Landscapes and Plant Population Genetics

Dyer, Rodney J.

doi:10.1002/9781118525258.ch11

Cited by 5 publications

(5 citation statements)

References 129 publications

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“…We chose this time span considering observations made by botanists from the Carajás Zoo Botanical Park, whom have planted both species for public exhibitions and estimate generation times of ~20 years for I. cavalcantei and ~3 years for I. maurandioides . Since elevation, terrain roughness, mean temperature and mean precipitation have been found to influence gene flow in other plant species (Dyer, 2016 ), we constructed resistance surfaces employing both the raw and inverted rasters for each one of these variables (see Table S2 for spatial data specifications). Finally, we used a land cover map to create a null model for isolation by resistance (isolation by geographic distance), where all pixels were coded with identical resistance values (0.1).…”

Section: Methodsmentioning

confidence: 99%

Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas

et al. 2018

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Although genetic diversity ultimately determines the ability of organisms to adapt to environmental changes, conservation assessments like the widely used International Union for Conservation of Nature (IUCN) Red List Criteria do not explicitly consider genetic information. Including a genetic dimension into the IUCN Red List Criteria would greatly enhance conservation efforts, because the demographic parameters traditionally considered are poor predictors of the evolutionary resilience of natural populations to global change. Here we perform the first genomic assessment of genetic diversity, gene flow, and patterns of local adaptation in tropical plant species belonging to different IUCN Red List Categories. Employing RAD-sequencing we identified tens of thousands of single-nucleotide polymorphisms in an endangered narrow-endemic and a least concern widespread morning glory (Convolvulaceae) from Amazonian savannas, a highly threatened and under-protected tropical ecosystem. Our results reveal greater genetic diversity and less spatial genetic structure in the endangered species. Whereas terrain roughness affected gene flow in both species, forested and mining areas were found to hinder gene flow in the endangered plant. Finally we implemented environmental association tests and genome scans for selection, and identified a higher proportion of candidate adaptive loci in the widespread species. These mainly contained genes related to pathogen resistance and physiological adaptations to life in nutrient-limited environments. Our study emphasizes that IUCN Red List Criteria do not always prioritize species with low genetic diversity or whose genetic variation is being affected by habitat loss and fragmentation, and calls for the inclusion of genetic information into conservation assessments. More generally, our study exemplifies how landscape genomic tools can be employed to assess the status, threats and adaptive responses of imperiled biodiversity.

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Section: Methodsmentioning

confidence: 99%

Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas

et al. 2018

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“…As functional connectivity is ultimately concerned with gene flow in time and space, landscape genetics provide a useful methodological toolbox to measure realized connectivity by explicitly incorporating spatial information to investigate gene flow in a landscape (Holderegger et al . ; Dyer ; Fig. ).…”

Section: Assessing Plant Functional Connectivitymentioning

confidence: 99%

Plant functional connectivity – integrating landscape structure and effective dispersal

et al. 2017

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Summary Dispersal is essential for species to survive the threats of habitat destruction and climate change. Combining descriptions of dispersal ability with those of landscape structure, the concept of functional connectivity has been popular for understanding and predicting species’ spatial responses to environmental change. Following recent advances, the functional connectivity concept is now able to move beyond landscape structure to consider more explicitly how other external factors such as climate and resources affect species movement. We argue that these factors, in addition to a consideration of the complete dispersal process, are critical for an accurate understanding of functional connectivity for plant species in response to environmental change. We use recent advances in dispersal, landscape and molecular ecology to describe how a range of external factors can influence effective dispersal in plant species, and how the resulting functional connectivity can be assessed. Synthesis. We define plant functional connectivity as the effective dispersal of propagules or pollen among habitat patches in a landscape. Plant functional connectivity is determined by a combination of landscape structure, interactions between plant, environment and dispersal vectors, and the successful establishment of individuals. We hope that this consolidation of recent research will help focus future connectivity research and conservation.

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“…By so doing we were able to evaluate the permeability to gene flow of each land cover class; and test whether habitat loss driven by mining hindered gene flow across our replicated landscapes. Additional variables found to be important predictors of gene flow in other plants (Dyer, 2016; Lanes et al, 2018) were modeled along with land cover, including geographic distance, elevation [digital elevation model (DEM) retrieved from the USGS Earth Explorer], terrain roughness (generated from the DEM using the Terrain Analysis plug-in from QGIS), and bioclimatic variables (retrieved from WorldClim). To select a set of orthogonal variables explaining most climatic variation across our study area, we first ran separate principal component analyses (PCA) for each species using the extracted values from all 19 WorldClim bioclimatic layers plus elevation (scaled) ( Figure S2 ).…”

Section: Methodsmentioning

confidence: 99%

Habitat Loss Does Not Always Entail Negative Genetic Consequences

et al. 2019

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Although habitat loss has large, consistently negative effects on biodiversity, its genetic consequences are not yet fully understood. This is because measuring the genetic consequences of habitat loss requires accounting for major methodological limitations like the confounding effect of habitat fragmentation, historical processes underpinning genetic differentiation, time-lags between the onset of disturbances and genetic outcomes, and the need for large numbers of samples, genetic markers, and replicated landscapes to ensure sufficient statistical power. In this paper we overcame all these challenges to assess the genetic consequences of extreme habitat loss driven by mining in two herbs endemic to Amazonian savannas. Relying on genotyping-by-sequencing of hundreds of individuals collected across two mining landscapes, we identified thousands of neutral and independent single-nucleotide polymorphisms (SNPs) in each species and used these to evaluate population structure, genetic diversity, and gene flow. Since open-pit mining in our study region rarely involves habitat fragmentation, we were able to assess the independent effect of habitat loss. We also accounted for the underlying population structure when assessing landscape effects on genetic diversity and gene flow, examined the sensitivity of our analyses to the resolution of spatial data, and used annual species and cross-year analyses to minimize and quantify possible time-lag effects. We found that both species are remarkably resilient, as genetic diversity and gene flow patterns were unaffected by habitat loss. Whereas historical habitat amount was found to influence inbreeding; heterozygosity and inbreeding were not affected by habitat loss in either species, and gene flow was mainly influenced by geographic distance, pre-mining land cover, and local climate. Our study demonstrates that it is not possible to generalize about the genetic consequences of habitat loss, and implies that future conservation efforts need to consider species-specific genetic information.

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Landscapes and Plant Population Genetics

Cited by 5 publications

References 129 publications

Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas

Landscape Genomic Conservation Assessment of a Narrow-Endemic and a Widespread Morning Glory From Amazonian Savannas

Plant functional connectivity – integrating landscape structure and effective dispersal

Habitat Loss Does Not Always Entail Negative Genetic Consequences

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