Demographic changes and loss of genetic diversity in two insular populations of bobcats (Lynx rufus)

Miller‐Butterworth, Cassandra M.; Diefenbach, Duane R.; Edson, Jessie; Hansen, Leslie A.; Jordan, James D.; Gingery, Tess M.; Russell, Amy L.

doi:10.1016/j.gecco.2021.e01457

Cited by 7 publications

(2 citation statements)

References 46 publications

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“…We used within‐population GD data collected and as presented elsewhere (Azizan & Paradis, 2021), including 10 additional studies published since 2020 found in Web of Science and Google Scholar ( n = 175). These additional studies provided data for Geoffroy's cat ( Leopardus geoffroyi ) (Bou et al, 2021), puma (Gallo et al, 2020; Zanin et al, 2021), European lynx (Herrero et al, 2021), jaguars (Kantek et al, 2021; Zanin et al, 2021), snow leopard (Korablev et al, 2021; Singh, Singh, Joshi, Chandra, et al, 2022), bobcat (Cancellare et al, 2021; Miller‐Butterworth et al, 2021) and leopard (Singh, Singh, Joshi, Singh, et al, 2022). Detailed methods for assembling this data set can be found elsewhere (Azizan & Paradis, 2021).…”

Section: Methodsmentioning

confidence: 99%

Population density and genetic diversity are positively correlated in wild felids globally

Azizan

Anile

Nielsen

et al. 2023

Global Ecol Biogeogr

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AimInsights into the biological and evolutionary traits of species, and their ability to cope with global changes, can be gained by studying genetic diversity within species. A cornerstone hypothesis in evolutionary and conservation biology suggests that genetic diversity decreases with decreasing population size, however, population size is difficult to estimate in threatened species with large distribution ranges, and evidence for this is limited to few species. To address this gap, we tested this hypothesis across multiple closely related species at a global scale using population density which is a more accessible measure.LocationGlobal.Time PeriodContemporary.Major Taxa StudiedWild felids in their natural habitats.MethodsWe obtained data from published estimates of population density assessed via camera trap and within‐population genetic diversity generated from microsatellite markers on 18 felid species across 41 countries from 354 studies. We propose a novel method to standardize population density estimates and to spatially join data using K‐means clustering. Linear mixed‐effect modelling was applied to account for confounding factors such as body mass, generation length and sample size used for the genetic estimates.ResultsWe found a significant positive correlation between population density and genetic diversity, particularly observed heterozygosity and allelic richness. While the confounding factors did not affect the main results, long generation length and large sample size were significantly associated with high genetic diversity. Body mass had no effect on genetic diversity, likely because large‐bodied species were over‐represented in our data sets.Main ConclusionsOur study emphasizes how recent demographic processes shape neutral genetic diversity in threatened and small populations where extinction vortex is a risk. Although caution is needed when interpreting the small population density effect in our findings, our methodological framework shows promising potential to identify which populations require actions to conserve maximal genetic variation.

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Section: Methodsmentioning

confidence: 99%

Population density and genetic diversity are positively correlated in wild felids globally

Azizan

Anile

Nielsen

et al. 2023

Global Ecol Biogeogr

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“…Inferring demographic history from genomic data has become routine in many research fields, from elucidating the anthropological origins and migration patterns of modern and archaic human populations (Gutenkunst et al 2009;Bergström et al 2020;Marchi et al 2022;Gopalan et al 2022), to inferring the population genetic trajectories of endangered animals (Mays Jr et al 2018;Miller-Butterworth et al 2021;Chavez et al 2022). Accounting for demographic history is also essential in setting the appropriate background for detecting signals of natural selection (Nielsen et al 2005;Boyko et al 2008;Kim et al 2017), disease associations (Mathieson & McVean 2012), and recombination hotspots (Johnston & Cutler 2012).…”

Section: Introductionmentioning

confidence: 99%

Computationally efficient demographic history inference from allele frequencies with supervised machine learning

Tran

Sun

Struck

et al. 2023

Preprint

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Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele frequency spectrum (AFS) and maximum likelihood optimization. However, dadi's maximum likelihood optimization procedure is computationally expensive. Here, we developed donni (demography optimization via neural network inference), a new inference method based on dadi that is more efficient while maintaining comparable inference accuracy. For each dadi-supported demographic model, donni simulates the expected AFS and trains a multilayer perceptron algorithm to infer the model parameters from input AFS. We demonstrated that for many demographic models, donni can infer some parameters, such as population size changes and inbreeding coefficients, very well (ρ≈0.9) and other parameters, such as migration rates and times of demographic events, fairly well (ρ≈0.6-0.7). Importantly, donni provides parameter inference instantaneously from input AFS, with accuracy comparable to parameters inferred by dadi's likelihood optimization while bypassing its long and computationally intensive evaluation process. Donni's performance demonstrates that supervised machine learning algorithms may be a promising avenue for developing more sustainable and computationally efficient demographic history inference methods.

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Long live the cat: Ocelot population viability in a planned reintroduced population in Texas, USA

Martinez,

Lombardi,

Parker

et al. 2024

Ecosphere

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Reintroductions are often needed to recover carnivore populations and restore ecological processes. Felids are common subjects of reintroduction efforts, but published population models informing felid reintroduction plans are uncommon, and poor planning has sometimes caused issues in felid reintroduction programs. In the United States, ocelots (Leopardus pardalis pardalis) are classified as endangered, and recovery requires population expansion into historic habitat. A multi‐organization effort is underway to establish a new ocelot population in Texas by releasing ocelots into an area of 478 km2 of suitable habitat in ocelots' historic but now unoccupied range. In this study, we used population viability analyses to compare different ocelot reintroduction strategies for the identified reintroduction area. Based on a potential ocelot breeding program's limitations, we modeled reintroduction using a founding population of no more than six ocelots and no more than four ocelots released per year for no more than 15 subsequent years. Within these limitations, we assessed projected population abundances and extinction risks after 30 years for 20 different reintroduction strategies. We found that long‐term releases are necessary to establish a viable population; under conservative model assumptions, releasing six ocelots in the initial year and then releasing four individuals annually for an additional 10–15 years is necessary for attaining a projected population greater than 36.62 ocelots (baseline) with <6% extinction risk. We also found that ocelot population abundance is about equally sensitive to post‐release mortality and inbreeding depression. This highlights the importance of not only supporting reintroduced ocelots' survival but also managing for high genetic diversity in the reintroduction program. Further, we found that realistic but more liberal assumptions on the carrying capacity of the reintroduction area and the age of first reproduction for ocelots increase projected population abundances (53.95 individuals and 61.26 individuals, respectively), and thus reintroduction success. The model's sensitivity to carrying capacity suggests that long‐term habitat protection and expansion are among the most important management actions to support ocelot reintroduction. Our study establishes the first population viability model for an ocelot reintroduction plan anywhere across the species' wide geographic range, and it reinforces several key considerations for wildlife reintroduction efforts worldwide.

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Demographic changes and loss of genetic diversity in two insular populations of bobcats (Lynx rufus)

Cited by 7 publications

References 46 publications

Population density and genetic diversity are positively correlated in wild felids globally

Population density and genetic diversity are positively correlated in wild felids globally

Computationally efficient demographic history inference from allele frequencies with supervised machine learning

Long live the cat: Ocelot population viability in a planned reintroduced population in Texas, USA

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