Inbreeding load and purging: implications for the short-term survival and the conservation management of small populations

Caballero, Armando; Bravo, Ignacio G.; Wang, J

doi:10.1038/hdy.2016.80

Cited by 97 publications

(104 citation statements)

References 60 publications

(82 reference statements)

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“…Accordingly, populations displaying high levels of individual inbreeding show a higher prevalence of monogenic disorders (e.g., Charlier et al., ) or complex diseases (e.g., Rudan et al., ). Inbreeding depression can thus increase the risk of extinction by reducing the population growth rate (Hedrick & Kalinowski, ; Keller & Waller, ) although it may be conversely favourable in some conditions by purging deleterious variants from the population (Caballero, Bravo, & Wang, ; Estoup et al., ). Assessing individual inbreeding is then of paramount interest to improve the management of populations under conservation or selection, and from a more general evolutionary perspective to better understand the genetic architecture of inbreeding depression.…”

Section: Introductionmentioning

confidence: 99%

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

2017

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Inbreeding results from the mating of related individuals and may be associated with reduced fitness because it brings together deleterious variants in one individual. In general, inbreeding is estimated with respect to an arbitrary base population consisting of ancestors that are assumed unrelated. We herein propose a model-based approach to estimate and characterize individual inbreeding at both global and local genomic scales by assuming the individual genome is a mosaic of homozygous-by-descent (HBD) and non-HBD segments. The HBD segments may originate from ancestors tracing back to different periods in the past defining distinct age-related classes. The lengths of the HBD segments are exponentially distributed with class-specific parameters reflecting that inbreeding of older origin generates on average shorter stretches of observed homozygous markers. The model is implemented in a hidden Markov model framework that uses marker allele frequencies, genetic distances, genotyping error rates and the sequences of observed genotypes. Note that genotyping errors, low-fold sequencing or genotype-by-sequencing data are easily accommodated under this framework. Based on simulations under the inference model, we show that the genomewide inbreeding coefficients and the parameters of the model are accurately estimated. In addition, when several inbreeding classes are simulated, the model captures them if their ages are sufficiently different. Complementary analyses, either on data sets simulated under more realistic models or on human, dog and sheep real data, illustrate the range of applications of the approach and how it can reveal recent demographic histories among populations (e.g., very recent bottlenecks or founder effects). The method also allows to clearly identify individuals resulting from extreme consanguineous matings.

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Section: Introductionmentioning

confidence: 99%

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

2017

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“…The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.Forests 2020, 11, 469 2 of 15 reproduction and development [2,3]. In addition to human disturbance, genetic factors can also represent threats to wild species [4]; such processes as mating systems, genetic drift, gene flow, evolution, and life history greatly affect the genetic diversity and spatial structure of plant populations [5][6][7][8][9].…”

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confidence: 99%

High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Deng

Liu

Xie

et al. 2020

Forests

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Research Highlights: This study is the first to examine the genetic diversity of Michelia shiluensis (Magnoliaceae). High genetic diversity and low differentiation were detected in this species. Based on these results, we discuss feasible protection measures to provide a basis for the conservation and utilization of M. shiluensis. Background and Objectives: Michelia shiluensis is distributed in Hainan and Guangdong province, China. Due to human disturbance, the population has decreased sharply, and there is thus an urgent need to evaluate genetic variation within this species in order to identify an optimal conservation strategy. Materials and Methods: In this study, we used eight nuclear single sequence repeat (nSSR) markers and two chloroplast DNA (cpDNA) markers to assess the genetic diversity, population structure, and dynamics of 78 samples collected from six populations. Results: The results showed that the average observed heterozygosity (Ho), expected heterozygosity (He), and percentage of polymorphic loci (PPL) from nSSR markers in each population of M. shiluensis were 0.686, 0.718, and 97.92%, respectively. For cpDNA markers, the overall haplotype diversity (Hd) was 0.674, and the nucleotide diversity was 0.220. Analysis of markers showed that the genetic variation between populations was much lower based on nSSR than on cpDNA (10.18% and 77.56%, respectively, based on an analysis of molecular variance (AMOVA)). Analysis of the population structure based on the two markers shows that one of the populations (DL) is very different from the other five. Conclusions: High genetic diversity and low population differentiation of M. shiluensis might be the result of rich ancestral genetic variation. The current decline in population may therefore be due to human disturbance rather than to inbreeding or genetic drift. Management and conservation strategies should focus on maintaining the genetic diversity in situ, and on the cultivation of seedlings ex-situ for transplanting back to their original habitat.

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“…5) The results of our analysis suggest that the subpopulation(s) on the Cleveland Peninsula are phenotypically and genetically differentiated from the adjacent GMU situated in southeast Alaska. Metrics of diversity suggest the Cleveland Peninsula is isolated with limited gene flow and is thus at risk for inbreeding depression and increased extinction risk (Caballero et al 2017).…”

Section: Resultsmentioning

confidence: 99%

Extensive field-sampling reveals the uniqueness of a trophy mountain goat population

Breen

Britt

Johnson

et al. 2018

Preprint

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Collaborations between academic researchers and agencies is crucial for genetic data to have a tangible impact on conservation and wildlife management. Such partnerships are particularly important elusive species where the difficult terrain requires that a significant amount of resources and a combination of methods be used to estimate population parameters needed for conservation. We report and multi-year academic-agency collaboration on the North American mountain goat that used an extensive field sampling of genetic and phenotypic data to determine whether, and to what degree, genetic and phenotypic differences separate an isolated population of mountain goats on the Cleveland Peninsula form those in southeast Alaska. We observed significantly larger horns on the peninsula and the population appears demographically isolated. Isolation-by-distance accompanied by limited migration and low effective population size on the Cleveland Peninsula suggest this population will continue to lose genetic diversity.While the large horns of mountain goats have generated interest in re-opening mountain goat harvest on Cleveland Peninsula, our genetic data suggest this population is vulnerable to demographic and environmental perturbations and is unlikely to support a sustained harvest.

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Inbreeding load and purging: implications for the short-term survival and the conservation management of small populations

Cited by 97 publications

References 60 publications

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

A model‐based approach to characterize individual inbreeding at both global and local genomic scales

High Genetic Diversity and Low Differentiation in Michelia shiluensis, an Endangered Magnolia Species in South China

Extensive field-sampling reveals the uniqueness of a trophy mountain goat population

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