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24 results for “genetic erosion”
Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
<p>Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation, and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity, and the fixation of maladaptive alleles, hindered adaptation, and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.</p>
Global warming leads to habitat loss and genetic erosion of alpine biodiversity
<p><span><strong>Aim</strong>:</span><span> Species living on steep environmental gradients are expected to be especially sensitive to global climate change. Here, we combined genetic, ecological niche modelling and climatic niche comparisons to investigate the influence of climate on the biogeography of three alpine species with overlapping ranges.</span></p> <p><span><strong>Location</strong>:</span><span> Te Waipounamu (South Island) Aotearoa</span>–<span>New Zealand.</span></p> <p><span><strong>Taxon</strong>:</span><span> Endemic alpine-adapted Cataontopinae grasshoppers.</span></p> <p><span><strong>Methods</strong>:</span><span> We used niche modelling to estimate and project the potential niche of three focal species under past and future climate scenarios.</span><span> Vulnerability assessments were</span><span> performed using </span><span>niche factor analyses. Demographic trends and phylogeographic structure were investigated using samples from 15 mountain tops to generate mitochondrial DNA haplotype networks and population genetic statistics.</span></p> <p><span><strong>Results</strong>:</span><span> Niche models and genetic data suggest suitable habitat for all three alpine species was more widespread and contiguous in the past than today. Demographic analyses indicate in situ survival rather than post-Pleistocene colonisation of current habitat. Population structuring and genetic divergence suggest that mountain uplift during the Pliocene and environmental barriers during Pleistocene glacial and interglacial stages shaped contemporary population structure of each species. Though geographically overlapping, niche analyses suggest these alpine species are not ecologically identical, and each shows similar but distinct responses to environmental change, but all will lose intraspecific diversity through population extinction.</span></p> <p><span><strong>Main</strong> <strong>conclusions</strong>:</span><span> Climatic, biological and geophysical factors controlled population structuring of three cold-adapted species during the Pleistocene with a legacy of spatially separate intraspecific lineages. Ecological niche models for each species emphasise distinct combinations of environmental proxies, but all are expected to experience severe habitat reduction during climate warming. Increased global temperatures drive available habitat to higher elevation resulting in population contractions, range shifts, habitat fragmentation, local extinctions, and genetic impoverishment. Despite alpine species not being ecologically identical, we predict all mountain biota will lose significant genetic diversity due to global warming.</span></p>
Genotyping results of the FabaPanel for: Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping
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Global warming leads to habitat loss and genetic erosion of alpine biodiversity
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Data from: Translocations spur population growth but fail to prevent genetic erosion in imperiled Florida Scrub-Jays
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Data from: How density dependence, genetic erosion, and the extinction vortex impact evolutionary rescue
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Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion
<p>The putatively positive association between host genetic diversity and the ability to defend against pathogens has long attracted the attention of evolutionary biologists. Chytridiomycosis, a disease caused by the chytrid fungus <em>Batrachochytrium dendrobatidis</em> (<em>Bd</em>), has emerged in recent decades as a cause of dramatic declines and extinctions across the amphibian clade. Bd susceptibility can vary widely across populations of the same species, but the relationship between standing genetic diversity and susceptibility has remained notably underexplored so far. Here, we focus on a putatively <em>Bd</em>-naive system of two mainland and two island populations of the common toad (<em>Bufo bufo</em>) at the edge of the species' range, and use controlled infection experiments and dd-RAD sequencing of >10,000 SNPs across 95 individuals to characterise the role of host population identity, genetic variation and individual body mass in mediating host response to the pathogen. We found strong genetic differentiation between populations and marked variation in their susceptibility to Bd. This variation was not, however, governed by isolation-mediated genetic erosion, and individual heterozygosity was even found to be negatively correlated with survival. Individual survival during infection experiments was strongly positively related to body mass, which itself was unrelated to population of origin or heterozygosity. Our findings underscore the general importance of context-dependency when assessing the role of host genetic variation for the ability of defence against pathogens.</p>
Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding
<p>Human water use combined with a recent megadrought have reduced river and stream flow through the Southwestern United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande Silvery Minnow. This species experiences 'boom-and-bust' population dynamics where large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We leveraged demographic and genetic data from wild and hatchery individuals to understand the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's <em>d</em>=1.34) and remains low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size (N<sub>eD</sub>) were positively associated (<em>r</em>=0.53) with wild/total abundance, but as the proportion of hatchery-origin spawners increased, N<sub>eD</sub> was reduced (N<sub>eD</sub> <em>r</em>= -0.55). Megadrought limits wild spawner abundance and precludes refreshment of hatchery brood stocks with wild fish, hence we predict an increasingly hatchery-dominated population, and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.</p>
Challenging a host-pathogen paradigm: Susceptibility to chytridiomycosis is decoupled from genetic erosion
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Genetic erosion in an endangered desert fish during a multi-decadal megadrought despite long-term supportive breeding
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Data from: Size-dependent genetic erosion due to human logging and conservation recommendation for an endangered Yew (Taxus fuana) in Tibet, China
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Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species' mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.
Data from: Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae)
Population extirpations are often precursors to species extinctions. Anthropogenic activities often lead to smaller populations that are more prone to extirpations and advocates for active conservation management have recently called for the preservation and monitoring of genetic diversity, particularly with regard to the adaptive potential of vulnerable populations. We used genomics and curated arrays of molecular markers, including those expected to impact key fitness traits, to quantify evidence of genomic erosion in core and peripheral populations of a gallinaceous bird. The Montezuma quail (Cyrtonyx montezumae) is a game species considered vulnerable to extirpation in Texas, but core populations in Arizona and New Mexico are robust and have the potential to serve as genetic reservoirs. We sequenced the Montezuma quail genome then developed a single nucleotide polymorphism (SNP) assay to quantify genetic variation, effective population sizes, signatures of natural selection, and population structure. We genotyped SNPs from gene deserts and from genes associated with fitness traits and found the isolated Texas population exhibits an extremely small effective population size, is genetically distinct from our Arizona and New Mexico samples, and has reduced heterozygosity at the fitness-related markers. Thus, our samples from Texas exhibit symptoms of genetic erosion that could exacerbate future risk of local extirpation. Management agencies must decide if active conservation efforts such as assisted gene flow or genetic rescue are now warranted. This decision may not be straightforward because the current conservation status of the Texas population reflects its isolated geographic locale on the periphery of the species' range.
Data from: Genetic erosion in wild populations makes resistance to a pathogen more costly
Populations that have suffered from genetic erosion are expected to exhibit reduced average trait values or decreased variation in adaptive traits when experiencing periodic or emergent stressors such as infectious disease. Genetic erosion may consequentially modify the ability of a potential host population to cope with infectious disease emergence. We experimentally investigate this relationship between genetic variability and host response to exposure to an infectious agent both in terms of susceptibility to infection and indirect parasite-mediated responses that also impact fitness. We hypothesized that the deleterious consequences of exposure to the pathogen (Batrachochytrium dendrobatidis) would be more severe for tadpoles descended from European tree frog (Hyla arborea) populations lacking genetic variability. Although all exposed tadpoles lacked detectable infection, we detected this relationship for some indirect host responses, predominantly in genetically depleted animals, as well as an interaction between genetic variability and pathogen dose on lifespan during the post-metamorphic period. Lack of infection and a decreased mass and post-metamorphic lifespan in low genetic diversity tadpoles lead us to conclude that genetic erosion, while not affecting the ability to mount effective resistance strategies, also erodes the capacity to invest in resistance, increased tadpole growth rate and metamorphosis relatively simultaneously.
Data, Code and Computational Environment for: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion
<p><strong>Data</strong></p> <p>The csv file "2023-06-27_data.csv" contains genetic profiles for all olive trees analyzed in the publication: Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion". The genotypes are provided in the GenAlEx format.</p> <p> </p> <p><strong>Code</strong></p> <p>Code is provided in the compressed folder "Tourvas_et_al_Olive". It is structured as a R project and can easily be opened, after decompressing, from the Rstudio interface. If you prefer to review and/or reuse code you can access it from the "analysis" folder inside the "Tourvas_et_al_Olive" folder.</p> <p> </p> <p><strong>Computational Environment</strong></p> <p>A tarball for the Docker image "tourvas_et_al_olive" is also provided. This is the recommended way to reproduce the results of the publication: "Wild olive tree genetic diversity in Greece: a diverse resource in danger of erosion".</p> <p>It is assumed that you already have Docker installed on your system. If not, please visit <a href="https://docs.docker.com/get-started/">https://docs.docker.com/get-started/</a></p> <p>To use it:</p> <ul> <li>download the image file tourvas_et_al_olive.tar</li> <li>load it with docker with the command:</li> </ul> <pre><code class="language-bash">docker load --input tourvas_et_al_olive.tar</code></pre> <ul> <li>then launch the Docker container with the command:</li> </ul> <pre><code class="language-bash">docker run --name popgen --rm -dp 8787:8787 -e ROOT=TRUE -e DISABLE_AUTH=true -v "`pwd`":/home/rstudio/working nikostourvas/tourvas_et_al_olive</code></pre> <ul> <li>start your favorite web browser and go to: http://localhost:8787/</li> <li>from the bottomright pane of the Rstudio server click on the directory "Tourvas_et_al_Olive" and open the project by clicking on the "Tourvas_et_al_Olive.Rproj" file</li> <li>launch the scripts inside the "analysis" directory and run them to reproduce results</li> </ul>
Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)
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Data from: Genetic erosion in wild populations makes resistance to a pathogen more costly
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Data from: Evidence of genetic erosion in a peripheral population of a North American game bird: the Montezuma quail (Cyrtonyx montezumae)
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Data from: Hybridization drives genetic erosion in sympatric desert fishes of western North America
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Data from: Within- and among-population impact of genetic erosion on adult fitness-related traits in the European tree frog Hyla arborea
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