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277 results for “invasion genetics”
Figure 1 in Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region - Greece
Figure 1. The study area in Kastoria region and capture locations (red dots) for the 75 living bears.
Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)
<p>The rapid expansion of wild pigs (<em>Sus scrofa</em>) throughout the United States (US) has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs – which overwhelmingly represent domestic pig-wild boar hybrids – pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pigs found within the US. We organized reference high-density single nucleotide polymorphism genotypes (1,039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed-commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well-established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (<em>sensu</em> genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis – that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6,566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.</p>
Fig. 1 MapshowingtherangeofthestudypopulationofEasternImperialEaglesinHungaryandthelocationofsampledandnotsampledterritoriesin 2003 in High Turnover Rate Revealed By Non-Invasive Genetic Analyses In An Expanding Eastern Imperial Eagle Population
Fig. 1 MapshowingtherangeofthestudypopulationofEasternImperialEaglesinHungaryandthelocationofsampledandnotsampledterritoriesin 2003 (35 ofthe 61 nesting
Fig. 2 in High Turnover Rate Revealed By Non-Invasive Genetic Analyses In An Expanding Eastern Imperial Eagle Population
Fig. 2. Firstidentification (1999, territorycodeBS-02) andre-identification (2003, BS-03) of afemale. Theterritorieswereapproximately 10 kmawayfromeachotherandtheoriginal BS-02 territorywasvacantin 2001-2002, butitwasoccupiedbyapairwithanewfemale in 2003; differentmarkingsrepresentdifferentgeneticallytaggedfemales, blackmarkings representthenestsfromtheBS-02 territory, greymarkingsrepresentnestsfromtheBS-03 territory; yearsinitalic (nestsmarkedbycircles) representnestingsiteswithoutsamples.
Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow
<p><span></span></p> <p>Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g., multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic.</p>
Fig. 2 in Analysis of propagule pressure and genetic diversity in the invasibility of a freshwater apex predator: the peacock bass (genus Cichla)
Fig. 2. Structure bar plots of probabilities of assignment of each individual from populations of CP in green (1 - TOC, 2 - ITU, 3 - ML and 4 - FU) and CK in red (5 - TOC, 6 - ITU, 7 - TRM, 8 - RD). Probabilities of assignment (q) of each individual to each cluster are shown along the x-axis.
Figure 2 in Reduced genetic diversity and the success of the invasive peacock bass (Cichliformes: Cichlidae)
Figure 2. Gray-greenish and yellowish types of Cichla collected in the reservoirs of the submiddle stretch of São Francisco River.
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
<p>1. Effective conservation requires accurate data on population genetic diversity, inbreeding, and genetic structure. Increasingly, scientists are adopting genetic non-invasive sampling as a cost-effective population-wide genetic monitoring approach. Genetic non-invasive sampling has, however, known limitations which may impact the accuracy of downstream genetic analyses.</p> <p>2. Here, using high quality SNP data from blood/tissue sampling of a free-ranging koala population (n = 430), we investigated how the reduced SNP panel size and call rate typical of genetic non-invasive samples (derived from experimental and field trials) impacts the accuracy of genetic measures, and also the effect of sampling intensity on these measures.</p> <p>3. We found that genetic non-invasive sampling at small sample sizes (14% of population) can provide accurate population diversity measures, but slightly underestimated population inbreeding coefficients. Accurate measures of internal relatedness required at least 33% of the population to be sampled. Accurate geographic and genetic spatial autocorrelation analysis requires between 28% and 51% of the population to be sampled.</p> <p>4. We show that genetic non-invasive sampling at low sample sizes can provide a powerful tool to aid conservation decision-making and provide recommendations for researchers looking to apply these techniques to free-ranging systems.</p>
Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: the case of Pseudocercospora fijiensis invasion in Africa
<p class="MsoNormal"><span>The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step towards improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana, <em>Pseudocercospora fijiensis</em>, by testing the historical hypothesis against other plausible hypotheses. We analysed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers, and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.</span></p>
The ash dieback invasion of Europe was founded by two genetically divergent individuals (https://doi.org/10.1038/s41559-018-0548-9)
<p>Hymenoscyphus fraxineus, genome, annotation and genetic diversity data used in analysis of the ash dieback invasion of Europe (McMullan et al., 2018; see README.txt)</p> <p>McMullan M, Rafiqi M, Kaithakottil G, Clavijo BJ, Bilham L, Orton E, et al. The ash dieback invasion of Europe was founded by two genetically divergent individuals. Nat Ecol Evol. 2018; Available from: https://doi.org/10.1038/s41559-018-0548-9</p>
Testing the effectiveness of genetic monitoring using genetic non-invasive sampling
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Population genetics and invasion history of the European Starling across Aotearoa New Zealand
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Data from: Population analysis reveals genetic structure of an invasive agricultural thrips pest related to invasion of greenhouses and suitable climatic space
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Data from: Genetic reconstruction of a bullfrog invasion to elucidate vectors of introduction and secondary spread
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Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow
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Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: the case of Pseudocercospora fijiensis invasion in Africa
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Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)
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Data from: Cropland connectivity affects genetic divergence of Colorado potato beetle along an invasion front
<p>The population genetic structure of invasive species can be strongly affected by environmental and landscape barriers to dispersal. Disentangling the relative contributions of these factors to genetic divergence among invading populations is a fundamental goal of landscape genetics with important implications for invasion management. Here, we relate patterns of genetic divergence in a global invasive agricultural pest, Colorado potato beetle (CPB; Leptinotarsa decemlineata), to environmental and landscape factors along an invasion front in Northwestern China. We first used microsatellite markers and spatial-temporal samples to assess broad patterns of genetic diversity as well as fine-scale changes in patterns of genetic divergence. We then distinguished the relative contributions of five factors to genetic divergence among front populations: geographic distance (isolation by distance), climate dissimilarity (isolation by environment), and least-cost distances (isolation by resistance) modelled with three factors: climate suitability, cropland cover, and road networks. Genetic diversity broadly decreased from West to East, with the exception being Eastern China. Low levels of genetic diversity and varying degrees of divergence were observed in Northwestern China, reflecting the potential effect of landscape heterogeneity. Least-cost distance across cropland cover was most positively correlated with genetic divergence, suggesting a role of croplands in facilitating gene flow. The contribution of climate to genetic divergence was secondary, whether modelled in terms of local adaptability or connectivity of the climatic landscape, suggesting that constraints to CPB gene flow imposed by a harsh climate may be ameliorated in agricultural landscapes. No evidence was found for an obvious effect of road networks on genetic divergence and population structuring. Our study provides an example of how agricultural landscape connectivity can facilitate the spread of invasive pests, even across a broad climatic gradient. More broadly, our findings can guide decisions about future land management for mitigating further spread.</p>
Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)
Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.
A lack of genetically compatible mates constrains the spread of an invasive weed
<ul> <li>Introduced populations often experience lag-times prior to invasion, but the mechanisms constraining rapid expansions of introduced populations are unclear. <i>Solidago altissima</i> is a North American native plant with highly invasive Japanese populations, and introduced Australian populations that are not invasive despite the climatic and ecological suitability of the region.</li> <li>By contrasting Australian with Japanese populations, we tested the hypothesis that Australian population growth is limited by a lack of long-distance dispersal via seeds due to limited number of compatible mates. </li> <li>In the field, Australian populations rarely produced viable seeds. A cross-pollination experiment found that Australian plants are fertile, yet lack compatible mates within Australia. Genetic analysis revealed that Australian individuals descend from a small set of self-incompatible genetic clones, which explains the negligible seed set within Australia.</li> <li>Our results show that low genetic diversity, leading to mate incompatibility, inhibits invasiveness of Australian <i>S. altissima</i>, and provides compelling evidence for genetic, rather than ecological, factors constraining invasion in Australia.</li> </ul>
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OpenNeuro
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