DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors
TLDR
A new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ' , χ2 test for population heterogeneity), among others.Abstract:
Summary
We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (θ, GST) and population differentiation statistics (DJost, GST ', χ2 test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective.
diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs).
Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis.read more
Citations
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Journal ArticleDOI
Evaluating the influence of life-history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes.
TL;DR: The difference in predictors of occupancy, abundance, and gene flow suggests that species‐specific responses to fragmentation are scale dependent.
Journal ArticleDOI
Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region
TL;DR: Sculpins in the Aare catchment appear to represent an early‐stage adaptive radiation involving the evolution of a lacustrine lineage distinct from parapatric stream sculpins and the repeated onset of depth‐related intralacustrine differentiation.
Journal ArticleDOI
Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales.
Christopher P. Kozakiewicz,Christopher P. Burridge,W. Chris Funk,Patricia E. Salerno,Daryl R. Trumbo,Roderick B. Gagne,Roderick B. Gagne,Erin E. Boydston,Robert N. Fisher,Lisa M. Lyren,Megan K. Jennings,Seth P. D. Riley,Laurel E. K. Serieys,Laurel E. K. Serieys,Sue VandeWoude,Kevin R. Crooks,Scott Carver +16 more
TL;DR: The results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure, and confirm a pervasive impact of urbanization largely independent of spatial scale.
Journal ArticleDOI
Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia.
Anurag Chaturvedi,Anurag Chaturvedi,Anurag Chaturvedi,Jiarui Zhou,Joost A. M. Raeymaekers,Joost A. M. Raeymaekers,Till Czypionka,Luisa Orsini,Craig Jackson,Katina I. Spanier,Joseph R. Shaw,John K. Colbourne,Luc De Meester,Luc De Meester,Luc De Meester +14 more
TL;DR: In this paper, the origin and maintenance of standing genetic variation that enables rapid evolutionary responses of natural populations is studied. But the authors lack a thorough understanding of the origin of standing genomic variation that enable rapid evolutionary response of natural population.
Journal ArticleDOI
Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus
Alex D. Twyford,Alex D. Twyford,Alex D. Twyford,Edgar L. Y. Wong,Edgar L. Y. Wong,Jannice Friedman,Jannice Friedman +6 more
TL;DR: This work uses reduced-representation sequencing and marker-based genotyping to understand dispersal dynamics and to characterise genetic structure in Mimulus guttatus, and demonstrates how dispersal affects spatial genetic variation at the local, regional, and range-wide scale.
References
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