Alencar LRV, Quental TB, Grazziotin FG, Alfaro ML, Martins M, Venzon M et al. (2016) Diversification in vipers: phylogenetic relationships, time of divergence and shifts in speciation rates. Mol Phylogenet Evol 105:50–62
Anger GR, Dean R (2010) The birds of Panama: a field guide. Zona Tropical Publication, San José, Costa Rica
Avise JC (1992) Molecular population structure and the biogeographic history of a regional fauna: a case history with lessons for conservation biology. Oikos 63:62–76
Bacon CD, Silvestro D, Jaramillo C, Smith BT, Chakrabarty P, Antonelli A (2015) Biological evidence supports an early and complex emergence of the Isthmus of Panama. Proc Natl Acad Sci 112:6110–6115
Bagley JC, Hickerson MJ, Johnson JB (2018) Testing hypotheses of diversification in Panamanian frogs and freshwater fishes using hierarchical approximate Bayesian computation with model averaging. Diversity 10:1–25
Bagley JC, Johnson JB (2014) Phylogeography and biogeography of the lower Central American Neotropics: diversification between two continents and between two seas. Biol Rev 89:767–790
Baird AB, Marchán-Rivadeneira MR, Pérez SG, Baker RJ (2012) Morphological analysis and description of two new species of Rhogeessa (Chiroptera: Vespertilionidae) from the neotropics. Occas Pap Mus Tex Tech Univ 307:1–25
Balkenhol N, Cushman SA, Storfer AT, Waits LP (2008) Landscape Genetics. Concepts, Methods, Applications. Wiley-Blackwell, West Sussex, UK
Beebee TJC (2005) Conservation genetics of amphibians. Heredity 95:423–7
Bloch JI, Woodruff ED, Wood AR, Rincon AF, Harrington AR, Morgan GS et al. (2016) First North American fossil monkey and early Miocene tropical biotic interchange. Nature 533:243–246
de Boer JZ, Drummond MS, Bordelon MJ, Defant MJ, Bellon H, Maury RC (1995) Cenozoic magmatic phases of the Costa Rican island arc (Cordillera de Talamanca). Geol Soc Am Spec Pap 295:35–56
Bogarín D, Pupulin F, Arrocha C, Warner J (2013) Orchids without borders: studying the hotspot of Costa Rica and Panama. Lankesteriana 13:13–26
Bolaños R, Watson V, Tosi J (2005) Mapa ecológico de Costa Rica (Zonas de Vida), según el sistema de clasificación de zonas de vida del mundo de LR Holdridge), Escala 1:750 000. Centro Científico Tropical, San José, Costa Rica. Centro Científico Tropical, San José, Costa Rica
Brumfield RT, Braun MJ (2001) Phylogenetic relationships in bearded manakins (Pipridae: Manacus) indicate that male plumage color is a misleading taxonomic marker. Condor 103:248–258
Carnaval AC, Hickerson MJ, Haddad CFB, Rodrigues MT, Moritz C (2009) Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science 323:785–789
Coates AG, Jackson JBC, Collins LS, Cronin TM, Dowtsett HJ, Bybell LM et al. (1992) Closure of the Isthmus of Panama: the near-shore marine record of Costa Rica and western Panama. Geol Soc Am Bull 104:814–828
Coen E (1991) Climate. In: Janzen DH (ed) Historia Natural de Costa Rica. Editorial de la Universidad de Costa Rica, San José, Costa Rica, p 822
Collins RA, Boykin LM, Cruickshank RH, Armstrong KF (2012) Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification. Methods Ecol Evol 3:457–465
Collins RA, Cruickshank RH (2012) The seven deadly sins of DNA barcoding. Mol Ecol Resour 13:969–975
Crawford AJ (2003) Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences. Mol Ecol 12:2525–2540
Crawford AJ, Bermingham E, Carolina PS (2007) The role of tropical dry forest as a long-term barrier to dispersal: a comparative phylogeographical analysis of dry forest tolerant and intolerant frogs. Mol Ecol 16:4789–807
Crawford AJ, Lips KR, Bermingham E (2010) Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. Proc Natl Acad Sci 107:13777–13782
Cruz-Piedrahita C, Navas CA, Crawford AJ (2018) Life on the edge: a comparative study of ecophysiological adaptations of frogs to Tropical semiarid environments. Physiol Biochem Zool 91:740–756
Doebeli M, Dieckmann U (2003) Speciation along environmental gradients. Nature 421:259–264
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Edwards S, Beerli P (2000) Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54:1839–1854
Feldman CR, Spicer GS (2006) Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Mol Ecol 15:2201–2222
Ferrier S, Manion G, Elith J, Richardson K (2007) Using generalized dissimilarity modelling to analyse and predict patterns of beta diversity in regional biodiversity assessment. Divers Distrib 13:252–264
Fitzpatrick MC, Mokany K, Manion G, Lisk M, Ferrier S, Nieto-Lugilde D (2020) gdm: Generalized dissimilarity modeling. https://CRANR-project.org/package=gdm.
Fouquet A, Vences M, Salducci M-D, Meyer A, Marty C, Blanc M et al. (2007) Revealing cryptic diversity using molecular phylogenetics and phylogeography in frogs of the Scinax ruber and Rhinella margaritifera species groups. Mol Phylogenet Evol 43:567–582
Frost DR (2019) Amphibian species of the world: an online reference. Version 6.0 (Date of access). Electronic database accessible at. Amphib Species World an Online Ref Version 60.
Funk WC, Caminer M, Ron SR (2012) High levels of cryptic species diversity uncovered in Amazonian frogs. Proc R Soc B 279:1806–1814
Gabb WM, Lücke OH, Gutiérrez V, Soto G (2007) On the geology of the Republic of Costa Rica. (Transcription of the original manuscript by: Oscar H. Lücke, Viviana Gutiérrez & Gerardo Soto). Rev Geológica América Cent 203:103–118
Garrigues R, Dean R (2014) The Birds of Costa Rica. Zona Tropical Publication, San José, Costa Rica
Grant T, Frost DR, Caldwell JP, Gagliardo R, Haddad CFB, Kok PJR et al. (2006) Phylogenetic systematics of dart-poison frogs and their relatives (Amphibia: Athesphatanura: Dendrobatidae). Bull Am Mus Nat Hist 299:1–262
Guarnizo CE, Cannatella DC (2013) Genetic divergence within frog species is greater in topographically more complex regions. J Zool Syst Evol Res 51:333–340
Hernandez PA, Graham CH, Master LL, Albert DL (2006) The effect of sample size and species characteristics on performance of different species distribution modeling methods. Ecography 29:773–785
Hijmans RJ, van Etten J (2010) raster: Geographic analysis and modeling with raster data. R Packag version 1.
Hijmans RJ, Phillips S, Leathwick J, Elith J (2012) Package ‘dismo’. Species distribution modeling. R Packag version 08-11.
Hilje B, Arévalo-Huezo E (2012) Aestivation in the cane toad Rhinella marina Linnaeus 1758 (Anura, Bufonidae) during the peak of a dry season in a tropical dry forest, Costa Rica. Herpetol Notes 5:533–534
Holdridge LR (1987) Ecología basada en zonas de vida. Instituto Interamericano de Cooperación para la Agricultura (IICA), San Jose, Costa Rica
Horn S (1990) Timing of deglaciation in the Cordillera de Talamanca. Costa Rica Clim Res 1:81–83
Hudson RR, Coyne JA (2002) Mathematical consequences of the genealogical species concept. Evolution 56:1557–1565
Islebe GA, Hooghiemstra H, van’t Veer R (1996) Holocene vegetation and water level history in two bogs of the Cordillera de Talamanca, Costa Rica. Vegetatio 124:155–171
Jacobson S (2018) Reproductive behavior and male mating success in two species of glass frogs. Herpetologica 41:396–404
Janzen DH (1991) Historia Natural de Costa Rica. Primera (D Janzen, Ed.). Editorial San José, Universidad de Costa Rica, San José, Costa Rica
Kaky E, Nolan V, Alatawi A, Gilbert F (2020) A comparison between Ensemble and MaxEnt species distribution modelling approaches for conservation: a case study with Egyptian medicinal plants. Ecol Inf 60:101150
Keigwin LD (1978) Pliocene closing of the Isthmus of Panama, based on biostratigraphic evidence from nearby Pacific Ocean and Caribbean Sea cores. Geology 6:630–634
Kessing B, Croom H, Martin A, McIntosh C, Owen MW, Palumbi SP (2004) The Simple Fool’s Guide to PCR, Version 1. Department of Zoology, University of Hawaii, Honolulu, USA
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kirby MX, Jones DS, MacFadden BJ (2008) Lower Miocene stratigraphy along the Panama Canal and its bearing on the Central American Peninsula. PLoS ONE 3:e2971
Kluge J, Kessler M (2006) Fern endemism and its correlates: contribution from an elevational transect in Costa Rica. Divers Distrib 12:535–545
Kubicki B (2007) Ranas de Vidrio de Costa Rica, 1st edn. Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica
Li X, Wang Y (2013) Applying various algorithms for species distribution modelling. Integr Zool 8:124–135
Luo A, Ling C, Ho SYW, Zhu CD (2018) Comparison of methods for molecular species delimitation across a range of speciation scenarios. Syst Biol 67:830–846
Luteyn J (1999) Paramos: a checklist of plant diversity, geographical distribution, and botanical literature. Mem N. Y Bot Gard 84:138–141
Manel S, Holderegger R (2013) Ten years of landscape genetics. Trends Ecol Evol 28:614–621
Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197
Manly B (1986) Randomization and regression methods for testing for associations with geographical, environmental and biological distances between populations. Res Popul Ecol 28:201–218
Marshall JS (2007) The geomorphology and physiographic provinces of Central America. In: Bundschuh & Alvarado (eds) Central America: Geology, Resources and Hazards, vol 1, CRC Press, Florida, USA, pp 1–51
Marshall LG (1988) Land mammals and the Great American interchange. Am Sci 76:380–388
Mayr E (1942) Systematics and the origin of species, 1st edn. Columbia University Press, New York, NY
McCann S, Greenlees MJ, Newell D, Shine R (2014) Rapid acclimation to cold allows the cane toad to invade montane areas within its Australian range. Funct Ecol 28:1166–1174
McRae BH (2006) Isolation by resistance. Evolution 60:1551–1561
Michaux JR, Libois R, Filippucci MG (2005) So close and so different: Comparative phylogeography of two small mammal species, the Yellow-necked fieldmouse (Apodemus flavicollis) and the Woodmouse (Apodemus sylvaticus) in the Western Palearctic region. Heredity 94:52–63
Montes C, Cardona A, McFadden R, Morón SE, Silva CA, Restrepo-Moreno S et al. (2012) Evidence for middle Eocene and younger land emergence in central Panama: implications for Isthmus closure. Bull Geol Soc Am 124:780–799
Muscarella R, Galante PJ, Soley-Guardia M, Boria RA, Kass JM, Uriarte M et al.(2014) ENMeval: an R package for conducting spatially independent evaluations and estimating optimal model complexity for MaxEnt ecological niche models Methods Ecol Evol 5:1198–1205
Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, da, Kent E (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858
Naimi B, Hamm NAS, Groen TA, Skidmore AK, Toxopeus AG (2014) Where is positional uncertainty a problem for species distribution modelling? Ecography 37:191–203
O’Dea A, Lessios HA, Coates AG, Eytan RI, Restrepo-Moreno SA, Cione AL et al. (2016) Formation of the Isthmus of Panama. Sci Adv 2:1–12
Oliveira BF, São-Pedro VA, Santos-Barrera G, Penone C, Costa GC (2017b) AmphiBIO, a global database for amphibian ecological traits. Sci Data 4:170123
Oliveira E, Martinez P, Sao-Pedro V, Gehara M, Burbrink FT, Mesquita D et al. (2017a) Climatic suitability, isolation by distance and river resistance explain genetic variation in a Brazilian whiptail lizard. Heredity 120:251–265
Padial JM, De La Riva I (2009) Integrative taxonomy reveals cryptic Amazonian species of Pristimantis (Anura: Strabomantidae). Zool J Linn Soc 155:97–122
Paz A, Crawford AJ (2012) Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians. J Biosci 37:887–896
Paz A, González A, Crawford AJ (2019) Testing effects of Pleistocene climate change on the altitudinal and horizontal distributions of frogs from the Colombian Andes: A species distribution modeling approach. Front Biogeogr 11:e37055
Paz A, Ibáñez R, Lips KR, Crawford AJ (2015) Testing the role of ecology and life history in structuring genetic variation across a landscape: a trait-based phylogeographic approach. Mol Ecol 24:3723–3737
Pinto-Sánchez NR, Ibañez R, Madriñán S, Sanjur OI, Bermingham E, Crawford AJ (2012) The Great American biotic interchange in frogs: multiple and early colonization of Central America by the South American genus Pristimantis (Anura: Craugastoridae). Mol Phylogenet Evol 62:954–972
Prum R, Rice NH, Mobley J, Dimmick W (2000) A preliminary phylogenetic hypothesis for the cotingas (Cotingidae) based on mitochondrial DNA. Auk 117:236–241
Puillandre N, Lambert A, Brouillet S, Achaz G (2012) ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Mol Ecol 21:1864–1877
Ramírez-Barahona S, Eguiarte LE (2013) The role of glacial cycles in promoting genetic diversity in the Neotropics: The case of cloud forests during the Last Glacial Maximum. Ecol Evol 3:725–738
Rich PV, Rich T (1991) La ruta de dispersión centroamericana: Historia biotica y paleográfica. In: Janzen DH (ed) Historia Natural de Costa Rica. Editorial San José, Universidad de Costa Rica, San José, Costa Rica, p 13–34
Riddle BR, Hafner DJ, Alexander LF, Jaeger JR (2000) Cryptic vicariance in the historical assembly of a Baja California Peninsular Desert biota. Proc Natl Acad Sci USA 97:14438–14443
Robertson JM, Duryea MC, Zamudio KR (2009) Discordant patterns of evolutionary differentiation in two Neotropical treefrogs. Mol Ecol 18:1375–1395
Robertson JM, Lips KR, Heist EJ (2008) Fine scale gene flow and individual movements among subpopulations of Centrolene prosoblepon (Anura: Centrolenidae). Rev Biol Trop 56:13–26
Rodríguez A, Börner M, Pabijan M, Gehara M, Haddad CFB, Vences M (2015) Genetic divergence in tropical anurans: deeper phylogeographic structure in forest specialists and in topographically complex regions. Evol Ecol 29:765–785
Savage J, Bolaños F (2009) A checklist of the amphibians and reptiles of Costa Rica: additions and nomenclatural revisions. Zootaxa 2005:1–23
Savage JM (2002) The Amphibians and Reptiles of Costa Rica: a herpetofauna between two continents, between two seas. University of Chicago press, Chicago, Illinois, USA
Sexton JP, Hangartner SB, Hoffmann AA (2014) Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution 68:1–15
Shah VB, McRae BH (2008) Circuitscape: a tool for landscape ecology. Proc 7th Python Sci Conf. 7:62–65
Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47:264–279
Smith AM, Green DM (2005) Dispersal and the metapopulation paradigm in amphibian ecology and conservation: are all amphibian populations metapopulations? Ecography 28:110–128
Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313
Steele CA, Storfer A (2007) Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution. Mol Phylogenet Evol 43:468–479
Stehli FG, Webb SD (eds) (1985) The Great American Biotic Interchange. Plenum Press, New York, NY (FG Stehli and SD Webb, Eds.)
Stiles G, Remsen JV, McGuire JA (2017) The generic classification of the Trochilini (Aves: Trochilidae): reconciling taxonomy with phylogeny. Zootaxa 4353:401–424
Stine R (1995) Graphical interpretation of variance inflation factors. Am Stat 49:53–56
Streicher JW, Crawford AJ, Edwards CW (2009) Multilocus molecular phylogenetic analysis of the montane Craugastor podiciferus species complex (Anura: Craugastoridae) in Isthmian Central America. Mol Phylogenet Evol 53:620–630
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Vences M, Thomas M, Van Der Meijden A, Chiari Y, Vieites DR (2005) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Front Zool 2:1–12
Wang I, Crawford AJ, Bermingham E (2008a) Phylogeography of the Pygmy Rain Frog (Pristimantis ridens) across the lowland wet forests of isthmian Central America. Mol Phylogenet Evol 47:992–1004
Wang IJ (2013) Examining the full effects of landscape heterogeneity on spatial genetic variation: A multiple matrix regression approach for quantifying geographic and ecological isolation. Evolution 67:3403–3411
Wang IJ, Bradburd GS (2014) Isolation by environment. Mol Ecol 23:5649–5662
Wang Y-H, Yang K-C, Bridgman CL, Lin L-K (2008b) Habitat suitability modelling to correlate gene flow with landscape connectivity. Landsc Ecol 23:989–1000
Webb SD (2006) The Great American Biotic Interchange: patterns and processes. Ann Mo Bot Gard 93:245–257
Weigt LA, Crawford AJ, Rand AS, Ryan MJ (2005) Biogeography of the túngara frog, Physalaemus pustulosus: a molecular perspective. Mol Ecol 14:3857–3876
Weir JT, Bermingham E, Schluter D (2009) The Great American biotic interchange in birds. Proc Natl Acad Sci USA 106:21737–21742
Werle E, Schneider C, Renner MV, W F (1994) Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res 22:4354–4355
Weyl R (1980) Geology of Central America. Gebrueder Borntraeger, Berlin-Stuttgart
Wilson JS, Carril OM, Sipes SD (2014) Revisiting the Great American Biotic Interchange through analyses of amphitropical bees. Ecography 37:791–796
Wollenberg KC, Vieites DR, Glaw F, Vences M (2011) Speciation in little: the role of range and body size in the diversification of Malagasy mantellid frogs. BMC Evol Biol 11:217
Wollenberg Valero KC (2015) Evidence for an intrinsic factor promoting landscape genetic divergence in Madagascan leaf-litter frogs. Front Genet 6:155
Wright S (1943) Isolation by distance. Genetics 28:114–138
Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354
Zhang J, Kapli P, Pavlidis P, Stamatakis A (2013) A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29:2869–2876
Zuur AF, Ieno EN, Elphick CS (2010) A protocol for data exploration to avoid common statistical problems. Methods Ecol Evol 1:3–14
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