Methylation Structure

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.

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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 gstudiopackage).

 

Loading and Cropping Rasters

We can load in the raster, and then crop it to just the are we need. These rasters were downloaded from [http://www.worldclim.org] and are much larger than the study area. This just makes it easier on the computer to not have to deal with such large areas. After cropping it, we will load in the annual precip and temperature data as well.

 

Getting Example Data from Araptus attenuatus

Now, lets grab the Araptus data and look at the data and plot out the locations.

 

 

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Extracting Point Data

To elevation, temperature and precipitation from the rasters for each sampling location, we need to translate them into points first. I’ll first grab the coordinate data as a data.frame.

 

Then we can grab them using the normal functions in the sp library.

 

 

Plotting Trend lines.

Cool, lets sort this by latitude

 

and then plot out some values to look at what is going on.

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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

 

Garrick RC, Meadows CA, Nason JD, Cognato AI, Dyer RJ. 2009. Variable markers for a Sonoran dessert bark beetle, Araptus attenuatus Wood (Curculionidae:Scolytinae), with applications to related genera. Conservation Genetics, 10 1177-1179.

Garrick RC, Meadows CA, Nason JD, Cognato AI, Dyer RJ. 2009. Variable markers for a Sonoran dessert bark beetle, Araptus attenuatus Wood (Curculionidae:Scolytinae), with applications to related genera. Conservation Genetics, 10 1177-1179.

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 levels of polymorphism (2–19 alleles per locus), and no loci showed significant deviations from Hardy–Weinberg or linkage equilibrium across both of the two populations examined, consistent with Mendelian inheritance patterns.

DOI: 10.1007/s10592-008-9738-3