| [1] | Beheregaray LB (2008) Twenty years of phylogeography: the state of the field and the challenges for the Southern Hemisphere. Molecular Ecology 17: 3754–3774.
|
| [2] | Pennington RT, Ratter JA, Lewis GP (2006) Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation. Boca RatonFL: CRC/Taylor & Francis. 484 p.
|
| [3] | Werneck FP (2011) The diversification of eastern South American open vegetation biomes: Historical biogeography and perspectives. Quaternary Science Reviews 30: 1630–1648.
|
| [4] | Scariot A, Sousa-Silva JC, Felfili JM, editors (2005) Cerrado: ecologia, biodiversidade e conserva？？o. Brasília: Ministério do Meio Ambiente. 439 p.
|
| [5] | Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853–858.
|
| [6] | Eiten G (1972) The Cerrado vegetation of Brazil. Botanical Review 38: 201–341.
|
| [7] | Klink CA, Machado RB (2005) Conservation of the Brazilian cerrado. Conservation Biology 19: 707–713.
|
| [8] | Fiaschi P, Pirani JR (2009) Review of plant biogeographic studies in Brazil. Journal of Systematics and Evolution 47: 477–496.
|
| [9] | Castro AAJF (1994) Compara？？o florístico-geográfica (Brasil) e fitossociológica (Piauí-S？o Paulo) de amostras de Cerrado [Ph.D. Thesis]. SP, Brazil: Universidade Estadual de Campinas.
|
| [10] | Castro AAJF, Martins FR (1999) Cerrados do Brasil e do Nordeste: caracteriza？？o, área de ocupa？？o e considera？？es sobre a sua fitodiversidade. Pesq Foco, S？o Luís 7: 147.
|
| [11] | Ratter JA, Bridgewater S, Ribeiro JF (2003) Analysis of the floristic composition of the Brazilian Cerrado vegetation III: comparison of the woody vegetation of 376 areas. Edinburgh Journal of Botany 60: 57–109.
|
| [12] | Haffer J (1969) Speciation in amazonian forest birds. Science 165: 131–137.
|
| [13] | Mayle FE (2004) Assessment of the Neotropical dry forest refugia hypothesis in the light of palaeoecological data and vegetation model simulations. Journal of Quaternary Science 19: 713–720.
|
| [14] | Behling H, Lichte M (1997) Evidence of dry and cold climatic conditions at glacial times in tropical southeastern Brazil. Quaternary Research 48: 348–358.
|
| [15] | Ledru M-P (2002) Late quaternary history and evolution of the Cerrados as revealed by palynological records. In: Oliveira PS, Marquis RJ, editors. The cerrados of Brazil: ecology and natural history of a neotropical savanna. New York: Columbia University Press. pp. 33–68.
|
| [16] | Hickerson MJ, Carstens BC, Cavender-Bares J, Crandall KA, Graham CH, et al. (2010) Phylogeography's past, present, and future: 10 years after Avise, 2000. Molecular Phylogenetics and Evolution 54: 291–301.
|
| [17] | Avise JC (2000) Phylogeography: the history and formation of species. Cambridge, Mass: Harvard University Press. viii, 447 p. p.
|
| [18] | Weiss S, Ferrand N (2007) Phylogeography of southern European refugia: evolutionary perspectives on the origins and conservation of European biodiversity. Dordrecht: Springer. ix, 377 p. p.
|
| [19] | Collevatti RG, Grattapaglia D, Hay JD (2003) Evidences for multiple maternal lineages of Caryocar brasiliense populations in the Brazilian Cerrado based on the analysis of chloroplast DNA sequences and microsatellite haplotype variation. Molecular Ecology 12: 105–115.
|
| [20] | Collevatti RG, Rabelo SG, Vieira RF (2009) Phylogeography and disjunct distribution in Lychnophora ericoides (Asteraceae), an endangered cerrado shrub species. Annals of Botany 104: 655–664.
|
| [21] | Novaes RM, Lemos-Filho JP, Ribeiro RA, Lovato MB (2010) Phylogeography of Plathymenia reticulata (Leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America. Molecular Ecology 19: 985–998.
|
| [22] | Ramos ACS, Lemos-Filho JP, Ribeiro RA, Santos FR, Lovato MB (2007) Phylogeography of the tree Hymenaea stigonocarpa (Fabaceae: Caesalpinioideae) and the influence of Quaternary climate changes in the Brazilian cerrado. Annals of Botany 100: 1219–1228.
|
| [23] | Bridgewater S, Ratter JA, Felipe Ribeiro J (2004) Biogeographic patterns, β-diversity and dominance in the cerrado biome of Brazil. Biodiversity and Conservation 13: 2295–2317.
|
| [24] | Carvalho AM (1989) Systematic studies of the genus Dalbergia L.f. in Brazil [Ph.D. Thesis]. Reading, England: University of Reading.
|
| [25] | Silva Júnior MC (2005) 100 árvores do Cerrado: guia de campo. Brasília, DF: Rede de Sementes do Cerrado.
|
| [26] | Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantitie.s of fresh leaf tissue. Phytochemical Bulletin 19: 11–15.
|
| [27] | Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of 3 noncoding regions of chloroplast DNA. Plant Molecular Biology 17: 1105–1109.
|
| [28] | Delgado-Salinas A, Turley T, Richman A, Lavin M (1999) Phylogenetic analysis of the cultivated and wild species of Phaseolus (Fabaceae). Systematic Botany 24: 438–460.
|
| [29] | Feliner GN, Rosselló JA (2007) Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44: 911–919.
|
| [30] | Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673–4680.
|
| [31] | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28: 2731–2739.
|
| [32] | Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. The American Journal of Human Genetics 68: 978–989.
|
| [33] | Garrick RC, Sunnucks P, Dyer RJ (2010) Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation. BMC Evolutionary Biology 10: 118.
|
| [34] | Machado M, Magalh？es WCS, Sene A, Araújo B, Faria-Campos AC, et al. (2011) Phred-Phrap package to analyses tools: a pipeline to facilitate population genetics re-sequencing studies. Investigative Genetics 2: 3.
|
| [35] | Excoffier L, Lischer HE (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564–567.
|
| [36] | Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.
|
| [37] | Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552–569.
|
| [38] | Tajima F (1989) Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585–595.
|
| [39] | Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915–925.
|
| [40] | Petit RJ, El Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12: 844–855.
|
| [41] | Jost L (2008) G(ST) and its relatives do not measure differentiation. Molecular Ecology 17: 4015–4026.
|
| [42] | Crawford NG (2010) SMOGD: software for the measurement of genetic diversity. Molecular Ecology Resources 10: 556–557.
|
| [43] | Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes - application to human mitochondrial-DNA restriction data. Genetics 131: 479–491.
|
| [44] | Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37–48.
|
| [45] | Templeton AR, Crandall KA, Sing CF (1992) A cladistic-analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA-sequence data.3. Cladogram estimation. Genetics 132: 619–633.
|
| [46] | Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657–1659.
|
| [47] | Corander J, Marttinen P, Siren J, Tang J (2008) Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539.
|
| [48] | Guillot G, Leblois R, Coulon A, Frantz AC (2009) Statistical methods in spatial genetics. Molecular Ecology 18: 4734–4756.
|
| [49] | Corander J, Marttinen P (2006) Bayesian identification of admixture events using multilocus molecular markers. Molecular Ecology 15: 2833–2843.
|
| [50] | Bitocchi E, Nanni L, Bellucci E, Rossi M, Giardini A, et al. (2012) Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proceedings of the National Academy of Science, USA 109: E788–E796.
|
| [51] | Kropf M, Comes HP, Kadereit JW (2012) Past, present and future of mountain species of the French Massif Central – the case of Soldanella alpina L. subsp. alpina (Primulaceae) and a review of other plant and animal studies. Journal of Biogeography 39: 799–812.
|
| [52] | Fang JY, Chung JD, Chiang YC, Chang CT, Chen CY, et al. (2013) Divergent selection and local adaptation in disjunct populations of an endangered conifer, Keteleeria davidiana var. formosana (Pinaceae). Plos One 8: 1–15.
|
| [53] | Jones FA, Cerón-Souza I, Hardesty BD, Dick CW (2013) Genetic evidence of Quaternary demographic changes in four rain forest tree species sampled across the Isthmus of Panama. Journal of Biogeography 40: 720–731.
|
| [54] | Manni F, Guerard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: How barriers can be detected by using Monmonier's algorithm. Human Biology 76: 173–190.
|
| [55] | Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583–590.
|
| [56] | Peakall ROD, Smouse PE (2005) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.
|
| [57] | Brante A, Fernández M, Viard F (2012) Phylogeography and Biogeography Concordance in the Marine Gastropod Crepipatella dilatata (Calyptraeidae) along the Southeastern Pacific Coast. Journal of Heredity 103: 630–637.
|
| [58] | Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
|
| [59] | Richardson JE, Pennington RT, Pennington TD, Hollingsworth PM (2001) Rapid diversification of a species-rich genus of neotropical rain forest trees. Science 293: 2242–2245.
|
| [60] | Petit RJ, Duminil J, Fineschi S, Hampe A, Salvini D, et al. (2005) Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology 14: 689–701.
|
| [61] | Albaladejo RG, Aguilar JF, Aparicio A, Feliner GN (2005) Contrasting nuclear-plastidial phylogenetic patterns in the recently diverged Iberian Phlomis crinita and P. lychnitis lineages (Lamiaceae). Taxon 54: 987–998.
|
| [62] | Queiroz CdS, Batista FRdC, De Oliveira LO (2011) Evolution of the 5.8 S nrDNA gene and internal transcribed spacers in Carapichea ipecacuanha (Rubiaceae) within a phylogeographic context. Molecular Phylogenetics and Evolution 59: 293–302.
|
| [63] | Vieira LT (2012) Padr？es de diversidade da flora lenhosa dos cerrados do nordeste do Brasil. Campinas: Universidade Estadual de Campinas.
|
| [64] | 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.
|
| [65] | Durigan G (2006) Observations on the Southern Cerrados and their Relationship with the Core Area. In: Pennington RT, Ratter JA, Lewis GP, editors. Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation. Boca RatonFL: CRC/Taylor & Francis. pp. 484 p.
|
| [66] | Ratter JA, Dargie TCD (1992) An analysis of the floristic composition of 26 cerrado areas in Brazil. Edinburgh Journal of Botany 49: 235–250.
|
| [67] | Durigan G, De Siqueira MF, Franco G, Bridgewater S, Ratter JA (2003) The vegetation of priority areas for cerrado conservation in S？o Paulo State, Brazil. Edinburgh Journal of Botany 60: 217–241.
|
| [68] | Avise JC (2009) Phylogeography: retrospect and prospect. Journal of Biogeography 36: 3–15.
|
| [69] | Brante A, Fernández M, Viard F (2012) Phylogeography and Biogeography concordance in the marine gastropod Crepipatella dilatata (Calyptraeidae). Journal of Heredity 103: 630–637.
|
| [70] | Li J, Foighil Dó, Park JK (2013) Triton's trident: cryptic Neogene divergences in a marine clam (Lasaea australis) correspond to Australia's three temperate biogeographic provinces. Molecular Ecology 22: 1933–1946.
|
| [71] | Ab'Saber AN (1983) O domínio dos cerrados: introdu？？o ao conhecimento. Revista do Servidor Público 11: 41–55.
|
| [72] | Oliveira-Filho AT, Ratter JA (2002) Vegetation physiognomies and woody flora of the Cerrado biome. In: Oliveira PS, Marquis RJ, editors. The cerrados of Brazil: ecology and natural history of a neotropical savanna. New York: Columbia University Press. pp. viii, 398 p.
|
| [73] | Simon MF, Grether R, de Queiroz LP, Skema C, Pennington RT, et al. (2009) Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proceedings of the National Academy of Sciences of the United States of America 106: 20359–20364.
|
| [74] | Rull V (2011) Neotropical biodiversity: timing and potential drivers. Trends in Ecology & Evolution 26: 508–513.
|
| [75] | Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, et al. (2010) Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science 330: 927–931.
|
| [76] | Turchetto-Zolet AC, Pinheiro F, Salgueiro F, Palma-Silva C (2013) Phylogeographical patterns shed light on evolutionary process in South America. Molecular Ecology 22: 1193–1213.
|
| [77] | Excoffier L, Foll M, Petit RJ (2009) Genetic consequences of range expansions. Annual Review in Ecology, Evolution, and Systematics 40: 481–501.
|
| [78] | Ledru MP, Braga PIS, Soubiès F, Fournier M, Martin L, et al. (1996) The last 50,000 years in the Neotropics (Southern Brazil): evolution of vegetation and climate. Palaeogeography, Palaeoclimatology, Palaeoecology 123: 239–257.
|
| [79] | Werneck FP, Nogueira C, Colli GR, Sites JW, Costa GC (2012) Climatic stability in the Brazilian Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot. Journal of Biogeography 39: 1695–1706.
|
| [80] | Prado DE, Gibbs PE (1993) Patterns of Species Distributions in the Dry Seasonal Forests of South-America. Annals of the Missouri Botanical Garden 80: 902–927.
|
| [81] | Behling H (2002) South and southeast Brazilian grasslands during Late Quaternary times: a synthesis. Palaeogeography, Palaeoclimatology, Palaeoecology 177: 19–27.
|
| [82] | Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology 21: 3907–3930.
|
| [83] | da Silva JMC, Bates JM (2002) Biogeographic patterns and conservation in the South American Cerrado: a tropical savanna hotspot. BioScience 52: 225–234.
|
| [84] | Nogueira C, Ribeiro S, Costa GC, Colli GR (2011) Vicariance and endemism in a Neotropical savanna hotspot: distribution patterns of Cerrado squamate reptiles. Journal of Biogeography 38: 1907–1922.
|
| [85] | Simon MF, Proen？a C (2000) Phytogeographic patterns of Mimosa (Mimosoideae, Leguminosae) in the Cerrado biome of Brazil: an indicator genus of high-altitude centers of endemism? Biological Conservation 96: 279–296.
|
