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.
Betrán
E
E
Departament de Genètica i de Microbiologia, Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Spain.
Rozas
J
J
Navarro
A
A
Barbadilla
A
A
D000818:Animals; D001483:Base Sequence; D004247:DNA; D004330:Drosophila / Q000235:genetics; D029721:Drosophila Proteins; D005785:Gene Conversion; D019476:Insect Proteins / Q000235:genetics; D008957:Models, Genetic; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D012269:Ribosomal Proteins
D029721:Drosophila Proteins; D019476:Insect Proteins; D012269:Ribosomal Proteins; C107533:RpL32 protein, Drosophila; D004247:DNA