The amplified fragment length polymorphism (AFLP) technique is being increasingly used in phylogenetic studies, especially in groups of rapidly radiating taxa. One of the key issues in the phylogenetic suitability of this technique is whether the DNA fragments generated via the AFLP method are homologous within and among the taxa being studied. We used a bioinformatics approach to assess homology based on both chromosomal location and sequence similarity of AFLP fragments. The AFLP technique was electronically simulated on genomes from eight organisms that represented a range of genome sizes. The results demonstrated that within a genome, the number of fragments is positively associated with genome size, and the degree of homology decreases with increasing numbers of fragments generated. The average homology of fragments was 89% for small genomes (< 400 Mb) but decreased to 59% for large genomes (> 2 Gb). Fragment homology for large genomes can be increased by excluding smaller fragments, although there is no clear upper limit for the size of fragments to exclude. A second approach is to increase the number of selective nucleotides in the final selective amplification step. For strains of the same organism, homology based on chromosome location and sequence similarity of fragments was 100%. Fragment homology for more distantly related taxa, however, decreased with greater time since divergence. We conclude that AFLP data are best suited for examining phylogeographic patterns within species and among very recently diverged species.

译文

扩增片段长度多态性 (AFLP) 技术越来越多地用于系统发育研究,尤其是在快速辐射的类群中。该技术的系统发育适用性的关键问题之一是,通过AFLP方法产生的DNA片段在所研究的分类单元内部和之间是否同源。我们使用生物信息学方法根据AFLP片段的染色体位置和序列相似性来评估同源性。AFLP技术是在代表一系列基因组大小的八种生物的基因组上进行电子模拟的。结果表明,在基因组中,片段的数量与基因组大小呈正相关,并且同源性程度随着生成片段数量的增加而降低。对于小基因组 (< 400 Mb),片段的平均同源性89%,但是对于大基因组 (> 2 gb),片段的平均同源性降低到59%。可以通过排除较小的片段来增加大基因组的片段同源性,尽管没有明确的上限来排除片段的大小。第二种方法是在最终的选择性扩增步骤中增加选择性核苷酸的数量。对于同一生物体的菌株,基于片段的染色体位置和序列相似性100% 了同源性。然而,自发散以来,远缘类群的片段同源性随时间的延长而降低。我们得出的结论是,AFLP数据最适合检查物种内部和最近分歧物种之间的系统地理模式。

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