Figure 1.
Topographic map depicting location of Santa Ana Mountains, eastern Peninsular Ranges in southern California, and adjacent regions.
Inset shows location in the state of California.
Figure 2.
Map of puma capture locations in the Santa Ana Mountains and eastern Peninsular Ranges of southern California.
Colors of symbols represent genetic group assignment inferred from Bayesian clustering analysis (STRUCTURE analysis, see Figure 4). Genetic group A-1 = green diamonds; A-2 = red triangles (apex at top). One male puma (M86) captured in the Santa Ana Mountains had predominant genetic assignment to the A-2 (red) genetic group. Five individuals (light green squares) captured in the Santa Ana Mountains had partial assignment to the A-2 group (M91, F92, M93, M97 and F102). Molecular kinship analysis showed that M86 and a female (F89) captured in the Santa Ana Mountains were parents of pumas M91, F92, and M93 (captured in the Santa Ana Mountains). Puma M97 assigned in parentage to M86 and F61, while F102 had unknown parentage (no parentage assignments; due possibly to her death early in project prior to collection of most of the samples). Three individuals (orange triangles, apex at bottom), had partial assignment (however, less than 20%) to A-1.
Table 1.
Genetic diversity summary statistics for southern California pumas (n = 97) relative to other populations in California (n = 257).
Figure 3.
California puma population genetic structure.
STRUCTURE bar plot displaying the genetic clustering relationship of southern California pumas relative to others in California. Three major genetic groups, A (blue, on right), B (brown, in center), and C (yellow, on left), are evident for analysis of 354 individuals sampled throughout California. Abbreviations: NC = North Coast, MP-ESN = Modoc Plateau & Eastern Sierra Nevada, WSN = Western Sierra Nevada, CC-N = Central Coast: north, CC-C = Central Coast: central, CC-S = Central Coast: South (Santa Monica Mountains), PR-E = Peninsular Range-East, SAM = Santa Ana Mountains. The plot is organized by grouping individuals in order of their geographic region sampling source. Proportional genetic assignment for each puma is represented by a vertical bar, most easily visualized for pumas that genetically assigned to a group different from most others sampled in its region (for example one individual with over 80% brown and 8% blue near far left of group A). Pumas primarily from the Sierra Nevada Range and northern California are represented by group A (yellow), group B (brown) includes primarily Central Coast pumas and group C (blue) represents primarily southern California pumas (Santa Ana Mountains and eastern Peninsular Ranges).
Figure 4.
Southern California puma population genetic structure.
Bar Plot displaying results of STRUCTURE analysis focused on genotypic data from 97 southern California pumas (the blue block from Figure 3). With removal of the strong genetic signal from northern California and Central Coast samples (see Figure 3), two distinct southern California groupings were inferred, C-1 (green, on right) and C-2 (red, on left). These reflect the two regions: Santa Ana Mountains to the west of I-15 (predominantly genetic group C-1) and eastern Peninsular Ranges to the east of I-15 (predominantly genetic group C-2). Genetic clustering is dependent on genetic variance among samples included in the analysis. One male puma (M86) captured in the Santa Ana Mountains has predominant genetic assignment to the C-2 (red) genetic group (the predominant genetic cluster for PR-E), and five others had partial assignment to the C-2 group (M91, F92, M93, M97 and F102). Molecular kinship analysis showed that M86 and a female (F89) assigning to the C-1 genetic group were parents of pumas M91, F92, and M93 (all were captured in the Santa Ana Mountains).
Figure 5.
Principal Coordinates analyses (PCoA) constructed using genetic covariance matrices (GenAlEx) for 354 California puma genetic profiles including 97 from southern California.
Patterns displayed for first two axes of variation within the genetic data set. Each point, color-coded to its sampling region, represents an individual puma. Note that colors in PCoA diagrams reflect geographic source of samples and not STRUCTURE genetic cluster assignment. Abbreviations and sample sizes per Table 1. Arrows denote pumas described in Figure 4.
Figure 6.
Principal Coordinates analyses (PCoA) via covariance matrices for 97 southern California puma genetic profiles as conducted in GenAlEx.
Patterns displayed for first two axes of variation within the genetic data set. Each point represents an individual puma, and has sample identification number and color-coding to sampling region. Note that colors in PCoA diagrams reflect geographic source of samples and not STRUCTURE genetic cluster assignment. Abbreviations and sample sizes per Table 1.
Table 2.
Wright’s FST values indicate that southern California mountain lion populations are genetically distinct from other populations in California.
Table 3.
Effective population size estimations and indications of recent genetic bottlenecks in southern California pumas.
Figure 7.
Average pairwise relatedness (r; blue bars with confidence intervals) for pumas sampled in southern California relative to other regions in California. Algorithm of Lynch and Ritland (1999) as implemented in GenAlEx.
Expected range for “unrelated” is shown as red bars with confidence intervals. The average relatedness of Santa Ana Mountain pumas is higher than those sampled in Peninsular Ranges east of I-15 and for any other region tested in California. Relatedness in the Santa Ana Mountains pumas approaches second order family relationship (half sibs, niece-aunt, grandparent-grandchild, etc.). Abbreviations listed in Table 1.
Figure 8.
Photographs of kinked tails of pumas F95 (a) and M96 (b).
Arrows indicate kink sites. Puma F95 had tail kink at base of tail and Puma M96 had tail kink near distal tip of tail. These two pumas had among the lowest genetic diversity measured in this study.