Rodney Dyer | Virginia Commonwealth University (original) (raw)

Papers by Rodney Dyer

Biochemical Systematics and Ecology, 2015

ABSTRACT Mountains as natural barriers often have important effects on intraspecific genetic stru... more ABSTRACT Mountains as natural barriers often have important effects on intraspecific genetic structure through restraining gene flow and enhancing differentiation among populations. While the Qinling and Daba mountains are considered significant geographic barriers, dividing China into temperate and subtropical regions, little is known about how this barrier influences the genetic patterns of sister species represented in distinct habitats. In this study, we analyzed genetic differentiation and the geographic boundary between Pinus henryi and Pinus tabuliformis using chloroplast microsatellite markers. Our data show high levels of among-population differentiation, consistent with the effects of historical demographic bottlenecks, local adaptation and climate effects. Three main geographic boundaries coinciding with mountain systems indicate natural landscapes, such as large rivers, and habitat loss caused by anthropogenic deforestation, are significant barriers to genetic exchange among populations. The divergence between populations in the eastern and western Qinling Mountains populations may possibly be ascribed to fragmentation driven by climate change. The genetic boundary of P. henryi and P. tabuliformis generally coincides with the previous morphological dividing line based on the unweighted pair group method using arithmetic averages and on spatial analysis of molecular variance.

A workshop was held at the National Center for Ecological Analysis and Synthesis to discuss gene ... more A workshop was held at the National Center for Ecological Analysis and Synthesis to discuss gene flow on an ecological, rather than an evolutionary, time scale. Recently, ecologists, conservation biologists, and ecosystem managers have been interested in monitoring on-going gene flow to understand environmental and landscape influences on genetic variation in existing populations. The current paradigm emphasizes the concern about isolation due to reduction in gene flow as a consequence of human landscape alteration. However, evidence also suggests that landscape change can increase gene flow with potential detrimental impact on local adaptation. This ambiguity in gene flow effects calls for a sensitive approach to the measurement of gene movement. During the workshop, our first goal was to review current approaches to the estimation of gene flow and their usefulness for measuring on-going gene flow. We concluded that indirect methods based on F-statistics are not sufficiently sensitive to measure gene flow on this scale. Instead, direct methods of genealogical analysis offer a reliable alternative at a small scale but may have more limited utility for scaling up. Because gene flow occurs on a landscape scale, we explored the usefulness of current population genetic approaches for scaling up our estimates and we discussed the potential contribution of metapopulation and landscape models. We evaluated the relationships between population genetic and metapopulation models, but concluded a new synthesis integrating the two approaches is not yet ready for development. However, workshop participants explored in detail a new approach to the study of gene flow that would be feasible at the landscape scale and might generate a parameter or estimator of migration needed for metapopulation and landscape models.

After this presentation, attendees will understand the principles of forensic palynology and how ... more After this presentation, attendees will understand the principles of forensic palynology and how Gas Chromatography-Mass Spectrometry (GC-MS) and trace metal profiling can be used to analyze pollen grains in a forensic sample. Further, attendees will learn about the interactions between pollen grains, organic compounds, and metal particles in the environment. This research will impact the forensic science community by introducing an integrated technique that will significantly improve the ability of forensic examiners to determine the geographic origin of trace evidence. Because pollen samples are found universally at crime scenes and are attached to various types of evidence, this technique has the potential to drastically increase the information gained from trace evidence analysis during a forensic investigation. Within forensic science, pollen identification is used to determine geographic origin of objects or people associated with a crime scene. However, pollen typing is a tim...

Background / Purpose: This poster summarizes the current work developing eDNA tools for Atlantic ... more Background / Purpose: This poster summarizes the current work developing eDNA tools for Atlantic Sturgeon management. Main conclusion: So far, 93% and 83% of positive control samples between tanks containing Atlantic Sturgeon samples and Atlantic Sturgeon DNA spiked environmental samples have returned correct identifications of Atlantic Sturgeon, respectively. Future work will finish the environmental sample dataset, and develop qPCR tools.

ABSTRACT The hardwood forests of eastern North America represent one of the most diverse temperat... more ABSTRACT The hardwood forests of eastern North America represent one of the most diverse temperate forests in the world. Over 120 tree species inhabit this region and have diversified into numerous niches defined by geoclimatic variables and biotic interactions. This diversification has occurred over evolutionary timescales that also included dramatic shifts in historical climate regimes. These forests, therefore, are ideal for the study of the interaction between phylogeographic history, historical climate change, and local adaptation. We have targeted a subset of eight species that largely represents this niche diversity: (1) yellow-poplar (Liriodendron tulipifera L.), (2) black tulepo (Nyssa sylvatica), (3) American beech (Fagus grandifolia), (3) green ash (Fraxinus pennsylvanica), (4) eastern redbud (Cercis canadensis L.), (6) flowering dogwood (Cornus florida), (7) boxelder (Acer negundo), and (8) American hophornbeam (Ostrya virginiana). Using flowering dogwood as a test case, we developed a genotype-by-sequencing (GBS) pipeline for a reference genotype of this species, the first step of which included the creation of a set of reference contigs. These contigs were assembled from Illumina short read data generated on the HiSeq2000 platform using a novel mixture of standard bioinformatics tools and custom scripts. Contigs were subsequently annotated and a GBS approach based on restriction digestion was conducted on 100 samples collected across the natural range of flowering dogwood. Preliminary data are being used to construct null models of the historical phylogeography of this species, with goals of scaling up to a full landscape genomic study of local adaption in the targeted eight species.

Molecular Ecology Notes, 2005

The server-based program GENER performs the two-generation analysis of pollen flow for data consi... more The server-based program GENER performs the two-generation analysis of pollen flow for data consisting of mother/offspring arrays using genetic markers. The GENER program decomposes the genetic variance sampled by maternal individuals within and among pollen pool components of genetic variance and is accessible from http://dyerlab.bio.vcu.edu. These estimates are used to construct the test statistic, Φ Φ Φ Φ ft , whose significance is tested via permutation. The Φ Φ Φ Φ ft statistic can subsequently be used to quantify genetic effective pollen donor population size ( N ep ), effective mating area and dispersal distance. Furthermore, the GENER program can calculate Φ Φ Φ Φ ft values for all pairs of substrata within the data set.

For a scientific discipline to be interdisciplinary it must satisfy two conditions; it must consi... more 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. This article is protected by copyright. All rights reserved.

Theoretical Population Biology, 2007

This manuscript explores the simultaneous evolution of population genetic parameters and topologi... more 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 Phi(ST) and M; (rho=-0.95;rho=-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 intraspecific genetic variation.

Oecologia, 2002

While floral herbivores and predispersal seed predators often reduce plant reproductive output, t... more While floral herbivores and predispersal seed predators often reduce plant reproductive output, their role in limiting plant fitness and population growth is less clear, especially for iteroparous perennial plant species. In this study we experimentally excluded floral herbivores and predispersal seed predators (insecticide spray versus water control) over a 2-year period to examine the effect of inflorescence-feeding insects on levels of seed production, seedling emergence, and juvenile establishment for Liatris cylindracea, an iteroparous perennial plant. In addition, we collected detailed demographic data on all life stage transitions for an additional set of individuals in the same population over 4 years. We used the experimental and demographic data to construct stochastic individual-based simulations to evaluate the overall effect of inflorescence-feeding insects on adult recruitment per maternal plant (a fitness component) and population growth rate. The insect exclusion experiments showed that damage due to insects decreased seed production, seedling emergence, and juvenile establishment for both years' experiments. These results indicate that recruitment was seed-limited through juvenile establishment, and that inflorescence-feeding insects influenced the degree of seed limitation. Results of the individual-based simulation models, which included individual demographic and temporal stochasticity, showed that inflorescence-feeding insects negatively affected the number of adult offspring per maternal plant recruited into the population and population growth rate for both years' experiments. Taken together, the results of the experimental exclusions and the individual-based models indicate that inflorescence-feeding insects can influence population growth rate, and have the potential to act as a selective force for the evolution of traits in this plant species.

Molecular Ecology Resources, 2009

The analysis of genetic marker data is increasingly being conducted in the context of the spatial... more 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.

Molecular Ecology, 2007

& Garcia present a compelling approach for quantifying seed dispersal in plant populations. Build... more & 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 behaviour 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.

Conservation Genetics, 2011

Patterns of spatial genetic structure produced following the expansion of an invasive species int... more 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.

Insects, 2015

Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests... more Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei) have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR) amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP) assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data). The assay is cost-and time-efficient, and will help improve knowledge of Reticulitermes species distributions.

Analyses of Araptus attenuatus mtCOI data inferred a phylogenetic tree topology in which major Cl... more Analyses of Araptus attenuatus mtCOI data inferred a phylogenetic tree topology in which major Clades C and S are sisters, and Clade B is early-branching in the main text; also supported by DIY-ABC analyses in ). Two alternative divergence histories that may have generated this topology where investigated further. The first scenario involves a single colonization of continental Sonora (where Clade S now resides) sourced from the Baja peninsula (i.e., the ancestor of Clade C), with a concomitant bottleneck of the Clade S lineage that occurred during long-distance overwater dispersal. The competing scenario involves two independent and temporally spaced colonizations of the Baja peninsula (with Clade B arrival postdating that of Clade C) from a continental ancestor. Again, each long-distance overwater dispersal event was assumed to be associated with a bottleneck. DIY-ABC v1.0.4.46b (Cornuet et al. 2010) was used to distinguish among the alternative scenarios, and closely followed the procedure used when reassessing relationships among major mtCOI clades (see main text Methods). In this case, two additional parameters were used to characterize a bottleneck, both with uniform priors: duration, which is number of number of generations for which N e remained low (Dur. = 10-1000), and severity, which is the actual N e during the bottleneck (Sev. = 10-1000, equivalent to at least a 99% reduction in size). Both

Molecular Ecology, 2013

Ecologically interacting species may have phylogeographical histories that are shaped both by fea... more 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 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 codistributed 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 phylogeographical patterns in the light of previous work on its host plant, Euphorbia lomelii. Using a combination of phylogenetic, coalescent-simulation-based and exploratory analyses of mitochondrial DNA sequences and nuclear genotypic data, we found that the evolutionary history of A. attenuatus exhibits similarities to its host plant that are attributable to both biotic and abiotic processes. Southward range expansion and recent colonization of continental Sonora from the Baja peninsula appear to be unique to this taxon pair and probably reflect influences of the host plant. On the other hand, abiotic factors with landscapelevel influences on a diverse suite of codistributed arid-adapted taxa, such as Plio-and Pleistocene-aged marine incursions in the region, also left genetic signatures in beetle and host plant populations. Superimposed on these similarities, bark beetle-specific patterns and processes were also evident: our data revealed two secondarily sympatric, reproductively isolated genetic lineages, as well as a previously unrecognized midpeninsular warm desert refuge. 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.

Molecular Ecology, 2014

Pollen-mediated gene flow is a major driver of spatial genetic structure in plant populations. Bo... more 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. Using spatially explicit simulations, we first tested the extent to which the inclusion of at-site variables influencing local pollination success improved the statistical characterization of genetic connectivity based upon examination of pollen pool genetic structure. The addition of at-site characteristics provided better models than those that only considered interindividual spatial distance (e.g. IBD). Models parameterized using conditional genetic covariance (e.g. population graphs) also outperformed those assuming panmixia. In a natural population of Cornus florida L. (Cornaceae), we showed that the addition of at-site characteristics (clumping of primary canopy opening above each maternal tree and maternal tree floral output) provided significantly better models describing gene flow than models including only between-site spatial (IBD) and ecological (isolation by resistance) variables. Overall, our results show that including interindividual and local ecological variation greatly aids in characterizing landscape-level measures of contemporary gene flow.