DOI: 10.5061/dryad.ksn02v733
title: Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species

description: Co-distributed species may exhibit similar phylogeographic patterns due to
 shared environmental factors or discordant patterns attributed to the
 influence of species-specific traits. Although either concordant or
 discordant patterns could occur due to chance, stark differences in key
 traits (e.g., dispersal ability) may readily explain differences between
 species. Multiple species’ attributes may affect genetic patterns, and it
 is difficult to isolate the contribution of each. Here we compare the
 relative importance of two attributes, range size and niche breadth, in
 shaping the spatial structure of genetic variation in four sedge species
 (genus Carex) from the Rocky Mountains. Within two pairs of co-distributed
 species, one species exhibits narrow niche breadth, while the other
 species has broad niche breadth. Furthermore, one pair of co-distributed
 species has a large geographical distribution, while the other has a small
 distribution. The four species represent a natural experiment to tease
 apart how these attributes (i.e., range size and niche breadth) affect
 phylogeographic patterns. Investigations of genetic variation and
 structure revealed that range size, but not niche breadth, is related to
 spatial genetic covariation across species of montane sedges. Our study
 highlights how isolating key attributes across multiple species can inform
 their impact on processes driving intraspecific differentiation.
description: <b>Sample collection</b> Samples
 were field-collected from 10 sites that represented the majority of the
 range for each species (see maps in manuscript: Fig. 2 and Fig. 3, and SI
 Table S1). In our experimental design, the small range species were
 sampled from 10 identical locations and the large range species were also
 sampled from 10 identical locations. Across all species, an average of 7.8
 individuals were collected per sampling location. Individuals were sampled
 from the same sites for the two small-range species (<i>C.
 bella</i> and <i>C. chalciolepis</i>) across Colorado,
 New Mexico, and Utah (a range of approximately 250,000
 km<sup>2</sup>) and for the two large-range species
 (<i>C. epapillosa</i> and <i>C. pelocarpa</i>)
 across Colorado, Idaho, Montana, Nevada, Oregon, Utah, and Wyoming (a
 range of approximately 1,000,000 km<sup>2</sup>). Due to the
 close proximity of different habitat types in montane regions, we were
 able to sample species with different habitat preferences from the same
 sampling sites. The average distance among sampled plants at a locality
 was 300m, and the minimum distance between samples was 35m to minimize the
 chance of sampling siblings or close relatives. For each sampled
 individual, leaf tissue was collected and placed directly into silica gel
 desiccant. Leaf tissue was kept in the dark and stored at room temperature
 until DNA extraction. DNA was extracted with DNeasy Plant Mini Kits
 (Qiagen, Hilden, Germany) using the manufacturer’s standard
 protocol. <b>RAD-seq library construction and
 processing</b> We used a restriction site
 associated DNA sequencing (RAD-seq) approach to generate thousands of
 anonymous loci using six single-end Illumina HiSeq 2500 sequencing lanes
 following the protocol of Peterson et al. 2012. We used ipyrad 0.7.20
 (Eaton 2014) to demultiplex and filter reads from each library, allowing
 one mismatch per barcode and using the most stringent filtering to
 identify and exclude contamination from adapters and/or primers. As some
 individuals were represented in more than one library, every library was
 initially demultiplexed and filtered separately (ipyrad steps one and
 two). Reads corresponding to the same individual were then combined and
 all reads were trimmed to a length of 41 bp using the fast-x toolkit
 (http://hannonlab.cshl.edu/fastx_toolkit/). We used a 90% clustering threshold for de novo assembly; all other parameter settings that affect steps three through seven were set as default (see SI Methods for additional details). Across all species, between two and 10 individuals were sequenced per sampling location, for a total of 89 <i>C. bella</i> individuals, 97 <i>C. chalciolepis</i> individuals, 71 <i>C. epapillosa</i> individuals, and 55 <i>C. pelocarpa</i> individuals (SI Table S1, S2). 
description: Please see README file.