Publications

Research manuscripts from students and faculty in the Center for Environmental Studies.  Student co-authors are indicated with (§) for undergraduates and () for graduates.

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McGarvey DJ, Faris SE. 2019An Arts-based approach to Science Communication Training. Scientia https://doi.org/10.26320/SCIENTIA311.

Undergraduate Author(s)
Rapid growth in the number and diversity of digital media outlets is creating novel opportunities to increase public engagement with science. Dr Daniel J. McGarvey and Sarah E. Faris, working at Virginia Commonwealth University, have developed an interdisciplinary training program that teaches STEM graduate students to use digital media to effectively communicate scientific topics to general audiences.
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Edwards J, Anderson J, Shuart W, Woolard J.2019An evaluation of reflectance calibration methods for UAV spectral imagery. Photogrammetric Engineering & Remote Sensing 85:61-70. https://doi.org/10.14358/PERS.85.3.221.

Graduate Author(s)
Spectral imagery using micro-unmanned aerial vehicles is rapidly advancing. This study compared reflectance calibration methods for imagery acquired using the Parrot Sequoia imager, a commercial multispectral sensor package. For the study, two orthomosaics were calibrated using 1) a manufacturer-suggested AIRINOV standard correction using PIX4D software and 2) the Empirical Line Calibration (ELC) method using ground radiometric data on specific in-scene targets. Both scenes were analyzed for target spectral agreement by ground radiometric survey. Regression analysis demonstrated more favorable target correlation for the ELC imagery than the AIRINOV-calibrated imagery, with Root Mean Square Error (RMSE) analysis supporting these results. Finally, classification maps were produced between the data sets. Error analysis resulted in an overall accuracy of 24% for the AIRINOV map compared to ELC-based truth data, with a considerable number of pixels associated with brighter targets unclassified. These results demonstrate the need for standardized calibration procedures in the spectral correction of small-format remote sensor data.
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Tonra CM, Hallworth MT, Boves TJ, Reese J, Bulluck LP, Johnson M, Viverette C, Percy K, Ames E, Matthews A, Slevin MC, Wilson RR, Johnson EI2019Concentration of a widespread breeding population in a few critically important nonbreeding areas: Migratory connectivity in the Prothonotary Warbler The Condor XX :1-15. https://doi.org/10.1093/condor/duz019.

Graduate Author(s)
One of the greatest challenges to informed conservation of migratory animals is elucidating spatiotemporal variation in distributions. Without such information, it is impossible to understand full-annual-cycle ecology and effectively implement conservation actions that address where and when populations are most limited. We deployed and recovered light-level geolocators (n = 34) at 6 breeding sites in North America across the breeding range of a declining long-distance migratory bird, the Prothonotary Warbler (Protonotaria citrea). We sought to determine migratory routes, stopover location and duration, and the location of overwintering grounds. We found that the species exhibits a large-scale, east‒west split in migratory routes and weak migratory connectivity across its range. Specifically, almost all individuals, regardless of breeding origin, overlapped in their estimated wintering location in northern Colombia, in an area 20% the size of the breeding range. Additionally, most of the individuals across all breeding locations concentrated in well-defined stopover locations in Central America while en route to Colombia. Although error inherent in light-level geolocation cannot be fully ruled out, surprisingly much of the estimated wintering area included inland areas even though the Prothonotary Warbler is considered a specialist on coastal mangroves in winter. Based on these results, conservation efforts directed at very specific nonbreeding geographical areas will potentially have benefits across most of the breeding population. Our findings highlight the importance of using modern technologies to validate assumptions about little-studied portions of a species’ annual cycle, and the need to distribute sampling across its range.
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Hendrick LRF, McGarvey DJ2019Climate change and mountaintop-removal mining: A MaxEnt assessment of the potential threat to West Virginia Fishes Northeastern Naturalist 26:499-522.

Graduate Author(s)
Accounts of species’ range shifts in response to climate change are rapidly accumulating. These range shifts are often attributed to species tracking their thermal niches as temperatures in their native ranges increase. Our objective was to estimate the degree to which shifts in water temperature driven by climate change may increase the exposure of West Virginia’s native freshwater fishes to mountaintop-removal surface coal mining. We projected mid century shifts in habitat suitability for 9 non-game West Virginian fishes via maximum entropy species distribution modeling, using a combination of physical habitat, historical climate conditions, and future climate data. Modeling projections for a high-emissions scenario (Representative Concentration Pathway 8.5) predict that habitat suitability will increase in high-elevation
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Slevin MC, Bulluck LP, Matthews AE, Boves TJ.2019Spatial variation in carotenoid plumage coloration and relationships between female coloration and quality in Prothonotary Warblers (Protonotaria citrea). The Auk 136:1-16. https://doi.org/10.1093/auk/ukz011.

Graduate Author(s)
Many birds use conspicuous plumage coloration to signal quality for sexual or social selection. However, it is still often unclear how intraspecific coloration and associated signaling vary spatially. Plumage coloration that is dependent on carotenoids may be ideal for studying spatial color variation because birds cannot naturally synthesize this pigment; therefore, bird coloration from carotenoids is at least partially contingent upon diet. As food availability often varies spatially, so might color and its signaling strength. While male coloration has received more research focus, less is known about female coloration and its relationships with social rank or sexual quality. To further improve our understanding of spatial variation in plumage coloration and correlations with individual quality, we compared Prothonotary Warblers breeding at 2 ecologically disparate sites separated by 1,300 km: in bottomland forests of Arkansas, USA, and the forests near the tidal freshwater James River in Virginia, USA. We assessed crown and breast plumage coloration for both sexes and compared several color metrics between sites. We then assessed surrogates of female quality (number of young fledged, number of eggs laid, provisioning rate, apparent annual survival, and nest depredation) and compared coloration-quality relationships between sites. We found that coloration of birds breeding in Arkansas was generally more elaborate than those breeding in Virginia. However, this was somewhat dependent on sex: females showed greater differences than males between sites. Additionally, color metrics of females breeding in Virginia showed stronger relationships with quality (all 5 quality metrics) than for birds breeding in Arkansas (only provisioning rate and nest depredation). Proximately, spatial variation in plumage coloration and the associated signaling may be explained by differences in diet between sites. Ultimately, spatial variation in intra- and intersexual selection pressures may explain how spatial variation in plumage signal strength evolved.
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Nickley B, Bulluck LP2019Spanning the habitat gradient: Red-headed woodpecker nest-site selection in three distinct cover types. Forest Ecology and Management 444:115-126. https://doi.org/10.1016/j.foreco.2019.04.048.

Graduate Author(s)
Understanding species habitat relationships is fundamental to ecology and underpins conservation-based management. Species with broad habitat preferences and wide geographic ranges are capable of fulfilling breeding requirements in different habitat contexts. Habitat selection in these species may vary in a context-specific way, so determining the factors driving habitat selection requires spanning the habitat gradient. Complex landscapes offer a unique opportunity to compare habitat selection across habitat gradients within a single study site. Here, we used a comparative approach to model scale-dependent nest-site selection of the red-headed woodpecker (Melanerpes erythrocephalus) in three distinct cover types at Fort A.P. Hill military installation, Virginia. We found that nest preferences varied among cover types for several patch-scale habitat features. In closed forests, red-headed woodpeckers selected patches with an open canopy characteristic that lacked holly (Ilex opaca) in the understory and contained large pines. In open forests, patches with a high percentage of canopy cover were also avoided. In wetlands, patches with low percent stem cover were preferred. We also found a single variable, medium/large snag density, was highly influential in models for all cover types at the patch scale, indicating the importance of suitable snags for nesting, irrespective of cover type. Models at the tree scale showed similar results for all cover types: red-headed woodpeckers consistently preferred large snags with less bark. Our results demonstrate the value of comparing habitat selection across a habitat gradient. Managers charged with promoting red-headed woodpecker populations would do well to manage for large, partially decayed snags while also considering context-specific habitat needs.
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Tassone SJ, Bukaveckas PA.2019Seasonal, interannual, and longitudinal patterns in estuarine metabolism derived from diel oxygen data using multiple computational approaches Estuaries & Coasts 42:1032-1051. https://doi.org/10.1007/s12237-019-00526-0.

Graduate Author(s)
Twenty-three station-years of diel oxygen data for the James River Estuary were analyzed to characterize longitudinal, seasonal, and interannual patterns of gross primary production (GPP) and ecosystem respiration (ER). We compared two commonly used methods for deriving metabolism (bookkeeping and Bayesian) to determine whether the observed patterns were robust with respect to computational methodology. The two methods revealed similar longitudinal patterns of increasing GPP and ER, and decreasing net ecosystem metabolism (NEM), with increasing salinity. Seasonal patterns in GPP and ER tracked water temperature and solar radiation, except during high discharge events when metabolism declined by 40%. The bookkeeping method yielded higher estimates of GPP and ER in the higher end of the range, and smaller estimates in the low end of the range, thereby accentuating seasonal and longitudinal differences. Inferences regarding net autotrophy and heterotrophy were robust, as both methods yielded positive estimates of NEM at the chlorophyll maximum (tidal fresh segment) and negative values for the saline portion of the estuary. Inferences regarding the relative importance of allochthonous inputs (based on inferred ER at GPP = 0) differed between the two methods. Values derived by the bookkeeping method indicated that respiration was largely supported by autochthonous production, whereas the Bayesian results indicated that autochthonous and allochthonous inputs were equally important. Overall, our findings show that methodological differences were small in the context of longitudinal, seasonal, and interannual variation but that the bookkeeping method yielded a wider range of values for GPP and ER relative to the Bayesian estimates.
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lores-Manzanero A, Luna-Bárcenas MA, Dyer RJ, Vázquez-Domínguez E.2019Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent. Ecology & Evolution 9:437-453. https://doi.org/10.1002/ece3.4762.

Graduate Author(s)
Gene flow in animals is limited or facilitated by different features within the landscape matrix they inhabit. The landscape representation in landscape genetics (LG) is traditionally modeled as resistance surfaces (RS), where novel optimization approaches are needed for assigning resistance values that adequately avoid subjectivity. Also, desert ecosystems and mammals are scarcely represented in LG studies. We addressed these issues by evaluating, at a microgeographic scale, the effect of landscape features on functional connectivity of the desert‐dwelling Dipodomys merriami. We characterized genetic diversity and structure with microsatellites loci, estimated home ranges and movement of individuals using telemetry—one of the first with rodents, generated a set of individual and composite environmental surfaces based on hypotheses of variables influencing movement, and assessed how these variables relate to individual‐based gene flow. Genetic diversity and structure results evidenced a family‐induced pattern driven by first‐order‐related individuals, notably determining landscape genetic inferences. The vegetation cover and soil resistance optimized surface (NDVI) were the best‐supported model and a significant predictor of individual genetic distance, followed by humidity and NDVI+humidity. Based on an accurate definition of thematic resolution, we also showed that vegetation is better represented as continuously (vs. categorically) distributed. Hence, with a nonsubjective optimization framework for RS and telemetry, we were able to describe that vegetation cover, soil texture, and climatic variables influence D. merriami's functional connectivity at a microgeographic scale, patterns we could further explain based on the home range, habitat use, and activity observed between sexes. We describe the relationship between environmental features and some aspects of D. merriami‘s behavior and physiology.
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Friedline CJ, Faske TM, Lind BM, Hobson EM, Parry D, Dyer RJ, Johnson DM, Thompson LM, Grayson KL, Eckert AJ.2019Evolutionary genomics of gypsy moth populations sampled along a latitudinal gradient. Molecular Ecology 28:2206-2223. https://doi.org/10.1111/mec.15069.

Undergraduate Author(s)
The European gypsy moth (Lymantria dispar L.) was first introduced to Massachusetts in 1869 and within 150 years has spread throughout eastern North America. This large‐scale invasion across a heterogeneous landscape allows examination of the genetic signatures of adaptation potentially associated with rapid geographical spread. We tested the hypothesis that spatially divergent natural selection has driven observed changes in three developmental traits that were measured in a common garden for 165 adult moths sampled from six populations across a latitudinal gradient covering the entirety of the range. We generated genotype data for 91,468 single nucleotide polymorphisms based on double digest restriction‐site associated DNA sequencing and used these data to discover genome‐wide associations for each trait, as well as to test for signatures of selection on the discovered architectures. Genetic structure across the introduced range of gypsy moth was low in magnitude (FST = 0.069), with signatures of bottlenecks and spatial expansion apparent in the rare portion of the allele frequency spectrum. Results from applications of Bayesian sparse linear mixed models were consistent with the presumed polygenic architectures of each trait. Further analyses indicated spatially divergent natural selection acting on larval development time and pupal mass, with the linkage disequilibrium component of this test acting as the main driver of observed patterns. The populations most important for these signals were two range edge populations established less than 30 generations ago. We discuss the importance of rapid polygenic adaptation to the ability of non‐native species to invade novel environments.
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Thornton V.2018DETERMINING TIDAL CHARACTERISTICS IN A RESTORED TIDAL WETLAND USING UNMANNED AERIAL VEHICLES AND DERIVED DATA MS Thesis https://scholarscompass.vcu.edu/etd/5369/.

Graduate Author(s)
Unmanned aerial vehicle (UAV) technology was used to determine tidal extent in Kimages Creek, a restored tidal wetland located in Charles City County, Virginia. A Sensefly eBee Real-Time Kinematic UAV equipped with the Sensor Optimized for Drone Applications (SODA) camera (20-megapixel RGB sensor) was flown during a single high and low tide event in Summer 2017. Collectively, over 1,300 images were captured and processed using Pix4D. Horizontal and vertical accuracy of models created using ground control points (GCP) ranged from 0.176 m to 0.363 m. The high tide elevation model was subtracted from the low tide using the ArcMap 10.5.1 raster calculator. The positive difference was displayed to show the portion of high tide that was above the low tide. These results show that UAVs offer numerous spatial and temporal advantages, but further research is needed to determine the best method of GCP placement in areas of similar forest structure.