Baja California

Talk at Temple!

Giving a talk up at Temple University, last seminar of the year but one I’ve been looking forward to giving for a while.

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.

Methylation Structure

Here is some interesting data coming out of the Baja Araptus attenuatus project. We looked at methylation variation, localized within the genome and compared the amount of among-population variation present. The underlying idea here is that in insects, methylation is more often encountered in coding regions, and has been shown in many cases to be influencing phenotype.

Merging data frames

In R, there is often the need to merge two data.frame objects (say one with individual samples and the other with population coordinates. The merge() function is a pretty awesome though it may take a little getting used to. Here are some things to remember: You need to have two data.frame objects to merge The first one in the function call will be the one merged _on-to _the second one is added to the first. Each will need a column to use as an index—it is a column that will be used to match rows of data. If they are the same column names then the function will do it automagically, if no common names are found in the names() of either data.frame objects, you can specify the columns using the optional by.x= and by.y= function arguments.

Extracting Data from Rasters

This document shows you how to extract data from rasters.  Getting The Libraries First, I’ll load in some packages to get the ability to work with raster data and to load in the Arapatus attenuatus data set (it is part of the default gstudio package). require(raster) ## Loading required package: raster ## Loading required package: sp require(gstudio) ## Loading required package: gstudio Loading and Cropping Rasters We can load in the raster, and then crop it to just the are we need.

Ecological coassociations influence species' responses to past climatic change: an example from a Sonoran Desert bark beetle

Ecologically interacting species may have phylogeographical histories that are shaped both by features of their abiotic landscape and by biotic constraints imposed by their coassociation. The Baja California peninsula provides an excellent …

Variable nuclear markers for a Sonoran Desert bark beetle, Araptus attenuatus Wood (Curculionidae: Scolytinae), with applications to related genera

We report eight new co-dominant nuclear markers for population genetics of the bark beetle Araptus attenuatus Wood. Several loci include introns from low-copy genes, and four cross-amplify in one or more related genera. The markers show moderate …

Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula

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 …