Genetic Sampling, DNA extraction and Sequencing
In this study, we included 566 beetles from 27 populations of theN. ingens complex in the Sierra Nevada, California (Figure 1 ). The sample beetles were collected with permits granted by Sequoia and Kings National Parks (Study# SEKI-0091), Yosemite National Park (Study# YOSE-00093), and the California Fish and Game Department (#SC-006997). Genomic DNA from these samples was extracted using the QIAamp 96 DNA Blood Kit (QIAGEN) or DNeasy Blood & Tissue Kits (QIAGEN) for both genotyping by sequencing (GBS) and mitochondrial COI gene sequencing. In addition to 219 samples from the study of Schoville et al. (2012), 104 beetles were selected to sequence an approximately 645 base pair region (after trimming the primer sequences) of the mitochondrial COI gene using the universal arthropod primers Jerry (5’-CAACATTTATTTTGATTTTTTGG-3’) and Pat (5’-TCCAATGCA CTAATCTGCCATATTA-3’) (Simon et al. 1994).). The resulting dataset of 323 COI gene sequences were aligned for downstream analyses. For nuclear genomic analyses, 381 samples were selected for genotyping by sequencing (GBS) (Elshire et al, 2011), with 3 individuals replicated. The restriction enzyme ApeKI was used to reduce the genome to an appropriate size distribution and 150 base pair single-end Illumina sequencing libraries were prepared by the Biotechnology Center of University of Wisconsin-Madison. All genetic data are deposited at NCBI (see Data Accessibility statement).