Mutations of alleles at microsatellite loci tend to result in alleles with repeat scores similar to those of the alleles from which they were derived. Therefore the difference in repeat score between alleles carries information about the amount of time that has passed since they shared a common ancestral allele. This information is ignored by genetic distances based on the infinite alleles model. Here we develop a genetic distance based on the stepwise mutation model that includes allelic repeat score. We adapt earlier treatments of the stepwise mutation model to show analytically that the expectation of this distance is a linear function of time. We then use computer simulations to evaluate the overall reliability of this distance and to compare it with allele sharing and Nei's distance. We find that no distance is uniformly superior for all purposes, but that for phylogenetic reconstruction of taxa that are sufficiently diverged, our new distance is preferable.
It has recently been suggested that observed levels of variation at microsatellite loci can be used to infer patterns of selection in genomes and to assess demographic history. In order to evaluate the feasibility of these suggestions it is necessary to know something about how levels of variation at microsatellite loci are expected to fluctuate due simply to stochasticity in the processes of mutation and inheritance (genetic sampling). Here we use recently derived properties of the stepwise mutation model to place confidence intervals around the variance in repeat score that is expected at mutation-drift equilibrium and outline a statistical test for whether an observed value differs significantly from expectation. We also develop confidence intervals for the time course of the buildup of variation following a complete elimination of variation, such as might be caused by a selective sweep or an extreme population bottleneck. We apply these methods to the variation observed at human Y-specific microsatellites. Although a number of authors have suggested the possibility of a very recent sweep, our analyses suggest that a sweep or extreme bottleneck is unlikely to have occurred anytime during the last approximately 74,000 years. To generate this result we use a recently estimated mutation rate for microsatellite loci of 5.6 x 10(-4) along with the variation observed at autosomal microsatellite loci to estimate the human effective population size. This estimate is 18,000, implying an effective number of 4,500 Y chromosomes. One important general conclusion to emerge from this study is that in order to reject mutation-drift equilibrium at a set of linked microsatellite loci it is necessary to have an unreasonably large number of loci unless the observed variance is far below that expected at mutation-drift equilibrium.
<p>La caracterización genética del ganado criollo colombiano (gcc) ha demostrado el valor de estas razas en los sistemas productivos tropicales, lo que ha despertado el interés para desarrollar programas de conservación y multiplicación. Se adelantó un estudio de análisis genético con las siete razas de ganado criollo colombiano, (rgcc): Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) y Casanareño (Ca), utilizando el Cebú (C) como control, con el objeto de evaluar su diversidad genética y relaciones filogenéticas. Se usaron 7 microsatélites (STR) para establecer las distancias genéticas amplificadas mediante PCR. El tamaño de los loci se definió mediante marcaje con ɣ<sup>32</sup> P seguido de un pase en geles de poliacrilamida (PAGE) o marcados con fluorescencia y electroforesis capilar. Los datos se analizaron usando los programas Genepop, GDA y Phylip. El número promedio de alelos por locus fue de 8,9 y Ia heterocigosidad promedia observada fue de o,52. El árbol filogenético construido con el programa Phylip, empleando la distancia de Nei y el algoritmo de Neighbour-joining, agrupó en dos las gcc. En el grupo uno las razas: BON, SM, R, CCC y H; y en el grupo dos las razas: Ch, Ca y C. Los resultados de evaluación filogenética de las gcc indicaron que existe diversidad genética adecuada en estas razas para programas de mejoramiento genético; sin embargo, se recomienda continuar el estudio con un mayor número de marcadores genéticos.</p><p><strong><br /></strong></p><p><strong>Diversity and Phylogenetic Relations of Colombian Criollo Cattle.</strong></p><p>Studies of genetic characterisation of Colombian criollo cattle (gcc) has shown the value of these breeds in tropical production systems; consequently attention is noticeably growing to develop conservation and multiplication programs. A genetic analysis study was conducted including the seven criollo cattle breeds: Blanco Orejinegro (BON), Romosinuano (R), Costeño Con Cuernos (CCC), Sanmartinero (SM), Chino Santandereano (Ch), Hartón del Valle (H) and Casanareño (C), using Cebu as external control breed, with the purpose to evaluate genetic diversity and philogenetic relations. Seven microsatellite (STR) were used to detect length variations amplified by the PCR and sized by means of ɣ<sup>32</sup> P, runned in PAGE or tagged with a fluorescent dye and electrophoresis. Data were analysed using Genepop, GDA and Phylip programs. Mean number of alleles by loci were 8.9 and mean heterozygocity was o.52. The phylogenetic tree developed using Phylip program, the Nei's distance and the neighbour-joining aglorithm grouped in two the gcc. Group one included: Bon, SM, R,CCC and H, and the second group included Ch, Ca, C. Results of the phylogenetic relations of gcc showed that these breeds have adequate genetic diversity for breeding Programs; however we suggest to carry out studies including higher number of genetic markers.</p>
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