RAD-seq library preparation, sequencing and read filtering
Restriction-site-associated DNA libraries of 519 ABFT individuals were prepared following Etter et al. (2012) . Input DNA (ranging from 50 to 500 ng) was digested with the SbfI restriction enzyme and ligated to modified Illumina P1 adapters containing 5bp unique barcodes. Pooled DNA of 32 individuals was sheared using the Covaris® M220 Focused-ultrasonicator™ Instrument (Life Technologies) and size selected to 300-500 pb on agarose gel. After Illumina P2 adaptor ligation, each library was amplified using 14 PCR cycles. Each pool was paired-end sequenced (100 pb) on an Illumina HiSeq2000. Demultiplexing, quality filtering (removing reads whose average Phred score is lower than 20 and truncating them to 90 nucleotides to remove low-quality bases at the end) and PCR duplicate removal were preformed using theprocess_radtags and clone_filter modules ofStacks version 2.3e (Rochette et al. 2019).