GStudio: An R Package for Spatial Analysis of Marker Data

This is the main package that provides data types and routines for spatial analysis of genetic marker data. The previous version is currently available on CRAN and you can install it rom within your R environtment by invoking the command

install.packages("gstudio")

If you want to keep up with the latest developments of this package, you can use the version found on GitHub.  Install it from within R as:

require(devtools)
install_github("dyerlab/gstudio")

and that should get you up-to-date.  You’ll need to have a fully working LaTeX install and some other stuff to build it if you fork.

The Users Manual for the package with several examples can be found here

I have started a github account for this package, you can get access to the whole codebase read about it on the wiki, and contribute to the project from its repo at https://github.com/dyerlab.

Dyer RJ. 2005. Gener: a server-based analysis of pollen pool structure. Molecular Ecology Notes, 5 971-973.

Dyer RJ. 2005. Gener: a server-based analysis of pollen pool structure. Molecular Ecology Notes, 5 971-973.

The server-based program GENER performs the two-generation analysis of pollen flow for data consisting of mother/offspring arrays using genetic markers. The GENER program decomposes the genetic variance sampled by maternal individuals within and among pollen pool components of genetic variance and is accessible from http://dyerlab.bio.vcu.edu. These estimates are used to construct the test statistic, Φft, whose significance is tested via permutation. The Φft statistic can subsequently be used to quantify genetic effective pollen donor population size (Nep), effective mating area and dispersal distance. Furthermore, the GENER program can calculate Φft values for all pairs of substrata within the data set.

DOI: 10.1111/j.1471-8286.2005.01113.x

Dyer RJ, Westfall RD, Sork VL, Smouse PE. 2004. Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure. Heredity, 92 204-211.

Dyer RJ, Westfall RD, Sork VL, Smouse PE. 2004. Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure. Heredity, 92 204-211.

Patterns of pollen dispersal are central to both the ecology and evolution of plant populations. However, the mechan- isms controlling either the dispersal process itself or our estimation of that process may be influenced by site-specific factors such as local forest structure and nonuniform adult genetic structure. Here, we present an extension of the AMOVA model applied to the recently developed TWOGENER analysis of pollen pool structure. This model, dubbed the Stepwise AMOVA (StAMOVA), focuses on determining to what extent ecological, demographic, and/or environmental factors influence the observed genetic variation in spatially separated pollen pools. The analysis is verified for efficacy, using an extensive battery of simulations, illustrating: (1) how nonuniform adult genetic structure influences the differentiation of spatially separated pollen pools, and (2) how effectively the Stepwise analysis performs in carrying out the appropriate corrections. Finally, the model is applied to a Quercus alba data set, from which we have prior evidence that the adult genetic structure is nonuniformly distributed across the sampling landscape. From this data set, we show how the Stepwise model can be applied to remove the effects of spatial adult genetic structure on pollen pool differentiation and contrast these results with those derived from the original TWOGENER analysis.

DOI: 10.1038/sj.hdy.6800397

Sork VL, Davis FW, Smouse PE, Apsit VJ, Dyer RJ, Fernandez-M JF, Kuhn B. 2002. Pollen movement in declining populations of California Valley oak, Quercus lobata: where have all the fathers gone? Molecular Ecology, 11 1657-1668.

Sork VL, Davis FW, Smouse PE, Apsit VJ, Dyer RJ, Fernandez-M JF, Kuhn B. 2002. Pollen movement in declining populations of California Valley oak, Quercus lobata: where have all the fathers gone? Molecular Ecology, 11 1657-1668.

The fragmented populations and reduced population densities that result from human disturbance are issues of growing importance in evolutionary and conservation biology. A key issue is whether remnant individuals become reproductively isolated. California Valley oak (Quercus lobata) is a widely distributed, endemic species in California, increasingly jeopardized by anthropogenic changes in biota and land use. We studied pollen movement in a savannah population of Valley oak at Sedgwick Reserve, Santa Barbara County, to estimate effective number of pollen donors (Nep) and average distance of effective pollen movement (δ). Using TWOGENER, our recently developed hybrid model of paternity and genetic structure treatments that analyses maternal and progeny multilocus genotypes, we found that current Nep = 3.68 individuals. Based on an average adult density of d = 1.19 stems/ha, we assumed a bivariate normal distribution to model current average pollen dispersal distance (δ) and estimated δ = 64.8 m. We then deployed our parameter estimates in spatially explicit models of the Sedgwick population to evaluate the extent to which Nep may have changed, as a consequence of progressive stand thinning between 1944 and 1999. Assuming that pollen dispersal distance has not changed, we estimate Nep was 4.57 individuals in 1944, when stand density was 1.48. Both estimates indicate fewer effective fathers than one might expect for wind-pollinated species and fewer than observed elsewhere. The results presented here provide a basis for further refinements on modelling pollen movement. If the trends continue, then ongoing demographic attrition could further reduce neighbourhood size in Valley oak resulting in increased risk of reproductive failure and genetic isolation.

DOI: 10.1046/j.1365-294X.2002.01574.x

Sork VL, Davis FW, Dyer RJ, Smouse PE. 2002. Mating patterns in a savanna population of Valley Oak (Quercus lobata Nee). USDA Forest SErvice Gen. Tech. Rep, PSW-GTR-184 427-439.

Sork VL, Davis FW, Dyer RJ, Smouse PE. 2002. Mating patterns in a savanna population of Valley Oak (Quercus lobata Nee). USDA Forest SErvice Gen. Tech. Rep, PSW-GTR-184 427-439.

California valley oak is threatened by landscape alteration and failing recruitment in remnant stands. Its reproductive ecology is a key element of the seedling recruitment process. We first examine the mating system, to determine the extent of inbreeding in a population at Sedgwick Reserve, in Santa Barbara County. We then quantify variation in germination success and acorn size, evaluating their spatial patterns across the site. We collected acorns from 21 mapped focal trees in fall 1999, measured their average seed weight and germination success, and identified their multilocus genotypes. Using a mixed mating model, we observed significant, but modest selfing (outcrossing rate: tm = 0.96) and no mating among relatives (tm – ts) = 0.0. The effective pollen donor number was estimated to be between 5 and 7 individuals, depending on the inbreeding coefficient of the adults. These mating results indicate relatively little inbreeding but low numbers of pollen donors. Mothers differed significantly in seed weight (range: ~ 4 – 10 g) and germination percentage (range: 0 – 90 percent), and a bivariate analysis showed a gradient across the study site. Such a pattern suggests that environment conditions influence acorn size and germination success. Future work will address whether isolated individuals are at risk of selfing, for the expression of inbreeding depression on seed traits, or a reduction in the effective pollen donor number.

USDA Forest Service Gen. Tech. Rep. PSW-GTR-184.

Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape I. Male gamete heterogeneity among females. Evolution, 55 260-271.

Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape I. Male gamete heterogeneity among females. Evolution, 55 260-271.

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processes and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model’s elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model’s effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by ΦFT, a male gametic analogue of Wright’s FST and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that ΦFT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

DOI: 10.1111/j.0014-3820.2001.tb01291.x

Dyer RJ, Sork VL. 2001. Pollen pool heterogeneity in shortleaf pine, Pinus echinata, Mill. Molecular Ecology, 10 859-866.

Pollen is the dominant vector of gamete exchange for most temperate tree species. Because pollen movement influences the creation, maintenance and erosion of genetic structure in adult populations, it is important to understand what factors influence the process of pollen movement. Isolation by distance in pollen donor populations can create highly structured pollen polls by increased sampling of local fathers. Extrinsic factors, such as the intervening vegetative structure and local pollen donor densities, can also influence the genetic composition of local pollen pools. Using paternally inherited chloroplast microsatellite markers, we examined the structure and diversity of pollen pools in Pinus echinata Mill. in southern Missouri, USA. Our analysis is based on a multivariate AMOVA analysis of stands (~1 ha; six per region) nested within regions (~800 ha; four each). Significant multilocus structure of the pollen pool within regions (ΦSR = 0.095), but not among regions (ΦRT = 0.010), indicates that pollen movement is relatively restricted. Furthermore, the significant correlation between pairwise genetic and physical distances (Mantel correlation; ρ = 0.32) provided support for the isolation by distance hypothesis. Our results indicated that availability of pollen donors did not affect diversity of the pollen pool, measured by the number of unique multilocus genotypes at each stand. However, pollen pool diversity was negatively associated with vegetative structure, measured as total forest tree density. Our findings indicated that on-going pollen movement within continuous forest is relatively restricted as a result of both isolation by distance and vegetative structure.

DOI: 10.1046/j.1365-294X.2001.01251.x

Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape I. Male gamete heterogeneity among females. Evolution, 55 260-271.

Smouse PE, Dyer RJ, Westfall RD, Sork VL. 2001. Two-generation analysis of pollen flow across a landscape I. Male gamete heterogeneity among females. Evolution, 55 260-271.

Gene flow is a key factor in the spatial genetic structure in spatially distributed species. Evolutionary biologists interested in microevolutionary processes and conservation biologists interested in the impact of landscape change require a method that measures the real time process of gene movement. We present a novel two-generation (parent-offspring) approach to the study of genetic structure (TwoGener) that allows us to quantify heterogeneity among the male gamete pools sampled by maternal trees scattered across the landscape and to estimate mean pollination distance and effective neighborhood size. First, we describe the model’s elements: genetic distance matrices to estimate intergametic distances, molecular analysis of variance to determine whether pollen profiles differ among mothers, and optimal sampling considerations. Second, we evaluate the model’s effectiveness by simulating spatially distributed populations. Spatial heterogeneity in male gametes can be estimated by ΦFT, a male gametic analogue of Wright’s FST and an inverse function of mean pollination distance. We illustrate TwoGener in cases where the male gamete can be categorically or ambiguously determined. This approach does not require the high level of genetic resolution needed by parentage analysis, but the ambiguous case is vulnerable to bias in the absence of adequate genetic resolution. Finally, we apply TwoGener to an empirical study of Quercus alba in Missouri Ozark forests. We find that ΦFT = 0.06, translating into about eight effective pollen donors per female and an effective pollination neighborhood as a circle of radius about 17 m. Effective pollen movement in Q. alba is more restricted than previously realized, even though pollen is capable of moving large distances. This case study illustrates that, with a modest investment in field survey and laboratory analysis, the TwoGener approach permits inferences about landscape-level gene movements.

DOI: 10.1111/j.0014-3820.2001.tb01291.x