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.

Garrick RC, Nason JD, Fernandez-Manjaress JFF, Dyer RJ. 2013. Ecological co-associations influence species’ responses to past climatic change: an example from a Sonoran Desert bark beetle. Molecular Ecology, 22, 3345-3361.

Garrick RC, Nason JD, Fernandez-Manjaress JFF, Dyer RJ. 2013. Ecological co-associations influence species’ responses to past climatic change: an example from a Sonoran Desert bark beetle. Molecular Ecology, 22, 3345-3361.

Ecologically interacting species may have phylogeographic histories that are shaped both by features of their abiotic landscape, and by biotic constraints imposed by their co-association. The Baja California peninsula provides an excellent opportunity to examine the influence of abiotic vs. biotic factors on patterns of diversity in plant-insect species. This is because past climatic and geological changes impacted the genetic structure of plants quite differently to that of co-distributed free-living animals (e.g., herpetofauna and small mammals). Thus, ‘plant-like’ patterns should be discernible in host-specific insect herbivores. Here we investigate the population history of a monophagous bark beetle, Araptus attenuatus, and consider drivers of phylogeographic patterns in light of previous work on its host plant, Euphorbia lomelii. Based on mitochondrial and nuclear markers, we found that the evolutionary history of A. attenuatus exhibits similarities to host plant that are attributable to both biotic and abiotic processes. Southward range expansion and recent colonization of continental Sonora peninsula appear to be unique to this taxon pair, and likely reflect influences of the host plant. On the other hand, abiotic factors with landscape-level influences on suites of co-distributed taxa, such as Plio- and Pleistocene-aged marine incursions in the region, also left genetic signatures in beetle populations. Superimposed on these similarities, bark beetle-specific patterns and processes were also evident. Taken together, this work illustrates that the evolutionary history of species-specific insect herbivores may represent a mosaic of influences, including, but not limited to, those imposed by the host plant.

 DOI: 10.1111/mec.12318

 

Dyer RJ, Nason JD, Garrick RC. 2010. Landscape modeling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology, 19 3746-3759.

Dyer RJ, Nason JD, Garrick RC. 2010. Landscape modeling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology, 19 3746-3759.

Landscape genetics is a burgeoning field of interest that focuses on how site-specific factors influence the distribution of genetic variation and the genetic connectivity of individuals and populations. In this manuscript, we focus on two methodological extensions for landscape genetic analyses: the use of conditional genetic distance (cGD) derived from population networks and the utility of extracting potentially confounding effects caused by correlations between phylogeographic history and contemporary ecological factors. Individual-based simulations show that when describing the spatial distribution of genetic variation, cGD consistently outperforms the traditional genetic distance measure of linearized FST under both 1- and 2-dimensional stepping stone models and Cavalli-Sforza and Edward’s chord distance Dc in 1-dimensional landscapes. To show how to identify and extract the effects of phylogeographic history prior to embarking on landscape genetic analyses, we use nuclear genotypic data from the Sonoran desert succulent Euphorbia lomelii (Euphrobiaceae), for which a detailed phylogeographic history has previously been determined. For E. lomelii, removing the effect of phylogeographic history significantly influences our ability to infer both the identity and the relative importance of spatial and bio-climatic variables in subsequent landscape genetic analyses. We close by discussing the utility of cGD in landscape genetic analyses.

DOI: 10.1111/j.1365-294X.2010.04748.x

Garrick RC, Sunnucks P, Dyer RJ. 2010. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evolutionary Biology, 10 118.

Garrick RC, Sunnucks P, Dyer RJ. 2010. Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evolutionary Biology, 10 118.

Background: A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses.

Results: We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters.
Conclusions: A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases.

DOI: 10.1186/1471-2148-10-118

Garrick RC, Nason JD, Meadows CA, Dyer RJ. 2009. Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Molecular Ecology, 18 1916-1931.

Garrick RC, Nason JD, Meadows CA, Dyer RJ. 2009. Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Molecular Ecology, 18 1916-1931.

To examine the generality of population-level impacts of ancient vicariance identified for numerous arid-adapted animal taxa along the Baja peninsula, we tested phylogeographical hypotheses in a similarly distributed desert plant, Euphorbia lomelii (Euphorbiaceae). In light of fossil data indicating marked changes in the distributions of Baja floristic assemblages throughout the Holocene and earlier, we also examined evidence for range expansion over more recent temporal scales. Two classes of complementary analytical approaches — hypothesis-testing and hypothesis-generating — were used to exploit phylogeographical signal from chloroplast DNA sequence data and genotypic data from six codominant nuclear intron markers. Sequence data are consistent with a scenario of mid-peninsular vicariance originating c. 1 million years ago (Ma). Alternative vicariance scenarios representing earlier splitting events inferred for some animals (e.g. Isthmus of La Paz inundation, c. 3 Ma; Sea of Cortez formation, c. 5 Ma) were rejected. Nested clade phylo- geographical analysis corroborated coalescent simulation-based inferences. Nuclear markers broadened the temporal spectrum over which phylogeographical scenarios could be addressed, and provided strong evidence for recent range expansions along the north– south axis of the Baja peninsula. In contrast to previous plant studies in this region, however, the expansions do not appear to have been in a strictly northward direction. These findings contribute to a growing appreciation of the complexity of organismal responses to past climatic and geological changes — even when taxa have evolved in the same landscape context.

DOI: 10.1111/j.1365-294X.2009.04148.x

Garrick RC, Dyer RJ, Beheregaray LB, Sunnucks P. 2008. Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis. Molecular Ecology, 17 1401-1403.

Garrick RC, Dyer RJ, Beheregaray LB, Sunnucks P. 2008. Babies and bathwater: a comment on the premature obituary for nested clade phylogeographical analysis. Molecular Ecology, 17 1401-1403.

A recent commentary in Molecular Ecology by Petit (2008) paints a rather grim picture of the utility of nested clade phylogeographical analysis (NCPA) for inferring population history. Drawing on simulation studies based on single locus data sets, including the recent work by Panchal & Beaumont (2007), the potential fallibility of NCPA was characterized as being so dire that the method should be abandoned until further evidence in support of its legitimacy emerges. Here, we reconsider the arguments presented by Petit in light of practical approaches for validating or strengthening inferences drawn from NCPA. As with any method that attempts to distinguish processes and events that shaped spatial-genetic structuring throughout complex evolutionary histories of natural populations, we propose that treatment of NCPA inferences should be set in the context of corroborating evidence (or lack thereof) that support those inferences. Indeed, results from computer simulation, studies lend no support to the idea that NCPA should not be employed for generating plausible hypotheses (i.e. consistent with species biology and landscape history) that can be further tested using other methods. Moreover, cross-validation of NCPA inferences via assessment of multiple independent loci, complementary analyses, and/or prior expectations, should at least partly — perhaps considerably — counter high false-positive rates reported for some inferences. NCPA uniquely offers the ability to explore patterns relating to complex, historical scenarios: an over-reaction to Panchal & Beaumont (2007) should not precipitate throwing out an approach currently with no computationally feasible substitute.

DOI: 10.1111/j.1365-294X.2008.03675.x