3.1 NextRAD and mitochondrial data
The nextRAD dataset consisted, on average, of 1.6 million single-end
reads per individual, with an average read length of 123 bp. The final
assembled genome contained 250,856 fragments with a total length of
240.6 Mb. Considering a set consisting of 173 samples, we identified
14,446 loci. However, we had to remove 32 individuals from further
analyses because of high numbers of missing data (<10%
missing genotypes). From the remaining 141 individuals, we recovered a
total of 5,383 loci. After filtering loci that were present in at least
90% of the individuals, we ended up with a final dataset containing
1,707 SNPs (average coverage 78X) used for further analyses. Numbers of
loci removed in each filtering step are detailed in Table S2. Since the
10% of missing data criterium used for filtering the SNPs dataset is
the strictest threshold, we evaluated other filtering thresholds that
yielded essentially the same results in population genetic structure and
species delimitation analyses.
The mtDNA dataset consisted of 233 sequences, 143 collected in the
native range and 90 in the non-native range. Additionally, we includedCOI sequences of five individuals from California, United States
on Cactaceae, but SNPs data at this location could not be generated. The
length of the amplified COI fragment was 413 bp, with 371
conserved (89.83%) and 42 (10.16%) variable sites, distributed in 27
haplotypes. The mtDNA sequences are available in GenBank under accession
numbers MT138921 - MT138931.