Published May 1, 2022
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Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae)
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Stopiglia, Renata, Barbosa, Waleska, Ferreira, Mateus, Raposo, Marcos A, Dubois, Alain, Harvey, Michael G, Kirwan, Guy M, Forcato, Giovanna, Bockmann, Flavio A, Ribas, Camila C (2022): Taxonomic challenges posed by discordant evolutionary scenarios supported by molecular and morphological data in the Amazonian Synallaxis rutilans group (Aves: Furnariidae). Zoological Journal of the Linnean Society 195 (1): 65-87, DOI: 10.1093/zoolinnean/zlab076, URL: https://academic.oup.com/zoolinnean/article/195/1/65/6457706
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- urn:lsid:plazi.org:pub:141FFFBCC858FFFAFF90FF98FFD2565A
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References
- Aberer AJ, Kobert K, Stamatakis A. 2014. ExaBayes: massively parallel bayesian tree inference for the wholegenome era. Molecular Biology and Evolution 31: 2553-2556.
- Addinsoft. 2017. XLSTAT (data analysis and statistics software for Microsoft Excel), version 2017. Paris: Addinsoft.
- Amaral F, Coelho M, Aleixo A, Luna L, Rego P, Araripe J, Souza T, Silva W, Thom G. 2018. Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins. Molecular Ecology 27: 4108-4120. http://dx.doi.org/10.1111/mec.14843
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics (Oxford, England) 30: 2114-2120.
- Chapman FM. 1914. Diagnoses of apparently new Colombian birds III. Bulletin of the American Museum of Natural History 33: 603-637.
- Claramunt S. 2014. Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Parana river basins. Molecular Phylogenetics and Evolution 78: 223-231.
- Clement M, Posada D, Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
- Cory CB, Hellmayr CE. 1925. Catalogue of birds of the Americas. Furnariidae - Dendrocolaptidae. Publications of the Field Museum of Natural History, Zoological Series 13: 1-390.
- Cracraft J. 1985. Historical biogeography and patterns of differentiation within the South American avifauna: areas of endemism. Ornithological Monographs 36: 49-84.
- Dayrat B. 2005. Toward integrative taxonomy. Biological Journal of the Linnean Society 85: 407-415.
- Dekker RWRJ. 2003. Type specimens of birds in the National Museum of Natural History, Leiden. Part 2. passerines: Eurylaimidae - Eopsaltriidae (Peters's sequence). Nationaal Natuurhistorisch Museum Technical Bulletin 6: 1-142.
- del Hoyo J, Elliott A, Sargatal J, Christie DA. 2013. Handbook of the birds of the world. Special volume. New species and global index. Barcelona: Lynx Edicions.
- del Hoyo J, Collar NJ. 2016. HBW and BirdLife International illustrated checklist of the birds of the world. Volume 2: Passerines. Barcelona: Lynx Edicions.
- de Queiroz K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879-886.
- Derryberry EP, Claramunt S, Derryberry G, Chesser RT, Cracraft J, Aleixo A, Perez-Eman J, Remsen JV Jr, Brumfield RT. 2011. Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae). Evolution; International Journal of Organic Evolution 65: 2973-2986.
- Dickinson EC, Christidis L, eds. 2014. The Howard and Moore complete checklist of the birds of the world, Vol. 2, 4th edn. Eastbourne: Aves Press.
- Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
- Dubois A. 2000. Synonymies and related lists in zoology: general proposals, with examples in herpetology. Dumerilia 4: 33-98.
- Dubois A. 2017. Diagnoses in zoological taxonomy and nomenclature. Bionomina 12: 63-85.
- Dubois A, Ohler A. 1996. Early scientific names of Amphibia Anura 1. Introduction. Bulletin du Museum National d'Histoire Naturelle (A) 18: 297-320.
- Dubois A, Raffaelli J. 2009. A new ergotaxonomy of the family Salamandridae Goldfuss, 1820 (Amphibia, Urodela). Alytes 26: 1-85.
- Dubois A, Raffaelli J. 2012. A new ergotaxonomy of the order Urodela Dumeril, 1805 (Amphibia, Batrachia).Alytes 28: 77-161.
- Ersts PJ. 2017. Geographic Distance Matrix Generator (v.1.2.3). American Museum of Natural History, Center for Biodiversity and Conservation. Available from http:// biodiversityinformatics.amnh.org/open_source/gdmg (accessed on 15 August 2017).
- Faircloth BC. 2013. Illumiprocessor: a trimmomatic wrapper for parallel adapater and quality trimming. http://dx.doi. org/10.6079/J9ILL.
- Faircloth BC. 2016. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics (Oxford, England) 32: 786-788.
- Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717-726.
- Fretey T, Dewynter M, Ohler A. 2018. Onymotopes in zoological nomenclature: some additional terms, with fixation of a lectonymotope for Xenopus petersii Bocage, 1895 (Amphibia, Anura). Bionomina 13: 37-50.
- GrabherrMG,HaasBJ,YassourM,LevinJZ,ThompsonDA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology 29: 644-652.
- Gyldenstolpe N. 1930. On a new spine-tail from east Ecuador together with some notes on the forms of the Synallaxis rutilans -group. Arkiv for Zoologi 25: 1-20.
- Haffer J. 1969. Speciation in Amazonian forest birds. Science (New York, N.Y.) 165: 131-137.
- Hartert EJO. 1901. [Synallaxis omissa n sp.]. Bulletin of the British Ornithologists' Club 11: 71.
- Harvey MG, Aleixo A, Ribas CC, Brumfield RT. 2017. Habitat association predicts genetic diversity and population divergence in amazonian birds. The American Naturalist 190: 631-648.
- Hellmayr CE. 1907. Another contribution to the ornithology of the lower Amazonas. Novitates Zoologicae 14: 1-38.
- Horandl E. 2010. Beyond cladistics: Extending evolutionary classifications into deeper time levels. Taxon 59: 345-350.
- ICZN. 1999. International code of zoological nomenclature. London : The International Trust for Zoological Nomenclature.
- Irestedt M, Fjeldsa J, Dalen L, Ericson PG. 2009. Convergent evolution, habitat shifts and variable diversification rates in the ovenbird-woodcreeper family (Furnariidae). BMC Evolutionary Biology 9: 268.
- Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A. 2012. Geneious Basic:an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England) 28: 1647-1649.
- Lanfear R, Frandsen PB, Wright AM, Senfeld T, Calcott B. 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34: 772-773.
- LeCroy M, Sloss R. 2000. Type specimens of birds in the American Museum of Natural History.Part 3: Passeriformes: Eurylaimidae, Dendrocolaptidae, Furnariidae, Formicariidae, Conopophagidae and Rhinocryptidae.Bulletin of the American Museum of Natural History 257: 1-88.
- Maia R , Eliason CM , Bitton PP , Doucet SM , Shawkey YMD. 2013. Pavo: an R package for the analysis, visualization and organization of spectral data. Methods in Ecology and Evolution 4: 906-913.
- Mayr E. 1931. Notes on Halcyon chloris and some of its subspecies. American Museum Novitates 469: 1-10.
- Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209-220.
- McKay BD, Mays HL Jr, Yao CT, Wan D, Higuchi H, Nishiumi I. 2014. Incorporating color into integrative taxonomy: analysis of the varied tit (Sittiparus varius) complex in East Asia. Systematic Biology 63: 505-517.
- Naka LN, Brumfield RT. 2018. The dual role of Amazonian rivers in the generation and maintenance of avian diversity. Science Advances 4: eaar8575.
- Ohlson JI, Irestedt M, Ericson PG, Fjeldsa J. 2013. Phylogeny and classification of the New World suboscines (Aves, Passeriformes). Zootaxa 3613: 1-35.
- Padial JM, Miralles A, De la Riva I, Vences M. 2010. The integrative future of taxonomy. Frontiers in Zoology 7: 16.
- Papavero N, Overal WL, Teixeira DM, Hinshaw J. 2008. The travels of Joseph Beal Steere in Brazil, Peru and Ecuador (1870-1873). Arquivos de Zoologia 39: 87-269.
- Paynter RA Jr. 1982. Ornithological gazetteer of Venezuela. Cambridge: Harvard University Press.
- Paynter RA Jr. 1997. Ornithological gazetteer of Colombia. Cambridge: Harvard University Press.
- Paynter RA Jr, Traylor MA. 1991. Ornithological gazetteer of Brazil. Cambridge: Harvard University Press.
- Peters JL. 1951. Check-list of birds of the world, Vol. VII. Cambridge: Harvard University Press.
- Pinto OMO. 1979. A ornitologia do Brasil atraves das idades. Seculo XVI a seculo XIX, Vol. XIII. Sao Paulo: Empresa Grafica da Revista dos Tribunais (Brasiliensia Documenta).
- Proctor NS, Lynch PJ. 1993. Manual of ornithology: avian structure and function. New Haven and London: Yale University Press.
- QGIS Development Team. 2014 . QGIS Geographic Information System. Open Source Geospatial Foundation Project. https://qgis.org.
- Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. 2018. Posterior summarization in bayesian phylogenetics using Tracer 1.7. Systematic Biology 67: 901-904.
- Raposo MA, Kirwan GM. 2017. What lies beneath the controversy as to the necessity of physical types for describing new species? Bionomina 12: 52-56.
- Raposo MA, Stopiglia R, Brito GRR, Bockman FA, Kirwan GM, Gayon J, Dubois A. 2017. What really hampers taxonomy and conservation? A riposte to Garnett and Christidis (2017). Zootaxa 4317: 179-184.
- Remsen JV Jr. 2003. Family Furnariidae (ovenbirds). In: del Hoyo J, Elliott A, Christie DA, eds. Handbook of the birds of the world, Vol. 8: Broadbills to Tapaculos. Barcelona: Lynx Edicions, 162-357.
- Ribas CC, Aleixo A, Nogueira AC, Miyaki CY, Cracraft J. 2012. A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years. Proceedings of the Royal Society B. Biological Sciences 279: 681-689.
- Ribas CC, Aleixo A, Gubili C, d'Horta FM, Brumfield RT, Cracraft J. 2018. Biogeography and diversification of Rhegmatorhina (Aves: Thamnophilidae): implications for the evolution of Amazonian landscapes during the Quaternary. Journal of Biogeography 45: 917-928.
- Ridgely RS, Tudor G. 1994. The birds of South America, Vol. 2. Austin: University of Texas Press.
- Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542.
- Silva JMC, Rylands AB, Fonseca GAB. 2005. The fate of the Amazonian Areas of Endemism. Conservation Biology 19: 689-694.
- Silva SM, Peterson AT, Carneiro L, Burlamaqui TCT, Ribas CC, Sousa-Neves T, Miranda LS, Fernandes AM, d'Horta FM , Araujo-Silva LE , Batista R , Bandeira CHMM, Dantas SM, Ferreira M, Martins DM, Oliveira J, Rocha TC, Sardelli CH, Thom G, Rego PS, Santos MP, Sequeira F, Vallinoto M, Aleixo A. 2019. A dynamic continental moisture gradient drove Amazonian bird diversification. Science Advances 5: eaat5752.
- Simpson GG. 1961. Principles of animal taxonomy. New York: Columbia University Press.
- Smith BT, McCormack JE, Cuervo AM, Hickerson MJ, Aleixo A, Cadena CD, Perez-Eman J, Burney CW, Xie X, Harvey MG, Faircloth BC, Glenn TC, Derryberry EP, Prejean J, Fields S, Brumfield RT. 2014. The drivers of tropical speciation. Nature 515: 406-409.
- Smithe FB. 1974. Naturalist's color guide. New York:American Museum of Natural History.
- Smithe FB. 1981. Naturalist's color guide. New York:American Museum of Natural History.
- Sorenson MD, Ast JC, Dimcheff DE, Yuri T, Mindell DP. 1999. Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates. Molecular Phylogenetics and Evolution 12: 105-114.
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England) 30: 1312-1313.
- StatSoft Inc. 2013. STATISTICA (Data Analysis Software System), v.12. version 12.
- Stephens L, Traylor MA. 1983. Ornithological gazetteer of Peru. Cambridge: Harvard University Press.
- Stephens L, Traylor MA. 1985. Ornithological gazetteer of the Guianas. Cambridge: Harvard University Press.
- 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.
- Temminck CJ. 1823. Nouveau recueil de planches coloriees d'oiseaux : pour servir de suite et de complement aux planches enluminees de Buffon, edition in-folio et in-40 de l'Imprimerie royale, 1770. Paris: F. G. Levrault, Livr. 38, 227 pl.
- Thom G, Amaral FR do, Hickerson MJ, Aleixo A, Araujo-Silva LE, Ribas CC, Choueri E, Miyaki CY. 2018. Phenotypic and genetic structure support gene flow generating gene tree discordances in an Amazonian Floodplain Endemic Species. Systematic Biology 67: 700- 718. http://dx.doi.org/doi.org/10.1093/sysbio/syy004
- Tobias JA, Seddon N, Spottiswoode CN, Pilgrim JD, Fishpool LDC, Collar NJ. 2010. Quantitative criteria for species delimitation. Ibis 152: 724-746.
- Tobias JA, Cornwallis CK, Derryberry EP, Claramunt S, Brumfield RT, Seddon N. 2014. Species coexistence and the dynamics of phenotypic evolution in adaptive radiation. Nature 506: 359-363.
- Vanzolini PE. 1992. A supplement to the Ornithological gazetteer of Brazil. Sao Paulo: Museu de Zoologia da Universidade de Sao Paulo.
- Vaurie C. 1965. Systematic notes on the bird family Cracidae, No. 3. Ortalis guttata, Ortalis superciliaris and Ortalis motmot. American Museum Novitates 2232: 1-21.
- Vaurie C. 1967. Systematic notes on the bird family Cracidae. No. 10. The genera Mitu and Pauxi and the generic relationships of the Cracini. American Museum Novitates 2307: 1-20.
- Vaurie C. 1980. Taxonomy and geographical distribution of the Furnariidae (Aves, Passeriformes). Bulletin of the American Museum of Natural History 166: 1-357.
- Wang X, Edwards RL, Auler AS, Cheng H, Kong X, Wang Y, Cruz FW, Dorale JA, Chiang H-W. 2017. Hydroclimate changes across the Amazon lowlands over the past 45,000 years. Nature 541: 204-207.
- Weir JT, Schluter D. 2008. Calibrating the avian molecular clock. Molecular Ecology 17: 2321-2328.
- Wiley RH. 2010. Alfonso Olalla and his family: the ornithological exploration of Amazonian Peru. Bulletin of the American Museum of Natural History 343: 1-68.
- Will KW, Mishler BD, Wheeler QD. 2005. The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54: 844-851.
- Zamudio KR, Bell RC, Mason NA. 2016. Phenotypes in phylogeography: species' traits, environmental variation, and vertebrate diversification. Proceedings of the National Academy of Sciences of the United States of America 113: 8041-8048.
- Zimmer JT. 1935. Studies of Peruvian birds. XVIII. Diagnoses of new species and subspecies of Furnariidae from Peru and other parts of South America. American Museum Novitates 819: 1-8.