Regional and scale-specific effects of land use on amphibian diversity [poster]

Background/Question/Methods Habitat loss and degradation influence amphibian distributions and are important drivers of population declines. Our previous research demonstrated that road disturbance, development and wetland area consistently influence amphibian richness across regions of the U.S. Here, we examined the relative importance of these factors in different regions and at multiple spatial scales. Understanding the scales at which habitat disturbance may be affecting amphibian distributions is important for conservation planning. Specifically, we asked: 1) Over what spatial scales do distinct landscape features affect amphibian richness? and 2) Do road types (non-rural and rural) have similar effects on amphibian richness? This is the second year of a collaborative, nationwide project involving 11 U.S. colleges integrated within undergraduate biology curricula. We summarized North American Amphibian Monitoring Program data in 13 Eastern and Central U.S states and used geographic information systems to extract landscape data for 471 survey locations. We developed models to quantify the influence of landscape variables on amphibian species richness and site occupancy across five concentric buffers ranging from 300m to 10,000m. Results/Conclusions Across spatial scales, development, road density and agriculture were the best predictors of amphibian richness and site occupancy by individual species. Across regions, we found that scale did not exert a large influence on how landscape features influenced amphibian richness as effects were largely comparable across buffers. However, development and percent impervious surface had stronger influence on richness at smaller spatial scales. Richness was lower at survey locations with higher densities of non-rural and rural roads, and non-rural road density had a larger negative effect at smaller scales. Within regions, landscape features driving patterns of species richness varied. The scales at which these factors were associated with richness were highly variable within regions, suggesting the scale effects may be region specific. Our project demonstrates that networks of undergraduate students can collaborate to compile and analyze large ecological data sets, while engaging students in authentic and inquiry-based learning in landscape-scale ecology

Phylogeography and non-invasive molecular monitoring of coyote (Canis latrans) and gray fox (Urocyon cinereoargenteus) in northern Virginia and the eastern United States

Molecular tools allow us to answer ecological questions about some of the most intriguing animals, including North America’s native gray fox (Urocyon cinereoargenteus) and Northern Virginia’s recent colonist, the coyote (Canis latrans). This dissertation is divided into four independent chapters, cohered by the common theme of molecular ecology of North American canids. The first chapter details a phylogeographical study of the gray fox, a widespread, but understudied, canid species. Fossil and historic records indicate that gray foxes were not present in the Northeastern United States until well after the Pleistocene (c. 900AD). To test the hypothesis that gray foxes experienced a post-Pleistocene range expansion, I sequenced a variable portion of the mitochondrial control region from gray fox tissue samples representing the range of all three East coast subspecies. Phylogeographic analyses indicated no clear pattern of genetic structuring of gray fox haplotypes across most of the Eastern United States. However, when haplotype frequencies were subdivided into a “Northeastern” and a “Southern” region, I detected a strong signal of differentiation between the Northeast and the rest of the Eastern United States. Indicators of molecular diversity and tests for demographic expansion confirmed this division and suggested a recent expansion of gray foxes into the Northeast. My results support the hypothesis that gray foxes first colonized the Northeast during a historic period of hemisphere-wide warming, which coincided with the range expansion of deciduous forest. The second chapter describes a novel method to genetically identify canid species from scat (feces) found in the field. I used a short fragment of the mitochondrial control region that is a different length in kit fox (Vulpes macrotis), red fox (V. vulpes), gray fox, coyote, and dog (C. familiaris) to differentiate their scat without using multiple primer sets, real-time PCR, or restriction enzyme digestion. All canid species included are potentially sympatric at the study site utilized in the following two chapters (Marine Corps Base Quantico, MCBQ and adjacent Prince William Forest Park, PWFP) except the kit fox. I extensively tested this technique using published and novel control region sequences and then applied it to two large scat data sets collected in California and Virginia (at MCBQ/PWFP). In the third chapter, I incorporate haplotype and genotype data obtained non-invasively from coyotes at MCBQ/PWFP into a regional analysis of patterns of coyote colonization across the Eastern United States. Coyotes have undergone a dramatic range expansion across North America since the early 19th century, colonizing east of the Mississippi River in two routes that have converged in the mid-Atlantic region in the past few decades. Notably, coyotes utilizing the Northern route of expansion show molecular evidence of admixture with the Great Lakes wolf (GLW). The study site at MCBQ/PWFP is located at the heart of the convergence of these two fronts. I screened scats collected at MCBQ/PWFP for species identification, then sequenced a hypervariable fragment of the mitochondrial control region to assign haplotype, and then used six microsatellite loci to identify individuals. I detected seven haplotypes (in 39 individuals), all of which have been previously reported in diverse surrounding geographic localities. Phylogeographic analyses indicated multiple sources of colonization of Northern Virginia and one common haplotype detected is of GLW origin, indicating the presence of admixed coyote/GLW individuals from the North. In the final chapter, I use the non-invasively collected genotype data to describe population demographics at MCBQ. I describe a population with low relatedness and minimal population genetic structure, reflective of the multiple geographic sources of colonization as described in the previous chapter. To estimate population density and size, I used a new class of spatially explicit capture-recapture models that address two key concerns of large carnivore demographic studies: violation of population closure and potentially sparse data sets. These models incorporate spatial data to eliminate the need for post hoc buffering and also use a Bayesian framework to effectively deal with a small sample size. Collectively, these studies are a significant contribution to the development and usage of non-invasive molecular technology, as well as to our understanding of phylogeography and population genetics of North American canids

Coyote colonization of northern Virginia and admixture with Great Lakes wolves

Ecological invasions of generalist species often are facilitated by anthropogenic disturbance. Coyotes (Canis latrans) have benefitted from anthropogenic changes to North American ecosystems and have experienced a dramatic range expansion since the early 19th century. The region east of the Mississippi River has been colonized via 2 routes that have converged in the mid-Atlantic region during the past few decades. Coyotes using the northern route of expansion show molecular evidence of admixture with the Great Lakes wolf (GLW). We used noninvasive molecular techniques to detect the geographic origins of the recent coyote colonization of northern Virginia as a representative of the mid-Atlantic region and to detect signatures of admixture with GLWs. Of 455 individual canid scats screened, we sequenced a variable 282-base pair fragment of the mitochondrial control region from 126 coyote scats, assigned individual identities to samples using 6 microsatellite loci, and conducted phylogeographic analyses by comparing our sequences to previously published haplotypes. In 39 individuals identified in our scat surveys we detected 7 mitochondrial DNA haplotypes, all of which have been previously reported in diverse surrounding geographic localities. Phylogeographic analyses indicate multiple sources of colonization of northern Virginia. One common haplotype detected in northern Virginia is of wolf origin, indicating the presence of admixed coyotes and GLWs from the north

Land use data and anuran species richness for North American Amphibian Monitoring Program survey sites

Data from 587 NAAMP survey sites. NAAMP survey locations are organized as "stops" within "routes," each of which has a unique SiteID. Land use variables were measured within buffers of 300m, 600m, 1000m, 5km, and 10km. Variables include "wet_prop" (proportion of area covered by wetland), "imperv" (proportion of area covered by impervious surface), "PROP_FOR" (proportion of area covered by forest), "PROP_DEV" (proportion of area covered by developed land uses, and "PROP_AGR" (proportion of area covered by row crop agriculture. Road-related variables are given as linear lengths (meters) within each buffer. Variables are T_ROAD_LEN (total road length), P_ROAD_LEN (primary (divided) roads), S_ROAD_LEN (secondary roads), O_ROAD_LEN (other roads, i.e. not P or S), and PS_ROAD_LEN (the sum of primary and secondary road lengths). Data also show the number of NAAMP surveys of each stop (Num.Surv), the number of years covered (Num.Years), mean car count during surveys (Car.Count), number of surveys with ambient noise (Noise.Num), and proportion of surveys that noted noise (NOISE_LEV = Noise.Num/Num.Surv). Amphibian presence/absence over all surveys are given for the species ANFO, HYCI, HYSQ, LICA, LICL, LIPA, LIPI, LISP, LISY, HYCV, PSTR (full scientific names are provided in the associated paper). NAs indicate sites outside the known range of each species. Richness is shown as the sum of all species detected at each stop, and NPP represents estimated Net Primary Productivity at that set (which provided a geographic expectation of anuran species richness)

Data from: Effects of roads and land use on frog distributions across spatial scales and regions in the eastern and central United States

Aim: Understanding the scales over which land use affects animal populations is critical for conservation planning, and it can provide information about the mechanisms that underlie correlations between species distributions and land use. We used a citizen-science database of anuran surveys to examine the relationship between road density, land use, and the distribution of frogs and toads across spatial scales and regions of the United States. Location: Eastern and Central United States Methods: We compiled data on anuran occupancy collected from 1999-2013 across 13 states in the North American Amphibian Monitoring Program, a citizen science survey of calling frogs. These data were indexed to measures of land use within buffers ranging from 300 m to 10 km. Results: The negative effects of road density and development on anuran richness were strongest at the smallest scales (300 – 1000 m), and this pattern was consistent across regions. In contrast, the relationships of anuran richness to agriculture and forest cover were similar across local scales but varied among regions. Richness had a negative relationship with agriculture/ forest loss in the Midwest but a positive relationship with agriculture in the Northeast. Anuran richness was more closely related to primary/secondary road density than to rural road density, and the negative effects of larger roads increased at smaller scales. Individual species differed in the scales over which roads and development affected their distributions, but these differences were not closely related to either body size or movement ability. Main conclusions: This study further refines our understanding of the relationship between roads and amphibian populations and highlights the need for research into the specific mechanisms by which roads affect amphibians. Additionally, we find that relationships between land use and species richness can differ substantially across regions, demonstrating that one should use caution in generalizing from one region to another, even when species composition is similar

Effects of Road and Land Use on Frog Distributions Across Spatial Scales and Regions in the Eastern and Central United States

Understanding the scales over which land use affects animal populations is critical for conservation planning, and it can provide information about the mechanisms that underlie correlations between species distributions and land use. We used a citizen science database of anuran surveys to examine the relationship between road density, land use and the distribution of frogs and toads across spatial scales and regions of the United States

Permanent genetic resources added to Molecular Ecology Resources Database 1 April 2010-31 May 2010

This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2010 – 31 May 2010: Isolation and characterization of microsatellite markers for the European shag, Phalacrocorax aristotelis.

This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii