Biamonte, E., Sandoval, L., Chacón, E. & Barrantes, G. Effect of urbanization on the avifauna in a tropical metropolitan area. Landsc. Ecol. 26, 183–194 (2011).
Google Scholar
Fahrig, L. Effects of habitat fragmentation on biodiversity. Annu. Rev. Ecol. Evol. Syst. 34, 487–515 (2003).
Google Scholar
Montgomery, M. R. The urban transformation of the developing world. Science 319, 761–764 (2008).
Google Scholar
Nuissl, H. & Siedentop, S. Urbanisation and Land Use Change. In Sustainable Land Management in a European Context: A Co-Design Approach (eds Weith, T. et al.) 75–99 (Springer International Publishing, 2021). https://doi.org/10.1007/978-3-030-50841-8_5.
Google Scholar
Scolozzi, R. & Geneletti, D. A multi-scale qualitative approach to assess the impact of urbanization on natural habitats and their connectivity. Environ. Impact Assess. Rev. 36, 9–22 (2012).
Google Scholar
Pauchard, A., Aguayo, M., Peña, E. & Urrutia, R. Multiple effects of urbanization on the biodiversity of developing countries: The case of a fast-growing metropolitan area (Concepción, Chile). Biol. Conserv. 127, 272–281 (2006).
Google Scholar
Xu, X., Xie, Y., Qi, K., Luo, Z. & Wang, X. Detecting the response of bird communities and biodiversity to habitat loss and fragmentation due to urbanization. Sci. Total Environ. 624, 1561–1576 (2018).
Google Scholar
Bélisle, M. & St. Clair, C. C. Cumulative effects of barriers on the movements of forest birds. Conserv. Ecol. 5, 9; http://www.consecol.org/vol5/iss2/art9 (2001).
Blair, R. B. Land use and avian species diversity along an urban gradient. Ecol. Appl. 6, 506–519 (1996).
Google Scholar
Tremblay, M. A. & St Clair, C. C. Permeability of a heterogeneous urban landscape to the movements of forest songbirds. J. Appl. Ecol. 48, 679–688 (2011).
Google Scholar
Johnson, M. T. J. & Munshi-South, J. Evolution of life in urban environments. Science 358, 8327 (2017).
Google Scholar
Isaksson, C. Impact of Urbanization on Birds. In Bird Species: How They Arise, Modify and Vanish (ed. Tietze, D. T.) 235–257 (Springer International Publishing, Berlin, 2018). https://doi.org/10.1007/978-3-319-91689-7_13.
Google Scholar
Miles, L. S., Rivkin, L. R., Johnson, M. T. J., Munshi-South, J. & Verrelli, B. C. Gene flow and genetic drift in urban environments. Mol. Ecol. 28, 4138–4151 (2019).
Google Scholar
Delaney, K. S., Riley, S. P. D. & Fisher, R. N. A rapid, strong, and convergent genetic response to urban Habitat fragmentation in four divergent and widespread vertebrates. PLoS ONE 5, e12767 (2010).
Google Scholar
Unfried, T. M., Hauser, L. & Marzluff, J. M. Effects of urbanization on Song Sparrow (Melospiza melodia) population connectivity. Conserv. Genet. 14, 41–53 (2013).
Google Scholar
Brewer, V. N., Lane, S. J., Sewall, K. B. & Mabry, K. E. Effects of low-density urbanization on genetic structure in the Song Sparrow. PLoS ONE 15, e0234008 (2020).
Google Scholar
Björklund, M., Ruiz, I. & Senar, J. C. Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city. Biol. J. Linn. Soc. 99, 9–19 (2010).
Google Scholar
Perrier, C. et al. Great tits and the city: Distribution of genomic diversity and gene–environment associations along an urbanization gradient. Evol. Appl. 11, 593–613 (2018).
Google Scholar
Tan, D. J. X. et al. Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis. Sci. Rep. 8, 12804 (2018).
Google Scholar
McRae, B. H., Dickson, B. G., Keitt, T. H. & Shah, V. B. Using circuit theory to model connectivity in ecology, evolution, and conservation. Ecology 89, 2712–2724 (2008).
Google Scholar
Howell, S. N. G. & Webb, S. A Guide to the Birds of Mexico and Northern Central America (Oxford University Press, 1995).
Sandoval, L. & Mennill, D. J. Breeding biology of White-eared Ground-sparrow (Melozone leucotis), with a description of a new nest type. Ornitol. Neotropical 23, 225–234 (2012).
Stiles, F. G. & Skutch, A. F. A Guide to the Birds of Costa Rica (Cornell University Press, 1989).
Carlson, T. N. & Sanchez-Azofeifa, G. A. Satellite remote sensing of land use changes in and around San José Costa Rica. Remote Sens. Environ. 70, 247–256 (1999).
Google Scholar
Sánchez, J. E., Criado, J., Sánchez, C. & Sandoval, L. Costa Rica. In Important Bird Areas of Americas: priority sites for biodiversity conservation (eds Davendish, C. et al.) 149–156 (Birdlife International, 2009).
Sandoval, L. et al. The forgotten habitats in conservation: early successional vegetation. Rev. Biol. Trop. 67, 36–52 (2019).
Google Scholar
Juárez, R., Chacón-Madrigal, E. & Sandoval, L. Urbanization has opposite effects on the territory size of two passerine birds. Avian Res. 11, 11 (2020).
Google Scholar
Skutch, A. F. Life history of the Southern House Wren. Condor 55, 121–149 (1953).
Google Scholar
Johnson, L. S. House Wren (Troglodytes aedon), Version 10. In Birds of the World (ed. Poole, A. F.) (Cornell Lab of Ornithology, 2020).
Markowski, M. et al. Genetic structure of urban and non-urban populations differs between two common parid species. Sci. Rep. 11, 10428. https://doi.org/10.1038/s41598-021-89847-4 (2021).
Google Scholar
Mueller, J. C. et al. Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proc. R. Soc. B Biol. Sci. 285, 20180206 (2018).
Google Scholar
Vangestel, C. et al. Genetic diversity and population structure in contemporary house sparrow populations along an urbanization gradient. Heredity 109, 163–172 (2012).
Google Scholar
Joyce, A. T. Land Use Change in Costa Rica: 1966–2006, as Influenced by Social, Economic, Political, and Environmental Factors (Litografía e imprenta LIL, 2016).
Fuchs, E. J. & Hamrick, J. L. Mating system and pollen flow between remnant populations of the endangered tropical tree, Guaiacum sanctum (Zygophyllaceae). Conserv. Genet. 12, 175–185 (2011).
Google Scholar
Stevens, K., Harrisson, K. A., Hogan, F. E., Cooke, R. & Clarke, R. H. Reduced gene flow in a vulnerable species reflects two centuries of habitat loss and fragmentation. Ecosphere 9, e02114 (2018).
Google Scholar
Quesada-Román, A., Villalobos-Portilla, E. & Campos-Durán, D. Hydrometeorological disasters in urban areas of Costa Rica Central America. Environ. Hazards 20, 264–278 (2021).
Google Scholar
Muñoz, P., García-Rodríguez, A. & Sandoval, L. Urbanization, habitat extension and spatial pattern, threaten a Costa Rican endemic bird. Rev. Biol. Trop. 69, 170–180 (2021).
Sandoval, L., Bitton, P. P., Doucet, S. M. & Mennill, D. J. Analysis of plumage, morphology, and voice reveals species-level differences between two subspecies of Prevost’s Ground-sparrow Melozone biarcuata (Prévost and Des Murs) (Aves: Emberizidae). Zootaxa 3895, 103–116 (2014).
Google Scholar
Arguedas, N. & Parker, P. G. Seasonal migration and genetic population structure in House Wrens. Condor 102, 517–528 (2000).
Google Scholar
Pujol, R. & Pérez, E. Crecimiento urbano en la región metropolitana de San José, Costa Rica. Una exploración espacial y temporal de los determinantes del cambio de uso del suelo, 1986–2010. Lincoln Institute of Land Policy https://www.lincolninst.edu/sites/default/files/pubfiles/2242_1578_Pujol_WP13RP1SP.pdf (2012).
Sandoval, L., Dabelsteen, T. & Mennill, D. J. Transmission characteristics of solo songs and duets in a neotropical thicket habitat specialist bird. Bioacoustics 24, 289–306 (2015).
Google Scholar
Sandoval, L., Méndez, C. & Mennill, D. J. Vocal behaviour of White-eared Ground-sparrows (Melozone leucotis) during the breeding season: repertoires, diel variation, behavioural contexts, and individual distinctiveness. J. Ornithol. 157, 1–12 (2016).
Google Scholar
Carro, M. E., Llambías, P. E., Mahler, B. & Fernández, G. J. Contrasting patterns of natal dispersal of a south temperate House Wren population at local and regional scales. J. Ornithol. 162, 895–907 (2021).
Google Scholar
Garrigues, R. & Dean, R. The Birds of Costa Rica: A Field Guide (Cornell University Press, 2014).
Sandoval, L., Epperly, K. L., Klicka, J. & Mennill, D. J. The biogeographic and evolutionary history of an endemic clade of Middle American sparrows: Melozone and Aimophila (Aves: Passerellidae). Mol. Phylogenet. Evol. 110, 50–59 (2017).
Google Scholar
MacGregor-Fors, I. & Escobar-Ibáñez, J. F. Birds from Urban Latin America, Where Economic Inequality and Urbanization Meet Biodiversity. In Avian Ecology in Latin American Cityscapes (eds MacGregor-Fors, I. & Escobar-Ibáñez, J. F.) 1–10 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-63475-3_1.
Google Scholar
MacGregor-Fors, I. & García-Arroyo, M. Who Is Who in the City? Bird Species Richness and Composition in Urban Latin America. In Avian Ecology in Latin American Cityscapes (eds MacGregor-Fors, I. & Escobar-Ibáñez, J. F.) 33–55 (Springer International Publishing, 2017). https://doi.org/10.1007/978-3-319-63475-3_3.
Google Scholar
Lande, R. & Barrowclough, G. F. Effective population size, genetic variation, and their use in population management. In Viable Populations for Conservation (ed. Soulé, M. E.) 87–124 (Cambridge University Press, 1987). https://doi.org/10.1017/CBO9780511623400.007.
Google Scholar
Newman, D. & Pilson, D. Increased probability of extinction due to decreased genetic effective population size: Experimental populations of Clarkia Pulchella. Evolution 51, 354–362 (1997).
Google Scholar
Longmire, J. L., Maltbie, M. & Baker, R. J. Use of ‘Lysis Buffer’ in DNA isolation and its implication for museum collections (Museum of Texas Tech University, 1997).
Google Scholar
Bulgin, N. L., Gibbs, H. L., Vickery, P. & Baker, A. J. Ancestral polymorphisms in genetic markers obscure detection of evolutionarily distinct populations in the endangered Florida grasshopper sparrow (Ammodramus savannarum floridanus). Mol. Ecol. 12, 831–844 (2003).
Google Scholar
Hanotte, O. et al. Isolation and characterization of microsatellite loci in a passerine bird: the reed bunting Emberiza schoeniclus. Mol. Ecol. 3, 529–530 (1994).
Google Scholar
Jeffery, K. J., Keller, L. F., Arcese, P. & Bruford, M. W. The development of microsatellite loci in the song sparrow, Melospiza melodia (Aves) and genotyping errors associated with good quality DNA. Mol. Ecol. Notes 1, 11–13 (2001).
Google Scholar
Petren, K. Microsatellite primers from Geospiza fortis and cross-species amplification in Darwin’s finches. Mol. Ecol. 7, 1782–1784 (1998).
Google Scholar
Brar, R. K. et al. Eleven microsatellite loci isolated from the banded wren (Thryothorus pleurostictus). Mol. Ecol. Notes 7, 69–71 (2007).
Google Scholar
Cabe, P. R. & Marshall, K. E. Microsatellite loci from the house wren (Troglodytes aedon). Mol. Ecol. Notes 1, 155–156 (2001).
Google Scholar
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing https://www.R-project.org/ (2021).
RStudio Team. RStudio: integrated development environment for R. RStudio http://www.rstudio.com/ (2021).
Goudet, J. hierfstat, a package for r to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184–186 (2005).
Google Scholar
Weir, B. S. & Cockerham, C. C. Estimating F-Statistics for the analysis of population structure. Evolution 38, 1358–1370 (1984).
Google Scholar
Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).
Google Scholar
Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945–959 (2000).
Google Scholar
Earl, D. A. & vonHoldt, B. M. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4, 359–361 (2012).
Google Scholar
Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol. Ecol. 14, 2611–2620 (2005).
Google Scholar
Shah, V. B. & McRae, B. Circuitscape: A Tool for Landscape Ecology. in Proceedings of the 7th Python in Science Conference (eds. Varoquaux, G., Vaught, T. & Millman, J.) 62–65 (2008).
Ortiz-Malavasi, E. Atlas digital de costa rica está a disposición del público. Invest. TEC 23, 1659–3383 (2015).
McRae, B., Shirk, A. & Platt, J. Gnarly landscape utilities: Resistance and habitat calculator user guide. The Nature Conservancy https://circuitscape.org/gnarly-landscape-utilities/ (2013).
Kass, J. M. et al. Wallace: A flexible platform for reproducible modeling of species niches and distributions built for community expansion. Methods Ecol. Evol. 9, 1151–1156 (2018).
Google Scholar
Source: Ecology - nature.com
