Effects of habitat fragment size and isolation on the density and genetics of urban red-backed salamanders (Plethodon cinereus)

adegenet: a R package for the multivariate analysis of genetic markers

Jombart, T. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn129 · Cited by 8,107

Inference of Population Structure Using Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies

Falush, D., Stephens, M., & Pritchard, J. K. (2003) · Genetics · doi:10.1093/genetics/164.4.1567 · Cited by 7,959

JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling

Plummer, M. (2003) · Cited by 4,720

Urbanization as a major cause of biotic homogenization

McKinney, M. L. (2005) · Biological Conservation · doi:10.1016/j.biocon.2005.09.005 · Cited by 4,066

Urbanization, Biodiversity, and Conservation

McKinney, M. L. (2002) · BioScience · doi:10.1641/0006-3568(2002)052[0883:ubac]2.0.co;2 · Cited by 3,848

Inferring weak population structure with the assistance of sample group information

HUBISZ, M. J., FALUSH, D., STEPHENS, M., & PRITCHARD, J. K. (2009) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2009.02591.x · Cited by 3,475

Inference of population structure using multilocus genotype data: dominant markers and null alleles

Falush, D., Stephens, M., & Pritchard, J. K. (2007) · Molecular Ecology Notes · doi:10.1111/j.1471-8286.2007.01758.x · Cited by 3,468

Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data

Piry, S., Luikart, G., & Cornuet, J.-M. (1999) · Journal of Heredity · doi:10.1093/jhered/90.4.502 · Cited by 3,336

Microsatellite Null Alleles and Estimation of Population Differentiation

Chapuis, M., & Estoup, A. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl191 · Cited by 2,873

pegas: an R package for population genetics with an integrated–modular approach

Paradis, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp696 · Cited by 2,687

Effects of urbanization on species richness: A review of plants and animals

McKinney, M. L. (2008) · Urban Ecosystems · doi:10.1007/s11252-007-0045-4 · Cited by 2,570

The role of urban parks for the sustainable city

Chiesura, A. (2004) · Landscape and Urban Planning · doi:10.1016/j.landurbplan.2003.08.003 · Cited by 2,555

A Meta-Analysis of Global Urban Land Expansion

Seto, K. C., Fragkias, M., Güneralp, B., & Reilly, M. K. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023777 · Cited by 2,344

Distortion of allele frequency distributions provides a test for recent population bottlenecks

Luikart, G. (1998) · Journal of Heredity · doi:10.1093/jhered/89.3.238 · Cited by 1,572

N‐Mixture Models for Estimating Population Size from Spatially Replicated Counts

Royle, J. A. (2004) · Biometrics · doi:10.1111/j.0006-341x.2004.00142.x · Cited by 1,541

Mutational processes of simple-sequence repeat loci in human populations.

Di Rienzo, A., Peterson, A. C., Garza, J. C., Valdes, A. M., Slatkin, M., & Freimer, N. B. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.8.3166 · Cited by 1,535

Effects of habitat loss and fragmentation on amphibians: A review and prospectus

Cushman, S. A. (2006) · Biological Conservation · doi:10.1016/j.biocon.2005.09.031 · Cited by 1,499

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

Lischer, H. E. L., & Excoffier, L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/btr642 · Cited by 1,316

Microclimate in Forest Ecosystem and Landscape Ecology

Chen, J., Saunders, S. C., Crow, T. R., Naiman, R. J., Brosofske, K. D., Mroz, G. D., Brookshire, B. L., & Franklin, J. F. (1999) · BioScience · doi:10.2307/1313612 · Cited by 976

Circuit theory predicts gene flow in plant and animal populations

McRae, B. H., & Beier, P. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706568104 · Cited by 945

How general are positive relationships between plant population size, fitness and genetic variation?

LEIMU, R., MUTIKAINEN, P., KORICHEVA, J., & FISCHER, M. (2006) · Journal of Ecology · doi:10.1111/j.1365-2745.2006.01150.x · Cited by 904

Who benefits from access to green space? A case study from Sheffield, UK

Barbosa, O., Tratalos, J. A., Armsworth, P. R., Davies, R. G., Fuller, R. A., Johnson, P., & Gaston, K. J. (2007) · Landscape and Urban Planning · doi:10.1016/j.landurbplan.2007.04.004 · Cited by 645

P op G en R eport: simplifying basic population genetic analyses in R

Adamack, A. T., & Gruber, B. (2014) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12158 · Cited by 640

How and why environmental noise impacts animals: an integrative, mechanistic review: Environmental noise and animals

Kight, C. R., & Swaddle, J. P. (2011) · Ecology Letters · doi:10.1111/j.1461-0248.2011.01664.x · Cited by 622

Animal behavior in urban ecosystems: Modifications due to human-induced stress

Ditchkoff, S. S., Saalfeld, S. T., & Gibson, C. J. (2006) · Urban Ecosystems · doi:10.1007/s11252-006-3262-3 · Cited by 582

Ecological consequences of habitat fragmentation: implications for landscape architecture and planning

Collinge, S. (1996) · Landscape and Urban Planning · doi:10.1016/s0169-2046(96)00341-6 · Cited by 548

Urban expansion dynamics and natural habitat loss in China: a multiscale landscape perspective

He, C., Liu, Z., Tian, J., & Ma, Q. (2014) · Global Change Biology · doi:10.1111/gcb.12553 · Cited by 508

Salamander Populations and Biomass in the Hubbard Brook Experimental Forest, New Hampshire

Burton, T. M., & Likens, G. E. (1975) · Copeia · doi:10.2307/1443655 · Cited by 457

The National Land Cover Database

Homer, C. G., Fry, J. A., & Barnes, C. A. (2012) · Fact sheet · doi:10.3133/fs20123020 · Cited by 444

The genetic implications of habitat fragmentation for animalsThis review is one of a series dealing with some aspects of the impact of habitat fragmentation on animals and plants. This series is one of several virtual symposia focussing on ecological topics that will be published in the Journal from time to time.

Keyghobadi, N. (2007) · Canadian Journal of Zoology · doi:10.1139/z07-095 · Cited by 430

Street Lighting Disturbs Commuting Bats

Stone, E. L., Jones, G., & Harris, S. (2009) · Current Biology · doi:10.1016/j.cub.2009.05.058 · Cited by 416

Biological Delineation of Terrestrial Buffer Zones for Pond‐Breeding Salamanders

Semlitsch, R. D. (1998) · Conservation Biology · doi:10.1046/j.1523-1739.1998.97274.x · Cited by 408

Vegetation and microclimatic edge effects in two mixed-mesophytic forest fragments

Gehlhausen, S. M., Schwartz, M. W., & Augspurger, C. K. (2000) · Plant Ecology · doi:10.1023/a:1009846507652 · Cited by 365

Do population size bottlenecks reduce evolutionary potential?

Frankham, R., Lees, K., Montgomery, M. E., England, P. R., Lowe, E. H., & Briscoe, D. A. (1999) · Animal Conservation · doi:10.1017/s136794309900058x · Cited by 332

Large trees are keystone structures in urban parks

Stagoll, K., Lindenmayer, D. B., Knight, E., Fischer, J., & Manning, A. D. (2012) · Conservation Letters · doi:10.1111/j.1755-263x.2011.00216.x · Cited by 295

ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms

Peterman, W. E. (2018) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12984 · Cited by 280

Synurbization-adaptation of animal wildlife to urban development

Luniak, M. (2004) · Cited by 262

Urbanization, oxidative stress and inflammation: a question of evolving, acclimatizing or coping with urban environmental stress

Isaksson, C. (2015) · Functional Ecology · doi:10.1111/1365-2435.12477 · Cited by 239

Urban amphibian assemblages as metacommunities.

Parris, K. (2006) · Journal of Animal Ecology · doi:10.1111/j.1365-2656.2006.01096.x · Cited by 222

Amphibian Movements in Response to Forest Edges, Roads, and Streambeds in Southern New England

Gibbs, J. P. (1998) · The Journal of Wildlife Management · doi:10.2307/3802333 · Cited by 213

Deleterious Effects of Restricted Gene Flow in Fragmented Populations

Couvet, D. (2002) · Conservation Biology · doi:10.1046/j.1523-1739.2002.99518.x · Cited by 211

Interpatch movements in spatially structured populations: a literature review

Bowne, D. R., & Bowers, M. A. (2004) · Landscape Ecology · doi:10.1023/b:land.0000018357.45262.b9 · Cited by 202

Amphibian Contributions to Ecosystem Services

Hocking, D. J., & Babbitt, K. J. (2014) · University of New Hampshire Scholars Repository (University of New Hampshire at Manchester) · Cited by 202

Small urban woodlands as biodiversity conservation hot-spot: a multi-taxon approach

Croci, S., Butet, A., Georges, A., Aguejdad, R., & Clergeau, P. (2008) · Landscape Ecology · doi:10.1007/s10980-008-9257-0 · Cited by 199

From connectivity to isolation: genetic consequences of population fragmentation in capercaillie across Europe

Segelbacher, G., Höglund, J., & Storch, I. (2003) · Molecular Ecology · doi:10.1046/j.1365-294x.2003.01873.x · Cited by 195

CRITICAL THRESHOLDS ASSOCIATED WITH HABITAT LOSS FOR TWO VERNAL POOL‐BREEDING AMPHIBIANS

Homan, R. N., Windmiller, B. S., & Reed, J. M. (2004) · Ecological Applications · doi:10.1890/03-5125 · Cited by 191

The city-fox phenomenon: genetic consequences of a recent colonization of urban habitat

Wandeler, P., Funk, S. M., Largiadèr, C. R., Gloor, S., & Breitenmoser, U. (2003) · Molecular Ecology · doi:10.1046/j.1365-294x.2003.01768.x · Cited by 189

Experimental assessment of salamanders as predators of detrital food webs: effects on invertebrates, decomposition and the carbon cycle

Wyman, R. L. (1998) · Biodiversity and Conservation · doi:10.1023/a:1008856402258 · Cited by 186

Impact of urban fragmentation on the genetic structure of the eastern red-backed salamander

Noël, S., Ouellet, M., Galois, P., & Lapointe, F. (2006) · Conservation Genetics · doi:10.1007/s10592-006-9202-1 · Cited by 180

Variation in Vegetation Structure and Composition across Urban Green Space Types

Threlfall, C. G., Ossola, A., Hahs, A. K., Williams, N. S. G., Lee, W., & Livesley, S. J. (2016) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2016.00066 · Cited by 180

Circuitscape in Julia: High Performance Connectivity Modelling to Support Conservation Decisions

(2020) · JuliaCon Proceedings · doi:10.21105/jcon.00058 · Cited by 163

Home Range and Homing Behavior of Plethodon cinereus in Northern Michigan

Kleeberger, S. R., & Werner, J. K. (1982) · Copeia · doi:10.2307/1444622 · Cited by 159

Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae:Stenopelmatus)

Vandergast, A. G., Bohonak, A. J., Weissman, D. B., & Fisher, R. N. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.03216.x · Cited by 157

Changes in bird species richness through different levels of urbanization: Implications for biodiversity conservation and garden design in Central Brazil

Reis, E., López-Iborra, G. M., & Pinheiro, R. T. (2012) · Landscape and Urban Planning · doi:10.1016/j.landurbplan.2012.04.009 · Cited by 152

Commensal ecology, urban landscapes, and their influence on the genetic characteristics of city‐dwelling Norway rats (Rattus norvegicus)

Gardner-Santana, L. C., Norris, D. E., Fornadel, C. M., Hinson, E. R., Klein, S. L., & Glass, G. E. (2009) · Molecular Ecology · doi:10.1111/j.1365-294x.2009.04232.x · Cited by 149

Geographical and genetic distances among zooplankton populations in a set of interconnected ponds: a plea for using GIS modelling of the effective geographical distance

Michels, E., Cottenie, K., Neys, L., Gelas, K. D., Coppin, P. R., & Meester, L. D. (2001) · Molecular Ecology · doi:10.1046/j.1365-294x.2001.01340.x · Cited by 147

Urban Green Space Fragmentation and Urbanization: A Spatiotemporal Perspective

Li, F., Zheng, W., Wang, Y. T., Liang, J., Xie, S., Guo, S., Li, X., & Yu, C. (2019) · Forests · doi:10.3390/f10040333 · Cited by 145

Influence of Cover and Moisture on Abundances of the Terrestrial Salamanders Plethodon cinereus and Plethodon glutinosus

Grover, M. C. (1998) · Journal of Herpetology · doi:10.2307/1565202 · Cited by 136

Forest Roads as Partial Barriers to Terrestrial Salamander Movement

Marsh, D. M., Milam, G. S., Gorham, N. P., & Beckman, N. G. (2005) · Conservation Biology · doi:10.1111/j.1523-1739.2005.00238.x · Cited by 124

Do cities represent sources, sinks or isolated islands for urban wild boar population structure?

Stillfried, M., Fickel, J., Börner, K., Wittstatt, U., Heddergott, M., Ortmann, S., Kramer‐Schadt, S., & Frantz, A. C. (2016) · Journal of Applied Ecology · doi:10.1111/1365-2664.12756 · Cited by 118

Fine-Scale Habitat Associations of a Terrestrial Salamander: The Role of Environmental Gradients and Implications for Population Dynamics

Peterman, W. E., & Semlitsch, R. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0062184 · Cited by 116

Multi-scaled habitat considerations for conserving urban biodiversity: native reptiles and small mammals in Brisbane, Australia

Garden, J. G., McAlpine, C., & Possingham, H. P. (2010) · Landscape Ecology · doi:10.1007/s10980-010-9476-z · Cited by 114

Declines in Woodland Salamander Abundance Associated with Non‐Native Earthworm and Plant Invasions

Maerz, J. C., Nuzzo, V., & Blossey, B. (2009) · Conservation Biology · doi:10.1111/j.1523-1739.2009.01167.x · Cited by 114

Fine-scale population differentiation and gene flow in a terrestrial salamander (Plethodon cinereus) living in continuous habitat

Cabe, P. R., Page, R. B., Hanlon, T. J., Aldrich, M. E., Connors, L., & Marsh, D. M. (2006) · Heredity · doi:10.1038/sj.hdy.6800905 · Cited by 114

landgenreport: a new r function to simplify landscape genetic analysis using resistance surface layers

Gruber, B., & Adamack, A. T. (2015) · Molecular Ecology Resources · doi:10.1111/1755-0998.12381 · Cited by 103

The effects of urbanization on North American amphibian species: Identifying new directions for urban conservation

Scheffers, B. R., & Paszkowski, C. A. (2011) · Urban Ecosystems · doi:10.1007/s11252-011-0199-y · Cited by 100

Effects of roads on patterns of genetic differentiation in red-backed salamanders, Plethodon cinereus

Marsh, D. M., Page, R. B., Hanlon, T. J., Corritone, R., Little, E. C., Seifert, D. E., & Cabe, P. R. (2007) · Conservation Genetics · doi:10.1007/s10592-007-9377-0 · Cited by 100

Female philopatry and male-biased dispersal in a direct-developing salamander, Plethodon cinereus

Liebgold, E. B., Brodie, E. D., & Cabe, P. R. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04946.x · Cited by 99

Ecology of Urban badgers Meles meles: Distribution in Britain and habitat selection, persecution, food and damage in the city of Bristol

Harris, S. E. (1984) · Biological Conservation · doi:10.1016/0006-3207(84)90041-7 · Cited by 96

The trophic role of a forest salamander: impacts on invertebrates, leaf litter retention, and the humification process

Best, M. L., & Welsh, H. H. (2014) · Ecosphere · doi:10.1890/es13-00302.1 · Cited by 96

Genetic structure of redback salamander Plethodon cinereus populations in continuous and fragmented forests

Gibbs, J. P. (1998) · Biological Conservation · doi:10.1016/s0006-3207(97)00173-0 · Cited by 67

Preference for Soil Moisture, Soil pH, and Light Intensity by the Salamander, Plethodon cinereus

Sugalski, M. T., & Claussen, D. L. (1997) · Journal of Herpetology · doi:10.2307/1565392 · Cited by 66

Urban conservation genetics: Study of a terrestrial salamander in the city

Noël, S., & Lapointe, F. (2010) · Biological Conservation · doi:10.1016/j.biocon.2010.07.033 · Cited by 59

Dispersal mode mediates the effect of patch size and patch connectivity on metacommunity diversity

Jones, N. T., Germain, R. M., Grainger, T. N., et al. (2015) · Journal of Ecology · doi:10.1111/1365-2745.12405 · Cited by 59

Role of Genetic Background in the Success of Reintroduced Peregrine Falcons

Tordoff, H. B., & Redig, P. T. (2001) · Conservation Biology · doi:10.1046/j.1523-1739.2001.015002528.x · Cited by 56

Conservation genetics of extremely isolated urban populations of the northern dusky salamander ( Desmognathus fuscus ) in New York City

Munshi‐South, J., Zak, Y., & Pehek, E. (2013) · PeerJ · doi:10.7717/peerj.64 · Cited by 52

Parapatric divergence of sympatric morphs in a salamander: incipient speciation on Long Island?

Fisher‐Reid, M. C., Engstrom, T. N., Kuczynski, C. A., et al. (2013) · Molecular Ecology · doi:10.1111/mec.12412 · Cited by 51

Multiple paternity in a salamander with socially monogamous behaviour

Liebgold, E. B., Cabe, P. R., Jaeger, R. G., & Leberg, P. L. (2006) · Molecular Ecology · doi:10.1111/j.1365-294x.2006.03076.x · Cited by 49

Dispersal Versus Site Tenacity of Adult and Juvenile Red-Backed Salamanders (Plethodon cinereus)

Ousterhout, B. H., & Liebgold, E. B. (2010) · Herpetologica · doi:10.1655/09-023.1 · Cited by 45

Ecological and genetic evidence that low-order streams inhibit dispersal by red-backed salamanders (Plethodon cinereus)

Marsh, D. M., Page, R. B., Hanlon, T. J., Bareke, H., Corritone, R., Jetter, N., Beckman, N. G., Gardner, K., Seifert, D. E., & Cabe, P. R. (2007) · Canadian Journal of Zoology · doi:10.1139/z07-008 · Cited by 42

Dealing with uncertainty in landscape genetic resistance models: a case of three co‐occurring marsupials

Dudaniec, R. Y., Wilmer, J. W., Hanson, J. O., Warren, M. J., Bell, S., & Rhodes, J. R. (2015) · Molecular Ecology · doi:10.1111/mec.13482 · Cited by 34

Urban park characteristics, genetic variation, and historical demography of white-footed mouse ( Peromyscus leucopus ) populations in New York City

Munshi‐South, J., & Nagy, C. M. (2014) · PeerJ · doi:10.7717/peerj.310 · Cited by 31

Linking physiological effects on activity and resource use to population level phenomena

O’Connor, M. P., Sieg, A., & Dunham, A. E. (2006) · Integrative and Comparative Biology · doi:10.1093/icb/icl031 · Cited by 27

Microsatellite Loci Analysis Reveals Post-bottleneck Recovery of Genetic Diversity in the Tibetan Antelope

Du, Y., Zou, X., Xu, Y., Guo, X., Li, S., Zhang, X., Su, M., Ma, J., & Guo, S. (2016) · Scientific Reports · doi:10.1038/srep35501 · Cited by 26

Isolation of dinucleotide microsatellite loci from red‐backed salamander (Plethodon cinereus)

Connors, L. M., & Cabe, P. R. (2003) · Molecular Ecology Notes · doi:10.1046/j.1471-8286.2003.00373.x · Cited by 23

Effects of land use legacies and habitat fragmentation on salamander abundance

Cosentino, B. J., & Brubaker, K. M. (2018) · Landscape Ecology · doi:10.1007/s10980-018-0686-0 · Cited by 23

The influence of historical landscape change on genetic variation and population structure of a terrestrial salamander (Plethodon cinereus)

Jordan, M. A., Morris, D. A., & Gibson, S. E. (2008) · Conservation Genetics · doi:10.1007/s10592-008-9741-8 · Cited by 21

Identification of Polymorphic Loci in Ambystoma annulatum and Review of Cross-species Microsatellite Use in the Genus Ambystoma

Peterman, W. E., Connette, G. M., Spatola, B. N., Eggert, L. S., & Semlitsch, R. D. (2012) · Copeia · doi:10.1643/ch-11-001 · Cited by 15

Development of microsatellite loci for the western slimy salamander (Plethodon albagula) using 454 sequencing

Spatola, B. N., Peterman, W. E., Stephens, N. T., Connette, G. M., Shepard, D. B., Kozak, K. H., Semlitsch, R. D., & Eggert, L. S. (2012) · Conservation Genetics Resources · doi:10.1007/s12686-012-9784-5 · Cited by 8

Circuitscape in julia: empowering dynamic approaches to connectivity assessment

Hall, K. R., Anantharaman, R., Landau, V. A., Clark, M., Dickson, B. G., Jones, A., Platt, J., Edelman, A., & Shah, V. B. (2021) · Land · doi:10.3390/land10030301 · Cited by 115