Fig 1.
Sampling sites of jaguars across five Mesoamerican countries.
Black triangles represent individual jaguar samples collected across five Mesoamerican countries (Mexico, Guatemala, Belize, Honduras, Costa Rica). Spatial data representing jaguar conservation units and movement corridors were obtained from Panthera.
Table 1.
Number of individual jaguars (n) and number of males and females detected across five Mesoamerican countries (Belize, Costa Rica, Guatemala, Honduras, Mexico).
Table 2.
Summary statistics of genetic diversity for Mesoamerican jaguars.
Fig 2.
Genetic structure in Mesoamerican jaguars.
Results were obtained from Bayesian clustering analysis (K = 3) using STRUCTURE, version 2.3.4 [47] and genotype data from 12 microsatellite loci for jaguars (n = 115) sampled across five Mesoamerican countries (Belize, Costa Rica, Guatemala, Honduras, Mexico). (a) STRUCTURE barplot—vertical bars represent individuals and the color of each bar visualizes the % of membership (Q) the individual belongs to the genetic clusters (K) identified. (b) Pie charts represent fractions of Q for groups of jaguar individuals studied across different sampling sites (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 Río-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.
Fig 3.
Results of the global STRUCTURE analysis in Mesoamerican jaguars.
The optimal number of genetic clusters (K) in Mesoamerican jaguars (n = 115) applying Bayesian clustering methods in STRUCTURE, version 2.3.4 [47] was chosen based on posterior probabilities (mean L(K); A) and delta K (ΔK, mean (|L”(K)|)/SD(L(K)); D) for each K value. SD, standard deviation; L’(K), mean rate of change of the likelihood distribution (B); |L”(K)|, absolute value of the 2nd order rate of change of the likelihood distribution (C).
Fig 4.
Hierarchical genetic structure in Mesoamerican jaguars.
Bayesian clustering analysis was conducted for all jaguar samples (a, n = 115) at a first (b, n = 72; c, n = 42) and a second hierarchy level (d, n = 65; e, n = 36) using STRUCTURE, version 2.3.4 [47]. 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 Río-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. K, number of genetics clusters inferred in STRUCTURE.
Fig 5.
Principal component analysis (PCA) based on Mesoamerican jaguar genotypes.
Scatterplot visualizes the first two principal components. Points represent individual genotypes, and geographical groups of jaguars sampled across five Mesoamerican countries (Belize, Costa Rica, Guatemala, Honduras, Mexico) are 95% inertia ellipses in different colors. Inserted barchart shows eigenvalues with corresponding components in dark grey. PC, principal component.
Table 3.
First-generation migrant analysis indicating dispersers in Mesoamerican jaguars.
Table 4.
Genetic differentiation in Mesoamerican jaguars.
Table 5.
Hierarchical analysis of molecular variance (AMOVA) in Mesoamerican jaguars.
Fig 6.
Regional and fine-scale isolation-by-distance patterns in Mesoamerican jaguars.
Isolation-by-distance in Mesoamerican jaguars was assessed by plotting pairwise codominant genotypic distance calculated in GenAlEx, version 6.41 [39] versus pairwise Euclidean distances (km) across (A) all sampling sites, (B) Mexico, Guatemala, and Belize, (C) Guatemala, Belize, and Honduras, and (D) Honduras and Costa Rica. Statistical significance was assessed using simple Mantel tests in ecodist, version 1.2.9 [62] in R, version 3.1.3 [41]. Each point represents a pairwise comparison among individual jaguars.
Fig 7.
Spatial autocorrelation in Mesoamerican jaguars.
Spatial correlogram for jaguars (n = 99) showing the genetic correlation coefficient (r) as a function of geographic distance across defined spatial distance classes. Dashed red lines represent upper (U) and lower (L) bounds of the null hypothesis of no spatial structure based on 10,000 random permutations. Error bars represent 95% confidence intervals about r based on 1,000 bootstraps.