scholarly journals A Survey of Chromosomal and Nucleotide Sequence Variation inDrosophila miranda

Genetics ◽  
2003 ◽  
Vol 164 (4) ◽  
pp. 1369-1381 ◽  
Author(s):  
Soojin Yi ◽  
Doris Bachtrog ◽  
Brian Charlesworth
Keyword(s):  
Nucleotide Sequence ◽  
Sequence Variation ◽  
General Pattern ◽  
Population Expansion ◽  
Convincing Evidence ◽  
Population Subdivision ◽  
Effective Population ◽  
Recent Population Expansion ◽  
Local Selection ◽  
Nucleotide Sequence Variation

AbstractThere have recently been several studies of the evolution of Y chromosome degeneration and dosage compensation using the neo-sex chromosomes of Drosophila miranda as a model system. To understand these evolutionary processes more fully, it is necessary to document the general pattern of genetic variation in this species. Here we report a survey of chromosomal variation, as well as polymorphism and divergence data, for 12 nuclear genes of D. miranda. These genes exhibit varying levels of DNA sequence polymorphism. Compared to its well-studied sibling species D. pseudoobscura, D. miranda has much less nucleotide sequence variation, and the effective population size of this species is inferred to be several-fold lower. Nevertheless, it harbors a few inversion polymorphisms, one of which involves the neo-X chromosome. There is no convincing evidence for a recent population expansion in D. miranda, in contrast to D. pseudoobscura. The pattern of population subdivision previously observed for the X-linked gene period is not seen for the other loci, suggesting that there is no general population subdivision in D. miranda. However, data on an additional region of period confirm population subdivision for this gene, suggesting that local selection is operating at or near period to promote differentiation between populations.

scholarly journals DNA Sequence Variation and the Recombinational Landscape in Drosophila pseudoobscura: A Study of the Second Chromosome

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 859-869 ◽  
Author(s):  
Martha T Hamblin ◽  
Charles F Aquadro
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Variation ◽  
Population Expansion ◽  
Drosophila Pseudoobscura ◽  
Effective Population ◽  
Standing Variation ◽  
Dna Sequence Polymorphism ◽  
Slightly Deleterious Mutations

Abstract The relationship between rates of recombination and DNA sequence polymorphism was analyzed for the second chromosome of Drosophila pseudoobscura. We constructed integrated genetic and physical maps of this chromosome using molecular markers at 10 loci spanning most of its physical length. The total length of the map was 128.2 cM, almost twice that of the homologous chromosome arm (3R) in D. melanogaster. There appears to be very little centromeric suppression of recombination, and rates of recombination are quite uniform across most of the chromosome. Levels of sequence variation (θW, based on the number of segregating sites) at seven loci (tropomyosin 1, Rhodopsin 3, Rhodopsin 1, bicoid, Xanthine dehydrogenase, Myosin light chain 1, and ribosomal protein 49) varied from 0.0036 to 0.0167. Generally consistent with earlier studies, the average estimate of θW at total sites is 1.5-fold higher than that in D. melanogaster, while average θW at silent sites is almost 3-fold higher. These estimates of variation were analyzed in the context of a background selection model under the same parameters of mutation rate and selection as have been proposed for D. melanogaster. It is likely that a significant fraction of the higher level of sequence variation in D. pseudoobscura can be explained by differences in regional rates of recombination rather than a larger species-level effective population size. However, the distribution of variation among synonymous, nonsynonymous, and noncoding sites appears to be quite different between the species, making direct comparisons of neutral variation, and hence inferences about effective population size, difficult. Tajima’s D statistics for 6 out of the 7 loci surveyed are negative, suggesting that D. pseudoobscura may have experienced a rapid population expansion in the recent past or, alternatively, that slightly deleterious mutations constitute an important component of standing variation in this species.

scholarly journals Cytochrome b Nucleotide Sequence Variation Among the Atlantic Alcidae

Hereditas ◽  
2004 ◽  
Vol 119 (3) ◽  
pp. 245-252 ◽  
Author(s):  
V. L. Friesen ◽  
W. A. Montevecchi ◽  
W. S. Davidson
Keyword(s):  
Nucleotide Sequence ◽  
Cytochrome B ◽  
Sequence Variation ◽  
Nucleotide Sequence Variation

scholarly journals Nucleotide sequence variation associated with β-amylase deficiency in the sweet potato Ipomoea batatas (L.) Lam

2009 ◽  
Vol 59 (3) ◽  
pp. 209-216 ◽  
Author(s):  
Nadia Anwar ◽  
Akira Kikuchi ◽  
Toru Kumagai ◽  
Kazuo N. Watanabe
Keyword(s):  
Nucleotide Sequence ◽  
Sweet Potato ◽  
Ipomoea Batatas ◽  
Sequence Variation ◽  
Nucleotide Sequence Variation
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