Table 2. Parameters varied in PyRAD runs.

Parameter (designation)	Default value	Other values tested
#8 (d): minimum depth for a statistical base call	6	2, 3, 4, 8, 10
#9 (n): maximum number of low quality sites per read	4	2, 8
#10 (c): clustering threshold within and between samples	0.88	0.82, 0.85, 0.91, 0.94, 0.97
#13 (h): maximum number of individuals sharing a heterozygous site	3	5, 10
#25 (pl): ploidy filter = maximum number of alleles per locus	2	4, 8
#34 (mr): minimum number of reads for a dereplicate in an individual	1	2, 4, 8, 10