Location of the study area in northwest Wyoming, USA.

<p>Location of the study area in northwest Wyoming, USA, and a close up of land ownership within the area of focus. The smaller rectangle delineated by a black line was the area in which we focused capture efforts and our interaction study using marked individuals.</p

Seasonal ranges of pronghorn, bighorn sheep, and cougars in the study area.

<p>Seasonal ranges of pronghorn and bighorn sheep in green in the study area, as they overlap with the seasonal ranges of cougars outlined in black. The large lake is Jackson Lake in Grand Teton National Park.</p

Seasonal habitat use by cougars.

<p>A comparison between Summer (A) and Winter (B) habitats utilized by cougars projected across the landscape based upon outputs from our Resource Selection Function outputs. The central body of water is Lower Slide Lake in the Bridger-Teton National Forest. Note the position of the Gros Ventre River, which we highlighted to emphasize the influence of “distance to water” in seasonal hunting.</p

DNA sample summary.

<p>Number of individual jaguars (<i>n</i>) and number of males and females detected across five Mesoamerican countries (Belize, Costa Rica, Guatemala, Honduras, Mexico).</p

Results of the global STRUCTURE analysis in Mesoamerican jaguars.

<p>The optimal number of genetic clusters (<i>K</i>) in Mesoamerican jaguars (<i>n</i> = 115) applying Bayesian clustering methods in STRUCTURE, version 2.3.4 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162377#pone.0162377.ref047" target="_blank">47</a>] was chosen based on posterior probabilities (mean L(<i>K</i>); A) and delta <i>K</i> (Δ<i>K</i>, mean (|L”(<i>K</i>)|)/SD(L(<i>K</i>)); D) for each <i>K</i> value. SD, standard deviation; L’(<i>K</i>), mean rate of change of the likelihood distribution (B); |L”(<i>K</i>)|, absolute value of the 2^nd order rate of change of the likelihood distribution (C).</p

Hierarchical analysis of molecular variance (AMOVA) in Mesoamerican jaguars.

<p>Hierarchical analysis of molecular variance (AMOVA) in Mesoamerican jaguars.</p

First-generation migrant analysis indicating dispersers in Mesoamerican jaguars.

<p>First-generation migrant analysis indicating dispersers in Mesoamerican jaguars.</p

Genetic differentiation in Mesoamerican jaguars.

<p>Genetic differentiation in Mesoamerican jaguars.</p

Summary statistics of genetic diversity for Mesoamerican jaguars.

<p>Summary statistics of genetic diversity for Mesoamerican jaguars.</p

Hierarchical genetic structure in Mesoamerican jaguars.

<p>Bayesian clustering analysis was conducted for all jaguar samples (a, <i>n</i> = 115) at a first (b, <i>n</i> = 72; c, <i>n</i> = 42) and a second hierarchy level (d, <i>n</i> = 65; e, <i>n</i> = 36) using STRUCTURE, version 2.3.4 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0162377#pone.0162377.ref047" target="_blank">47</a>]. Hierarchical structure analysis identified four genetic clusters (cluster 1: sites A and B; cluster 2: sites F, G, and H; cluster 3: C, D, and E; cluster 4: I, J, and K). A, Sierra del Abra Tanchipa Biosphere Reserve, Mexico; B, Sierra Mixe, Oaxaca, Mexico; C, northern Guatemala (Laguna del Tigre National Park, Maya Biosphere Reserve, Mirador R<b>í</b>o-Azul National Park); D, Central Belize Corridor Area, Belize; E, Cockscomb Basin Wildlife Sanctuary, Belize; F, Jeanette Kawas National Park, Honduras; G, Pico Bonito National Park, Honduras; H, Río Plátano Biosphere Reserve, Honduras; I, northeastern Costa Rica (Tortuguero National Park, Barra del Colorado Wildlife Refuge, and Barbilla National Park); J, several sites across northern and northwestern Costa Rica; K, Corcovado National Park, Costa Rica. <i>K</i>, number of genetics clusters inferred in STRUCTURE.</p