Number of samples used in this study from each stratigraphic layer in Lamar Cave, and ages and the climatic periods represented by each layer.

<p>Period, climate and age of layers from.</p

AMOVAs of genetic subdivision in modern northern Yellowstone based on the four identified mitochondrial haplotypes.

<p>DF = degrees of freedom; SS = sum squares, MS = mean squares.</p

Map of field site with approximate locations of sampled ponds and proportion of individuals at each site that possessed each haplotype.

<p>Map area shows the Lamar Valley in northern Yellowstone National Park in Wyoming, USA. Thin grey lines show rivers, thick grey lines show park and state boundaries, black lines show roads. Lamar Cave site indicated with arrow. Samples collected from Lamar Cave = 16 (all Haplotype 1), samples collected from Ice Lake (Ice) = 17, Rainbow Lake (R) = 12, Pond A = 7, Pond F = 12, Pond J = 16, Pond 47 = 5, Pond 1 = 5, Pond 5 = 11, Pond 26 = 18, Pond 34 = 8, Pond 38 = 6, Pond 36 = 17, Pond 49 = 9.</p

Morphological Adaptations for Digging and Climate-Impacted Soil Properties Define Pocket Gopher (<i>Thomomys</i> spp.) Distributions

<div><p>Species ranges are mediated by physiology, environmental factors, and competition with other organisms. The allopatric distribution of five species of northern Californian pocket gophers (<i>Thomomys</i> spp.) is hypothesized to result from competitive exclusion. The five species in this environmentally heterogeneous region separate into two subgenera, <i>Thomomys</i> or <i>Megascapheus</i>, which have divergent digging styles. While all pocket gophers dig with their claws, the tooth-digging adaptations of subgenus <i>Megascapheus</i> allow access to harder soils and climate-protected depths. In a Northern Californian locality, replacement of subgenus <i>Thomomys</i> with subgenus <i>Megascapheus</i> occurred gradually during the Pleistocene-Holocene transition. Concurrent climate change over this transition suggests that environmental factors – in addition to soil – define pocket gopher distributional limits. Here we show 1) that all pocket gophers occupy the subset of less energetically costly soils and 2) that subgenera sort by percent soil clay, bulk density, and shrink-swell capacity (a mineralogical attribute). While clay and bulk density (without major perturbations) stay constant over decades to millennia, low precipitation and high temperatures can cause shrink-swell clays to crack and harden within days. The strong yet underappreciated interaction between soil and moisture on the distribution of vertebrates is rarely considered when projecting species responses to climatic change. Furthermore, increased precipitation alters the weathering processes that create shrink-swell minerals. Two projected outcomes of ongoing climate change—higher temperatures and precipitation—will dramatically impact hardness of soil with shrink-swell minerals. Current climate models do not include factors controlling soil hardness, despite its impact on all organisms that depend on a stable soil structure.</p></div

Full occupancy model with traits

R and JAGS code for the full phylogenetic occupancy model with influence of traits include

Array of Costa Rican bat capture data

Capture data collected from the field and arranged in an R data array. Array includes: (1) the capture array (X), with the site, year, visit and species information; (2) matrix of the number of visits conducted at each site by year combination (nrep); (3) the pairwise distance between sites (D); (4) scaled and centered proportion of area covered by trees across all spatial scales; see full model explanation (Env); (5) relative elevation of site compared to surroundings (terrain); (6) whether or not the site was a coffee field (coffee.dummy

cytbFig2a Mrbayes

cytbFig2a Mrbaye

divergence_CytbND4_xml

divergence_CytbND4_xm

Species tree ND4 alignment

Species tree ND4 alignmen

Species Tree xml

Species Tree xm