title: Viral diversity and biogeographic dynamics in wild rodents from Baja California
design: 2 to 5 fecal pellets were transfered to a 1.5-ml screw-cap tube containing stainless steel beads (Next-Advance, Inc., USA) and 800 l of SM buffer (0.1 M NaCl, 50 mM Tris-HCl [pH 7.4], and 10 mM MgSO4). We used a Bullet Blender Storm 24 (Next-Advance, Inc., USA) to homogenize the pellets for 3 min at a speed setting of 10. We then used a benchtop centrifuge (Eppendorf, Germany) to centrifuge the homogenate for 1 min at 5,000  g. To enrich for viral particles, we filtered the supernatant through 0.45-m and 0.2-m syringe filters (Cole-Parmer LLC., USA) and aliquoted 200 l of filtrate for extract viral DNA using a High Pure Viral Nucleic Acid Kit (Roche Diagnostics, USA) following the manufacturers protocol. We performed a rolling-circle amplification (RCA) step with 2 l of viral nucleic acid extract from each sample using a TempliPhi Kit (GE Healthcare, USA) to target circular DNA preferentially. We used RCA amplicons combined 50/50 with viral nucleic acid extract to generate Illumina sequencing libraries with an Illumina DNA Prep Kit and IDT Illumina Nextera DNA Unique Dual Indexes. Libraries were sequenced on an Illumina HiSeq 2500 sequencer.