in

Contrasting environmental drivers of genetic and phenotypic divergence in an Andean poison frog (Epipedobates anthonyi)

[adace-ad id="91168"]
  • Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387

    Article 

    Google Scholar 

  • Allendorf FW (2017) Genetics and the conservation of natural populations: allozymes to genomes. Mol Ecol 26:420–430

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Van Asch B, Pinheiro R, Pereira R, Alves C, Pereira V, Pereira F et al. (2010) A framework for the development of STR genotyping in domestic animal species: characterization and population study of 12 canine X‐chromosome loci. Electrophoresis 31:303–308

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • Bates D, Maechler M, Bolker B, Walker S, Bojesen RH, Singmann H et al. (2014) Package Lme4: Linear mixed-effects models using Eigen andS4. R package version 1.1-10

  • Blaszczynski JS (1997) Landform characterization with Geographic Information Systems. Photogramm Eng Remote Sens 63:183–191

    Google Scholar 

  • Bolnick DI, Fitzpatrick BM (2007) Sympatric Speciation: Models and Empirical Evidence. Annu Rev Ecol Evol Syst 38:459–487

    Article 

    Google Scholar 

  • Cadena CD, Kozak KH, Gomez JP, Parra JL, McCain CM, Bowie RC et al. (2012) Latitude, elevational climatic zonation and speciation in New World vertebrates. Proc R Soc Lond B Biol Sci 279:194–201

    Google Scholar 

  • Caro LM, Caycedo‐Rosales PC, Bowie RCK, Slabbekoorn H, Cadena CD (2013) Ecological speciation along an elevational gradient in a tropical passerine bird? J Evol Biol 26:357–374

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Clarke RT, Rothery P, Raybould AF (2002) Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. J Agric Biol Environ Stat 7:361–372

    Article 

    Google Scholar 

  • Crandall KA, Bininda-Emonds OR, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trends Ecol Evol 15:290–295

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. Am Nat 168:486–499

    PubMed 
    Article 

    Google Scholar 

  • Do C, Waples RS, Peel D, Macbeth GM, Tillett BJ, Ovenden JR (2014) NeEstimator v2: re‐implementation of software for the estimation of contemporary effective population size (Ne) from genetic data. Mol Ecol Resour 14:209–214

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Dormann CF, Elith J, Bacher S, Buchmann C, Carl G, Carré G et al. (2012) Collinearity: a review of methods to deal with it and a simulation study evaluating their performance. Ecography 36:27–46

    Article 

    Google Scholar 

  • Dreher CE, Cummings ME, Pröhl H (2015) An analysis of predator selection to affect aposematic coloration in a poison frog species. PloS One 10:e0130571

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Dugas MB, Halbrook SR, Killius AM, Sol JF, Richards‐Zawacki CL (2015) Colour and escape behaviour in polymorphic populations of an aposematic poison frog. Ethology 121:813–822

    Article 

    Google Scholar 

  • Earl DA, vonHoldt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article 

    Google Scholar 

  • Ebersbach J, Posso-Terranova A, Bogdanowicz S, Gómez‐Díaz M, García‐González MX, Bolívar‐García W et al. (2020) Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs. Mol Ecol 29:1944–1956

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Farr TG, Kobrick M (2000) Shuttle radar topography mission produces a wealth of data. Eos 81:583–585

    Article 

    Google Scholar 

  • Funk WC, Murphy MA (2010) Testing evolutionary hypotheses for phenotypic divergence using landscape genetics. Mol Ecol 19:427–430

    PubMed 
    Article 

    Google Scholar 

  • Funk WC, McKay JK, Hohenlohe PA, Allendorf FW (2012) Harnessing genomics for delineating conservation units. Trends Ecol Evol 27:489–496

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Funk WC, Murphy MA, Hoke KL, Muths E, Amburgey SM, Lemmon EM et al. (2016) Elevational speciation in action? Restricted gene flow associated with adaptive divergence across an altitudinal gradient. J Evol Biol 29:241–252

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Funk WC, Blouin MS, Corn PS, Maxell BA, Pilliod DS, Amish S, Allendorf FW (2005) Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Mol Ecol 14:483–496

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Galeano SP, Harms KE (2016) Coloration in the polymorphic frog Oophaga pumilio associates with level of aggressiveness in intraspecific and interspecific behavioral interactions. Behav Ecol Sociobiol 70:83–97

    Article 

    Google Scholar 

  • García-Rodríguez A, Guarnizo CE, Crawford AJ, Garda AA, Costa GC (2021) Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America. Heredity 126:251–265

    PubMed 
    Article 

    Google Scholar 

  • Gessler PE, Moore ID, McKenzie NJ, Ryan PJ (1995) Soil-landscape modeling and spatial prediction of soil attributes. Int J Geogr Inf Sci 9:421–432

    Article 

    Google Scholar 

  • Graham CH, Ron SR, Santos JC, Schneider CJ, Moritz C (2004) Integrating phylogenetics and environmental niche models to explore speciation mechanisms in dendrobatid frogs. Evolution 58:1781–1793

    PubMed 
    Article 

    Google Scholar 

  • 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

    Article 

    Google Scholar 

  • Guarnizo CE, Amézquita A, Bermingham E (2009) The relative roles of vicariance versus elevational gradients in the genetic differentiation of the high Andean tree frog, Dendropsophus labialis. Mol Phylogenet Evol 50:84–92

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Hansen MC, Townshend JRG, DeFries RS, Carroll M (2005) Estimation of tree cover using MODIS data at global, continental and regional/local scales. Int J Remote Sens 26:4359–4380

    Article 

    Google Scholar 

  • Harvey MG, Aleixo A, Ribas CC, Brumfield RT (2017) Habitat association predicts genetic diversity and population divergence in Amazonian birds. Am Nat 190:631–648

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A (2005) Very high resolution interpolated climate surface for global land areas. Int J Climatol 25:1965–1978

    Article 

    Google Scholar 

  • Hoffman AA, Sgrò CM (2011) Climate change and evolutionary adaptation. Nature 470:479–485

    Article 
    CAS 

    Google Scholar 

  • Holleley CE, Geerts PG (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. Biotechniques 46:511–517

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Huete A, Didan K, Miura T, Rodriguez EP, Gao X, Ferreira LG (2002) Overview of the radiometric and biophysical performance of the MODIS vegetation indices. Remote Sens Environ 83:195–213

    Article 

    Google Scholar 

  • Hutter CR, Lambert SM, Wiens JJ (2017) Rapid diversification and time explain amphibian richness at different scales in the Tropical Andes, Earth’s most biodiverse hotspot. Am Nat 190:828–843

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Jombart T (2008) Adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Kalinowski ST (2005) hp‐rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5:187–189

    CAS 
    Article 

    Google Scholar 

  • Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7:1225–1241

    Article 

    Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S et al. (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Keller I, Seehausen O (2012) Thermal adaptation and ecological speciation. Mol Ecol 21:782–799

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Keller I, Alexander JM, Holderegger R, Edwards PJ (2013) Widespread phenotypic and genetic divergence along altitudinal gradients in animals. J Evol Biol 26:2527–2543

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Leinonen T, Cano JM, Mäkinen H, Merilä J (2006) Contrasting patterns of body shape and neutral genetic divergence in marine and lake populations of threespine sticklebacks. J Evol Biol 19:1803–1812

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Lowe WH, McPeek MA, Likens GE, Cosentino BJ (2012) Decoupling of genetic and phenotypic divergence in a headwater landscape. Mol Ecol 21:2399–2409

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Lynch JD, Duellman WE (1997) Frogs of the genus Eleutherodactylus (Leptodactylidae) in western Ecuador: systematics, ecology and biogeography. University of Kansas, Natural History Museum. Special Publication No. 23. University of Kansas Printing Service, Lawrence, Kansas

  • Maan ME, Cummings ME (2009) Sexual dimorphism and directional sexual selection on aposematic signals in a poison frog. Proc Natl Acad Sci USA 106:19072–19077

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Márquez R, Linderoth TP, Mejía-Vargas D, Nielsen R, Amézquita A, Kronforst MR (2020) Divergence, gene flow and the origin of leapfrog geographic distributions: The history of color pattern variation in Phyllobates poison-dart frogs. Mol Ecol 29:3702–3719

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Mayr E (1963) Animal Species and Evolution. Harvard University Press, Cambridge, MA

    Book 

    Google Scholar 

  • McCune B, Keon D (2002) Equations for potential annual direct incident radiation and heat load index. J Veg Sci 13:603–606

    Article 

    Google Scholar 

  • McKay JK, Latta RG (2002) Adaptive population divergence: markers, QTL and traits. Trends Ecol Evol 17:285–291

    Article 

    Google Scholar 

  • McRae BH (2006) Isolation by resistance. Evolution 60:1551–1561

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • McRae BH, Dickson BG, Keitt TH, Shah VB (2008) Using circuit theory to model connectivity in ecology and conservation. Ecology 10:2712–2724

    Article 

    Google Scholar 

  • Moore ID, Gessler PE, Nielsen GA, Petersen GA (1993) Terrain attributes: estimation methods and scale effects. In: Jakeman AJ, Beck MB, McAleer M (eds) Modeling Change in Environmental Systems. Wiley, London, p 189–214

    Google Scholar 

  • Morrison C, Hero JM (2003) Geographic variation in life‐history characteristics of amphibians: a review. J Anim Ecol 72:270–279

    Article 

    Google Scholar 

  • Muir AP, Biek R, Thomas R, Mable BK (2014) Local adaptation with high gene flow: temperature parameters drive adaptation to altitude in the common frog (Rana temporaria). Mol Ecol 23:561–574

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403:853–858

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Naimi B, Hamm NA, Groen TA, Skidmore AK, Toxopeus AG (2014) Where is positional uncertainty a problem for species distribution modelling. Ecography 37:191–203

    Article 

    Google Scholar 

  • Nali RC, Becker CG, Zamudio KR, Prado CP (2020) Topography, more than land cover, explains genetic diversity in a Neotropical savanna tree frog. Divers Distrib 26:1798–1812

    Article 

    Google Scholar 

  • Noonan BP, Comeault AA (2009) The role of predator selection on polymorphic aposematic poison frogs. Biol Lett 5:51–54

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Nosil P (2008) Speciation with gene flow could be common. Mol Ecol 17:2103–2106

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO‐CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

    Article 
    CAS 

    Google Scholar 

  • Orr MR, Smith TB (1998) Ecology and speciation. Trends Ecol Evol 13:502–506

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Páez-Vacas MI, Oleas NH (2019) Isolation and characterization of 12 microsatellite loci in Epipedobates anthonyi (Amphibia: Anura: Dendrobatidae) for population genetic analysis. Mol Biol Rep. 46:3519–3522

    PubMed 
    Article 
    CAS 
    PubMed Central 

    Google Scholar 

  • Pfennig DW, Wund MA, Snell-Rood EC, Cruickshank T, Schlichting CD, Moczek AP (2010) Phenotypic plasticity’s impacts on diversification and speciation. Trends Ecol Evol 25:459–467

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Pilliod DS, Peterson CR, Ritson PI (2002) Seasonal migration of Columbia spotted frogs (Rana luteiventris) among complementary resources in a high mountain basin. CAN J ZOOL 80:1849–1862

    Article 

    Google Scholar 

  • Pinho C, Hey J (2010) Divergence with gene flow: models and data. Annu Rev Ecol Evol Systs 41:215–230

    Article 

    Google Scholar 

  • Pintanel P, Tejedo M, Ron SR, Llorente GA, Merino‐Viteri A (2019) Elevational and microclimatic drivers of thermal tolerance in Andean Pristimantis frogs. J Biogeogr 46:1664–1675

    Article 

    Google Scholar 

  • Polato NR, Gill BA, Shah AA, Gray MM, Casner KL, Barthelet A et al. (2018) Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. Proc Natl Acad Sci USA 115:12471–12476

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Posso-Terranova A, Andrés JA (2016) Complex niche divergence underlies lineage diversification in Oophaga poison frogs. J Biogeogr 43:2002–2015

    Article 

    Google Scholar 

  • Prates I, Paz A, Brown JL, Carnaval AC (2019) Links between prey assemblages and poison frog toxins: a landscape ecology approach to assess how biotic interactions affect species phenotypes. Ecol Evol 9:14317–14329

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Räsänen K, Hendry AP (2008) Disentangling interactions between adaptive divergence and gene flow when ecology drives diversification. Ecol Lett 11:624–636

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 83:248–249

    Article 

    Google Scholar 

  • Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225

    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Richards‐Zawacki CL (2009) Effects of slope and riparian habitat connectivity on gene flow in an endangered Panamanian frog, Atelopus varius. Divers Distrib 15:796–806

    Article 

    Google Scholar 

  • Richter-Boix A, Quintela M, Kierczak M, Franch M, Laurila A (2013) Fine-grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of nonrandom gene flow in restricting effective migration among wetlands. Mol Ecol 22:1322–1340

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Robertson JM, Murphy MA, Pearl CA, Adams MJ, Páez‐Vacas MI, Haig SM, Funk WC (2018) Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the US Pacific Northwest. Mol Ecol 27:3242–3256

    Article 

    Google Scholar 

  • Rojas D, Lima AP, Momigliano P, Simões PI, Dudaniec RY, De Avila-Pires TCS et al. (2020) The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus. Heredity 124:439–456

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar 

  • Roland AB, Santos JC, Carriker BC, Caty SN, Tapia EE, Coloma LA et al. (2017) Radiation of the polymorphic Little Devil poison frog (Oophaga sylvatica) in Ecuador. Ecol Evol 7:9750–9762

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Row JR, Knick ST, Oyler‐McCance SJ, Lougheed SC, Fedy BC (2017) Developing approaches for linear mixed modeling in landscape genetics through landscape directed dispersal simulations. Ecol Evol 7:3751–3761

    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Rundle HD, Nosil P (2005) Ecological speciation. Ecol Lett 8:336–352

    Article 

    Google Scholar 

  • Santos JC, Cannatella DC (2011) Phenotypic integration emerges from aposematism and scale in poison frogs. Proc Natl Acad Sci USA 108:6175–6180

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Savolainen O, Lascoux M, Merilä J (2013) Ecological genomics of local adaptation. Nat Rev Genet 14:807–820

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Schluter D (2009) Evidence for ecological speciation and its alternative. Science 323:737–741

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nat Biotechnol 18:233–234

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Servedio MR, Van Doorn GS, Kopp M, Frame AM, Nosil P (2011) Magic traits in speciation: ‘magic’ but not rare? Trends Ecol Evol 26:389–397

    PubMed 
    Article 

    Google Scholar 

  • 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

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Shafer AB, Wolf JBW, Alves PC, Bergström L, Bruford MW, Brännström I et al. (2015) Genomics and the challenging translation into conservation practice. Trends Ecol Evol 30:78–87

    PubMed 
    Article 

    Google Scholar 

  • Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787–792

    CAS 
    PubMed 
    Article 

    Google Scholar 

  • Stevens M, Hopkins E, Hinde W, Adcock A, Connolly Y, Troscianko T et al. (2007) Field experiments on the effectiveness of ‘eyespots’ as predator deterrents. Anim Behav 74:1215–1227

    Article 

    Google Scholar 

  • Storfer A, Patton A, Fraik AK (2018) Navigating the interface between landscape genetics and landscape genomics. Front Genet 9:68

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 

  • Van Strien MJ, Keller D, Holderegger R (2012) A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Mol Ecol 21:4010–4023

    Article 

    Google Scholar 

  • Summers K, Symula R, Clough M, Cronin T (1999) Visual mate choice in poison frogs. Proc R Soc Lond B Biol Sci 266:2141–2145

    CAS 
    Article 

    Google Scholar 

  • Tarvin RD, Powell EA, Santos JC, Ron SR, Cannatella DC (2017) The birth of aposematism: High phenotypic divergence and low genetic diversity in a young clade of poison frogs. Mol Phylogenet Evol 109:283–295

    PubMed 
    Article 

    Google Scholar 

  • Thomé MTC, Carstens BC, Rodrigues MT, Galetti Jr PM, Alexandrino J, Haddad CF (2021) A role of asynchrony of seasons in explaining genetic differentiation in a Neotropical toad. Heredity 2021:1–10

    Google Scholar 

  • Twomey E, Vestergaard JS, Venegas PJ, Summers K (2016) Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator. Am Nat 187:205–224

    PubMed 
    Article 

    Google Scholar 

  • Wang IJ, Summers K (2010) Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison‐dart frog. Mol Ecol 19:447–458

    PubMed 
    Article 

    Google Scholar 

  • Warren DL, Glor RE, Turelli M (2010) ENMTools: a toolbox for comparative studies of environmental niche models. Ecography 33:607–611

    Article 

    Google Scholar 

  • Willink B, García‐Rodríguez A, Bolaños F, Pröhl H (2014) The interplay between multiple predators and prey colour divergence. Biol J Linn Soc Lond 113:580–589

    Article 

    Google Scholar 

  • Womack MC, Bell RC (2020) Two‐hundred million years of anuran body‐size evolution in relation to geography, ecology and life history. J Evol Biol 33:1–16

    Article 

    Google Scholar 

  • Wright S (1943) Isolation by distance. Genetics 28:114–138

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 

  • Zamudio KR, Bell RC, Mason NA (2016) Phenotypes in phylogeography: Species’ traits, environmental variation, and vertebrate diversification. Proc Natl Acad Sci USA 113:8041–8048

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 


  • Source: Ecology - nature.com

    Central America drying

    Scientists say Australian plan to cull up to 10,000 wild horses doesn’t go far enough