lunes, 2 de mayo de 2016

Estimates of Genetic Differentiation Measured by F ST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

Willing E-M, Dreyer C, Oosterhout C van (2012) Estimates of Genetic Differentiation Measured by F ST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers. PLOS ONE, 7, e42649.


Elegido por: Vero R.

Abstract
Population genetic studies provide insights into the evolutionary processes that influence the distribution of sequence variants within and among wild populations. FST is among the most widely used measures for genetic differentiation and plays a central role in ecological and evolutionary genetic studies. It is commonly thought that large sample sizes are required in order to precisely infer FST and that small sample sizes lead to overestimation of genetic differentiation. Until recently, studies in ecological model organisms incorporated a limited number of genetic markers, but since the emergence of next generation sequencing, the panel size of genetic markers available even in non-reference organisms has rapidly increased. In this study we examine whether a large number of genetic markers can substitute for small sample sizes when estimating FST. We tested the behavior of three different estimators that infer FST and that are commonly used in population genetic studies. By simulating populations, we assessed the effects of sample size and the number of markers on the various estimates of genetic differentiation. Furthermore, we tested the effect of ascertainment bias on these estimates. We show that the population sample size can be significantly reduced (as small as n = 4–6) when using an appropriate estimator and a large number of bi-allelic genetic markers (k>1,000). Therefore, conservation genetic studies can now obtain almost the same statistical power as studies performed on model organisms using markers developed with next-generation sequencing.

Este artículo se basa en que los estudios genéticos de población proporcionan una visión de los procesos evolutivos que influyen en la distribución de las variantes de secuencia dentro y entre las poblaciones silvestres. Y dentro de los análisis el FST es una de las medidas más utilizadas para la diferenciación genética ya que desempeña un papel central en los estudios genéticos ecológicos y evolutivos. Se piensa comúnmente que se requieren grandes tamaños de muestra con el fin de inferir con precisión los FST y que los tamaños de muestra pequeños conducen a la sobreestimación de la diferenciación genética.  Probado el comportamiento de tres estimadores diferentes que infieren FST (1.-Wright, 2.-Cockerham y Weir, 3.-Reich y colegas) y que se utilizan comúnmente en los estudios de genética de poblaciones. 

Es de mi interes checar este articulo debido a que todos realizaremos este análisis y se nos pueden cruzar problemas a la hora de elegir el estimador o simplemente saber que nos esta arrojando para poder interpretarlo de la manera más adecuada. (Este articulo me lo recomendo Idalia ya que tuvimos unos inconvenientes al determinar los Fst en R y este artículo aclaró unas dudas).