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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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:

  1. You need to have two data.frame objects to merge
  2. The first one in the function call will be the one merged on-to the second one is added to the first.
  3. 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.

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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

 

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

Meadows CA, Garrick RC, Dyer RJ. 2009. Analysis of genetic structure in Euphorbia lomelii, a desert euphorb. Actus, 1 19-24.

Meadows CA, Garrick RC, Dyer RJ. 2009. Analysis of genetic structure in Euphorbia lomelii, a desert euphorb. Actus, 1 19-24.

The distribution of genetic variation within species is the result of both historical and ongoing demographic and evolutionary processes. Here we examine how genetic variation in Euphorbia lomelii (Euphorbaceae) among populations in Baja Mexico to understand how region-wide historical processes may have influenced this species. Specifically, we examined how the formation of the Sea of Cortéz, separating mainland and peninsular populations, and range expansion caused by Post Pleistocene climate change have influenced genetic variation. Samples were obtained from 37 sites in Baja California and mainland Sonora with a total of 324 individuals genotyped using six nuclear DNA markers. Analysis of genetic structure showed that while there was considerable differentiation among sites (ΦST=0.19) there was no significant difference between mainland and peninsular populations. The genetic structure of E. lomelii also has a gradual change with a northward reduction in heterozygosity, most likely caused by the relatively rapid range expansion during the current interglacial period. This research is important in understanding how genetic structure is influenced by historical processes that have operated on species in this region.

DOI:

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, Meadows CA, Nicolas AN, Nason JD, Dyer RJ. 2008. A set of polymorphic nuclear intron markers for conservation genetics and phylogeography of Euphorbia species (Pedilanthus clade). Conservation Genetics, 9 1673-1676.

Garrick RC, Meadows CA, Nicolas AN, Nason JD, Dyer RJ. 2008. A set of polymorphic nuclear intron markers for conservation genetics and phylogeography of Euphorbia species (Pedilanthus clade). Conservation Genetics, 9 1673-1676.

We developed seven nuclear intron markers for Euphorbia lomelii. New exon-primed intron-crossing (EPIC) oligonucleotides were used for initial amplification and sequencing, then locus-specific primers and restriction fragment length polymorphism genotyping assays were designed. Loci showed no significant deviation from Hardy–Weinberg and linkage equilibrium, and they cross-amplify in at least three congeneric species.

DOI: 10.1007/s10592-008-9521-5

Dyer RJ, Nason JD. 2004. Population Graphs: the graph theoretic shape of genetic structure. Molecular Ecology, 13 1713-1727.

Dyer RJ, Nason JD. 2004. Population Graphs: the graph theoretic shape of genetic structure. Molecular Ecology, 13 1713-1727.

Patterns of intraspecific genetic variation result from interactions among both historical and contemporary evolutionary processes. Traditionally, population geneticists have used methods such as F-statistics, pairwise isolation by distance models, spatial autocorrelation and coalescent models to analyses this variation and to gain insight about causal evolutionary processes. Here we introduce a novel approach (Population Graphs) that focuses on the analysis of marker-based population genetic data within a graph theoretic framework. This method can be used to estimate traditional population genetic summary statistics, but its primary focus is on characterizing the complex topology resulting from historical and con- temporary genetic interactions among populations. We introduce the application of Population Graphs by examining the range-wide population genetic structure of a Sonoran Desert cactus (Lophocereus schottii). With this data set, we evaluate hypotheses regarding historical vicariance, isolation by distance, population-level assignment and the importance of specific populations to species-wide genetic connectivity. We close by discussing the applicability of Population Graphs for addressing a wide range of population genetic and phylogeographical problems.

DOI:  10.1111/j.1365-294X.2004.02177.x