Published October 29, 2021 | Version v1
Journal article Restricted

A new genus and species of tanager (Passeriformes, Thraupidae) from the lower Yungas of western Bolivia and southern Peru

Description

Lane, D. F., Justiniano, M. A. A., Terrill, R. S., Rheindt, F. E., Klicka, L. B., Rosenberg, G. H., Schmitt, C. J., Burns, K. J. (2021): A new genus and species of tanager (Passeriformes, Thraupidae) from the lower Yungas of western Bolivia and southern Peru. Ornithology 138 (4): 1-17, DOI: 10.1093/ornithology/ukab059

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FFA6E3514215A003FE124A669D129A17
URL
http://publication.plazi.org/id/FFA6E3514215A003FE124A669D129A17

References

  • Barker, F. K., K. J. Burns, J. Klicka, S. M. Lanyon, and I. J. Lovette (2013). Going to extremes: Contrasting rates of diversification in a recent radiation of New World passerine birds. Systematic Biology 62:298-320.
  • Bates, J. M. (2006). The seasonal movements of southern populations of Dull-colored Grassquit (Tiaris obscura obscura). Bulletin of the British Ornithologists' Club 126:50-53.
  • Bolger, A. M., M. Lohse, and B. Usadel (2014). Trimmomatic: Aflexible trimmer for Illumina Sequence Data. Bioinformatics 30:2114-2120.
  • Burns,K.J.(1997).Molecular systematics of tanagers (Thraupinae): Evolution and biogeography of a diverse radiation of Neotropical birds. Molecular Phylogenetics and Evolution 8:334-348.
  • Burns, K. J., and R. A. Racicot (2009). Molecular phylogenetics of a clade of lowland tanagers: Implications for avian participation in the great American interchange. The Auk 126:635-648.
  • Burns, K. J., A. J. Schultz, P. O. Title, N. A. Mason, F. K. Barker, J. Klicka, S. M. Lanyon, and I. J. Lovette (2014). Phylogenetics and diversification of tanagers (Passeriformes: Thraupidae), the largest radiation of Neotropical songbirds. Molecular Phylogenetics and Evolution 75:41-77.
  • Burns, K. J., P. Unitt, and N. A. Mason (2016). Agenus-level classification of the family Thraupidae (Class Aves: Order Passeriformes). Zootaxa 4088:329-354.
  • Castresana, J. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17:540-552.
  • Cayola, L., A. Fuentes, and P. M. JOrgensen (2005). Estructura y composicionfloristicadeunbosquesecosubandinoyungueno en elvalle del Tuichi, Area Natural de Manejo Integrado Madidi, La Paz (Bolivia). Ecologia en Bolivia 40:396-417.
  • Chifman, J., and L. Kubatko. (2014). Quartet inference from SNP data under the coalescent model. Bioinformatics 30:3317-3324.
  • Clements, J. F., T. S. Schulenberg, M. J. Iliff, S. M. Billerman, T. A. Fredericks, B. L. Sullivan, and C. L. Wood (2019). The eBird/ Clements Checklist of Birds of the World: v2019. https://www. birds.cornell.edu/clementschecklist/download/
  • Del Fabbro, C., S. Scalabrin, M. Morgante, and F. M. Giorgi (2013). An extensive evaluation of read trimming effects on Illumina NGS data analysis. PLoS One 8:e85024.
  • Degnan, J. H., and L. A. Salter. (2005). Gene tree distributions under the coalescent process. Evolution 59:24-37.
  • Degnan, J. H., and N. A. Rosenberg. (2006). Discordance of species trees with their most likely gene trees. PLOS Genetics 2:e68.
  • Demery, A.-J. C., K. J. Burns, and N. A. Mason (2021). Bill size, bill shape, and body size constrain bird song evolution on a macroevolutionary scale. Ornithology 138:ukab011. https:// doi.org/10.1093/ornithology/ukab011
  • Drummond, A. J., and A. Rambaut (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7:214.
  • Faircloth, B. C. (2013). illumiprocessor: Atrimmomatic wrapper for parallel adapter and quality trimming. http://dx.doi. org/10.6079/J9ILL.
  • Faircloth, B. C. (2016). PHYLUCE is a software package for the analysis of conservedgenomic loci.Bioinformatics 32:786-788.
  • Faircloth, B. C., J. E. McCormack, N. G. Crawford, M. G. Harvey, R. T. Brumfield, and T. C. Glenn (2012). Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61:717-726.
  • Glenn, T. C., R. A. Nilsen, T. J. Kieran, J. G. Sanders, N. J. Bayona-Vasquez, J. W. Finger, T.W. Pierson, K. E. Bentley, S. L. Hoffberg, Louha S., F. J. Garcia-De Leon, M. A. del Rio Portilla, et al. (2019). Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorically indexed Illumina libraries (iTru & iNext). PeerJ 7:e7755
  • Grabherr, M. G., B. J. Haas, M. Yassour, J. Z. Levin, D. A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, Q. Zeng et al. (2011). Trinity: Reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nature Biotechnology 29:644-652.
  • Hackett, S. J. (1996). Molecular phylogenetics and biogeography of tanagers in the genus Ramphocelus (Aves). Molecular Phylogenetics and Evolution 5:368-382.
  • Harvey,M. G., D.F.Lane,J.Hite, R. S.Terrill,S.Figueroa R., B.T.Smith, J. Klicka, and W. Vargas C. (2014). Notes on bird species in bamboo in northern Madre de Dios, Peru, including the first Peruvian record of Acre Tody-Tyrant (Hemitriccus cohnhafti). Occasional Papers of the Louisiana State University Museum of Natural Science 81:1-38.
  • Hijmans, R. J., S. Cameron, J. Parra, P. Jones, A. Jarvis, and K. Richardson (2005). WorldClim, version 1.3. University of California, Berkeley, CA, USA. https://www.worldclim.org/ data/worldclim21.html
  • Hijmans, R. J., S. Phillips, J. Leathwick, J. Elith, and M. R. J. Hijmans (2017). Package "dismo". Circles 9:1-68.
  • Hilty, S. L. (2011). Family Thraupidae (tanagers). In Handbook of the Birds of the World,vol. 16 (J.del Hoyo,A.Elliott, and D.A.Christie, Editors). Lynx Edicions, Barcelona, Spain. pp. 46-329
  • Isler, M. L., and P. R. Isler (1987). The Tanagers: Natural History, Distribution, and Identification. Smithsonian Institution Press, Washington, D.C., USA.
  • Johnson, E. I., P. C. Stouffer, and R. O. Beirregaard, Jr. (2012). The phenology of molt, breeding and their overlap in central Amazonian birds. Journal of Avian Biology 43:141-154.
  • Katoh, K., and D. M. Standley (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30:772-780.
  • Kessler, M., and M. Helme (1999). Floristic diversity and phytogeography of the central Tuichi Valley, and isolated dry forest locality in the Bolivian Andes. Candollea 54:341-366.
  • Lanfear, R., B. Calcott, S. Y. W. Ho, and S. Guindon (2012). PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29:1695-1701.
  • Larkin, M. A. (2007). ClustalW and ClustalX version 2.0. Bioinformatics 23:2947-2948.
  • Lobo-y-Henriques, J. C., Y., J. Bates, and D. Willard (2012). First record for the Black-and-white Tanager (Conothraupis speculigera) in Colombia. Conservacion Colombiana 17:45-51.
  • Lohse, M., A. M. Bolger, A. Nagel, A. R. Fernie, J. E. Lunn, M. Stitt, and B. Usadel. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research 40:622-627.
  • Lowery, G. H., Jr., and J. P. O'Neill (1964). Anew genus and species of tanager from Peru.The Auk 81:125-131.
  • Lowery, G. H., Jr., and D. A. Tallman (1976). Anew genus and species of nine-primaried oscine of uncertain affinities from Peru.The Auk 93:415-428.
  • Maddison, W., and D. Maddison (2010). MESQUITE: Amodular system for evolutionary analysis, version 2.6. mesquiteproject. org
  • Mason, N. A., and K. J. Burns (2015). The effect of habitat and body size on the evolution of vocal displays in Thraupidae (tanagers), the largest family of songbirds. Biological Journal of the Linnean Society 114:538-551.
  • Mauck, W. M., and K. J. Burns (2009). Phylogeny, biogeography, and recurrent evolution of divergent bill types in the nectarstealing flowerpiercers (Thraupini: Diglossa and Diglossopis). Biological Journal of the Linnean Society 98:14-28.
  • Mirarab, S., R. Reaz, M. S. Bayzid, T. Zimmermann, M. S. Swenson, and T. Warnow. (2014). ASTRAL: genome-scale coalescentbased species tree estimation. Bioinformatics 30:i541-i548.
  • Munsell. [No date]. The Munsell book of color. Gretag Macbeth LLC; New Britain, NY, USA.
  • Neudorf, D. L., and P. J. Blanchfield (1994). The Slate-colored Seedeater (Sporophila schistacea): Abamboo specialist? Ornitologia Neotropical 5:129-132.
  • O'Neill, J. P. (1966). Notes on the distribution of Conothraupis speculigera (Gould).The Condor 68:598-600.
  • Pamilo, P., and M. Nei (1988). Relationships between gene trees and species trees. Molecular Biology and Evolution 5:568-583.
  • Parker, T. A., III (1982). Observations of some unusual rainforest and marsh birds of southeastern Peru. The Wilson Bulletin 94:477-493.
  • Parker, T. A., III, and B. Bailey (Editors) (1991). A Biological Assessment of the Alto Madidi Region and Adjacent Areas of Northwest Bolivia, May l8-June 15, 1990. RAP Working Papers 1, Conservation International, Washington, D.C., USA.
  • Patterson, B. D., D. F. Stotz,and S. Solari (2006). Mammals and birds of the Manu Biosphere Reserve.Fieldiana Zoology 2006:110.https:// doi.org/10.3158/0015-0754(2006)110[1:MABOTM]2.0.CO;2
  • Patterson, B. D., D. F.Stotz,S. Solari, J.W. Fitzpatrick,and V. Pacheco (1998). Contrasting patterns of elevational zonation for birds and mammals in the Andes of southeastern Peru. Journal of Biogeography 25:593-607.
  • Pearman,M. (1993).The avifauna of the Rio Machariapodry forest, northern depto. La Paz, Bolivia: Apreliminary investigation. Bird Conservation International 3:105-117.
  • Perry, A., M. Kessler, and N. Helme (1997). Birds of the central Rio Tuichi Valley, with emphasis on dry forest, Parque Nacional Madidi, depto. La Paz, Bolivia. In Studies in Neotropical Ornithology Honoring Ted Parker (J. V. Remsen, Jr., Editor). American Ornithologist's Union, Washington (DC).
  • Piacentini, V., P. Unitt, and K. J. Burns (2019). Two overlooked generic synonyms in the Thraupidae (Aves: Passeriformes). Zootaxa 4608 (3): 593-594.
  • Posada, D. (2008). JModelTest: Phylogenetic model averaging. Molecular Biology and Evolution 25:1253-1256.
  • R Core Team (2019). R: Alanguage and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
  • Rambaut, A., and A. Drummond (2007). Tracer, v1.5. http://tree. bio.ed.ac.uk/software/tracer/
  • Rand, A. L. (1959).Tarsal scutellation of song birds as a taxonomic character.The Wilson Bulletin 71:274-277.
  • Reaz, R., M. S. Bayzid, and M. S. Rahman. (2014). Accurate phylogenetic tree reconstruction from quartets: Aheuristic approach. PLoS One 9:e104008.
  • Remsen, J. V., Jr., J. I. Areta, E. Bonaccorso, S. Claramunt, A. Jaramillo, J. F. Pacheco, M. B. Robbins, F. G. Stiles, D. F. Stotz, and K. J. Zimmer (2020). Aclassification of the bird species of South America. American Ornithological Society. http://www. museum.lsu.edu/~Remsen/SACCBaseline.htm
  • Sayyari E., and S. Mirarab. (2016). Fast coalescent-based computationof localbranch supportfromquartet frequencies. Molecular Biology and Evolution 33:1654-1668.
  • Shultz, A. J., and K. J. Burns (2013). Plumage evolution in relation to light environment in a novel clade of Neotropical tanagers. Molecular Phylogenetics and Evolution 66:112-125.
  • Shultz, A. J., and K. J. Burns. (2017). The role of sexual and natural selection in shaping patterns of sexual dichromatism in the largest family of songbirds (Aves: Thraupidae). Evolution 71:1061-1074.
  • Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312-1313.
  • Storer, R. W. (1970). Subfamilies Thraupinae and Tersininae. In Check-List of Birds of the World, vol. 13 (R. A. Paynter, Jr., Editor). Museum of Comparative Zoology, Cambridge, MA, USA. pp. 246-409.
  • Swofford, D. L. (1998). PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer, Sunderland, MA.
  • Talavera,G., and J.Castresana (2007).Improvementof phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56:564-577.
  • Terborgh, J. (1985). The role of ecotones in the distribution of Andean birds. Ecology 66:1237-1246.
  • Title, P. O., and K. J. Burns (2015). Rates of climatic niche evolution are correlated with species richness in a large and ecologically diverse radiation of songbirds. Ecology Letters 18:433-440.
  • Vallely, A. C., and D. Dyer (2018). Birds of Central America, Princeton University Press, Princeton, NJ, USA.
  • Vinciguerra, N. T., and K. J. Burns (2021). Species diversification and ecomorphological evolution in the radiation of tanagers (Passeriformes: Thraupidae). Biological Journal of the Linnean Society 133:3. https://doi.org/10.1093/ biolinnean/blab042
  • Walker, B., D. F. Stotz, T. Pequeno, and J. W. Fitzpatrick (2006). Birds of the Manu Biosphere Reserve. In Mammals and Birds of the Manu Biosphere Reserve, Peru (Patterson, B. D., D. F. Stotz, and S. Solari, Editors). Field Museum of Natural History, Chicago, IL, USA. Fieldiana Zoology 2006:110. pp. 23-49.
  • Witt, C. C. (2005). Syntopic breeding suggests mimicry of the Black-and-white Seedeater (Sporophila luctuosa) by the Blackand-white Tanager (Conothraupis speculigera). Ornitologia Neotropical 16:387-396.