3. Results
The number of Illumina reads for each sample varied from 58,930 to 1,151,143, with an average of 326,580 sequences per sample, with 7.3 to 75.3% of reads mapped to the Niebla reference using Bowtie2 (Appendix 1). The number of Niebla RADseq loci (within sample clusters) that STACKs generated from these sequences ranged from 2,534 to 39,941 (mean=22,373 loci/sample). Our final RADseq dataset resulted in a total of 25,086 143-bp loci. The total length of the concatenated RADseq loci was 3.6 Mb, including 198K variable sites.