Using AFLP markers and the Geneland program for the inference

The use of dominant markers such as Amplified Fragment Length Polymorphism (AFLP) for population 5 genetics analyses is often impeded by the lack of appropriate computer programs and rarely motivated by 6 objective considerations. The point of the present note is two-fold: (i) we describe how the computer program 7 Geneland designed to infer population structure has been adapted to deal with dominant markers; (ii) 8 we use Geneland for numerical comparison of dominant and codominant markers to perform clustering. 9 AFLP markers lead to less accurate results than bi-allelic codominant markers such as Single Nucleotide 10 Polymorphisms (SNP) markers but this difference becomes negligible for datasets of common size (number 11 of individuals n ≥ 100, number of markers L ≥ 200). The latest Geneland version (3.2.1) handling dominant 12 markers is freely available as an R package with a fully clickable graphical interface. Installation instructions 13 and documentation can be found on www2.imm.dtu.dk/̃ gigu/Geneland. 14