Ultraconserved elements improve resolution of marmot phylogeny and offer insights into biogeographic history

Marmots (Marmota spp.) comprise a lineage of large-bodied ground squirrels that diversified rapidly in the Pleistocene, when the planet quickly transitioned to a drier, colder, and highly seasonal climate—particularly at high latitudes. Fossil evidence indicates the genus spread from North America, across Beringia, and into the European Alps over the course of only a few million years, beginning in the late Pliocene. Marmots are highly adapted to survive long and severely cold winters, and this likely favored their expansion and diversification over this time period. Previous phylogenetic studies have identified two major subgenera of marmots, but the timing of important speciation events and some species relationships have been difficult to resolve. Here we use ultraconserved elements and mitogenomes, with samples from all 15 extant species, to more precisely retrace how and when marmots came to inhabit a vast Holarctic range. Our results indicate marmots arose in North America in the ..., We obtained frozen tissues from 56 individuals representing all 15 currently recognized extant marmot species. Genomic DNA was extracted following the PureGene kit protocol for animal tissue (Gentra Systems Inc.). Sequence capture of ultraconserved elements (UCEs) was performed on a pilot dataset of 15 individuals according to the original UCE capture and sequencing protocols (Faircloth et al. 2012). Briefly, genomic libraries were prepared using KAPA library kits (Kapa Biosystems) and barcoded adapters for multiplexing (Faircloth & Glenn 2012). Enrichment was performed using the UCE Tetrapods 5kv1 probe set (http://ultraconserved.org/), and post-enrichment libraries were pooled and sequenced on one lane of an Illumina HiSeq 2000 instrument with 150 bp paired-end reads at the University of California Los Angeles Neuroscience Genomics Core. An additional 41 individuals were then sent to RAPiD Genomics (Gainesville, FL, USA) for library prep and sequencing using the same lab protocols...,