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31.
The partition matrix: exploring variable phylogenetic signals along nucleotide sequence alignments 总被引:6,自引:2,他引:4
The partition matrix is a graphical tool for comparative analysis of
nucleotide sequences following alignment. It is particularly useful for
investigating the divergent phylogenies of sequence regions undergoing
reticulate evolution. A partition matrix is generated by determining the
consistency of the parsimoniously informative sites in a set of aligned
sequences with the binary partitions inferred from the sequences. Since the
linear order of sites is maintained, the matrix can be used to assess
whether the distribution of sites either supporting or conflicting with
particular partitions changes along the length of the alignment. The
usefulness of the matrix in allowing visual identification of differences
in evolutionary history among regions depends on the order in which
partitions are shown; several suitable ordering schemes are proposed. We
demonstrate the use of the partition matrix in interpreting the evolution
of the pseudoautosomal boundary region on the sex chromosome of catarrhine
primates. Its routine use should help to avoid attempts to derive single
phylogenies from sequences whose evolution has been reticulate and to
identify the gene conversion or recombination events underlying the
reticulation. The method is relatively fast. It is exploratory, and it can
form the basis for more formal analysis, which we discuss.
相似文献
32.
Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin 总被引:27,自引:12,他引:15
Bindin is a gamete recognition protein of sea urchins that mediates
species-specific attachment of sperm to an egg-surface receptor during
fertilization. Sequences of bindin from closely related urchins show fixed
species-specific differences. Within species, highly polymorphic bindin
alleles result from point substitution, insertion/deletion, and
recombination. Since speciation, positive selection favoring allelic
variants has generated diversity in bindin polypeptides. Intraspecific
bindin variation can be tolerated by the egg receptor, which suggests
functional parallels between this system and other flexible recognition
systems, including immune recognition. These results show that polymorphism
in mate recognition loci required for rapid evolution of sexual isolation
can arise within natural populations.
相似文献
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Ubiquitin has been purified to homogeneity, through a dialysis membrane having a NMW cutoff of 12 kDa, by taking advantage of its non-dialysable nature under these conditions. The dialysate was continuously recycled through a CM-52 cation exchange column at pH 4.5. The adsorbed fraction was eluted selectively at pH 7.2. Ubiquitin (25 mg) was obtained from 500 ml of packed RBCs. On SDS PAGE, ubiquitin showed varying mobility depending on the time of boiling in SDS. With 2 min of boiling, the molecular weight seemed to be 10.5 kDa, whereas 10 min of boiling resulted in a molecular weight of 8.5 kDa. Ubiquitin showed a slow intrinsic proteolytic activity against SDS-denatured beta-galactosidase in the absence of ATP. For the first 4 hr, there was no detectable degradation, but degradation was nearly complete after 8 hr. These data are not in agreement with those of Freid et al. [Proc. Natl Acad. Sci, USA, 84 (1987), 3685] who have reported a proteolytic activity comparable to that of other proteolytic enzymes. 相似文献
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36.
Danillo S Silva Susana SR Milhomem Julio C Pieczarka Cleusa Y Nagamachi 《BMC genetics》2009,10(1):1-8
Background
Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set.Results
The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern.Conclusion
In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens. 相似文献37.
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39.
F. R. Parakh 《BMJ (Clinical research ed.)》1930,2(3636):449-450
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