population graphs

Population Graph Stability

A population graph is a network structure based upon inter-stratum conditional genetic covariance (see Dyer & Nason 2004 for a more complete discussion). In this context, it is often of interest to know the statistical stability of your loci in determining the topology you see in the popgraph. Here is a way to subsample the loci you have and identify the extent to which you are asymptotically estimating a stable topology.

Jane Remfert, Doctoral Candidate

Jane Remfert has successfully completed the necessary steps to proceed to Doctoral Candidate by completing her written and oral defense and submitting her research proposal. Thank you to Drs. Eckert, Gough, Johnson, and Keyghobadi for their insightful comments and expertise in helping to shape a dynamic and exciting research project. Now, you just have to do it!

Applied Population Genetics Textbook Release

I will be posting portions of all 10 chapters of my upcoming textbook, Applied Population Genetics, as early draft chapters to this website over the spring semester.

Population Graphs and Landscape Genetics

At the heart of the analyses of landscape genetics are isolation models seeking to explain either interindividual or interpopulation connectivity. These models use spatial, ecological, and topographic predictor variables measured between sites in an …

Compiling the GSL Library for OSX

I’ve been working on integrating the Swift language into my analysis workflow but much of what I do involves the GNU Scientific Libraries for matrix analysis and other tools. Here is a quick tutorial on how to install the GSL library on a clean OSX platform. It is easiest if you have XCode installed. You can get this from the App Store for free. Go download it and install it.

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”)

The gravity of pollination: integrating at-site features into spatial analysis of contemporary pollen movement

Pollen-mediated gene flow is a major driver of spatial genetic structure in plant populations. Both individual plant characteristics and site-specific features of the landscape can modify the perceived attractiveness of plants to their pollinators …

DiLeo MF, Siu JC, Rhodes MK, López-Villalobos A, Redwine A, Ksiazek K, Dyer RJ. 2014. The gravity of pollination: integrating at-site features into spatial analysis of contemporary pollen movement. Molecular Ecology, 23, 2973-2982.

Pollen-mediated gene flow is a major driver of spatial genetic structure in plant populations. Both individual plant characteristics and site-specific features of the landscape can modify the perceived attractiveness of plants to their pollinators and thus play an important role in shaping spatial genetic variation. Most studies of landscape-level genetic connectivity in plants have focused on the effects of interindividual distance using spatial and increasingly ecological separation, yet have not incorporated individual plant characteristics or other at-site ecological variables.

GeneticStudio: a suite of programs for spatial analysis of genetic-marker data

The analysis of genetic marker data is increasingly being conducted in the context of the spatial arrangement of strata (e.g. populations) necessitating a more flexible set of analysis tools. GeneticStudio consists of four interacting programs: (i) …

The evolution of genetic topologies

This manuscript explores the simultaneous evolution of population genetic parameters and topological features within a population graph through a series of Monte Carlo simulations. I show that node centrality and graph breadth are significantly …