A short-range endemic species from south-eastern Atlantic Rain Forest shows deep signature of historical events: phylogeography of harvestmen Acutisoma longipes (Arachnida: Opiliones)

References

• Almeida, F., & Carneiro, C. (1998). Origem e evolução da Serra do Mar. Revista Brasileira de Geociências, 28, 135–150.
   Google Scholar
• Álvarez-Presas, M., Sánchez-Gracia, A., Carbayo, F., Rozas, J., & Riutort, M. (2014). Insights into the origin and distribution of biodiversity in the Brazilian Atlantic forest hot spot: A statistical phylogeographic study using a low-dispersal organism. Heredity, 112, 656–665.
   PubMed Web of Science ®Google Scholar
• Amaro, R. C., Rodrigues, M. T., Yonenaga-Yassuda, Y., & Carnaval, A. C. (2012). Demographic processes in the montane Atlantic rainforest: Molecular and cytogenetic evidence from the endemic frog. Proceratophrys boiei. Molecular Phylogenetics and Evolution, 62, 880–888.
   PubMed Web of Science ®Google Scholar
• Amorim, D. S., & Pires, M. R. S. (1996). Neotropical biogeography and a method for a maximum biodiversity estimation. In: C. E. M. Bicudo & N. A. Menezes (Eds.). Biodiversity in Brazil. A First Approach (pp. 183–219). São Paulo: Conselho Nacional de Desenvolvimento Científico e Tecnológico.
   Google Scholar
• Batalha-Filho, H., Cabanne, G. S., & Miyaki, C. Y. (2012). Phylogeography of an Atlantic forest passerine reveals demographic stability through the last glacial maximum. Molecular Phylogenetics and Evolution, 65, 892–902.
   PubMed Web of Science ®Google Scholar
• Batalha-Filho, H., Waldschmidt, A. M., Campos, L. A. O., Tavares, M. G., & Fernandes-Salomão, T. M. (2010). Phylogeography and historical demography of the neotropical stingless bee Melipona quadrifasciata (Hymenoptera, Apidae): Incongruence between morphology and mitochondrial DNA. Apidologie, 41, 534–547.
   Web of Science ®Google Scholar
• Bouckaert, R. (2010). DensiTree: Making sense of sets of phylogenetic trees. Bioinformatics, 26, 1372–1373.
   PubMed Web of Science ®Google Scholar
• Boyer, S. L., Baker, J. M., & Giribet, G. (2007). Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): A widespread ‘mite harvestman’ defies DNA taxonomy. Molecular Ecology, 16, 4999–5016.
   PubMed Web of Science ®Google Scholar
• Bragagnolo, C., Pinto-da-Rocha, R., Antunes, M., & Clouse, R. M. (2015). Phylogenetics and phylogeography of a long-legged harvestman (Arachnida: Opiliones) in the Brazilian Atlantic Rain Forest reveals poor dispersal, low diversity, and extensive mitochondrial introgression. Invertebrate Systematics, 29, 386–404.
   Web of Science ®Google Scholar
• Brunes, T. O., Sequeira, F., Haddad, C. F. B., & Alexandrino, J. (2010). Gene and species trees of a Neotropical group of treefrogs: Genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species. Molecular Phylogenetics and Evolution, 57, 1120–1133.
   PubMed Web of Science ®Google Scholar
• Cabanne, G. S., Calderón, L., Trujillo-Arias, N., Flores, P., Pessoa, R., D'Horta, F. M., & Miyaki, C. Y. (2016). Effects of Pleistocene climate changes on species ranges and evolutionary processes in the Neotropical Atlantic Forest. Biological Journal of the Linnean Society, 119, 856–872.
   Web of Science ®Google Scholar
• Cabanne, G. S., Santos, F. R., & Miyaki, C. Y. (2007). Phylogeography of Xiphorhynchus fuscus (Passeriformes, Dendrocolaptidae): Vicariance and recent demographic expansion in southern Atlantic forest. Biological Journal of the Linnean Society, 91, 73–84.
   Web of Science ®Google Scholar
• Cabanne, G. S., Trujillo-Arias, N., Calderón, L., D'Horta, F. M., & Miyaki, C. Y. (2014). Phenotypic evolution of an Atlantic Forest passerine (Xiphorhynchus fuscus): Biogeographic and systematic implications. Biological Journal of the Linnean Society, 113, 1047–1066.
   Web of Science ®Google Scholar
• Caetano, D. S., & Machado, G. (2013). The ecological tale of Gonyleptidae (Arachnida, Opiliones) evolution: Phylogeny of a Neotropical lineage of armoured harvestmen using ecological, behavioural and chemical characters. Cladistics, 29, 589–609.
   Web of Science ®Google Scholar
• Carnaval, A. C., Hickerson, M. J., Haddad, C. F. B., Rodrigues, M. T., & Moritz, C. (2009). Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science, 323, 785–789.
   PubMed Web of Science ®Google Scholar
• Cavarzere, V., Silveira, L. F., Vasconcelos, M. F., Grantsau, R., & Straube, F. C. (2014). Taxonomy and biogeography of Stephanoxis Simon, 1897 (Aves: Trochilidae). Papéis Avulsos de Zoologia (São Paulo), 54, 69–79.
   Google Scholar
• Clement, M., Posada, D., & Crandall, K. A. (2000). TCS: A computer program to estimate gene genealogies. Molecular Ecology, 9, 1657–1659.
   PubMed Web of Science ®Google Scholar
• Clouse, R. M., Sharma, P. P., Stuart, J. C., Davis, L. R., Giribet, G., Boyer, S. L., & Wheeler, W. C. (2016). Phylogeography of the harvestman genus Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox. Organisms Diversity and Evolution, 16, 167–184.
   Google Scholar
• Costa, L. P. (2003). The historical bridge between the Amazon and the Atlantic Forest of Brazil: A study of molecular phylogeography with small mammals. Journal of Biogeography, 30, 71–86.
   Web of Science ®Google Scholar
• D'Horta, F. M., Cabanne, G. S., Meyer, D., & Miyaki, C. Y. (2011). The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: Diversification of an Atlantic Forest passerine. Molecular Ecology, 20, 1923–1935.
   PubMed Web of Science ®Google Scholar
• Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nature Methods, 9, 772–772.
   PubMed Web of Science ®Google Scholar
• DaSilva, M. B., & Gnaspini, P. (2010). A systematic revision of Goniosomatinae (Arachnida: Opiliones: Gonyleptidae), with a cladistic analysis and biogeographical notes. Invertebrate Systematics, 23, 530–624.
   Web of Science ®Google Scholar
• DaSilva, M. B., Pinto-da-Rocha, R., & DeSouza, A. M. (2015). A protocol for the delimitation of areas of endemism and the historical regionalization of the Brazilian Atlantic Rain Forest using harvestmen distribution data. Cladistics, 31, 692–705. doi:10.1111/cla.12121
   PubMed Web of Science ®Google Scholar
• DaSilva, M. B., Pinto-da-Rocha, R., & DeSouza, A. M. (2016). História Biogeográfica da Mata Atlântica: Opiliões (Arachnida) como modelo para sua inferência. In C. Carvalho & E. Almeida (Eds.), Biogeografia da América do Sul: Análise de tempo, espaço e forma (pp. 227–244). Rio de Janeiro: Roca.
   Google Scholar
• Drummond, A. J., Suchard, M. A., Xie, D., & Rambaut, A. (2012). Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.
   PubMed Web of Science ®Google Scholar
• Excoffier, L., & Lischer, H. E. L. (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.
   PubMed Web of Science ®Google Scholar
• Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances amongst DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.
   PubMed Web of Science ®Google Scholar
• Fiaschi, P., & Pirani, J. R. (2009). Review of plant biogeographic studies in Brazil. Journal of Systematics and Evolution, 47, 477–496.
   Web of Science ®Google Scholar
• Fitzpatrick, S. W., Brasileiro, C. A., Haddad, C. F. B., & Zamudio, K. R. (2009). Geographical variation in genetic structure of an Atlantic Coastal Forest frog reveals regional differences in habitat stability. Molecular Ecology, 18, 2877–2896.
   PubMed Web of Science ®Google Scholar
• Flot, J. F. (2010). SEQPHASE: A web tool for interconverting phase input/output files and fasta sequence alignments. Molecular Ecology Resources, 10, 162–166.
   PubMed Web of Science ®Google Scholar
• Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925.
   PubMed Web of Science ®Google Scholar
• Gnaspini, P. (1996). Population ecology of Goniosoma spelaeum, a cavernicolous harvestman from south-eastern Brazil (Arachnida: Opiliones: Gonyleptidae). Journal of Zoology, 239, 417–435.
   Web of Science ®Google Scholar
• Grazziotin, F. G., Monzel, M., Echeverrigaray, S., & Bonatto, S. L. (2006). Phylogeography of the Bothrops jararaca complex (Serpentes: Viperidae): Past fragmentation and island colonization in the Brazilian Atlantic Forest. Molecular Ecology, 15, 3969–3982.
   PubMed Web of Science ®Google Scholar
• Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52, 696–704.
   PubMed Web of Science ®Google Scholar
• Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.
   Google Scholar
• Harpending, H. C. (1994). Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology, 66, 591–600.
   PubMed Web of Science ®Google Scholar
• Heled, J., & Drummond, A. J. (2008). Bayesian inference of population size history from multiple loci. BioMedCentral Evolutionary Biology, 8, 289.
   Google Scholar
• Heled, J., & Drummond, A. J. (2010). Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570–580.
   PubMed Web of Science ®Google Scholar
• Heller, R., Chikhi, L., & Siegismund, H. R. (2013). The confounding effect of population structure on Bayesian skyline plot inferences of demographic history. Public Library of Science One, 8, e62992.
   Google Scholar
• Ji, Y. J., Zhang, D. X., & He, L. J. (2003). Evolutionary conservation and versatility of a new set of primers for amplifying the ribosomal internal transcribed spacer regions in insects and other invertebrates. Molecular Ecology Notes, 3, 581–585.
   Web of Science ®Google Scholar
• Katoh, K., & Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–780.
   PubMed Web of Science ®Google Scholar
• Ledru, M. P., Mourguiart, P., & Riccomini, C. (2009). Related changes in biodiversity, insolation and climate in the Atlantic rainforest since the last interglacial. Palaeogeography, Palaeoclimatology, Palaeoecology, 271, 140–152.
   Web of Science ®Google Scholar
• Leigh, J. W., & Bryant, D. (2015). popart: Full-feature software for haplotype network construction. Methods in Ecology and Evolution, 6, 1110–1116.
   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
• Machado, G. (2002). Maternal care, defensive behavior, and sociality in neotropical Goniosoma harvestmen (Arachnida, Opiliones). Insectes Sociaux, 49, 388–393.
   Web of Science ®Google Scholar
• Machado, G., Raimundo, R. L. G., & Oliveira, P. S. (2000). Daily activity schedule, gregariousness, and defensive behaviour in the Neotropical harvestman Goniosoma longipes (Opiliones: Gonyleptidae). Journal of Natural History, 34, 587–596.
   Web of Science ®Google Scholar
• Martins, F. M. (2011). Historical biogeography of the Brazilian Atlantic forest and the Carnaval-Moritz model of Pleistocene refugia: What do phylogeographical studies tell us? Biological Journal of the Linnean Society, 104, 499–509.
   Web of Science ®Google Scholar
• Mestre, L. A. M., & Pinto-da-Rocha, R. (2004). Population dynamics of an isolated population of the harvestman Ilhaia cuspidata(Opiliones, Gonyleptidae), in Araucaria Forest (Curitiba, Paraná, Brazil). Journal of Arachnology, 32, 208–220.
   Google Scholar
• Meyer, C. P. (2003). Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics. Biological Journal of the Linnean Society, 79, 401–459.
   Web of Science ®Google Scholar
• Mittermeier, R. A., Gil, P. R., Hoffman, M., Pilgrim, J., Brooks, T., Mittermeier, C. G., … DaFonseca, G. A. B. (2005). Hotspots Revisited: Earth's biologically richest and most endangered ecoregions. Washington, DC: Conservation International.
   Google Scholar
• Moulton, J. K., & Wiegmann, B. M. (2004). Evolution and phylogenetic utility of CAD (rudimentary) amongst Mesozoic-aged Eremoneuran Diptera (Insecta). Molecular Phylogenetics and Evolution, 31, 363–378.
   PubMed Web of Science ®Google Scholar
• Müller, P. (1973). The dispersal centers of terrestrial vertebrates in the Neotropical realm: A study in the evolution of the Neotropical biota and its native landscape. Biogeographica, 2, 1–250.
   Google Scholar
• Myers, N., Mittermeier, R. A., Mittermeier, C. G., DaFonseca, G. A., & Kent, J. (2000). Biodiversity hotspots for conservation priorities. Nature, 403, 853–858.
   PubMed Web of Science ®Google Scholar
• Nazareth, T. M., & Machado, G. (2015). Egg production constrains chemical defenses in a Neotropical arachnid. Public Library of Science One, 10, e0134908.
   Google Scholar
• Oliveira-Filho, A. T., & Ratter, J. A. (1995). A study of the origin of central Brazilian forests by the analysis of plant species distribution patterns. Edinburgh Journal of Botany, 52, 141–194.
   Google Scholar
• Pellegrino, K. C. M., Rodrigues, M. T., Waite, A. N., Morando, M., Yonenaga-Yassuda, Y., & Sites, J. W. (2005). Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): Genetic structure coincides with river systems in the Brazilian Atlantic Forest. Biological Journal of the Linnean Society, 85, 13–26.
   Web of Science ®Google Scholar
• Peres, E. A., Sobral-Souza, T., Perez, M. F., Bonatelli, I. A. S., Silva, D. P., … Solferini, V. N. (2015). Pleistocene niche stability and lineage diversification in the subtropical spider Araneus omnicolor (Araneidae). Public Library of Science One, 10, e0121543.
   Google Scholar
• Peres, E. A., Silva, M. J., & Solferini, V. N. (2017). Phylogeography of the spider Araneus venatrix (Araneidae) suggests past connections between Amazon and Atlantic rainforests. Biological Journal of the Linnean Society, 121, 771–785.
   Web of Science ®Google Scholar
• Pinto-da-Rocha, R., Bragagnolo, C., Marques, F. P. L., & Antunes Junior, M. (2014). Phylogeny of harvestmen family Gonyleptidae inferred from a multilocus approach (Arachnida: Opiliones). Cladistics, 30, 519–539.
   PubMed Web of Science ®Google Scholar
• Pinto-da-Rocha, R., DaSilva, M. B., & Bragagnolo, C. (2005). Faunistic similarity and historic biogeography of the harvestmen of southern and southeastern Atlantic Rain Forest of Brazil. Journal of Arachnology, 33, 290–299.
   Web of Science ®Google Scholar
• Prance, G. T. (1982). Forest refuges: Evidence from woody angiosperms. In G. T. Prance (Ed.). Biological diversification in the tropics (pp. 137–158). New York: Columbia University Press.
   Google Scholar
• Prugnolle, F., & de Meeus, T. (2002). Inferring sex-biased dispersal from population genetic tools: A review. Heredity, 88, 161–165.
   PubMed Web of Science ®Google Scholar
• Ramos-Onsins, S. E., & Rozas, J. (2002). Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092–2100.
   PubMed Web of Science ®Google Scholar
• Ravelo, A. C., Andreasen, D. H., Lyle, M., Olivarez-Lyle, A., & Wara, M. W. (2004). Regional climate shifts caused by gradual global cooling in the Pliocene epoch. Nature, 429, 263–267.
   PubMed Web of Science ®Google Scholar
• Resende, H. C., Yotoko, K. S. C., Delabie, J. H. C., Costa, M. A., Campiolo, S., Tavares, M. G., … Fernandes-Salomão, T. M. (2010). Pliocene and Pleistocene events shaping the genetic diversity within the central corridor of the Brazilian Atlantic Forest. Biological Journal of the Linnean Society, 101, 949–960.
   Web of Science ®Google Scholar
• Ribeiro, A. C. (2006). Tectonic history and the biogeography of the freshwater fishes from the coastal drainages of eastern Brazil: An example of faunal evolution associated with a divergent continental margin. Neotropical Ichthyology, 4, 225–246.
   Web of Science ®Google Scholar
• Riccomini, C., Santanna, L., & Ferrari, A. (2004). Evolução geológica do Rift Continental do Sudeste do Brasil. In V. Mantesso Neto, A. Bartorelli, C. Carneiro, & B. Brito Neves (Eds.), Geologia do Continente Sul-Americano: Evolução da Obra de Fernando Flávio Marques de Almeida (pp. 383–405). São Paulo: Beca.
   Google Scholar
• Rogers, A. R., & Harpending, H. C. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552–569.
   PubMed Web of Science ®Google Scholar
• Ronquist, F., Teslenko, M., Van Der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). Mrbayes 3.2: Efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61, 539–542.
   PubMed Web of Science ®Google Scholar
• Saia, S., Pessenda, L., Gouveia, S., Aravena, R., & Bendassolli, J. (2008). Last glacial maximum (LGM) vegetation changes in the Atlantic Forest, southeastern Brazil. Quaternary International, 184, 195–201.
   Web of Science ®Google Scholar
• Salis, S. M., Shepherd, G. J., & Joly, C. A. (1995). Floristic Comparison of Mesophytic Semideciduous Forests of the Interior of the State of São Paulo, Southeast Brazil. Vegetatio, 119, 155–164.
   Google Scholar
• Santos, F. (2007). Ecophysiology. In R. Pinto-da-Rocha, G. Machado, & G. Giribet (Eds.), Harvestmen: The biology of opiliones (pp. 473–488). Cambridge, MA: Harvard University Press.
   Google Scholar
• Sharma, P. P., & Giribet, G. (2011). The evolutionary and biogeographic history of the armoured harvestmen – Laniatores phylogeny based on ten molecular markers, with the description of two new families of Opiliones (Arachnida). Invertebrate Systematics, 25, 106–142.
   Web of Science ®Google Scholar
• Sigrist, M. S., & Carvalho, C. J. B. (2009). Historical relationships amongst areas of endemism in the tropical South America using Brooks Parsimony Analysis (BPA). Biota Neotropica, 9, 79–90.
   Google Scholar
• Silva, J. M. C., & Casteleti, C. H. M. (2005). Estado da biodiversidade da Mata Atlântica brasileira. In C. Galindo–Leal & I. G. Câmara (Eds.), Mata Atlântica: Biodiversidade, Ameaças e Perspectivas (pp. 43–59). São Paulo: Fundação SOS Mata Atlântica.
   Google Scholar
• Silva, S. M., Moraes-Barros, N., Ribas, C. C., Ferrand, N., & Morgante, J. S. (2012). Divide to conquer: A complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest. Biological Journal of the Linnean Society, 107, 39–55.
   Web of Science ®Google Scholar
• Stamatakis, A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30, 1312–1313.
   PubMed Web of Science ®Google Scholar
• Stephens, M., & Donnelly, P. (2003). A Comparison of bayesian methods for haplotype reconstruction from population genotype data. The American Journal of Human Genetics, 73, 1162–1169.
   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., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.
   PubMed Web of Science ®Google Scholar
• Thomas, S. M., & Hedin, M. (2008). Multigenic phylogeographic divergence in the paleoendemic southern Appalachian opilionid Fumontana deprehendor Shear (Opiliones, Laniatores, Triaenonychidae). Molecular Phylogenetics and Evolution, 46, 645–658.
   PubMed Web of Science ®Google Scholar
• Thomé, M. T. C., Zamudio, K. R., Giovanelli, J. G. R., Haddad, C. F. B., Baldissera, F. A., & Alexandrino, J. (2010). Phylogeography of endemic toads and post-Pliocene persistence of the Brazilian Atlantic Forest. Molecular phylogenetics and Evolution, 55, 1018–1031.
   PubMed Web of Science ®Google Scholar
• Thomé, M. T. C., Zamudio, K. R., Haddad, C. F. B., & Alexandrino, J. (2014). Barriers, rather than refugia, underlie the origin of diversity in toads endemic to the Brazilian Atlantic Forest. Molecular Ecology, 23, 6152–6164.
   PubMed Web of Science ®Google Scholar
• Toews, D. P. L., & Brelsford, A. (2012). The biogeography of mitochondrial and nuclear discordance in animals. Molecular Ecology, 21, 3907–3930.
   PubMed Web of Science ®Google Scholar
• 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, 1193–1213.
   PubMed Web of Science ®Google Scholar
• Vaschetto, L. M., González-Ittig, R. E., Vergara, J., & Acosta, L. E. (2015). High genetic diversity in the harvestman Geraeocormobius sylvarum (Arachnida, Opiliones, Gonyleptidae) from subtropical forests in north-eastern Argentina revealed by mitochondrial DNA sequences. Journal of Zoological Systematics and Evolutionary Research, 53, 211–218.
   Web of Science ®Google Scholar
• Willemart, R. H., & Gnaspini, P. (2004). Spatial distribution, mobility, gregariousness, and defensive behaviour in a Brazilian cave harvestman Goniosoma albiscriptum (Arachnida, Opiliones, Gonyleptidae). Animal Biology, 54, 221–235.
   Web of Science ®Google Scholar