Neither barriers nor refugia explain genetic structure in a major biogeographic break: phylogeography of praying mantises in the Brazilian Atlantic Forest

References

• Amaro RC, Rodrigues MT, Yonenaga-Yassuda Y, Carnaval AC. 2012. Demographic processes in the montane Atlantic rainforest: molecular and cytogenetic evidence from the endemic frog Proceratophrys boiei. Mol Phylogenet Evol. 62:880–888.
   PubMed Web of Science ®Google Scholar
• Ayers M, Clutton-Brock T. 1992. River boundaries and species range size in Amazonian primates. Am Nat. 140:531–537.
   PubMed Web of Science ®Google Scholar
• Batalha-Filho H, Cabanne GS, Miyaki CY. 2012. Phylogeography of an Atlantic Forest passerine reveals demographic stability through the last glacial maximum. Mol Phylogenet Evol. 65:892–902.
   PubMed Web of Science ®Google Scholar
• Behling H. 1997. Late Quaternary vegetation, climate and fire history from the tropical mountain region of Morro de Itapeva, SE Brazil. Palaeogeogr Palaeoclimatol Palaeoecol. 129:407–422.
   Web of Science ®Google Scholar
• Behling H. 1998. Late Quaternary vegetational and climatic changes in Brazil. Rev Palaeobot Palynol. 99:143–156.
   Web of Science ®Google Scholar
• Behling H. 2003. Late glacial and Holocene vegetation, climate and fire history inferred from Lagoa Nova in the southeastern Brazilian lowland. Veg Hist Archaeobot. 12:263–270.
   Web of Science ®Google Scholar
• Brunes TO, Thomé MTC, Alexandrino J, Haddad CF, Sequeira F. 2015. Ancient divergence and recent population expansion in a leaf frog endemic to the southern Brazilian Atlantic forest. Org Divers Evol. 15:695–710.
   Web of Science ®Google Scholar
• Cabanne GS, Calderón L, Trujillo Arias N, Flores P, Pessoa R, D’Horta FM, Miyaki CY. 2016. Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest. Biol J Linn Soc. 119:856–872.
   Web of Science ®Google Scholar
• Cabanne GS, Santos FR, Miyaki CY. 2007. Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): vicariance and recent demographic expansion in southern Atlantic forest. Biol J Linn Soc. 91:73–84.
   Web of Science ®Google Scholar
• Cabanne GS, d’Horta FM, Sari EH, Santos FR, Miyaki CY. 2008. Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications. Mol Phylogenet Evol. 49:760–773.
   PubMed Web of Science ®Google Scholar
• Cardoso DC, Cristiano MP, Tavares MG, Schubart CD, Heinze J. 2015. Phylogeography of the sand dune ant Mycetophylax simplex along the Brazilian Atlantic Forest coast: remarkably low mtDNA diversity and shallow population structure. BMC Evol Biol. 15:106.
   PubMed Web of Science ®Google Scholar
• Carnaval AC, Moritz C. 2008. Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest. J Biogeogr. 35:1–15.
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Carnaval AC, Waltari E, Rodrigues MT, Rosauer D, VanDerWal J, Damasceno R, Prates I, Strangas M, Spanos Z, Rivera D, et al. 2014. Prediction of phylogeographic endemism in an environmentally complex biome. Proc Royal Soc B. 281:20141461.
   Web of Science ®Google Scholar
• Cazé ALR, Mälder G, Nunes TS, Queiroz LP, de Oliveira G, Diniz-Filho JAF, Bonatto SL, Freitas LB. 2016. Could refuge theory and rivers acting as barriers explain the genetic variability distribution in the Atlantic Forest? Mol Phylogenet Evol. 101:242–251.
   PubMed Web of Science ®Google Scholar
• Che Y, Gui S, Lo N, Ritchie A, Wang Z. 2017. Species delimitation and phylogenetic relationships in Ectobiid Cockroaches (Dictyoptera, Blattodea) from China. PLoS One. 12:e0169006.
   PubMed Web of Science ®Google Scholar
• Colinvaux P, de Oliveira P, Moreno J, Miller M, Bush M. 1996. A long pollen record from lowland Amazonia: forest and cooling in glacial times. Science. 274:85–88.
   Web of Science ®Google Scholar
• Costa LP, Leite YLR. 2012. Historical fragmentation shaping vertebrate diversification in the Atlantic Forest biodiversity hotspot. In: Paterson BD, Costa LP, editors. Bones, clones, and biomes: the history and geography of recent neotropical mammals. Chicago (IL): The University of Chicago Press; p. 284–306.
   Google Scholar
• Costa LP, Leite YLR, Fonseca GAB, Fonseca MT. 2000. Biogeography of South American forest mammals: endemism and diversity in the Atlantic Forest. Biotropica. 32:872–881.
   Web of Science ®Google Scholar
• Costa LP. 2003. The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals. J Biogeogr. 30:71–86.
   Web of Science ®Google Scholar
• Drummond AJ, Rambaut A, Shapiro B, Pybus OG. 2005. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 22:1185–1192.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29:1969–1973.
   PubMed Web of Science ®Google Scholar
• Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11:2571–2581.
   PubMed Web of Science ®Google Scholar
• Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792–1797.
   PubMed Web of Science ®Google Scholar
• Farrell BD. 2001. Evolutionary assembly of the milkweed fauna: cytochrome oxidase I and the age of Tetraopes beetles. Mol Phylogenet Evol. 18:467–478.
   PubMed Web of Science ®Google Scholar
• Fitzpatrick SW, Brasileiro CA, Haddad CFB, Zamudio KR. 2009. Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability. Mol Ecol. 18:2877–2896.
   PubMed Web of Science ®Google Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147:915–925.
   PubMed Web of Science ®Google Scholar
• Gascon CSJ, Malcom JR, Patton JL, da Silva MNF, Bogart JP, Lougheed SC, Peres CA, Neckel S, Boag PT. 2000. Riverine barriers and the geographic distribution of Amazonian species. Proc Natl Acad Sci. 97:13672–13677.
   PubMed Web of Science ®Google Scholar
• Glick PA. 1939. The distribution of insects, spiders and mites in the air. US Dep Agric Tec Bull. 673:1–150.
   Google Scholar
• Grazziotin FG, Monzel M, Echeverrigaray S, Bonatto SL. 2006. Phylogeography of the Bothrops jararaca complex (Serpentes: Viperidae): past fragmentation and island colonization in the Brazilian Atlantic Forest. Mol Ecol. 15:3969–3982.
   PubMed Web of Science ®Google Scholar
• Haffer J. 1969. Speciation in amazonian forest birds. Science. 165:131–137.
   PubMed Web of Science ®Google Scholar
• Haffer J. 1997. Alternative models of vertebrate speciation in Amazonia: an overview. Biodivers Conserv. 6:451–476.
   Web of Science ®Google Scholar
• Hebert PDN, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci. 270:313–321.
   PubMed Web of Science ®Google Scholar
• Hewitt G. 2000. The genetic legacy of the quaternary ice ages. Nature. 405:907–913.
   PubMed Web of Science ®Google Scholar
• Hudson RR, Slatkin M, Maddison WP. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics. 132:583–589.
   PubMed Web of Science ®Google Scholar
• Kalliola R, Puhakka M, Danjoy W. 1993. Amazonia Peruana: vegetation húmeda en el llano subandino. Jyväskylä: Paut & Onern.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Frandsen P, Wright A, Senfeld T, Calcott B. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol Biol Evol. 34:772–773.
   PubMed Web of Science ®Google Scholar
• Laurance WF. 2009. Conserving the hottest of the hotspots. Biol Conserv. 142:1137.
   Web of Science ®Google Scholar
• Ledru MP, Rousseau DD, Cruz FW, Riccomini C, Karmann I, Martin L. 2005. Paleoclimate changes during the last 100,000 yr from a record in the Brazilian Atlantic rainforest region and interhemispheric comparison. Quat Res. 64:444–450.
   Web of Science ®Google Scholar
• Leigh JW, Bryant D. 2015. PopART. Full-feature software for haplotype network construction. Methods Ecol Evol. 6:1110–1116.
   Web of Science ®Google Scholar
• Leite YLR. 2003. Evolution and systematics of the Atlantic Tree Rats, genus Phyllomys (Rodentia. Echimyidae), with description of two new species. Univ Calif Publ Zool. 132:1–118.
   Google Scholar
• Leite YL, Costa LP, Loss AC, Rocha RG, Batalha-Filho H, Bastos AC, Quaresma VS, Fagundes V, Paresque R, Passamani M, et al. 2016. Neotropical forest expansion during the last glacial period challenges refuge hypothesis. Proc Natl Acad Sci USA. 113:1008–1013.
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25:1451–1452.
   PubMed Web of Science ®Google Scholar
• Mayrose I, Friedman N, Pupko T. 2005. A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics. 21:151–158.
   Web of Science ®Google Scholar
• Menezes RS, Brady SG, Carvalho AF, Del Lama MA, Costa MA. 2017. The roles of barriers, refugia, and chromosomal clines underlying diversification in Atlantic Forest social wasps. Sci Rep. 7:7689.
   PubMed Web of Science ®Google Scholar
• Moraes-Barros N, Silva JAB, Myiaki CY, Morgante JS. 2006. Comparative phylogeography of the Atlantic forest endemic sloth (Bradypus torquatus) and the widespread three-toed sloth (Bradypus variegatus) (Bradypodidade, Xenarthra). Genetica. 126:189–198.
   PubMed Web of Science ®Google Scholar
• Myers N, Mittermeier RA, Mittermeier CG, Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature. 403:853–858.
   PubMed Web of Science ®Google Scholar
• Papadopoulou A, Anastasiou I, Vogler AP. 2010. Revisiting the insect mitochondrial molecular clock: the Mid-Aegean Trench calibration. Mol Biol Evol. 27:1659–1672.
   PubMed Web of Science ®Google Scholar
• Patton JL, da Silva MNF. 1998. Rivers, refuges and ridges: the geography of speciation of Amazonian mammals. In: Howard DJ, Berlocher SH, editors. Endless forms: species and speciation. New York (NY): Oxford University Press.
   Google Scholar
• Patton JL, da Silva MNF, Malcom JR. 2000. Mammals of the Rio Juruá and the evolutionary and ecological diversification of Amazonia. Bull Am Mus Nat Hist. 244:1–306.
   Web of Science ®Google Scholar
• Pellegrino KCM, Rodrigues MT, Waite AN, Morando M, Yassuda YY, Sites JW Jr. 2005. Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic Forest. Biol J Linn Soc. 85:13–26.
   Web of Science ®Google Scholar
• Pessenda LCR, De Oliveira PE, Mofatto M, de Medeiros VB, Garcia RJF, Aravena R, Bendassoli JA, Leite AZ, Saad AR, Etchebehere ML. 2009. The evolution of a tropical rainforest/grassland mosaic in southeastern Brazil since 28,000 14C yr BP based on carbon isotopes and pollen records. Quat Res. 71:437–452.
   Web of Science ®Google Scholar
• Prance GT. 1982. Biological diversification in the tropics. New York (NY): Columbia University Press.
   Google Scholar
• Rambaut A, Suchard MA, Xie D, Drummond AJ. 2014. Tracer v1.6. [accessed 2017 Jun 16]. http://tree.bio.ed.ac.uk/software/tracer.
   Google Scholar
• Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 19:2092–2100.
   PubMed Web of Science ®Google Scholar
• Rebijith KB, Asokan R, Krishna V, Ranjitha HH, Kumar NK, Ramamurthy VV. 2014. DNA barcoding and elucidation of cryptic diversity in thrips (Thysanoptera). Fla Entomol. 97:1328–1347.
   Web of Science ®Google Scholar
• Resende HC, Yotoko KS, Delabie JH, Costa MA, Campiolo S, Tavares MG, Campos LA, Fernandes-Salomao TM. 2010. Pliocene and Pleistocene events shaping the genetic diversity within the central corridor of the Brazilian Atlantic Forest. Biol J Linn Soc. 101:949–960.
   Web of Science ®Google Scholar
• Schenk JJ. 2016. Consequences of secondary calibrations on divergence time estimates. PLoS One. 11:e0148228.
   PubMed Web of Science ®Google Scholar
• Scherrer MV. 2014. A revision of Miobantia Giglio-Tos, 1917 (Mantodea: Thespidae, Miobantiinae), with molecular association of dimorphic sexes and immature stages. Zootaxa. 3797:207–268.
   Web of Science ®Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–2690.
   PubMed Web of Science ®Google Scholar
• Svenson GJ, Whiting MF. 2009. Reconstructing the origins of praying mantises (Dictyoptera, Mantodea): the roles of Gondwanan vicariance and morphological convergence. Cladistics. 25:468–514.
   PubMed Web of Science ®Google Scholar
• Svenson GJ, Rodrigues HM. 2017. A Cretaceous-aged Palaeotropical dispersal established an endemic lineage of Caribbean Praying Mantises. Proc R Soc B. 284:20171280.
   PubMed Web of Science ®Google Scholar
• Symula R, Schulte R, Summers K. 2003. Molecular systematics and phylogeography of Amazonian poison frogs of the genus Dendrobates. Mol Phylogenet Evol. 26:452–475.
   PubMed Web of Science ®Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123:585–595.
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Terra PS. 1995. Revisão Sistemática dos gêneros de louva-a-deus da região Neotropical (Mantodea). Rev Bras Entomol. 39:13–94.
   Google Scholar
• Thomé MTC, Zamudio KR, Giovanelli JGR, Haddad CFB, Baldissera JFA, Alexandrino J. 2010. Phylogeography of endemic toads and post-Pliocene persistence of the Brazilian Atlantic Forest. Mol Phylogenet Evol. 55:1018–1031.
   PubMed Web of Science ®Google Scholar
• Thomé MTC, Zamudio KR, Haddad CF, Alexandrino J. 2014. Barriers, rather than refugia, underlie the origin of diversity in toads endemic to the Brazilian Atlantic Forest. Mol Ecol. 23:6152–6164.
   PubMed Web of Science ®Google Scholar
• Tonini JFR, Costa LP, Carnaval AC. 2013. Phylogeographic structure is strong in the Atlantic Forest; predictive power of correlative paleodistribution models, not always. J Zool Syst Evol Res. 51:114–121.
   Web of Science ®Google Scholar
• Ventura K, Sato-Kuwabara Y, Fagundes V, Geise L, Leite YLR, Costa LP, Silva MJJ, Yonenaga-Yassuda Y, Rodrigues MT. 2012. Phylogeographic structure and karyotypic diversity of the Brazilian shrew mouse (Blarinomys breviceps, Sigmodontinae) in the Atlantic Forest. Cytogenet Genome Res. 138:19–30.
   PubMed Web of Science ®Google Scholar
• Wallace AR. 1852. On the monkeys of the Amazon. Proc Zool Soc Lond. 20:107–110.
   Google Scholar
• Wang G, Li C, Guo X, Xing D, Dong Y, Wang Z, Zhang Y, Liu M, Zheng M, Zhang H, et al. 2012. Identifying the main mosquito species in China based on DNA barcoding. PLoS One. 7:e47051.
   PubMed Web of Science ®Google Scholar
• Zamudio KR, Greene HW. 1997. Phylgeography of the Bushmaster (Lachesis muta, Viperidae): implications for neotropical biogeography, systematics, and conservation. Biol J Linn Soc. 62:421–442.
   Web of Science ®Google Scholar