Fractured Genetic Connectivity Threatens a Southern California Puma (Puma concolor) Population

Ernest, Holly B.; Vickers, T. Winston; Morrison, Scott; Buchalski, Michael R.; Boyce, Walter M.

doi:10.1371/journal.pone.0107985

Cited by 69 publications

(114 citation statements)

References 42 publications

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“…Mountain lions from the Santa Ana Mountains (south of Los Angeles) and the Santa Monica Mountains (north of Los Angeles) have high average pairwise relatedness, small estimated effective population sizes, and strong evidence of past genetic bottlenecks (44,45). While our phylogenetic data suggest that PLVA in California mountain lions is acquired primarily from bobcats versus intraspecific contacts, the condition of these small, isolated populations may similarly predispose them to chains of intraspecific infection and emergence of a mountain lion-adapted PLVA infection over time.…”

Section: Figmentioning

confidence: 99%

Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

Lee

Malmberg

Wood

et al. 2017

J Virol

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Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of human immunodeficiency virus (HIV) emergence following human exposures to simian immunodeficiency virus (SIV), an understanding of processes that promote successful cross-species lentiviral transmissions is highly relevant. We previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats (Lynx rufus) and mountain lions (Puma concolor) for a small number of animals in California and Florida. In this study, we investigate host-specific selection pressures, within-host viral fitness, and inter-versus intraspecies transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analyses of proviral and viral RNA levels demonstrate that PLVA fitness is severely restricted in mountain lions compared to that in bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but we did not detect selection among 20 PLVA isolates from bobcats. These findings support the hypothesis that PLVA is a bobcat-adapted virus which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals that intraspecific PLVA transmission has occurred among panthers (Puma concolor coryi) in Florida following the initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to the emergence of HIV from nonhuman primates.IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. We used molecular techniques to evaluate the transmission, fitness, and adaptation of puma lentivirus A (PLVA) between bobcats and mountain lions in two geographic regions. Our findings illustrate that mountain lion exposure to PLVA is relatively common but does not routinely result in communica-

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Section: Figmentioning

confidence: 99%

Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

Lee

Malmberg

Wood

et al. 2017

J Virol

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Section: Introductionmentioning

confidence: 99%

“…The process of landscape modification may impose barriers to gene flow [2][3][4], which in turn reduces the genetic diversity and decreases population viability in long term [2,5]. Several species are already in a process of genetic diversity and presenting certain level of isolation of their populations [3,4,[6][7][8]. Even those species with generalist habits or high dispersal behavior have already experienced negative genetic consequences (e.g., gene flow reduction and population structuring) in human-modified landscapes [2][3][4]9].…”

Section: Introductionmentioning

confidence: 99%

Evidence of Recent Fine-Scale Population Structuring in South American Puma concolor

Saranholi¹,

Chávez-Congrains²,

Galetti³

2017

Diversity

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Habitat loss and fragmentation are considered the major treats to worldwide biodiversity. Carnivores in particular can be more sensitive to landscape modification due to their low occurrence density and large home ranges. Population structuring of Puma concolor has been already reported as a consequence of extensive human activities in the North American continent. Here, we investigated the occurrence of fine-scale population structuring in the South American cougar population, contrasting two conservation areas immersed in a highly human-fragmented landscape dominated by the presence of sugar cane monoculture, roads, and urbanization, including a series of dams in the Tietê River which enlarges its water body. Seven microsatellites were amplified using non-invasive DNA obtained from fecal samples. We conducted genetic clustering analyses using Bayesian and factorial components. We also performed genetic differentiation analyses by fixation indices (F st and D est ). Two genetic clusters represented by individuals from each area were found, indicating the occurrence of gene flow reduction between the areas. The intense human-induced landscape modification-which includes the Tietê River water body enlargement, imposing physical barriers to the movement of the individuals-could explain the gene flow reduction. Increasing connectivity among the preserved areas can mitigate such effects, and the creation of corridors or further management actions such as individual translocation to ensure gene flow in the highly-modified landscape may be essential for maintaining the genetic and demographic health of the species and its long-term persistence.

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“…Loss of genetic connectivity across landscapes can depress genetic diversity and potentially increase extinction risks (Epps et al, 2005;Dixo et al, 2009;Clark et al, 2010;Ernest et al, 2014), so landscape genetics can provide information to help understand and potentially mitigate the effects of land cover change in natural populations (for example, fragmentation, habitat loss, anthropogenic disturbance; Segelbacher et al, 2010). To understand how landscape heterogeneity may impact genetic connectivity within a focal species, researchers typically utilize field studies (for example, habitat selection or occupancy) to develop landscape resistance models.…”

Section: Introductionmentioning

confidence: 99%

Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species

Kierepka

Latch

2015

Heredity

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Landscape genetics is a powerful tool for conservation because it identifies landscape features that are important for maintaining genetic connectivity between populations within heterogeneous landscapes. However, using landscape genetics in poorly understood species presents a number of challenges, namely, limited life history information for the focal population and spatially biased sampling. Both obstacles can reduce power in statistics, particularly in individual-based studies. In this study, we genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to identify alternative statistical approaches that can be applied to poorly understood species in an individual-based framework. Badgers are protected in Wisconsin owing to an overall lack in life history information, so our study utilized partial redundancy analysis (RDA) and spatially lagged regressions to quantify how three landscape factors (Wisconsin River, Ecoregions and land cover) impacted gene flow. We also performed simulations to quantify errors created by spatially biased sampling. Statistical analyses first found that geographic distance was an important influence on gene flow, mainly driven by fine-scale positive spatial autocorrelations. After controlling for geographic distance, both RDA and regressions found that Wisconsin River and Agriculture were correlated with genetic differentiation. However, only Agriculture had an acceptable type I error rate (3-5%) to be considered biologically relevant. Collectively, this study highlights the benefits of combining robust statistics and error assessment via simulations and provides a method for hypothesis testing in individual-based landscape genetics.

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Fractured Genetic Connectivity Threatens a Southern California Puma (Puma concolor) Population

Cited by 69 publications

References 42 publications

Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections

Evidence of Recent Fine-Scale Population Structuring in South American Puma concolor

Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species

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