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J Rozas

Publications and source records attributed to J Rozas.

12 recordsLinked to original sources
PubMed1999

DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.

UNLABELLED: DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY: For academic uses, DnaSP is available free of charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es

Computer Simulation↗
PubMed1999

Molecular population genetics of the rp49 gene region in different chromosomal inversions of Drosophila subobscura.

Nucleotide variation at the ribosomal protein 49 (rp49) gene region has been studied in 75 lines of Drosophila subobscura belonging to four chromosomal arrangements (Ost, O3+4, O3+4+8, and O3+4+23). The location of the rp49 gene region within the inversion loop differs among heterokaryotypes: it is very close to one of the breakpoints in heterozygotes involving Ost chromosomes, while it is in a more central position in all other heterokaryotypes. The distribution of nucleotide polymorphism in the different arrangements is consistent with a monophyletic origin of the inversions. The data also provide evidence that gene conversion and possibly double crossover are involved in shuffling nucleotide variation among gene arrangements. The analyses reveal that the level of genetic exchange is higher when the region is located in a more central position of the inverted fragment than when it is close to the breakpoints. The pairwise difference distributions as well as the negative values of Tajima's and Fu and Li's statistics further support the hypothesis that nucleotide variation within chromosomal arrangements still reflects expansion after the origin of the inversions. Under the expansion model, we have estimated the time of origin of the studied inversions.

Animals↗
PubMed1998

Molecular and chromosomal phylogeny in the obscura group of Drosophila inferred from sequences of the rp49 gene region.

A region of approximately 1.6 kb encompassing the ribosomal protein 49 gene (rp49) has been sequenced and compared in nine species of the obscura group of Drosophila: four species belonging to the obscura subgroup, three to the pseudoobscura subgroup, and two to the affinis subgroup. Our data provide strong support that the nearctic species (pseudoobscura and affinis subgroups) are monophyletic and place D. bifasciata with the other species of the obscura subgroup. Nucleotide sequence information at the rp49 gene region (located very close to one of the breakpoints of inversion O3) has also been used to infer the phylogeny of the O chromosome in the subobscura species cluster. Analysis based both on parsimony-informative sites and on genetic distances confirms that the O3 gene arrangement, present in D. guanche (together with inversion g) and in D. madeirensis, is ancestral to gene arrangements O3 + 4 and Ost present in extant populations of D. subobscura.

Animals↗
PubMed1997

The estimation of the number and the length distribution of gene conversion tracts from population DNA sequence data.

DNA sequence variation studies report the transfer of small segments of DNA among different sequences caused by gene conversion events. Here, we provide an algorithm to detect gene conversion tracts and a statistical model to estimate the number and the length distribution of conversion tracts for population DNA sequence data. Two length distributions are defined in the model: (1) that of the observed tract lengths and (2) that of the true tract lengths. If the latter follows a geometric distribution, the relationship between both distributions depends on two basic parameters: psi, which measures the probability of detecting a converted site, and phi, the parameter of the geometric distribution, from which the average true tract length, 1/(1-phi), can be estimated. Expressions are provided for estimating phi by the method of the moments and that of the maximum likelihood. The robustness of the model is examined by computer simulation. The present methods have been applied to the published rp49 sequences of Drosophila subobscura. Maximum likelihood estimate of phi for this data set is 0.9918, which represents an average conversion tract length of 122 bp. Only a small percentage of extant conversion events is detected.

Animals↗
PubMed1997

DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis.

MOTIVATION: Several methods in molecular population genetics have recently been described to estimate the amount and pattern of the DNA polymorphism in natural populations, and also to test the neutral theory of molecular evolution. These methods are essential for understanding the molecular evolutionary process. However, a comprehensive computer program for the analysis is not currently available. RESULTS: Here we present DnaSP (DNA Sequence Polymorphism) version 2.0, a software package for Windows that performs extensive population genetics analyses on DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion (a new algorithm to detect gene conversion tracts has been included). DnaSP can also carry out several tests of neutrality: those of Fu and Li; Hudson, Kreitman and Aguadé; and Tajima. The results of the analyses are displayed in tabular and graphic form. AVAILABILITY: For academic uses, DnaSP is available via anonymous ftp: ftp.ebi.ac.uk in the directory/pub/software/dos.

Algorithms↗
PubMed1995

DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data.

DnaSP, DNA sequence polymorphism, is an interactive computer program for the analysis of DNA polymorphism from nucleotide sequence data. The program, addressed to molecular population geneticists, calculates several measures of DNA sequence variation within and between populations, linkage disequilibrium parameters and Tajima's D statistic. The program, which is written in Visual Basic v. 3.0 and runs on an IBM-compatible PC under Windows, can handle a large number of sequences of up to thousands of nucleotides each.

Animals↗
PubMed1994

Gene conversion is involved in the transfer of genetic information between naturally occurring inversions of Drosophila.

The DNA sequences of the ribosomal protein 49 (rp49) region were determined for 34 isochromosomal strains of Drosophila subobscura representing two chromosomal arrangements, the OST and the O3 + 4 gene arrangements, which differ by two overlapping inversions. The data reveal that gene conversion is a mechanism responsible for the transfer of genetic information between naturally occurring inversions of Drosophila. The estimated rate of gene transfer by gene conversion at this region, which is close to an inversion breakpoint, is lower than previous estimates obtained experimentally at the rosy (ry) gene in Drosophila melanogaster. Our data indicate that gene arrangements OST and O3 + 4 are monophyletic and rather old (0.58 and 0.73 million years old, respectively).

Animals↗
PubMed1993

Transfer of genetic information in the rp49 region of Drosophila subobscura between different chromosomal gene arrangements.

Nucleotide variation in the region including the ribosomal protein 49 (rp49) gene was investigated by direct sequencing of 10 alleles of Drosophila subobscura from chromosomes differing in gene arrangements. Fifty-six nucleotide and seven length polymorphisms were detected over a 1.5-kb region. Of the 20 nucleotide polymorphisms present more than once in the sample, 13 were segregating in O[3 + 4], 9 in O[3 + 4 + 8], and 4 in O[st] chromosomal classes. Several of these polymorphisms were segregating in more than one chromosomal class, a strong indication of genetic transfer between different chromosomal gene arrangements either by double crossover or gene conversion. Given the probable role played by gene conversion in the history of the rp49 region in D. subobscura, estimates of nucleotide diversity within chromosomal class indicate that the O[3 + 4] chromosomal gene arrangement is older than the O[st] arrangement.

Alleles↗
PubMed1993

Latitudinal differences in sex chromosome inversions, sex linked allozymes, and mitochondrial DNA variation in Drosophila subobscura.

Mitochondrial DNA, sex linked allozymes, and chromosome A gene arrangement data, from eight European natural populations of Drosophila subobscura, were analyzed to determine the existence of latitudinal clines. Strong north-south correlations with latitude were found for gene arrangements and for the Hbdh and 6Pgdh allozymes. Gametic associations between the A2 gene arrangement, the Hbdh96 and the 6Pgdh96 alleles, point out some kind of epistatic interaction. At mtDNA level, the Hae III, A variant did not show a previously found north-south clinal variation.

Alleles↗
PubMed1990

Evidence of extensive genetic exchange in the rp49 region among polymorphic chromosome inversions in Drosophila subobscura.

Restriction map variation in 107 lines extracted from two natural populations of Drosophila subobscura was investigated with seven four-nucleotide-recognizing enzymes in a 1.6-kb region including the rp49 gene, that is located very close to the proximal breakpoint of inversion O3. Fourteen restriction site and 8 length polymorphisms, resulting in 73 haplotypes, have been identified. Estimated heterozygosity per nucleotide, pi = 0.0045, is comparable to the average nucleotide variation observed in Drosophila melanogaster. Because of the location of the rp49 region in D. subobscura, variation in three different gene arrangements-Ost, O3 + 4 and O3 + 4 + 8-has been compared. Out of 14 restriction site polymorphisms, 3 are shared by Ost, O3 + 4 and O3 + 4 + 8, and 3 additional ones are shared by Ost and O3 + 4, evidencing extensive genetic exchange among these polymorphic inversions. In agreement with previous data, the higher level of variation of O3 + 4 (as measured by haplotype diversity and nucleotide variation) suggests that O3 + 4 may be ancestral in relationship to extant gene arrangements.

Animals↗