scholarly journals Simulating Pattern-Process Relationships to Validate Landscape Genetic Models

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
A. J. Shirk ◽  
S. A. Cushman ◽  
E. L. Landguth
Keyword(s):  
Gene Flow ◽  
Genetic Model ◽  
Strong Relationship ◽  
Genetic Isolation ◽  
Landscape Resistance ◽  
Oreamnos Americanus ◽  
Landscape Models ◽  
Genetic Pattern ◽  
Alternative Hypotheses ◽  
Landscape Genetic

Landscapes may resist gene flow and thereby give rise to a pattern of genetic isolation within a population. The mechanism by which a landscape resists gene flow can be inferred by evaluating the relationship between landscape models and an observed pattern of genetic isolation. This approach risks false inferences because researchers can never feasibly test all plausible alternative hypotheses. In this paper, rather than infer the process of gene flow from an observed genetic pattern, we simulate gene flow and determine if the simulated genetic pattern is related to the observed empirical genetic pattern. This is a form of inverse modeling and can be used to independently validate a landscape genetic model. In this study, we used this approach to validate a model of landscape resistance based on elevation, landcover, and roads that was previously related to genetic isolation among mountain goats (Oreamnos americanus) inhabiting the Cascade Range, Washington (USA). The strong relationship between the empirical and simulated patterns of genetic isolation we observed provides independent validation of the resistance model and demonstrates the utility of this approach in supporting landscape genetic inferences.

scholarly journals Using empirical datasets to quantify uncertainty in inferences of landscape genetic resistance due to variation of individual-based genetic distance metrics

2021 ◽  
Author(s):  
Joscha Beninde ◽  
Alain C. Frantz
Keyword(s):  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Resistance ◽  
List Type ◽  
Distance Metrics ◽  
Factorial Correspondence Analysis ◽  
Landscape Resistance ◽  
Landscape Factors ◽  
Landscape Genetic ◽  
The Impact

AbstractEstimates of gene flow are commonly based on inferences of landscape resistance in ecological and evolutionary research and they frequently inform decision-making processes in conservation management. It is therefore imperative that inferences of a landscape factors relevance and its resistance are robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 160 different individual-based pairwise genetic metrics on consistency of landscape genetic inferences.We used three empirical datasets that adopted individual-based sampling schemes and varied in scale (35-25,000 km2) and total number of samples (184-790) and comprise the wild boar, Sus scrofa, the red fox, Vulpes vulpes and the common wall lizard, Podarcis muralis. We made use of a machine-learning algorithm implemented in ResistanceGA to optimally fit resistances of landscape factors to genetic distance metrics and ranked their importance. Employed for nine landscape factors this resulted in 4,320 unique combinations of dataset, landscape factor and genetic distance metric, which provides the basis for quantifying uncertainty in inferences of landscape resistance.Our results demonstrate that there are clear differences in Akaike information criteria (AICc)-based model support and marginal R2-based model fit between different genetic distance metrics. Metrics based on between 1-10 axes of eigenvector-based multivariate analyses (Factorial correspondence analysis, FCA; Principal component analysis, PCA) outperformed more widely used metrics, including the proportion of shared alleles (DPS), with AICc and marginal R2 values often an order of magnitude greater in the former. Across datasets, inferences of the directionality of a landscape factors influence on gene flow, e.g. facilitating or impeding it, changed across different genetic distance metrics. The directionality of the inferred resistance was largely consistent when considering metrics based on between 1-10 FCA/PCA axes.Inferences of landscape genetic resistance need to be corroborated using calculations of multiple individual-based pairwise genetic distance metrics. Our results call for the adoption of eigenvector-based quantifications of pairwise genetic distances. Specifically, a preliminary step of analysis should be incorporated, which explores model ranks across genetic distance metrics derived from FCA and PCA, and, contrary to findings of a simulation study, we demonstrate that it suffices to quantify these distances spanning the first ten axes only.

scholarly journals Using simulations to evaluate Mantel‐based methods for assessing landscape resistance to gene flow

2016 ◽  
Vol 6 (12) ◽  
pp. 4115-4128 ◽  
Author(s):  
Katherine A. Zeller ◽  
Tyler G. Creech ◽  
Katie L. Millette ◽  
Rachel S. Crowhurst ◽  
Robert A. Long ◽  
...  
Keyword(s):  
Gene Flow ◽  
Landscape Resistance

Landscape Genetic Approaches to Understanding Movement and Gene Flow in Cities

2020 ◽  
pp. 54-73
Author(s):  
Jason Munshi-South ◽  
Jonathan L. Richardson
Keyword(s):  
Gene Flow ◽  
Urban Landscape ◽  
Bare Soil ◽  
Urban Environments ◽  
Urban Habitats ◽  
Urban Neighbourhoods ◽  
Direct Tracking ◽  
Landscape Genetic ◽  
The Many ◽  
Socioeconomic Data

Cities are home to a continuum of species that range from those specially adapted to exploit urban habitats, to others passing through as transient dispersers. Urbanization often has a profound impact on the movement and gene flow of these species. Compared to natural landscapes, urban environments are complex matrices of roads, buildings, bare soil, slopes, green space, and subterranean infrastructure. Urban neighbourhoods also vary greatly in their socioeconomic and cultural characteristics. This heterogeneity can lead to complex movement patterns in wildlife that are difficult or impossible to characterize using direct tracking methods. Population genetic analyses provide powerful approaches to evaluate spatial patterns of genetic variation and even signatures of adaptive evolution across the genome. When analysed with landscape, environmental, and socioeconomic data, genetic approaches may also identify which features of urban habitats impede or facilitate gene flow. These landscape genetic approaches, when paired with high-resolution sampling and replicated studies across multiple cities, identify dynamic processes that underpin wildlife movement in cities. This chapter reviews the use of spatially explicit genetic approaches in understanding urban wildlife movement, and highlights the many insights gained from rodents in particular as models for urban landscape genetics.

scholarly journals Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 135 ◽  
Author(s):  
Jingxue Zhang ◽  
Miaoli Wang ◽  
Zhipeng Guo ◽  
Yongzhuo Guan ◽  
Jianyu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Genetic ◽  
Cynodon Dactylon ◽  
Latitudinal Gradients ◽  
Wind Pollination ◽  
Ploidy Levels ◽  
Sexual And Asexual Reproduction ◽  
Genetic Pattern

Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.

Temporal landscape genetic data indicate an ongoing disruption of gene flow in a relict bird species

2020 ◽  
Vol 21 (2) ◽  
pp. 329-340
Author(s):  
Peter Klinga ◽  
Martin Mikoláš ◽  
Ivan V. Delegan ◽  
Gabriel Dănilă ◽  
Peter Urban ◽  
...  
Keyword(s):  
Gene Flow ◽  
Bird Species ◽  
Genetic Data ◽  
Landscape Genetic

scholarly journals Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

2019 ◽  
Vol 9 (6) ◽  
pp. 3059-3074 ◽  
Author(s):  
Mei Yang ◽  
Chengyuan Xu ◽  
Pierre Duchesne ◽  
Qiang Ma ◽  
Ganqiang Yin ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Scirpus Mariqueter ◽  
Landscape Genetic ◽  
Adaptive Differentiation

scholarly journals Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

2020 ◽  
Vol 29 (3) ◽  
pp. 466-484 ◽  
Author(s):  
Sophia E. Kimmig ◽  
Joscha Beninde ◽  
Miriam Brandt ◽  
Anna Schleimer ◽  
Stephanie Kramer‐Schadt ◽  
...  
Keyword(s):  
Gene Flow ◽  
Metropolitan Area ◽  
Landscape Resistance

The interplay between dispersal and gene flow in anadromous Arctic char (Salvelinus alpinus): implications for potential for local adaptation

2013 ◽  
Vol 70 (9) ◽  
pp. 1327-1338 ◽  
Author(s):  
Jean-Sébastien Moore ◽  
Les N. Harris ◽  
Ross F. Tallman ◽  
Eric B. Taylor
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Genetic Model ◽  
Salvelinus Alpinus ◽  
Arctic Char ◽  
Baffin Island ◽  
Assignment Method ◽  
Natal Habitat ◽  
Breeding Condition ◽  
Assignment Approach

Dispersal can influence the process of local adaptation, particularly when the dispersers successfully breed in the non-natal habitat. Anadromous Arctic char (Salvelinus alpinus) display a complex migratory behaviour that makes the distinction between breeding and nonbreeding dispersal especially important. This species does not reproduce every year, but individuals must migrate to fresh water to overwinter such that a large proportion of fish running up-river are not in breeding condition and have no potential for gene flow. We used a genetic assignment approach to identify dispersers among populations of char from Baffin Island, Canada. Estimates of dispersal varied between 15.8% and 25.5% depending on the assignment method, suggesting that Arctic char disperse at a higher rate than other salmonids. Nonbreeding individuals were more likely to use non-natal habitats than breeding individuals, thus resulting in estimates of dispersal that overestimate the potential for gene flow among populations. Finally, we parameterized a population genetic model showing that gene flow is probably sufficiently low to allow for local adaptation among populations, given realistic selection coefficients. Our results underscore the importance of understanding patterns of dispersal to appropriately evaluate their potential consequences for local adaptation and management.

scholarly journals Sex-biased dispersal and spatial heterogeneity affect landscape resistance to gene flow in fisher

Ecosphere ◽  
2017 ◽  
Vol 8 (6) ◽  
pp. e01839 ◽  
Author(s):  
Jody M. Tucker ◽  
Fred W. Allendorf ◽  
Richard L. Truex ◽  
Michael K. Schwartz
Keyword(s):  
Gene Flow ◽  
Spatial Heterogeneity ◽  
Landscape Resistance
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