Ecological niche modelling and genetic analyses reveal lack of geographic differentiation of Leptolobium dasycarpum (Leguminosae, Papilionoideae) across the Brazilian savannah

Wellington Santos Fava1, Priscila Canesqui da Costa2, Aline Pedroso Lorenz1
1Laboratory of Ecology and Evolutionary Biology, Institute of Biosciences, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, 79070-900 Brazil
2Institute of Natural, Human and Social Sciences, Federal University of Mato Grosso, Sinop, Mato Grosso, 78557-267 Brazil

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Araújo, 2005, Validation of species-climate impact models under climate change, Glob. Change Biol., 11, 1504, 10.1111/j.1365-2486.2005.01000.x Avise, 2000 Bandelt, 1999, Median-joining networks for inferring intraspecific phylogenies, Mol. Biol. Evol., 16, 37, 10.1093/oxfordjournals.molbev.a026036 Baranzelli, 2017, Travelling to the south: phylogeographic spatial diffusion model in Monttea aphylla (Plantaginaceae), an endemic plant of the Monte Desert, PLoS One, 12, e0178827, 10.1371/journal.pone.0178827 Behling, 1995, A high resolution Holocene pollen record from Lago do Pires, SE Brazil: vegetation, climate and fire history, J. Paleolimnol., 14, 253, 10.1007/BF00682427 Behling, 1998, Late quaternary vegetational and climatic changes in Brazil, Rev. Paleobot. and Palyno., 99, 143, 10.1016/S0034-6667(97)00044-4 Behling, 2002, South and southeast Brazilian grasslands during late quaternary times: a synthesis, Palaeogeogr. Palaeoclimatol. Palaeoecol., 177, 19, 10.1016/S0031-0182(01)00349-2 Behling, 2001, Neotropical savanna environments in space and time: late quaternary interhemispheric comparison, 307 Behling, 1997, Evidence of dry and cold climatic conditions at glacial times in tropical southeastern Brazil, Quaternary Res., 48, 348, 10.1006/qres.1997.1932 Beyra-M, 1999, Monograph of Pictetia Leguminosae-Papilionoideae and review of the Aeschynomeneae, Syst. Bot. Monogr., 56, 1, 10.2307/25096650 Bielejec, 2011, SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics, Bioinformatics, 27, 2910, 10.1093/bioinformatics/btr481 Buzatti, 2018, Genetic and historical colonization analyses of an endemic savanna tree, Qualea grandiflora, reveal ancient connections between Amazonian savannas and Cerrado core, Front. Plant Sci., 9, 981, 10.3389/fpls.2018.00981 Cassino, 2018, A late quaternary palynological record of a palm swamp in the Cerrado of central Brazil interpreted using modern analog data, Palaeogeogr. Palaeoclimatol. Palaeoecol., 490, 1, 10.1016/j.palaeo.2017.08.036 Collevatti, 2012, A coupled phylogeographical and species distribution modelling approach recovers the demographical history of a Neotropical seasonally dry forest tree species, Mol. Ecol., 21, 5845, 10.1111/mec.12071 Collevatti, 2012, Recovering the demographical history of a Brazilian Cerrado tree species Caryocar brasiliense: coupling ecological niche modelling and coalescent analyses, Nat. Conservação., 10, 169, 10.4322/natcon.2012.024 Collevatti, 2013, Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas, Heredity, 111, 97, 10.1038/hdy.2013.23 Collevatti, 2014, High genetic diversity and contrasting fine-scale spatial genetic structure in four seasonally dry tropical forest tree species, Plant Syst. Evol., 300, 1671, 10.1007/s00606-014-0993-0 Collevatti, 2015, Relaxed random walk model coupled with ecological niche modeling unravel the dispersal dynamics of a Neotropical savanna tree species in the deeper Quaternary, Front. Plant Sci., 6, 653, 10.3389/fpls.2015.00653 Corander, 2008, Bayesian spatial modelling of genetic population structure, Computation. Stat., 23, 111, 10.1007/s00180-007-0072-x Costa, 2017, Biome stability in South America over the last 30 kyr: inferences from long‐term vegetation dynamics and habitat modelling, Glob. Ecol. Biogeogr., 27, 285, 10.1111/geb.12694 CRIA, 2005 Darriba, 2012, jModelTest 2: more models, new heuristics and parallel computing, Nat. Methods, 9, 772, 10.1038/nmeth.2109 Desfeux, 1996, Systematics of Euromediterranean Silene Caryophyllaceae: evidence from a phylogenetic analysis using ITS sequences, Comptes Rendus Acad. Sci. Serie III, Sciences de la vie., 319, 351 Diniz-Filho, 2013, Mantel test in population genetics, Genet. Mol. Biol., 36, 475, 10.1590/S1415-47572013000400002 Doyle, 1987, Preservation of plant samples for DNA restriction endonuclease analysis, Taxon, 36, 715, 10.2307/1221122 Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075 Eiten, 1972, The Cerrado vegetation of Brazil, Bot. Rev., 38, 201, 10.1007/BF02859158 Excoffier, 2010, Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 10, 564, 10.1111/j.1755-0998.2010.02847.x Fava, 2019, Reproductive phenology of Leptolobium dasycarpum and L. elegans across the Brazilian savanna based on herbarium records, Flora, 255, 34, 10.1016/j.flora.2019.03.020 Fielding, 1997, A review of methods for the assessment of prediction errors in conservation presence/ absence models, Environ. Conserv., 24, 38, 10.1017/S0376892997000088 Fu, 1997, Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, 147, 915, 10.1093/genetics/147.2.915 Fu, 1993, Statistical tests of neutrality of mutations, Genetics, 133, 693, 10.1093/genetics/133.3.693 Giorgetta, 2013, Climate and carbon cycle changes from 1850 to 2100 in MPI‐ESM simulations for the Coupled Model Intercomparison Project phase 5, J. Adv. Model. Earth Sy., 5, 572, 10.1002/jame.20038 Hamilton, 1999, Tropical tree gene flow and seed dispersal, Nature, 401, 129, 10.1038/43597 Hanley, 1982, The meaning and use of the area under a receiver operating characteristic ROC curve, Radiology, 143, 29, 10.1148/radiology.143.1.7063747 Hare, 2001, Prospects for nuclear gene phylogeography, Trends Ecol. Evol., 16, 700, 10.1016/S0169-5347(01)02326-6 Hasumi, 2004 Heled, 2008, Bayesian inference of population size history from multiple loci, BMC Evol. Biol., 8, 289, 10.1186/1471-2148-8-289 Hijmans, 2005, Very high resolution interpolated climate surfaces for global land areas, Int. J. Climatol., 25, 1965, 10.1002/joc.1276 Klink, 2005, Conservação do Cerrado brasileiro, Megadiversidade, 1, 147 Lemey, 2009, Bayesian phylogeography finds its roots, PLoS Comput. Biol., 5, 10.1371/journal.pcbi.1000520 Lemey, 2010, Phylogeography takes a relaxed random walk in continuous space and time, Mol. Biol. Evol., 27, 1877, 10.1093/molbev/msq067 Librado, 2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data, Bioinformatics, 25, 1451, 10.1093/bioinformatics/btp187 Lima, 2017, Demographic stability and high historical connectivity explain the diversity of a savanna tree species in the Quaternary, Ann. Bot., 119, 645 Mantel, 1967, The detection of disease clustering and a generalized regression approach, Cancer Res., 27, 209 Melo, 2016, Coalescent simulation and paleodistribution modeling for Tabebuia rosealba do not support South American dry forest refugia hypothesis, PLoS One, 11, e0159314, 10.1371/journal.pone.0159314 Miller, 2005, Alleles In Space AIS: computer software for the joint analysis of interindividual spatial and genetic information, J. Hered., 96, 722, 10.1093/jhered/esi119 Myers, 2000, Biodiversity hotspots for conservation priorities, Nature, 403, 853, 10.1038/35002501 Novaes, 2010, Phylogeography of Plathymenia reticulata Leguminosae reveals patterns of recent range expansion towards northeastern Brazil and southern Cerrados in Eastern Tropical South America, Mol. Ecol., 19, 985, 10.1111/j.1365-294X.2010.04530.x Novaes, 2013, Concordance between phylogeographical and biogeographical patterns in the Cerrado: Diversification of the endemic tree Dalbergia miscolobium (Fabaceae), PLoS One, 8, e82198, 10.1371/journal.pone.0082198 Oliveira, 2017, Biodiversity conservation gaps in the Brazilian protected areas, Sci. Rep., 7, 9141, 10.1038/s41598-017-08707-2 Oliveira-Filho, 2002, Vegetation physiognomies and woody flora of the Cerrado biome, 91 Otto-Bliesner, 2006, Simulating Arctic climate warmth and icefield retreat in the last interglaciation, Science, 311, 1751, 10.1126/science.1120808 Phillips, 2006, Maximum entropy modelling of species geographic distributions, Ecol. Model., 190, 231, 10.1016/j.ecolmodel.2005.03.026 Prado, 1993, Patterns of species distributions in the dry seasonal forest South America, Ann. Mo. Bot. Gard., 80, 902, 10.2307/2399937 Rambaut, 2014 Ramos, 2007, Phylogeography of the tree Hymenaea stigonocarpa Fabaceae: Caesalpinioideae and the influence of Quaternary climate changes in the Cerrado, Ann. Bot., 100, 1219, 10.1093/aob/mcm221 Ramos, 2009, Phylogeographical structure of the neotropical forest tree Hymenaea courbaril Leguminosae: Caesalpinioideae and its relationship with the vicariant Hymenaea stigonocarpa from Cerrado, J. Hered., 100, 206, 10.1093/jhered/esn092 Ribeiro, 2011, Phylogeography of the endangered rosewood Dalbergia nigra Fabaceae: insights into the evolutionary history and conservation of the Brazilian Atlantic Forest, Heredity, 106, 46, 10.1038/hdy.2010.64 Richardson, 2001, Rapid diversification of a species–rich genus of neotropical rain forest trees, Science, 293, 2242, 10.1126/science.1061421 Rizzini, 1997 Rodrigues, 2012, A taxonomic revision of Leptolobium Papilionoideae, Leguminosae. Acta Bot. Bras., 26, 146, 10.1590/S0102-33062012000100016 Rogers, 1992, Population growth makes waves in the distribution of pairwise genetic differences, Mol. Biol. Evol., 9, 552 Schneider, 2012, NIH Image to ImageJ: 25 years of image analysis, Nat. Methods, 9, 671, 10.1038/nmeth.2089 Shin, 2003, A simulation of the Last Glacial Maximum climate using the NCAR–CCSM, Clim. Dynam., 20, 127, 10.1007/s00382-002-0260-x Sokal, 1978, Spatial autocorrelation in biology: 1, Methodol. Biol. J. Linn. Soc., 10, 199, 10.1111/j.1095-8312.1978.tb00013.x Souza, 2017, A large historical refugium explains spatial patterns of genetic diversity in a Neotropical savanna tree species, Ann. Bot., 119, 239, 10.1093/aob/mcw096 Strassburg, 2017, Moment of truth for the Cerrado hotspot, Nat. Ecol. Evol., 1, 0099, 10.1038/s41559-017-0099 Swets, 1988, Measuring the accuracy of diagnostic systems, Science., 240, 1285, 10.1126/science.3287615 Tajima, 1989, Statistical–method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, 123, 585, 10.1093/genetics/123.3.585 Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197 Terribile, 2012, Areas of climate stability of species ranges in the Brazilian Cerrado: disentangling uncertainties through time, Nat. Conservação., 10, 152, 10.4322/natcon.2012.025 Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position–specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673 Turchetto-Zolet, 2012, Large-scale phylogeography of the disjunct Neotropical tree species Schizolobium parahyba Fabaceae–Caesalpinioideae, Mol. Phylogenet. Evol., 65, 174, 10.1016/j.ympev.2012.06.012 Velazco, 2019, A dark scenario for Cerrado plant species: effects of future climate, land use and protected areas ineffectiveness, Divers. Distrib., 25, 660, 10.1111/ddi.12886 Viana e Souza, 2010, Genetic diversity and structure of the critically endangered tree Dimorphandra wilsonii and of the widespread in the Cerrado Dimorphandra mollis: implications for conservation, Biochem. Syst. Ecol., 38, 49, 10.1016/j.bse.2009.12.038 Vitorino, 2016, Demographical history and palaeodistribution modelling show range shift towards Amazon Basin for a Neotropical tree species in the LGM, BMC Evol. Biol., 16, 213, 10.1186/s12862-016-0779-9 Vitorino, 2018, Demographical expansion of Handroanthus ochraceus in the Cerrado during the Quaternary: implications for the genetic diversity of Neotropical trees, Biol. J. Linn. Soc. Lond., 123, 561, 10.1093/biolinnean/blx163 Werneck, 2012, Climatic stability in the Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot, J. Biogeogr., 39, 1695, 10.1111/j.1365-2699.2012.02715.x Wright, 1943, Isolation by distance, Genetics, 28, 114, 10.1093/genetics/28.2.114 Wright, 1978