Comparative phylogeography reveals the demographic patterns of neotropical ancient mountain species

. 2023 Jun ; 32 (12) : 3165-3181. [epub] 20230326

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid36934376

Mountains are renowned for their bountiful biodiversity. Explanations on the origin of such abundant life are usually regarded to their orogenic history. However, ancient mountain systems with geological stability also exhibit astounding levels of number of species and endemism, as illustrated by the Brazilian Quartzitic Mountains (BQM) in Eastern South America. Thus, cycles of climatic changes over the last couple million years are usually assumed to play an important role in the origin of mountainous biota. These climatic oscillations potentially isolated and reconnected adjacent populations, a phenomenon known as flickering connectivity, accelerating speciation events due to range fragmentation, dispersion, secondary contact, and hybridization. To evaluate the role of the climatic fluctuations on the diversification of the BQM biota, we estimated the ancient demography of distinct endemic species of animals and plants using hierarchical approximate Bayesian computation analysis and Ecological Niche Modelling. Additionally, we evaluated if climatic oscillations have driven a genetic spatial congruence in the genetic structure of codistributed species from the Espinhaço Range, one of the main BQM areas. Our results show that the majority of plant lineages underwent a synchronous expansion over the Last Glacial Maximum (LGM, c. 21 thousand years ago), although we could not obtain a clear demographic pattern for the animal lineages. We also obtained a signal of a congruent phylogeographic break between lineages endemic to the Espinhaço Range, suggesting how ancient climatic oscillations might have driven the evolutionary history of the Espinhaço's biota.

Zobrazit více v PubMed

Allouche, O., Tsoar, A., & Kadmon, R. (2006). Assessing the accuracy of species distribution models: Prevalence, kappa and the true skill statistic (TSS). Journal of Applied Ecology, 43(6), 1223-1232. https://doi.org/10.1111/j.1365-2664.2006.01214.x

Ané, C., Larget, B., Baum, D. A., Smith, S. D., & Rokas, A. (2007). Bayesian estimation of concordance among gene trees. Molecular Biology and Evolution, 24(2), 412-426. https://doi.org/10.1093/molbev/msl170

Antonelli, A., Ariza, M., Albert, J., Andermann, T., Azevedo, J., Bacon, C., Faurby, S., Guedes, T., Hoorn, C., Lohmann, L. G., Matos-Maraví, P., Ritter, C. D., Sanmartín, I., Silvestro, D., Tejedor, M., ter Steege, H., Tuomisto, H., Werneck, F. P., Zizka, A., & Edwards, S. V. (2018). Conceptual and empirical advances in neotropical biodiversity research. PeerJ, 6, e5644. https://doi.org/10.7717/peerj.5644

Antonelli, A., Kissling, W. D., Flantua, S. G. A., Bermúdez, M. A., Mulch, A., Muellner-Riehl, A. N., Kreft, H., Linder, H. P., Badgley, C., Fjeldså, J., Fritz, S. A., Rahbek, C., Herman, F., Hooghiemstra, H., & Hoorn, C. (2018). Geological and climatic influences on mountain biodiversity. Nature Geoscience, 11(10), 718-725. https://doi.org/10.1038/s41561-018-0236-z

Antonelli, A., Nylander, J. A. A., Persson, C., & Sanmartín, I. (2009). Tracing the impact of the Andean uplift on neotropical plant evolution. Proceedings of the National Academy of Sciences, 106(24), 9749-9754. https://doi.org/10.1073/pnas.0811421106

Antonelli, A., Verola, C., Parisod, C., & Gustafsson, A. L. S. (2010). Climate cooling promoted the expansion and radiation of a threatened group of south American orchids (Epidendroideae: Laeliinae). Biological Journal of the Linnean Society, 100(3), 597-607. https://doi.org/10.1111/j.1095-8312.2010.01438.x

Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, J. E., Reeb, C. A., & Saunders, N. C. (1987). Intraspecific Phylogeography: The mitochondrial dna bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.

Barberi, M., Salgado-Labouriau, M. L., & Suguio, K. (2000). Paleovegetation and paleoclimate of “Vereda de Águas Emendadas”, central Brazil. Journal of South American Earth Sciences, 13(3), 241-254. https://doi.org/10.1016/S0895-9811(00)00022-5

Barbosa, N. P. U., & Fernandes, G. W. (2016). Rupestrian grassland: Past, present and future distribution. In G. W. Fernandes (Ed.), Ecology and conservation of mountaintop grasslands in Brazil (pp. 531-544). Springer International Publishing. https://doi.org/10.1007/978-3-319-29808-5_22

Barres, L., Batalha-Filho, H., Schnadelbach, A. S., & Roque, N. (2019). Pleistocene climatic changes drove dispersal and isolation of Richterago discoidea (Asteraceae), an endemic plant of Campos rupestres in the central and eastern Brazilian sky islands. Botanical Journal of the Linnean Society, 189(2), 132-152. https://doi.org/10.1093/botlinnean/boy080

Beichman, A. C., Huerta-Sanchez, E., & Lohmueller, K. E. (2018). Using genomic data to infer historic population dynamics of nonmodel organisms. Annual Review of Ecology, Evolution, and Systematics, 49(1), 433-456. https://doi.org/10.1146/annurev-ecolsys-110617-062431

Bitencourt, C., Rapini, A., Santos Damascena, L., & De Marco Junior, P. (2016). The worrying future of the endemic flora of a tropical mountain range under climate change. Flora-Morphology, Distribution, Functional Ecology of Plants, 218, 1-10. https://doi.org/10.1016/j.flora.2015.11.001

Bochorny, T., Bacci, L. F., Reginato, M., Vasconcelos, T., Michelangeli, F. A., & Goldenberg, R. (2022). Similar diversification patterns in “sky islands”: A comparative approach in lineages from campo rupestre and campo de altitude. Perspectives in Plant Ecology, Evolution and Systematics, 57, 125700. https://doi.org/10.1016/j.ppees.2022.125700

Bonatelli, I. A. S., Gehara, M., Carstens, B. C., Colli, G. R., & Moraes, E. M. (2022). Comparative and predictive phylogeography in the south American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography. Molecular Ecology, 31(1), 331-342. https://doi.org/10.1111/mec.16210

Bonatelli, I. A. S., Perez, M. F., Peterson, A. T., Taylor, N. P., Zappi, D. C., Machado, M. C., Koch, I., Pires, A. H. C., & Moraes, E. M. (2014). Interglacial microrefugia and diversification of a cactus species complex: Phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies. Molecular Ecology, 23(12), 3044-3063. https://doi.org/10.1111/mec.12780

Borowiec, M. L., Dikow, R. B., Frandsen, P. B., McKeeken, A., Valentini, G., & White, A. E. (2022). Deep learning as a tool for ecology and evolution. Methods in Ecology and Evolution, 13(8), 1640-1660. https://doi.org/10.1111/2041-210X.13901

Breiman, L. (2001). Random forests. Machine Learning, 45(1), 5-32. https://doi.org/10.1023/A:1010933404324

Campos, L., Moro, M. F., Funk, V. A., & Roque, N. (2019). Biogeographical review of Asteraceae in the Espinhaço Mountain range, Brazil. The Botanical Review, 85(4), 293-336. https://doi.org/10.1007/s12229-019-09216-9

Camurugi, F., Gehara, M., Fonseca, E. M., Zamudio, K. R., Haddad, C. F. B., Colli, G. R., Thomé, M. T. C., Prado, C. P. A., Napoli, M. F., & Garda, A. A. (2021). Isolation by environment and recurrent gene flow shaped the evolutionary history of a continentally distributed neotropical treefrog. Journal of Biogeography, 48(4), 760-772. https://doi.org/10.1111/jbi.14035

Carnaval, A. C., & Moritz, C. (2008). Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic Forest. Journal of Biogeography, 35(7), 1187-1201. https://doi.org/10.1111/j.1365-2699.2007.01870.x

Carpenter, G., Gillison, A. N., & Winter, J. (1993). DOMAIN: A flexible modelling procedure for mapping potential distributions of plants and animals. Biodiversity and Conservation, 2(6), 667-680. https://doi.org/10.1007/BF00051966

Chan, Y. L., Schanzenbach, D., & Hickerson, M. J. (2014). Detecting concerted demographic response across community assemblages using hierarchical approximate bayesian computation. Molecular Biology and Evolution, 31(9), 2501-2515. https://doi.org/10.1093/molbev/msu187

Chaves, A. V., Freitas, G. H. S., Vasconcelos, M. F., & Santos, F. R. (2015). Biogeographic patterns, origin and speciation of the endemic birds from eastern Brazilian mountaintops: A review. Systematics and Biodiversity, 13(1), 1-16. https://doi.org/10.1080/14772000.2014.972477

Chaves, M. L. S. C., & Benitez, L. (2004). Depósitos superficiais diamantíferos da região de Diamantina, Serra do Espinhaço (Minas Gerais). Geosciences, 23, 31-42.

Collevatti, R. G., de Castro, T. G., de Souza Lima, J., & de Campos Telles, M. P. (2012). Phylogeography of Tibouchina papyrus (Pohl) Toledo (Melastomataceae), an endangered tree species from rocky savannas, suggests bidirectional expansion due to climate cooling in the Pleistocene. Ecology and Evolution, 2(5), 1024-1035. https://doi.org/10.1002/ece3.236

Collevatti, R. G., Rabelo, S. G., & Vieira, R. F. (2009). Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species. Annals of Botany, 104(4), 655-664. https://doi.org/10.1093/aob/mcp157

Collevatti, R. G., Terribile, L. C., Diniz-Filho, J. A. F., & Lima-Ribeiro, M. S. (2015). Multi-model inference in comparative phylogeography: An integrative approach based on multiple lines of evidence. Frontiers in Genetics, 6(31), 1-8. https://doi.org/10.3389/fgene.2015.00031

Colli-Silva, M., Vasconcelos, T. N. C., & Pirani, J. R. (2019). Outstanding plant endemism levels strongly support the recognition of campo rupestre provinces in mountaintops of eastern South America. Journal of Biogeography, 46(8), 1723-1733. https://doi.org/10.1111/jbi.13585

Conceição, A. A., Rapini, A., do Carmo, F. F., Brito, J. C., Silva, G. A., Neves, S. P. S., & Jacobi, C. M. (2016). Rupestrian grassland vegetation, diversity, and origin. In G. W. Fernandes (Ed.), Ecology and conservation of mountaintop grasslands in Brazil (pp. 105-127). Springer International Publishing. https://doi.org/10.1007/978-3-319-29808-5_6

Costa, C. R., Pinto da Luz, C. F., Horák-Terra, I., de Camargo, P. B., Barral, U. M., Mendonça-Filho, C. V., Gonçalves, T. S., & Silva, A. C. (2022). Paleoenvironmental dynamics in Central-Eastern Brazil during the last 23 000 years: Tropical peatland record in the Cerrado biome. Journal of Quaternary Science, Early View., 38, 61-75. https://doi.org/10.1002/jqs.3459

Couto, D. R., Kessous, I. M., Neves, B., Paixão-Souza, B., Faria, C. G., Barfuss, M. H. J., Salgueiro, F., Sá-Haiad, B., & Costa, A. F. (2022). Molecular phylogenetics and trait evolution in Stigmatodon (Bromeliaceae, Tillandsioideae), an endemic genus to Brazilian rocky outcrops. Systematic Botany, 47(2), 347-362. https://doi.org/10.1600/036364422X16512564801696

Csilléry, K., François, O., & Blum, M. G. B. (2012). Abc: An R package for approximate Bayesian computation (ABC). Methods in Ecology and Evolution, 3(3), 475-479. https://doi.org/10.1111/j.2041-210X.2011.00179.x

Dantas-Queiroz, M. V., Cacossi, T. C., Leal, B. S. S., Chaves, C. J. N., Vasconcelos, T. N. C., Versieux, L. M., & Palma-Silva, C. (2021). Underlying microevolutionary processes parallel macroevolutionary patterns in ancient neotropical mountains. Journal of Biogeography, 48(9), 2312-2327. https://doi.org/10.1111/jbi.14154

Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9(8), 772. https://doi.org/10.1038/nmeth.2109

de Oliveira, F. F. R., Gehara, M., Solé, M., Lyra, M., Haddad, C. F. B., Silva, D. P., Magalhães, R. F., Leite, F. S. F., & Burbrink, F. T. (2021). Quaternary climatic fluctuations influence the demographic history of two species of sky-Island endemic amphibians in the neotropics. Molecular Phylogenetics and Evolution, 160, 107113. https://doi.org/10.1016/j.ympev.2021.107113

DeForest Safford, H. (2007). Brazilian Páramos IV. Phytogeography of the Campos de altitude. Journal of Biogeography, 34(10), 1701-1722. https://doi.org/10.1111/j.1365-2699.2007.01732.x

Drouin, G., Daoud, H., & Xia, J. (2008). Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants. Molecular Phylogenetics and Evolution, 49(3), 827-831. https://doi.org/10.1016/j.ympev.2008.09.009

Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7(1), 214. https://doi.org/10.1186/1471-2148-7-214

Duchen, P., Hautphenne, S., Lehmann, L., & Salamin, N. (2020). Linking micro and macroevolution in the presence of migration. Journal of Theoretical Biology, 486, 110087. https://doi.org/10.1016/j.jtbi.2019.110087

Echternacht, L., Trovó, M., Oliveira, C. T., & Pirani, J. R. (2011). Areas of endemism in the Espinhaço range in Minas Gerais, Brazil. Flora-Morphology, Distribution, Functional Ecology of Plants, 206(9), 782-791. https://doi.org/10.1016/j.flora.2011.04.003

Edwards, S. V., Robin, V. V., Ferrand, N., & Moritz, C. (2022). The evolution of comparative phylogeography: Putting the geography (and more) into comparative population genomics. Genome Biology and Evolution, 14(1), evab176. https://doi.org/10.1093/gbe/evab176

Ehlers, J., Gibbard, P. L., & Hughes, P. D. (2018). Chapter 4-Quaternary glaciations and chronology. In J. Menzies & J. J. M. van der Meer (Eds.), Past glacial environments (2nd ed., pp. 77-101). Elsevier. https://doi.org/10.1016/B978-0-08-100524-8.00003-8

Eterovick, P. C., Rievers, C. R., Kopp, K., Wachlevski, M., Franco, B. P., Dias, C. J., Barata, I. M., Ferreira, A. D. M., & Afonso, L. G. (2010). Lack of phylogenetic signal in the variation in anuran microhabitat use in southeastern Brazil. Evolutionary Ecology, 24(1), 1-24. https://doi.org/10.1007/s10682-008-9286-9

Farber, O., & Kadmon, R. (2003). Assessment of alternative approaches for bioclimatic modeling with special emphasis on the Mahalanobis distance. Ecological Modelling, 160(1), 115-130. https://doi.org/10.1016/S0304-3800(02)00327-7

Ferris, K. G., & Willis, J. H. (2018). Differential adaptation to a harsh granite outcrop habitat between sympatric mimulus species. Evolution, 72(6), 1225-1241. https://doi.org/10.1111/evo.13476

Fiaschi, P., & Pirani, J. R. (2009). Review of plant biogeographic studies in Brazil. Journal of Systematics and Evolution, 47(5), 477-496. https://doi.org/10.1111/j.1759-6831.2009.00046.x

Fiorini, C. F., Miranda, M. D., Silva-Pereira, V., Barbosa, A. R., Oliveira, U. D., Kamino, L. H. Y., Mota, N. F. O., Viana, P. L., & Borba, E. L. (2019). The phylogeography of Vellozia auriculata (Velloziaceae) supports low zygotic gene flow and local population persistence in the campo rupestre, a neotropical OCBIL. Botanical Journal of the Linnean Society, 191(3), 381-398. https://doi.org/10.1093/botlinnean/boz051

Flantua, S. G. A., & Hooghiemstra, H. (2018). Historical connectivity and mountain biodiversity. In C. Hoorn, A. Perrigo, & A. Antonelli (Eds.), Mountains, climate and biodiversity (pp. 171-185). Wiley Blackwell.

Flantua, S. G. A., O'Dea, A., Onstein, R. E., Giraldo, C., & Hooghiemstra, H. (2019). The flickering connectivity system of the north Andean páramos. Journal of Biogeography, 46(8), 1808-1825. https://doi.org/10.1111/jbi.13607

Fonseca, E. M., Colli, G. R., Werneck, F. P., & Carstens, B. C. (2021). Phylogeographic model selection using convolutional neural networks. Molecular Ecology Resources, 21(8), 2661-2675. https://doi.org/10.1111/1755-0998.13427

Fujisawa, T., & Barraclough, T. G. (2013). Delimiting species using single-locus data and the generalized mixed yule coalescent approach: A revised method and evaluation on simulated data sets. Systematic Biology, 62(5), 707-724. https://doi.org/10.1093/sysbio/syt033

GBIF.org. (2022). GBIF Home Page. Retrieved March 1, 2020, from https://www.gbif.org

Gehara, M., Garda, A. A., Werneck, F. P., Oliveira, E. F., da Fonseca, E. M., Camurugi, F., Magalhães, F. M., Lanna, F. M., Sites, J. W., Jr., Marques, R., Silveira-Filho, R., São Pedro, V. A., Colli, G. R., Costa, G. C., & Burbrink, F. T. (2017). Estimating synchronous demographic changes across populations using hABC and its application for a herpetological community from northeastern Brazil. Molecular Ecology, 26(18), 4756-4771. https://doi.org/10.1111/mec.14239

Giulietti, A. M., & Pirani, J. R. (1987). Patterns of geographic distribution of some plant species from the Espinhaço range, Minas Gerais and Bahia. In. P. E. Vanzolini & W. R. Heyer (Eds), Proceedings of a workshop on neotropical distribution patterns, 1.

Gomes, F. R., Rezende, E. L., Grizante, M. B., & Navas, C. A. (2009). The evolution of jumping performance in anurans: Morphological correlates and ecological implications. Journal of Evolutionary Biology, 22(5), 1088-1097. https://doi.org/10.1111/j.1420-9101.2009.01718.x

Hijmans, R. J. (2022). Raster: Geographic data analysis and modeling. Retrieved from https://CRAN.R-project.org/package=raster

Hijmans, R. J., Phillips, S., Leathwick, J., & Elith, J. (2022). dismo: Species Distribution Modeling. Retrieved from https://CRAN.R-project.org/package=dismo

Horák-Terra, I., Cortizas, A. M., Da Luz, C. F. P., Silva, A. C., Mighall, T., De Camargo, P. B., Mendonça-Filho, C. V., Oliveira, P. E., Cruz, F. W., & Vidal-Torrado, P. (2020). Late quaternary vegetation and climate dynamics in Central-Eastern Brazil: Insights from a 35k cal a bp peat record in the Cerrado biome. Journal of Quaternary Science, 35(5), 664-676. https://doi.org/10.1002/jqs.3209

Horák-Terra, I., Martínez Cortizas, A., da Luz, C. F. P., Rivas López, P., Silva, A. C., & Vidal-Torrado, P. (2015). Holocene climate change in Central-Eastern Brazil reconstructed using pollen and geochemical records of Pau de Fruta mire (Serra do Espinhaço meridional, Minas Gerais). Palaeogeography, Palaeoclimatology, Palaeoecology, 437, 117-131. https://doi.org/10.1016/j.palaeo.2015.07.027

Hornik, K., & Zeileis, A. (2004). kernlab-An S4 package for kernel methods in R. Journal of Statistical Software, 11(9), 1-20. Retrieved from http://www.jstatsoft.org/v11/i09/paper

Hughes, C. E., & Atchison, G. W. (2015). The ubiquity of alpine plant radiations: From the Andes to the Hengduan Mountains. New Phytologist, 207(2), 275-282. https://doi.org/10.1111/nph.13230

Karger, D. N., Conrad, O., Böhner, J., Kawohl, T., Kreft, H., Soria-Auza, R. W., Zimmermann, N., Linder, H. P., & Kessler, M. (2017). Climatologies at high resolution for the earth's land surface areas. Scientific Data, 4(1), 170122. https://doi.org/10.1038/sdata.2017.122

Knowles, L. L., & Maddison, W. P. (2002). Statistical Phylogeography. Molecular Ecology, 11(12), 2623-2635. https://doi.org/10.1046/j.1365-294X.2002.01410.x

Kok, P. J. R., Russo, V. G., Ratz, S., Means, D. B., MacCulloch, R. D., Lathrop, A., Aubret, F., & Bossuyt, F. (2017). Evolution in the south American ‘Lost World’: Insights from multilocus phylogeography of stefanias (Anura, Hemiphractidae, Stefania). Journal of Biogeography, 44(1), 170-181. https://doi.org/10.1111/jbi.12860

Körner, C., Jetz, W., Paulsen, J., Payne, D., Rudmann-Maurer, K., & Spehn, E. M. (2017). A global inventory of mountains for bio-geographical applications. Alpine Botany, 127(1), 1-15. https://doi.org/10.1007/s00035-016-0182-6

Lagomarsino, L. P., Condamine, F. L., Antonelli, A., Mulch, A., & Davis, C. C. (2016). The abiotic and biotic drivers of rapid diversification in Andean bellflowers (Campanulaceae). New Phytologist, 210(4), 1430-1442. https://doi.org/10.1111/nph.13920

Lanfear, R., Kokko, H., & Eyre-Walker, A. (2014). Population size and the rate of evolution. Trends in Ecology & Evolution, 29(1), 33-41. https://doi.org/10.1016/j.tree.2013.09.009

Larget, B. R., Kotha, S. K., Dewey, C. N., & Ané, C. (2010). BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis. Bioinformatics, 26(22), 2910-2911. https://doi.org/10.1093/bioinformatics/btq539

Leal, B. S. S., Chaves, C. J. N., Koehler, S., & Borba, E. L. (2016). When hybrids are not hybrids: A case study of a putative hybrid zone between Cattleya coccinea and C. brevipedunculata (Orchidaceae). Botanical Journal of the Linnean Society, 181(4), 621-639. https://doi.org/10.1111/boj.12437

Leal, B. S. S., Palma-Silva, C., & Pinheiro, F. (2016). Phylogeographic studies depict the role of space and time scales of plant speciation in a highly diverse neotropical region. Critical Reviews in Plant Sciences, 35(4), 215-230. https://doi.org/10.1080/07352689.2016.1254494

Leigh, D. M., van Rees, C. B., Millette, K. L., Breed, M. F., Schmidt, C., Bertola, L. D., Hand, B. K., Hunter, M. E., Jensen, E. L., Kershaw, F., Liggins, L., Luikart, G., Manel, S., Mergeay, J., Miller, J. M., Segelbacher, G., Hoban, S., & Paz-Vinas, I. (2021). Opportunities and challenges of macrogenetic studies. Nature Reviews Genetics, 22(12), 791-807. https://doi.org/10.1038/s41576-021-00394-0

Leite, Y. L. R., Costa, L. P., Loss, A. C., Rocha, R. G., Batalha-Filho, H., Bastos, A. C., Quaresma, V. S., Fagundes, V., Paresque, R., Passamani, M., & Pardini, R. (2016). Neotropical forest expansion during the last glacial period challenges refuge hypothesis. Proceedings of the National Academy of Sciences, 113(4), 1008-1013. https://doi.org/10.1073/pnas.1513062113

Li, J., Huang, J.-P., Sukumaran, J., & Knowles, L. L. (2018). Microevolutionary processes impact macroevolutionary patterns. BMC Evolutionary Biology, 18(1), 123. https://doi.org/10.1186/s12862-018-1236-8

Liaw, A., & Wiener, M. (2002). Classification and regression by randomForest. R News, 2/3, 18-22.

Magalhães, R. F., Lemes, P., Santos, M. T. T., Mol, R. M., Ramos, E. K. S., Oswald, C. B., Pezzuti, T. L., Santos, F. R., Brandão, R. A., & Garcia, P. C. A. (2021). Evidence of introgression in endemic frogs from the campo rupestre contradicts the reduced hybridization hypothesis. Biological Journal of the Linnean Society, 133(2), 561-576. https://doi.org/10.1093/biolinnean/blaa142

Miller, M. A., Pfeiffer, W., & Schwartz, T. (2011). The CIPRES science gateway: A community resource for phylogenetic analyses. In Proceedings of the 2011 TeraGrid conference: Extreme digital discovery (pp. 1-8). Association for Computing Machinery. https://doi.org/10.1145/2016741.2016785

Mota, M. R., Pinheiro, F., Leal, B. S. S., Sardelli, C. H., Wendt, T., & Palma-Silva, C. (2020). From micro- to macroevolution: Insights from a neotropical bromeliad with high population genetic structure adapted to rock outcrops. Heredity, 125(5), 353-370. https://doi.org/10.1038/s41437-020-0342-8

Mota, M. R., Pinheiro, F., Leal, B. S. S., Wendt, T., & Palma-Silva, C. (2019). The role of hybridization and introgression in maintaining species integrity and cohesion in naturally isolated inselberg bromeliad populations. Plant Biology, 21(1), 122-132. https://doi.org/10.1111/plb.12909

Muellner-Riehl, A. N. (2019). Mountains as evolutionary arenas: Patterns, emerging approaches, paradigm shifts, and their implications for plant phylogeographic research in the Tibeto-Himalayan region. Frontiers in Plant Science, 10(195), 1-8. https://doi.org/10.3389/fpls.2019.00195

Muellner-Riehl, A. N., Schnitzler, J., Kissling, W. D., Mosbrugger, V., Rijsdijk, K. F., Seijmonsbergen, A. C., Versteegh, H., & Favre, A. (2019). Origins of global mountain plant biodiversity: Testing the ‘mountain-geobiodiversity hypothesis’. Journal of Biogeography, 46(12), 2826-2838. https://doi.org/10.1111/jbi.13715

Nascimento, A. C., Chaves, A. V., Leite, F. S. F., Eterovick, P. C., & dos Santos, F. R. (2018). Past vicariance promoting deep genetic divergence in an endemic frog species of the Espinhaço range in Brazil: The historical biogeography of Bokermannohyla saxicola (Hylidae). PLoS One, 13(11), e0206732. https://doi.org/10.1371/journal.pone.0206732

Neves, D. M., Dexter, K. G., Pennington, R. T., Bueno, M. L., de Miranda, P. L. S., & Oliveira-Filho, A. T. (2018). Lack of floristic identity in Campos rupestres-A hyperdiverse mosaic of rocky montane savannas in South America. Flora, 238, 24-31. https://doi.org/10.1016/j.flora.2017.03.011

Nix, H. A. (1986). A biogeographic analysis of Australian elapid snakes. Atlas of Elapid Snakes of Australia, 7, 4-15.

Norder, S. J. (2019). Alexander von Humboldt (1769-1859): Connecting geodiversity, biodiversity and society. Journal of Biogeography, 46(8), 1627-1630. https://doi.org/10.1111/jbi.13500

Ornelas, J. F., Sosa, V., Soltis, D. E., Daza, J. M., González, C., Soltis, P. S., Gutiérrez-Rodríguez, C., de los Monteros, A. E., Castoe, T. A., Bell, C., & Ruiz-Sanchez, E. (2013). Comparative phylogeographic analyses illustrate the complex evolutionary history of threatened cloud forests of northern Mesoamerica. PLoS One, 8(2), e56283. https://doi.org/10.1371/journal.pone.0056283

Ortego, J., & Knowles, L. L. (2020). Incorporating interspecific interactions into phylogeographic models: A case study with Californian oaks. Molecular Ecology, 29(23), 4510-4524. https://doi.org/10.1111/mec.15548

Oswald, C. B., Lemes, P., Thomé, M. T. C., Pezzuti, T. L., Santos, F. R., Garcia, P. C. A., Leite, F. S. F., & de Magalhães, R. F. (2022). Colonization rather than fragmentation explains the geographical distribution and diversification of treefrogs endemic to Brazilian shield sky islands. Journal of Biogeography, 49(4), 682-698. https://doi.org/10.1111/jbi.14320

Otto-Bliesner, B. L., Marshall, S. J., Overpeck, J. T., Miller, G. H., Hu, A., & Cape Last Interglacial Project Members. (2006). Simulating arctic climate warmth and icefield retreat in the last interglaciation. Science, 311(5768), 1751-1753. https://doi.org/10.1126/science.1120808

Palma-Silva, C., Lexer, C., Paggi, G. M., Barbará, T., Bered, F., & Bodanese-Zanettini, M. H. (2009). Range-wide patterns of nuclear and chloroplast DNA diversity in Vriesea gigantea (Bromeliaceae), a neotropical forest species. Heredity, 103(6), 503-512. https://doi.org/10.1038/hdy.2009.116

Palma-Silva, C., Wendt, T., Pinheiro, F., Barbará, T., Fay, M. F., Cozzolino, S., & Lexer, C. (2011). Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in neotropical inselbergs. Molecular Ecology, 20(15), 3185-3201. https://doi.org/10.1111/j.1365-294X.2011.05143.x

Pannell, J. R. (2003). Coalescence in a metapopulation with recurrent local extinction and recolonization. Evolution, 57(5), 949-961. https://doi.org/10.1111/j.0014-3820.2003.tb00307.x

Papadopoulou, A., & Knowles, L. L. (2016). Toward a paradigm shift in comparative phylogeography driven by trait-based hypotheses. Proceedings of the National Academy of Sciences, 113(29), 8018-8024. https://doi.org/10.1073/pnas.1601069113

Pelletier, T. A., & Carstens, B. C. (2014). Model choice for phylogeographic inference using a large set of models. Molecular Ecology, 23(12), 3028-3043. https://doi.org/10.1111/mec.12722

Perez, M. F., Bonatelli, I. A. S., Moraes, E. M., & Carstens, B. C. (2016). Model-based analysis supports interglacial refugia over long-dispersal events in the diversification of two south American cactus species. Heredity, 116(6), 550-557. https://doi.org/10.1038/hdy.2016.17

Perez, M. F., Bonatelli, I. A. S., Romeiro-Brito, M., Franco, F. F., Taylor, N. P., Zappi, D. C., & Moraes, E. M. (2022). Coalescent-based species delimitation meets deep learning: Insights from a highly fragmented cactus system. Molecular Ecology Resources, 22(3), 1016-1028. https://doi.org/10.1111/1755-0998.13534

Perrigo, A., Hoorn, C., & Antonelli, A. (2020). Why mountains matter for biodiversity. Journal of Biogeography, 47(2), 315-325. https://doi.org/10.1111/jbi.13731

Pfanzelt, S., Albach, D. C., & von Hagen, K. B. (2017). Tabula rasa in the Patagonian channels? The phylogeography of Oreobolus obtusangulus (Cyperaceae). Molecular Ecology, 26(15), 4027-4044. https://doi.org/10.1111/mec.14156

Pinheiro, F., Dantas-Queiroz, M. V., & Palma-Silva, C. (2018). Plant species complexes as models to understand speciation and evolution: A review of south American studies. Critical Reviews in Plant Sciences, 37(1), 54-80. https://doi.org/10.1080/07352689.2018.1471565

Prates, I., Xue, A. T., Brown, J. L., Alvarado-Serrano, D. F., Rodrigues, M. T., Hickerson, M. J., & Carnaval, A. C. (2016). Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proceedings of the National Academy of Sciences, 113(29), 7978-7985. https://doi.org/10.1073/pnas.1601063113

QGIS Development Team. (2022). QGIS Geographic Information System. Open Source Geospatial Foundation. Retrieved from http://qgis.org

R Core Team. (2019). R: A language and environment for statistical computing. R Foundation for Statistical Computing. Retrieved from https://www.R-project.org/

Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarization in bayesian phylogenetics using tracer 1.7. Systematic Biology, 67(5), 901-904. https://doi.org/10.1093/sysbio/syy032

Rapini, A., Bitencourt, C., Luebert, F., & Cardoso, D. (2021). An escape-to-radiate model for explaining the high plant diversity and endemism in Campos rupestres. Biological Journal of the Linnean Society, 133(2), 481-498. https://doi.org/10.1093/biolinnean/blaa179

Reid, B. N., Naro-Maciel, E., Hahn, A. T., FitzSimmons, N. N., & Gehara, M. (2019). Geography best explains global patterns of genetic diversity and postglacial co-expansion in marine turtles. Molecular Ecology, 28(14), 3358-3370. https://doi.org/10.1111/mec.15165

Reid, N. M., & Carstens, B. C. (2012). Phylogenetic estimation error can decrease the accuracy of species delimitation: A Bayesian implementation of the general mixed yule-coalescent model. BMC Evolutionary Biology, 12(1), 196. https://doi.org/10.1186/1471-2148-12-196

Revelle, W. (2022). Psych: Procedures for psychological, psychometric, and personality research. Northwestern University.

Ribeiro, P. L., Rapini, A., Damascena, L. S., & van den Berg, C. (2014). Plant diversification in the Espinhaço range: Insights from the biogeography of Minaria (Apocynaceae). Taxon, 63(6), 1253-1264. https://doi.org/10.12705/636.16

Rull, V. (2005). Biotic diversification in the Guayana highlands: A proposal. Journal of Biogeography, 32(6), 921-927. https://doi.org/10.1111/j.1365-2699.2005.01252.x

Rull, V., Montoya, E., Nogué, S., Safont, E., & Vegas-Vilarrúbia, T. (2019). Chapter 2-Climatic and ecological history of Pantepui and surrounding areas. In V. Rull, T. Vegas-Vilarrúbia, O. Huber, & C. Señaris (Eds.), Biodiversity of Pantepui (pp. 33-54). Academic Press. https://doi.org/10.1016/B978-0-12-815591-2.00002-1

Sanín, M. J., Borchsenius, F., Paris, M., Carvalho-Madrigal, S., Gómez Hoyos, A. C., Cardona, A., Marín, N. A., Ospina, Y., Hoyos-Gómez, S. E., Manrique, H. F., & Bernal, R. (2022). The tracking of moist habitats allowed Aiphanes (Arecaceae) to cover the elevation gradient of the northern Andes. Frontiers in Plant Science, 13, 881879. https://doi.org/10.3389/fpls.2022.881879

Satler, J. D., & Carstens, B. C. (2016). Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system. Evolution, 70(5), 1105-1119. https://doi.org/10.1111/evo.12924

Schaefer, C. E., Cândido, H. G., Corrêa, G. R., Nunes, J. A., & Arruda, D. M. (2016). Soils associated with rupestrian grasslands. In G. W. Fernandes (Ed.), Ecology and conservation of mountaintop grasslands in Brazil (pp. 55-69). Springer International Publishing. https://doi.org/10.1007/978-3-319-29808-5_3

Schwery, O., Onstein, R. E., Bouchenak-Khelladi, Y., Xing, Y., Carter, R. J., & Linder, H. P. (2015). As old as the mountains: The radiations of the Ericaceae. New Phytologist, 207(2), 355-367. https://doi.org/10.1111/nph.13234

Sérsic, A. N., Cosacov, A., Cocucci, A. A., Johnson, L. A., Pozner, R., Avila, L. J., Sites, J. W., Jr., & Morando, M. (2011). Emerging phylogeographical patterns of plants and terrestrial vertebrates from Patagonia. Biological Journal of the Linnean Society, 103(2), 475-494. https://doi.org/10.1111/j.1095-8312.2011.01656.x

Silva, A. C., Horàk-Terra, I., Barral, U. M., Costa, C. R., Gonçalves, S. T., Pinto, T., Silva, B. P. C., Fernandes, J. S. C., Filho, C. V. M., & Vidal-Torrado, P. (2020). Altitude, vegetation, paleoclimate, and radiocarbon age of the basal layer of peatlands of the Serra do Espinhaço meridional, Brazil. Journal of South American Earth Sciences, 103, 102728. https://doi.org/10.1016/j.jsames.2020.102728

Silveira, F. A. O., Negreiros, D., Barbosa, N. P. U., Buisson, E., Carmo, F. F., Carstensen, D. W., Conceição, A. A., Cornelissen, T. G., Echternach, L., Wilson Fernandes, G., Garcia, Q. S., Guerra, T. J., Jacobi, C. M., Lemos-Filho, J. P., Stradic, S. L., Morellato, L. P. C., Neves, F. S., Oliveira, R. S., Schaefer, C. E., … Lambers, H. (2016). Ecology and evolution of plant diversity in the endangered campo rupestre: A neglected conservation priority. Plant and Soil, 403(1), 129-152. https://doi.org/10.1007/s11104-015-2637-8

Smith, C. I., Tank, S., Godsoe, W., Levenick, J., Strand, E., Esque, T., & Pellmyr, O. (2011). Comparative phylogeography of a coevolved community: Concerted population expansions in Joshua trees and four yucca moths. PLoS One, 6(10), e25628. https://doi.org/10.1371/journal.pone.0025628

Soltis, D. E., Morris, A. B., McLachlan, J. S., Manos, P. S., & Soltis, P. S. (2006). Comparative phylogeography of unglaciated eastern North America. Molecular Ecology, 15(14), 4261-4293. https://doi.org/10.1111/j.1365-294X.2006.03061.x

Tax, D. M. J., & Duin, R. P. W. (2004). Support vector data description. Machine Learning, 54(1), 45-66. https://doi.org/10.1023/B:MACH.0000008084.60811.49

Thom, G., Smith, B. T., Gehara, M., Montesanti, J., Lima-Ribeiro, M. S., Piacentini, V. Q., Miyaki, C. Y., & do Amaral, F. R. (2020). Climatic dynamics and topography control genetic variation in Atlantic Forest montane birds. Molecular Phylogenetics and Evolution, 148, 106812. https://doi.org/10.1016/j.ympev.2020.106812

Thomé, M. T. C., & Carstens, B. C. (2016). Phylogeographic model selection leads to insight into the evolutionary history of four-eyed frogs. Proceedings of the National Academy of Sciences, 113(29), 8010-8017. https://doi.org/10.1073/pnas.1601064113

Turchetto-Zolet, A. C., Pinheiro, F., Salgueiro, F., & Palma-Silva, C. (2013). Phylogeographical patterns shed light on evolutionary process in South America. Molecular Ecology, 22(5), 1193-1213. https://doi.org/10.1111/mec.12164

Vasconcelos, T. N. C., Alcantara, S., Andrino, C. O., Forest, F., Reginato, M., Simon, M. F., & Pirani, J. R. (2020). Fast diversification through a mosaic of evolutionary histories characterizes the endemic flora of ancient neotropical mountains. Proceedings of the Royal Society B: Biological Sciences, 287(1923), 20192933. https://doi.org/10.1098/rspb.2019.2933

Wieringa, J. G., Boot, M. R., Dantas-Queiroz, M. V., Duckett, D., Fonseca, E. M., Glon, H., Hamilton, N., Kong, S., Lanna, F. M., Mattingly, K. Z., Parsons, D. J., Smith, M. L., Stone, B. W., Thompson, C., Zuo, L., & Carstens, B. C. (2020). Does habitat stability structure intraspecific genetic diversity? It's Complicated…. Frontiers of Biogeography, 12(2), e45377. https://doi.org/10.21425/F5FBG45377

Zappi, D. C., Moro, M. F., Meagher, T. R., & Nic Lughadha, E. (2017). Plant biodiversity drivers in Brazilian Campos rupestres: Insights from phylogenetic structure. Frontiers in Plant Science, 8(2141), 1-15. https://doi.org/10.3389/fpls.2017.02141

Zobrazit více v PubMed

Dryad
10.5061/dryad.80gb5mkvf

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...