3.1 Patterns of genetic diversity, numts and the presence of a duplicated region
We obtained an average of 192 sequences per marker (length range 307-1323 bp; Table 1). Mitochondrial data produced 148 polymorphic sites yielding 150 haplotypes, while nuclear data exhibited a total of 111 variable sites and 150 alleles (see Table 1 for summary of polymorphic sites, haplotypes and diversities per marker). Mitochondrial markers were twice as variable as nuclear markers, though nuclear haplotype and nucleotide diversity in βfib reached a level similar to mitochondrial haplotype diversity (Table 1).
None of the coding markers (cox1 , cytb and pax ) presented any insertion, deletion, nonsense or stop-codon following translation (see Supplementary Material 1). Double peaks on Sanger chromatograms were however detected for each of the three mtDNA markers. While all double peaks at cox1 were removed by the exonuclease treatment, 60 CR sequences (33%) still showed double-peaks at 73 positions, as well as 37 positions for 22 individuals (10%) forcytb . Double-peaks were not specific to any population or sex, and were not linked to the position of the individuals in the sequencing plate (see Supplementary Material 3). Only 12 (5%) individuals showed double-peaks both at CR and cytb , so the presence of double peaks seemed unlinked between the two markers. Replicating DNA extractions, PCR and sequencing confirmed these results, making laboratory contamination unlikely. Contamination in the field was also unlikely since new sampling supplies were used for every sample. Given that only 10% of the cytb sequences presented such ambiguities (which may be due to heteroplasmy, Torres et al 2018), we removed such sequences for further analyses expecting little impact on the analyses. However, for the CR, since a third of the total sequences were involved, we kept all CR data in further analyses, considering two haplotypic phases for MrBayes and *BEAST analyses (although this is a violation of the assumption that mixed sequences to be phased are under Hardy-Weinberg equilibrium; see discussion below).