencing mutations. These observations reinforce the hypothesis
that the maintenance of the ABO gene polymorphism in primates reflects convergent evolution more than transpecies inheritance of ancestor alleles.
Received: 30 July 1998 / Revised: 12 December 1998 相似文献
4.
5.
Nonhuman primates express varying responses to Mycobacterium tuberculosis: New World monkeys appear to be resistant to tuberculosis (TB) while Old World monkeys seem to be particularly susceptible. The aim of this study was to elucidate the presence of the regulatory guanine–thymine (GT) repeat polymorphisms in intron 2 of Toll-like receptor 2 (TLR2) associated with the development of TB in humans and to determine any variations in these microsatellite polymorphisms in primates. We sequenced the region encompassing the regulatory GT repeat microsatellites in intron 2 of TLR2 in 12 different nonhuman primates using polymerase chain reaction amplification, TA cloning, and automatic sequencing. The nonhuman primates included for this study were as follows: chimpanzee (Pan troglodytes), bonobo (Pan paniscus), gorilla (Gorilla gorilla), orangutan (Pongo pygmaeus), Celebes ape (Macaca nigra), rhesus monkey (Macaca mulatta), pigtail macaque (Macaca nemestrina), patas monkey (Erythrocebus patas), spider monkey (Ateles geoffroyi), Woolly monkey (Lagothrix lagotricha), tamarin (Saguinus labiatus), and ring-tailed lemur (Lemur catta). Nucleotide sequences encompassing the regulatory GT repeat region are similar across species and are completely conserved in great apes. However, Old World monkeys lack GT repeats altogether, while New World monkeys and ring-tailed lemurs have much more complex structures around the position of the repeats. In conclusion, the genetic structures encompassing the regulatory GT repeats in intron 2 of human TLR2 are similar among nonhuman primates. The sequence is most conserved in New World monkeys and less in Old World monkeys. 相似文献
6.
The complete mitochondrial DNA (mtDNA) molecule of Sumatran orangutan, plus the complete mitochondrial control region of
another Sumatran specimen and the control regions and five protein-coding genes of two specimens of Bornean orangutan were
sequenced and compared with a previously reported complete mtDNA of Bornean orangutan. The two orangutans are presently separated
at the subspecies level. Comparison with five different species pairs—namely, harbor seal/grey seal, horse/donkey, fin whale/blue
whale, common chimpanzee/pygmy chimpanzee, and Homo/common chimpanzee—showed that the molecular difference between Sumatran and Bornean orangutan is much greater than that between
the seals, and greater than that between the two chimpanzees, but similar to that between the horse and the donkey and the
fin and blue whales. Considering their limited morphological distinction the comparison revealed unexpectedly great molecular
difference between the two orangutans. The nucleotide difference between the orangutans is about 75% of that between Homo and the common chimpanzee, whereas the amino acid difference exceeds that between Homo and the common chimpanzee. On the basis of their molecular distinction we propose that the two orangutans should be recognized
as different species, Pongo pygmaeus, Bornean orangutan, and P. abelii, Sumatran orangutan.
Received: 15 May 1996 / Accepted: 21 June 1996 相似文献
7.
8.
We have examined the length distribution of perfect dimer repeats, where perfect means uninterrupted by any other base, using
data from GenBank on primates and rodents. Virtually no lengths greater than 30 repeats are found, except for rodent AG repeats,
which extend to 35. Comparable numbers of long AC and AG repeats suggest that they have not been selected for special functions
or DNA structures. We have compared the data with predictions of two models: (1) a Bernoulli Model in which bases are assumed
equally likely and distributed at random and (2) an Unbiased Random Walk Model (URWM) in which repeats are permitted to change
length by plus or minus one unit, with equal probabilities, and in which base substitutions are allowed to destroy long perfect
repeats, producing two shorter perfect repeats. The source of repeats is assumed to be from single base substutions from neighboring
sequences, i.e., those differing from the perfect repeat by a single base. Mutation rates either independent of repeat length
or proportional to length were considered. An upper limit to the lengths L≈ 30 is assumed and isolated dimers are assumed unable to expand, so that there are absorbing barriers to the random walk
at lengths 1 and L+ 1, and a steady state of lengths is reached. With these assumptions and estimated values for the rates of length mutation
and base substitution, reasonable agreement is found with the data for lengths > 5 repeats. Shorter repeats, of lengths ≤
3 are in general agreement with the Bernoulli Model. By reducing the rate of length mutations for n≤ 5, it is possible to obtain reasonable agreement with the full range of data. For these reduced rates, the times between
length mutations become comparable to those suggested for a bottleneck in the evolution of Homo sapiens, which may be the reason for low heterozygosity of short repeats. 相似文献
9.
New copies of the mammalian retrotransposon L1 arise in the germline at an undetermined rate. Each new L1 copy appears at
a specific evolutionary time point that can be estimated by phylogenetic analysis. In humans, the active L1 sequence L1.2
resides at the genomic locus LRE1. Here we analyzed the region surrounding the LRE1 locus in humans and gorillas to determine the evolutionary history of the region and to estimate the age of L1.2. We found
that the region was composed of an ancient L1, L1Hs-Lrg, which was significantly divergent from all other L1 sequences available
in the databases. We also determined that L1.2 was absent from the gorilla genome and arose in humans after the divergence
of gorilla and human lineages. In the gorilla LRE1 region, we discovered a different full-length L1 element, L1Gg-1, which
was allelic and present at a high gene frequency in gorillas but absent from other primates. We determined the nucleotide
sequence of L1Gg-1 and found that it was 98% identical to L1.2, suggesting a close relationship between active L1s in gorillas
and humans.
Received: 28 December 1997 / Accepted: 20 March 1998 相似文献
10.
A DNA fragment containing short tandem repeat sequences (approximately 86-bp repeat) was isolated from a Xenopus laevis cDNA library. Southern blot and in situ hybridization analyses revealed that the repeat was highly dispersed in the genome and was present at approximately 1 million
copies per haploid genome. We named this element Xstir (Xenopus short tandemly and invertedly repeating element) after its arrangement in the genome. The majority of the genomic Xstir sequences
were digested to monomer and dimer sizes with several restriction enzymes. Their sequences were found to be highly homogeneous
and organized into tandem arrays in the genome. Alignment analyses of several known sequences showed that some of the Xstir-like
sequences were also organized into interspersed inverted repeats. The inverted repeats consisted of an inverted pair of two
differently modified Xstirs separated by a short insert. In addition, these were framed by another novel inverted repeat (Xstir-TIR).
The Xstir-TIR sequence was also found at the ends of tandem Xstir arrays. Furthermore, we found that Xstir-TIR was linked
to a motif characterizing the T2 family which belonged to a vertebrate MITE (miniature inverted-repeat transposable element)
family, suggesting the importance of Xstir-TIR for their amplification and transposition. The present study of 11 anuran and
2 urodele species revealed that Xstir or Xstir-like sequences were extensively amplified in the three Xenopus species. Genomic Xstir populations of X. borealis and X. laevis were mutually indistinguishable but significantly different from that of X. tropicalis.
Received: 5 April 2000 / Accepted: 3 August 2000 相似文献
11.
We have analysed 136 newly identified human Y-chromosomal microsatellites in five (sub)species of nonhuman primates. We identified 83 male-specific loci for central chimpanzees, 82 for western chimpanzees, 67 for gorillas, 45 for orangutans and 19 loci for mandrills. Polymorphism was detected at 56 loci in central chimpanzees, 29 in western chimpanzees, 24 in western gorillas, 17 in orangutans and at three in mandrills. Success in male-specific amplification of human Y-chromosomal microsatellites in nonhuman primates was significantly negatively correlated with divergence time from the human lineage. We observed significantly more Y-chromosomal microsatellite diversity in central chimpanzees than in western chimpanzees. There were significantly more male-specific loci with longer alleles in humans than with longer alleles in the nonhuman primates; however, this significant difference disappeared when only the loci which are polymorphic in nonhuman primates were analysed, suggesting that ascertainment bias is responsible. This study provides primatologists with a large number of polymorphic, male-specific microsatellite markers that will be valuable for investigating relevant questions in behavioural ecology such as male reproductive strategies, kin-based cooperation among males and male-specific dispersal patterns in wild groups of nonhuman primates. 相似文献
12.
We have previously shown that GAA trinucleotide repeats have undergone significant expansion in the human genome. Here we present the analysis of the length distribution of all 10 nonredundant trinucleotide repeat motifs in 20 complete eukaryotic genomes (6 mammalian, 2 nonmammalian vertebrates, 4 arthropods, 4 fungi, and 1 each of nematode, amoebozoa, alveolate, and plant), which showed that the abundance of large expansions of GAA trinucleotide repeats is specific to mammals. Analysis of human-chimpanzee-gorilla orthologs revealed that loci with large expansions are species-specific and have occurred after divergence from the common ancestor. PCR analysis of human controls revealed large expansions at multiple human (GAA)(30+) loci; nine loci showed expanded alleles containing >65 triplets, analogous to disease-causing expansions in Friedreich ataxia, including two that are in introns of genes of unknown function. The abundance of long GAA trinucleotide repeat tracts in mammalian genomes represents a significant mutation potential and source of interindividual variability. 相似文献
13.
Divergent Human Y-Chromosome Microsatellite Evolution Rates 总被引:5,自引:0,他引:5
Denise R. Carvalho-Silva Fabrício R. Santos Mara H. Hutz Francisco M. Salzano Sérgio D.J. Pena 《Journal of molecular evolution》1999,49(2):204-214
In this work, we analyze several characteristics influencing the low variability of the microsatellite DYS19 in the major founder Amerindian Y chromosome lineage containing the point mutation DYS199-T. Variation of DYS19 was compared with that of five other Y-linked tetranucleotide repeat loci (DYS389A, DYS389B, DYS390, DYS391, and DYS393) in the DYS199-T lineage. All the other microsatellites showed significantly higher levels of variability than DYS19 as measured by gene diversity and repeat number variance. Moreover, we had previously shown that DYS19 had high diversity in Brazilians and in several other populations worldwide. Thus, the slow DYS19 evolution in the DYS199-T lineage seems to be both locus and allele specific. To understand the slow DYS19 evolutionary rate, the microsatellite loci were compared according to their mapping on the Y chromosome and also on the basis
of structural aspects such as the base composition of the repeat motif and flanking regions and the degree of perfection and
size (repeat number) of the variable blocks. The only observed difference that might be related to the low DYS19 variability is its small average number of repeats, a value expected to be closer to the founder DYS19 allele in the DYS199-T lineage. These data were also compared to other derived Y lineages. The Tat-C lineage displayed a lower DYS19 variability correlated to a small average repeat number, while in the DYS234-G lineage, a high DYS19 variability was found associated to a larger average repeat number. This approach reveals that evolution of Y microsatellites
in lineages defined by slowly evolving markers, such as point mutations, can be greatly influenced by the size (number of
repeats of the variable block) of the founder allele in each microsatellite locus. Thus lineage-dating methods using microsatellite
variation should be practiced with great care.
Received: 7 November 1998 / Accepted: 9 April 1999 相似文献
14.
15.
Microsatellite DNA sequences have become the dominant source of nuclear genetic markers for most applications. It is important
to investigate the basis of variation between alleles and to know if current assumptions about the mechanisms of microsatellite
mutation (that is to say, variations involving simple changes in the number of repeat) are correct. We have characterized,
by DNA sequencing, the human alleles of a new highly informative (CA)n repeat localized approximately 20 kb centromeric to
the HLA-B gene. Although 12 alleles were identified based on conventional length criteria, sequencing of the alleles demonstrated
that differences between alleles were found to be more complex than previously assumed: A high degree of microsatellite variability
is due to variation in the region immediately flanking the repeat. These data indicate that the mutational process which generates
polymorphism in this region has involved not only simple changes in the number of dinucleotide CA repeats but also perturbations
in the nonrepeated 5′ and 3′ flanking sequences. Three families of alleles (not visible from the overall length of the alleles),
with presumably separate evolutionary histories, exist and can yield to homoplasy of size. Effectively, we can observe alleles
of the same size with different internal structures which are separated by a significant amount of variation. Although allelic
homoplasy for noninterrupted microsatellite loci has been suggested between different species, it has not been unequivocally
demonstrated within species. A strong association is noted between alleles defined at the sequence level and HLA-B alleles.
The observation of several families of alleles at the population level provides information about the evolutionary history
and mutation processes of microsatellites and may have implications for the use of these markers in phylogenetic, linkage
disequilibrium studies, and gene mapping.
Received: 14 May 1996 / Accepted: 9 September 1996 相似文献
16.
17.
Most Neotropical primate species possess a polymorphic X-linked and a monomorphic autosomal color vision gene. Consequently,
populations are composed of both dichromatics and trichromatics. Most theories on the maintenance of this genetic system revolve
around possible advantages for foraging ecology. To examine the issue from a different angle, we compared the numbers and
relative frequencies of alleles at the X-linked locus among three species of Saimiri representing a wide range of geographical and behavioral variation in the genus. Exons 3, 4, and 5 of the X-linked opsin
gene were sequenced for a large number of X chromosomes for all three species. Several synonymous mutations were detected
in exons 4 and 5 for the originally reported alleles but only a single nonsynonymous change was detected. Two alleles were
found that appeared to be the result of recombination events. The low occurrence of recombinant alleles and absence of mutations
in the amino acids critical for spectral tuning indicates that stabilizing selection acts to maintain the combinations of
critical sites specific to each allele. Allele frequencies were approximately the same for all Saimiri species, with a slight but significant difference between S. boliviensis and S. oerstedii. No apparent correlation exists between allele frequencies and behavioral or biogeographical differences between species,
casting doubt on the speculation that the spectral sensitivities of the alleles have been maintained because they are specifically
well-tuned to Saimiri visual ecology. Rather, the spectral tuning peaks might have been maintained because they are as widely spaced as possible
within the limited range of middlewave to longwave spectra useful to all primates. This arrangement creates a balance between
maximizing the distance between spectral tuning peaks (allowing the color opponency of the visual system to distinguish between
peaks) and maximizing the number of alleles within a limited range (yielding the greatest possible frequency of heterozygotes). 相似文献
18.
In human populations, a null allele having several nucleotide differences from the wild-type allele is segregating at the
FUT2 locus (the ABO-Secretor locus) encoding α(1,2)fucosyltransferase. To estimate the age of the most recent common ancestor
(MRCA) of these two alleles, we sequenced FUT2 homologues from chimpanzee, gorilla, orangutan, and green monkey. Since we did not detect acceleration or any heterogeneity
in the substitution rate at this locus among these species, the age of the MRCA was estimated to be around 3 MYA, assuming
the divergence time of human and chimpanzee to be 5 MYA. We developed a simple test to examine whether or not the old age
of the MRCA of the FUT2 is consistent with that expected for two divergent neutral alleles sampled from a random mating population. An application
of the test to the data at FUT2 indicated that the age of the MRCA is too old to be explained by the simple neutral assumptions, although our test depends
on accurate estimation of the divergence time of human and chimpanzee in units of twice the human population size. Various
possibilities including balancing selection are discussed to explain this old age of the MRCA.
Received: 9 May 1999 / Accepted: 20 September 1999 相似文献
19.
In order to understand evolutionary aspects of the highly polymorphicHLA-F microsatellite (heterozygosity>90%), several alleles of primates were characterized. 576 meioses from 35 CEPH families were
investigated for regular transmission. Furthermore 364 healthy, non-related individuals belonging to four populations from
distant ethnic groups were analysed to determine the applicability of this locus in population studies.
Sequencing revealed alternate (GAGGAA)n blocks spaced by (GAA)n repeats in all primates analysed. The mutation rate of this locus amounts to 1.5%. The mutational patterns follow approximately
the one step mutation model. Differential analysis suggests that mutation rates depend on the repeat length. Paternal mutation
rates exceed maternal ones. The presence of both allele classes in all human populations investigated indicates that this
polymorphism predated raciation. Evidence is provided that the short alleles originated from the longer ones by deletion.
Finally the differential analysis of each allele class corroborates the biological history of the studied populations as traced
by other genetic markers. 相似文献
20.
Frédérique Viard Pierre Franck Marie-Pierre Dubois Arnaud Estoup Philippe Jarne 《Journal of molecular evolution》1998,47(1):42-51
Size homoplasy was analyzed at microsatellite loci by sequencing electromorphs, that is, variants of the same size (base
pairs). This study was conducted using five interrupted and/or compound loci in three invertebrate species, the honey bee
Apis mellifera, the bumble bee Bombus terrestris, and the freshwater snail Bulinus truncatus. The 15 electromorphs sequenced turned out to hide 31 alleles (i.e., variants identical in sequence). Variation in the amount
of size homoplasy was detected among electromorphs and loci. From one to seven alleles were detected per electromorph, and
one locus did not show any size homoplasy in both bee species. The amount of size homoplasy was related to the sequencing
effort, since the number of alleles was correlated with the number of copies of electromorphs sequenced, but also with the
molecular structure of the core sequence at each locus. Size homoplasy within populations was detected only three times, meaning
that size homoplasy was detected mostly among populations. We analyzed population structure, estimating F
st and a genetic distance, based on either electromorphs or alleles. Whereas little difference was found in A. mellifera, uncovering size homoplasy led to a more marked population structure in B. terrestris and B. truncatus. We also showed in A. mellifera that the detection of size homoplasy may alter phylogenetic reconstructions.
Received: 21 July 1997 / Accepted: 29 January 1998 相似文献