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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Dyer RJ. 2015  Is there such a thing as landscape genetics?  Molecular Ecology.

Dyer RJ. 2015 Is there such a thing as landscape genetics? Molecular Ecology.

For a scientific discipline to be interdisciplinary it must satisfy two conditions; it must consist of contributions from at least two existing disciplines and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this paper, I examine the complete body of peer-reviewed literature self-identified as landscape genetics using the statistical approaches of text mining and natural language processing. The goal here is to quantify the kinds of questions being addressed in landscape genetic studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published landscape genetic papers examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual- and population-based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if landscape genetics is to serve as a real bridge connecting evolution and ecology sensu lato.

DOI http://dx.doi.org/10.1111/mec.13249

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.

Klütsch CFC, Dyer RJ, Misof B. 2012. Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera). Conservation Genetics, 13 21-37.

Klütsch CFC, Dyer RJ, Misof B. 2012. Combining multiple analytical approaches for the identification of population structure and genetic delineation of two subspecies of the endemic Arabian burnet moth Reissita simonyi (Zygaenidae; Lepidoptera). Conservation Genetics, 13 21-37.

Habitat fragmentation and landscape topology may influence the genetic structure and connectivity between natural populations. Six microsatellite loci were used to infer the population structure of 35 populations (N = 788) of the alpine Arabian burnet moth Reissita simonyi (Lepidoptera, Zygaenidae) in Yemen and Oman. Due to the patchy distribution of larval food plants, R. simonyi is not continuously distributed throughout the studied area and the two recognized subspecies of this endemic species (Reissita s. simonyi/R. s. yemenicola) are apparently discretely distributed. All microsatellites showed prevalence of null alleles and therefore a thorough investigation of the impact of null alleles on different population genetic parameters (FST, inbreeding coefficients, and Population Graph topologies) is given. In general, null alleles reduced genetic covariance and independence of allele frequencies resulting in a more connected genetic topology in Population Graphs and an overestimation of pairwise FST values and inbreeding coefficients. Despite the presence of null alleles, Population Graphs also showed a much higher genetic connectivity within subspecies (and lower genetic differentiation, via FST) than between; supporting existing taxonomic distinction. Partial Mantel tests showed that both geo- graphical distance and altitude were highly correlated with the observed distribution of genetic structure within R. simonyi. In conclusion, we identified geographical and altitudinal distances in R. simonyi as well as an intervening desert area to be the main factors for spatial genetic structure in this species and show that the taxonomic division into two subspecies is confirmed by genetic analysis.

DOI: 10.1007/s10592-011-0259-0

Baker SA, Dyer RJ. 2011. Invasion genetics of Microstegium vimineum (Poaceae) within the James River Basin of Virginia, USA. Conservation Genetics, 12 793-803.

Baker SA, Dyer RJ. 2011. Invasion genetics of Microstegium vimineum (Poaceae) within the James River Basin of Virginia, USA. Conservation Genetics, 12 793-803.

Patterns of spatial genetic structure produced following the expansion of an invasive species into novel habitats reflect demographic processes that have shaped the genetic structure we see today. We examined 359 individuals from 23 populations over 370 km within the James River Basin of Virginia, USA as well as four populations outside of the basin. Population diversity levels and genetic structure was quantified using several analyses. Within the James River Basin there was evidence for three separate introductions and a zone of secondary contact between two distinct lineages suggesting a relatively recent expansion within the basin. Microstegium vimineum possesses a mixed-mating system advantageous to invasion and populations with low diversity were found suggesting a recent founder event and self-fertilization. However, surprisingly high levels of diversity were found in some populations suggesting that out-crossing does occur. Understanding how invasive species spread and the genetic consequences following expansion may provide insights into the cause of invasiveness and can ultimately lead to better management strategies for control and eradication.

DOI: 10.1007/s10592-011-0186-0

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

Dyer RJ. 2009 GeneticStudio: a suite of programs for spatial analysis of genetic-marker data. Molecular Ecology Resources, 9 110-113.

Dyer RJ. 2009 GeneticStudio: a suite of programs for spatial analysis of genetic-marker data. Molecular Ecology Resources, 9 110-113.

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) Geno a spreadsheet-like interface for the analysis of spatially explicit marker-based genetic variation; (ii) Graph software for the analysis of Population Graph and network topologies, (iii) Manteller, a general purpose for matrix analysis program; and (iv) SNPFinder, a program for identifying single nucleotide polymorphisms. The GeneticStudio suite is available as source code as well as binaries for OSX and Windows and is distributed under the GNU General Public License.

DOI: 10.1111/j.1755-0998.2008.02384.x

Dyer RJ. 2007. Powers of discerning: challenges to understanding dispersal processes in natural populations. Molecular Ecology,16, 4881-4882.

Dyer RJ. 2007. Powers of discerning: challenges to understanding dispersal processes in natural populations. Molecular Ecology,16, 4881-4882.

In this issue of Molecular Ecology, authors Robledo-Arnuncio & Garcia present a compelling approach for quantifying seed dispersal in plant populations. Building upon methods previously used for quantification of pollen dispersal, the authors not only examine the behavior of the model with respect to sample sizes, dispersal distance, and the kurtosis of the dispersal function but also provide an empirical example using Prunus mahaleb.

DOI: 10.1111/j.1365-294X.2007.03581.x

Dyer RJ. 2007. The evolution of genetic topologies. Theoretical Population Biology, 71 71-79.

Dyer RJ. 2007. The evolution of genetic topologies. Theoretical Population Biology, 71 71-79.

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 correlated to population genetic parameters FST and M (ρ = -0.95; ρ -0.98, respectively), which are commonly used in quantifying among population genetic structure and isolation by distance. Next, the topological consequences of migration patterns are examined by contrasting N-island and stepping stone models of gene movement. Finally, I show how variation in migration rate influences the rate of formation of specific topological features with particular emphasis to the phase transition that occurs when populations begin to become fixed due to restricted movement of genes among populations. I close by discussing the utility of this method for the analysis of intra-specific genetic variation.

DOI: 10.1016/j.tpb.2006.07.001

Gonzales E, Hamrick JL, Smouse PE, Dyer RJ. 2006. Pollen-mediated gene dispersal within continuous and fragmented populations of a forest understory species, Trillium cuneatum. Molecular Ecology, 15 2047-2058.

Pollen movement plays a critical role in the distribution of genetic variation within and among plant populations. Direct measures of pollen movement in the large, continuous populations that characterize many herbaceous plant species are often technically difficult and biologically unreliable. Here, we studied contemporary pollen movement in four large populations of Trillium cuneatum. Three populations, located in the Georgia Piedmont, are exposed to strong anthropogenic disturbances, while the fourth population, located in the Southern Appalachian Mountains, is relatively undisturbed. Using the recently developed TwoGener analysis, we extracted estimates of the effective number of pollen donors (Nep), effective mating neighbourhood size (Aep) and the average distance of pollen movement (δ) for each population. We extended the TwoGener method by developing inference on the paternal gametic contribution to the embryo in situations where offspring genotypes are inferred from seeds and elaiosomes of species with bisporic megagametogenesis. Our estimates indicate that maternal plants do not sample pollen randomly from a global pool; rather, pollen movement in all four populations is highly restricted. Although the effective number of pollen donors per maternal plant is low (Nep = 1.22–1.66) and pollen movement is highly localized in all populations, Nep in the disturbed Piedmont populations is higher and there is more pollen movement than in the mountains. The distance pollen moves is greater in disturbed sites and fragmented populations, possibly due to edge effects in Trillium habitats.

DOI: 10.1111/j.1365-294X.2006.02913.x

Sork VL, Smouse PE, Apsit VJ, Dyer RJ, Westfall RD. 2005. A two-generation analysis of pollen pool genetic structure in flowering dogwood, Cornus florida (Cornaceae), in the Missouri Ozarks. American Journal of Botany, 92 262-271.

Anthropogenic landscape change can disrupt gene flow. As part of the Missouri Ozark Forest Ecosystem Project, this study examined whether silvicultural practices influence pollen-mediated gene movement in the insect-pollinated species, Cornus florida L., by comparing pollen pool structure (Φst) among clear-cutting, selective cutting, and uncut regimes with the expectation that pollen movement should be least in the uncut regime. Using a sample of 1500 seedlings—10 each from 150 seed parents (43 in clear-cut, 74 in selective, and 33 in control sites) from six sites (each ranging from 266 to 527 ha), eight allozyme loci were analyzed with a pollen pool structure approach known as TWOGENER (Smouse et al., 2001; Evolution 55: 260–271). This analysis revealed that pollen pool structure was less in clear-cut (&PhiC = 0.090, P < 0.001) than in uncut areas (ΦU = 0.174, P < 0.001), with selective-cut intermediate (ΦS = 0.125, P < 0.001). These estimates translate into more effective pollen donors (Nep) in clear-cut (Nep = 5.56) and selective-cut (Nep = 4.00) areas than in uncut areas (Nep = 2.87). We demonstrate that &PhiC ≤ ΦS ≤ ΦU, with ΦC significantly smaller than ΦU (P < 0.034). The findings imply that, as long as a sufficiently large number of seed parents remain to provide adequate reproduction and to avoid a genetic bottleneck in the effective number of mothers, silvicultural management may not negatively affect the effective number of pollen parents, and hence subsequent genetic diversity in Cornus florida.

DOI: 10.3732/ajb.92.2.262.

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

Dyer RJ, Westfall RD, Sork VL, Smouse PE. 2004. Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure. Heredity, 92 204-211.

Dyer RJ, Westfall RD, Sork VL, Smouse PE. 2004. Two-generation analysis of pollen flow across a landscape V: a stepwise approach for extracting factors contributing to pollen structure. Heredity, 92 204-211.

Patterns of pollen dispersal are central to both the ecology and evolution of plant populations. However, the mechan- isms controlling either the dispersal process itself or our estimation of that process may be influenced by site-specific factors such as local forest structure and nonuniform adult genetic structure. Here, we present an extension of the AMOVA model applied to the recently developed TWOGENER analysis of pollen pool structure. This model, dubbed the Stepwise AMOVA (StAMOVA), focuses on determining to what extent ecological, demographic, and/or environmental factors influence the observed genetic variation in spatially separated pollen pools. The analysis is verified for efficacy, using an extensive battery of simulations, illustrating: (1) how nonuniform adult genetic structure influences the differentiation of spatially separated pollen pools, and (2) how effectively the Stepwise analysis performs in carrying out the appropriate corrections. Finally, the model is applied to a Quercus alba data set, from which we have prior evidence that the adult genetic structure is nonuniformly distributed across the sampling landscape. From this data set, we show how the Stepwise model can be applied to remove the effects of spatial adult genetic structure on pollen pool differentiation and contrast these results with those derived from the original TWOGENER analysis.

DOI: 10.1038/sj.hdy.6800397

Dyer RJ, Sork VL. 2001. Pollen pool heterogeneity in shortleaf pine, Pinus echinata, Mill. Molecular Ecology, 10 859-866.

Pollen is the dominant vector of gamete exchange for most temperate tree species. Because pollen movement influences the creation, maintenance and erosion of genetic structure in adult populations, it is important to understand what factors influence the process of pollen movement. Isolation by distance in pollen donor populations can create highly structured pollen polls by increased sampling of local fathers. Extrinsic factors, such as the intervening vegetative structure and local pollen donor densities, can also influence the genetic composition of local pollen pools. Using paternally inherited chloroplast microsatellite markers, we examined the structure and diversity of pollen pools in Pinus echinata Mill. in southern Missouri, USA. Our analysis is based on a multivariate AMOVA analysis of stands (~1 ha; six per region) nested within regions (~800 ha; four each). Significant multilocus structure of the pollen pool within regions (ΦSR = 0.095), but not among regions (ΦRT = 0.010), indicates that pollen movement is relatively restricted. Furthermore, the significant correlation between pairwise genetic and physical distances (Mantel correlation; ρ = 0.32) provided support for the isolation by distance hypothesis. Our results indicated that availability of pollen donors did not affect diversity of the pollen pool, measured by the number of unique multilocus genotypes at each stand. However, pollen pool diversity was negatively associated with vegetative structure, measured as total forest tree density. Our findings indicated that on-going pollen movement within continuous forest is relatively restricted as a result of both isolation by distance and vegetative structure.

DOI: 10.1046/j.1365-294X.2001.01251.x