Bonin A, Ehrich D, Manel S
Diversity Arrays Technology P/L, Yarralumla, ACT 2600, Australia.
Mol Ecol. 2007 Sep;16(18):3737-58. doi: 10.1111/j.1365-294X.2007.03435.x.
Recently, the amplified fragment length polymorphism (AFLP) technique has gained a lot of popularity, and is now frequently applied to a wide variety of organisms. Technical specificities of the AFLP procedure have been well documented over the years, but there is on the contrary little or scattered information about the statistical analysis of AFLPs. In this review, we describe the various methods available to handle AFLP data, focusing on four research topics at the population or individual level of analysis: (i) assessment of genetic diversity; (ii) identification of population structure; (iii) identification of hybrid individuals; and (iv) detection of markers associated with phenotypes. Two kinds of analysis methods can be distinguished, depending on whether they are based on the direct study of band presences or absences in AFLP profiles ('band-based' methods), or on allelic frequencies estimated at each locus from these profiles ('allele frequency-based' methods). We investigate the characteristics and limitations of these statistical tools; finally, we appeal for a wider adoption of methodologies borrowed from other research fields, like for example those especially designed to deal with binary data.
最近，扩增片段长度多态性（AFLP）技术已广受欢迎，如今常被应用于各种各样的生物体。多年来，AFLP程序的技术细节已有详尽记载，但相反，关于AFLP统计分析的信息却很少且零散。在本综述中，我们描述了处理AFLP数据的各种可用方法，重点关注群体或个体分析层面的四个研究主题：（i）遗传多样性评估；（ii）群体结构识别；（iii）杂交个体识别；以及（iv）与表型相关的标记检测。根据分析方法是基于对AFLP图谱中条带的存在与否进行直接研究（“基于条带”的方法），还是基于从这些图谱中估计的每个位点的等位基因频率（“基于等位基因频率”的方法），可以区分出两种分析方法。我们研究了这些统计工具的特点和局限性；最后，我们呼吁更广泛地采用从其他研究领域借鉴的方法，例如那些专门设计用于处理二元数据的方法。
