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).