Fractured genetic connectivity threatens a southern california puma (Puma concolor) population - PubMed (original) (raw)

Fractured genetic connectivity threatens a southern california puma (Puma concolor) population

Holly B Ernest et al. PLoS One. 2014.

Abstract

Pumas (Puma concolor; also known as mountain lions and cougars) in southern California live among a burgeoning human population of roughly 20 million people. Yet little is known of the consequences of attendant habitat loss and fragmentation, and human-caused puma mortality to puma population viability and genetic diversity. We examined genetic status of pumas in coastal mountains within the Peninsular Ranges south of Los Angeles, in San Diego, Riverside, and Orange counties. The Santa Ana Mountains are bounded by urbanization to the west, north, and east, and are separated from the eastern Peninsular Ranges to the southeast by a ten lane interstate highway (I-15). We analyzed DNA samples from 97 pumas sampled between 2001 and 2012. Genotypic data for forty-six microsatellite loci revealed that pumas sampled in the Santa Ana Mountains (n = 42) displayed lower genetic diversity than pumas from nearly every other region in California tested (n = 257), including those living in the Peninsular Ranges immediately to the east across I-15 (n = 55). Santa Ana Mountains pumas had high average pairwise relatedness, high individual internal relatedness, a low estimated effective population size, and strong evidence of a bottleneck and isolation from other populations in California. These and ecological findings provide clear evidence that Santa Ana Mountains pumas have been experiencing genetic impacts related to barriers to gene flow, and are a warning signal to wildlife managers and land use planners that mitigation efforts will be needed to stem further genetic and demographic decay in the Santa Ana Mountains puma population.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

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

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.

Figure 3

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

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

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

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.

Figure 7

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

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.

References

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