amplified fragment length homoplasy in silico analysis for model and non-model species扩增片段长度在硅片分析模型和non-model物种相似.pdfVIP

Paris et al. BMC Genomics 2010, 11:287 /1471-2164/11/287 M E T H O D O L O G Y A R T I C L E Open Access Methodology article Amplified fragment length homoplasy: in silico analysis for model and non-model species Margot Paris*, Benjamin Bonnes, Gentile Francesco Ficetola, Bénédicte N Poncet and Laurence Després Abstract Background: AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences available for model species to study AFLP homoplasy and to predict it in non-model species. Results: In this study we performed in silico AFLPs on the complete genome of three model species to predict intra- individual homoplasy in a prokaryote (Bacillus thuringiensis ser. konkukian), a plant (Arabidopsis thaliana) and an animal (Aedes aegypti). In addition, we compared in silico AFLPs to empirical data obtained from three related non-model species (Bacillus thuringiensis ser. israelensis, Arabis alpina and Aedes rusticus). Our results show that homoplasy rate sharply increases with the number of peaks per profile. However, for a given number of peaks per profile, genome size or taxonomical range had no effect on homoplasy. Furthermore, the number of co-migrating fragments in a single peak was dependent on the genome richness in repetitive sequences: we found up to 582 co-migrating fragments in Ae. aegypti . Finally, we show that in silico AFLPs can help to accurately predict AFLP profiles in related non-model species. Conclusions: These predictions can be used to tackle current issues in the planning of AFLP studies by limiting homoplasy rate and popula