Dataset Information

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

ABSTRACT: Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an invasive population of the Javan Myna Acridotheres javanicus across the island of Singapore. We inferred limited population subdivision at a micro-geographic level, a genetic patch size (~13-14?km) indicative of a pronounced dispersal ability, and barely an increase in effective population size since introduction despite an increase of four to five orders of magnitude in actual population size, suggesting that low population-genetic diversity following a bottleneck has not impeded establishment success. Landscape genomic analyses identified urban features, such as low-rise neighborhoods, that constitute pronounced barriers to gene flow. Based on our data, we consider an approach targeting the complete eradication of Javan Mynas across Singapore to be unfeasible. Instead, a mixed approach of localized mitigation measures taking into account urban geographic features and planning policy may be the most promising avenue to reducing the adverse impacts of this urban pest. Our study demonstrates how genomic methods can directly inform the management and control of invasive species, even in geographically limited datasets with high gene flow rates.

SUBMITTER: Low GW

PROVIDER: S-EPMC5837122 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Low G W GW Chattopadhyay B B Garg K M KM Irestedt M M Ericson Pgp P Yap G G Tang Q Q Wu S S Rheindt F E FE

Heredity 20171211 2

Invasive species exert a serious impact on native fauna and flora and have been the target of many eradication and management efforts worldwide. However, a lack of data on population structure and history, exacerbated by the recency of many species introductions, limits the efficiency with which such species can be kept at bay. In this study we generated a novel genome of high assembly quality and genotyped 4735 genome-wide single nucleotide polymorphic (SNP) markers from 78 individuals of an in ...[more]

PMID: 29225353

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Project description:Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators.

Project description:Simple Summary Restoration of biodiversity in urban green spaces frequently requires eradication or management of invasive species. We aimed to identify fine- and landscape-scale habitat features associated with the presence of five invasive urban mammals (Rattus species, European hedgehogs, mice, and brushtail possums) in three urban green space types (forest fragment, amenity park, residential garden) across three New Zealand cities, and across two seasons, to identify where management effort should be focused. All species were detected in all greenspace types; however, rodents were detected least in residential gardens, possums were detected most often in forest fragments, and hedgehogs least in forest fragments. Proximity of amenity parks to forest patches was positively associated with possum and hedgehog presence and negatively with rats. Conversely, proximity of residential gardens to forest patches was positively associated with rat presence. Management of rats should focus on sites with shrub and lower canopy cover and of mice on sites with herb layer cover, while micro-habitat features were not important for hedgehogs and possums. Rats were most likely to be found in residential gardens with compost heaps. The wide distributions of these species suggest that in order to be successful, ecological restoration must be coordinated, target all green space types, and engage urban residents. Abstract A barrier to successful ecological restoration of urban green spaces in many cities is invasive mammalian predators. We determined the fine- and landscape-scale habitat characteristics associated with the presence of five urban predators (black and brown rats, European hedgehogs, house mice, and brushtail possums) in three New Zealand cities, in spring and autumn, in three green space types: forest fragments, amenity parks, and residential gardens. Season contributed to variations in detections for all five taxa. Rodents were detected least in residential gardens; mice were detected more often in amenity parks. Hedgehogs were detected least in forest fragments. Possums were detected most often in forest fragments and least often in residential gardens. Some of this variation was explained by our models. Proximity of amenity parks to forest patches was strongly associated with presence of possums (positively), hedgehogs (positively), and rats (negatively). Conversely, proximity of residential gardens to forest patches was positively associated with rat presence. Rats were associated with shrub and lower canopy cover and mice with herb layer cover. In residential gardens, rat detection was associated with compost heaps. Successful restoration of biodiversity in these cities needs extensive, coordinated predator control programmes that engage urban residents.

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Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

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Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

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