F. cf. subanescens:RAD-Seq
We used a double-digest restriction site-associated DNA sequencing (RADseq) approach to sequence samples, following the protocol outlined in Brelsford et al. (2016). DNA from individuals sequenced in the 2016, 2017, and 2019 batches was digested using the restriction enzymes MseI and SbfI, while DNA from individuals sequenced in the 2021 batch was digested using MseI and PstI. Subsequently, a universal MseI adapter and uniquely barcoded Sbfl or PstI adapter were ligated to each sample. Small DNA fragments were removed using Sera-Mag magnetic beads (Rohland & Reich, 2012) in a 0.8:1 ratio (beads:sample solution). Amplification of each sample occurred in four separate 5 l  PCR reactions with Q5 Hot Start DNA Polymerase, incorporating plate-specific indexed Illumina primers. The replicate PCR products for each sample were pooled, additional dNTP and primer mix were added, and a final PCR cycle was conducted. We visualized the PCR product using gel electrophoresis and pooled samples that amplified successfully.  For the 2016 and 2017 libraries, we ran pooled samples on a 2.5 % agarose gel, excised DNA in the 300-500 bp range, and used the QIAGEN MinElute gel extraction kit following the manufacturer's protocol to extract DNA from the gel fragment. For the 2019 and 2021 libraries, we removed small fragments using Sera-Mag beads in a 0.8-1 ratio (beads: sample solution).