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Cueva D, Bravo GA, Silveira LF. Systematics of Thraupis (Aves, Passeriformes) reveals an extensive hybrid zone between T. episcopus (Blue-gray Tanager) and T. sayaca (Sayaca Tanager). PLoS One 2022; 17:e0270892. [PMID: 36197923 PMCID: PMC9534438 DOI: 10.1371/journal.pone.0270892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
The Neotropical avian genus Thraupis (Passeriformes, Thraupidae) currently comprises seven species that are widespread and abundant throughout their ranges. However, no phylogenetic hypothesis with comprehensive intraspecific sampling is available for the group and, therefore, currently accepted species limits remain untested. We obtained sequence data for two mitochondrial (ND2, cyt-b) and three non-coding nuclear (TGFB2, MUSK, and βF5) markers from 118 vouchered museum specimens. We conducted population structure and coalescent-based species-tree analyses using a molecular clock calibration. We integrated these results with morphometric and coloration analyses of 1,003 museum specimens to assess species limits within Thraupis. Our results confirm that Thraupis is a monophyletic group and support its origin in the late Miocene and subsequent diversification during the Pleistocene. However, we found conflicts with previous phylogenies. We recovered Thraupis glaucocolpa to be sister to all other species in the genus, and T. cyanoptera to the remaining five species. Our phylogenetic trees and population structure analyses uncovered phylogeographic structure within Thraupis episcopus that is congruent with geographic patterns of phenotypic variation and distributions of some named taxa. The first genetic and phenotypic cluster in T. episcopus occurs east of the Andes and is diagnosed by the white patch on the lesser and median wing coverts, whereas the second group has a blue patch on the wing and distributes to the west of Colombia's eastern Andes. Finally, we present evidence of hybridization and ongoing gene flow between several taxa at different taxonomic levels and discuss its taxonomic implications.
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Affiliation(s)
- Diego Cueva
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- * E-mail:
| | - Gustavo A. Bravo
- Museu de Zoologia da Universidade de São Paulo, São Paulo, SP, Brazil
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
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Turbek SP, Browne M, Di Giacomo AS, Kopuchian C, Hochachka WM, Estalles C, Lijtmaer DA, Tubaro PL, Silveira LF, Lovette IJ, Safran RJ, Taylor SA, Campagna L. Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater. Science 2021; 371:371/6536/eabc0256. [PMID: 33766854 DOI: 10.1126/science.abc0256] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022]
Abstract
Behavioral isolation can catalyze speciation and permit the slow accumulation of additional reproductive barriers between co-occurring organisms. We illustrate how this process occurs by examining the genomic and behavioral bases of pre-mating isolation between two bird species (Sporophila hypoxantha and the recently discovered S. iberaensis) that belong to the southern capuchino seedeaters, a recent, rapid radiation characterized by variation in male plumage coloration and song. Although these two species co-occur without obvious ecological barriers to reproduction, we document behaviors indicating species recognition by song and plumage traits and strong assortative mating associated with genomic regions underlying male plumage patterning. Plumage differentiation likely originated through the reassembly of standing genetic variation, indicating how novel sexual signals may quickly arise and maintain species boundaries.
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Affiliation(s)
- Sheela P Turbek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Melanie Browne
- Centro de Ecología Aplicada del Litoral (CECOAL, CONICET), Corrientes, Argentina
| | - Adrián S Di Giacomo
- Centro de Ecología Aplicada del Litoral (CECOAL, CONICET), Corrientes, Argentina
| | - Cecilia Kopuchian
- Centro de Ecología Aplicada del Litoral (CECOAL, CONICET), Corrientes, Argentina
| | - Wesley M Hochachka
- Center for Avian Population Studies, Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Cecilia Estalles
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN, CONICET), Buenos Aires, Argentina
| | - Darío A Lijtmaer
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN, CONICET), Buenos Aires, Argentina
| | - Pablo L Tubaro
- Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN, CONICET), Buenos Aires, Argentina
| | | | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Rebecca J Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Leonardo Campagna
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA. .,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, USA
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Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci U S A 2020; 117:30554-30565. [PMID: 33199636 DOI: 10.1073/pnas.2015987117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Numerous studies of emerging species have identified genomic "islands" of elevated differentiation against a background of relative homogeneity. The causes of these islands remain unclear, however, with some signs pointing toward "speciation genes" that locally restrict gene flow and others suggesting selective sweeps that have occurred within nascent species after speciation. Here, we examine this question through the lens of genome sequence data for five species of southern capuchino seedeaters, finch-like birds from South America that have undergone a species radiation during the last ∼50,000 generations. By applying newly developed statistical methods for ancestral recombination graph inference and machine-learning methods for the prediction of selective sweeps, we show that previously identified islands of differentiation in these birds appear to be generally associated with relatively recent, species-specific selective sweeps, most of which are predicted to be soft sweeps acting on standing genetic variation. Many of these sweeps coincide with genes associated with melanin-based variation in plumage, suggesting a prominent role for sexual selection. At the same time, a few loci also exhibit indications of possible selection against gene flow. These observations shed light on the complex manner in which natural selection shapes genome sequences during speciation.
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