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Long KM, Rivera-Colón AG, Bennett KFP, Catchen JM, Braun MJ, Brawn JD. Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone. Evolution 2024; 78:1539-1553. [PMID: 38753474 DOI: 10.1093/evolut/qpae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.
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Affiliation(s)
- Kira M Long
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Jeffrey D Brawn
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Porzio NS, Crottini A, Leite RN, Mota PG. Song determined by phylogeny and body mass in two differently constrained groups of birds: manakins and cardinals. BMC Ecol Evol 2024; 24:109. [PMID: 39160456 PMCID: PMC11331619 DOI: 10.1186/s12862-024-02298-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/01/2024] [Indexed: 08/21/2024] Open
Abstract
The songs of birds are complex signals that may have several functions and vary widely among species. Different ecological, behavioural and morphological factors, as well as phylogeny, have been associated as predictors of the evolution of song structure. However, the importance of differences in development, despite their relevance, has seldom been considered. Here, we analysed the evolution of song in two families of songbirds that differ in song development, manakins (suboscines) and cardinals (oscines), with their phylogeny, morphology, and ecology. Our results show that song characteristics had higher phylogenetic signal in cardinals than in manakins, suggesting higher evolutionary lability in the suboscines. Body mass was the main predictor of song parameters in manakins, and together with habitat type, had a major effect on cardinals' song structure. Precipitation and altitude were also associated with some song characteristics in cardinals. Our results bring unexpected insights into birdsong evolution, in which non-learners (manakins) revealed greater evolutionary lability than song learners (cardinals).
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Affiliation(s)
- Natália S Porzio
- Departamento de Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade de Coimbra, 3000-456, Coimbra, Portugal.
- CIBIO, Centro de Investigação Em Biodiversidade E Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal.
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.
| | - Angelica Crottini
- CIBIO, Centro de Investigação Em Biodiversidade E Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade Do Porto, Rua Do Campo Alegre S/N, 4169- 007, Porto, Portugal
| | - Rafael N Leite
- Graduate Program in Genetics, Conservation and Evolutionary Biology, National Institute for Amazonian Research, Manaus, AM, Brazil
| | - Paulo G Mota
- Departamento de Ciências da Vida, Faculdade de Ciências E Tecnologia, Universidade de Coimbra, 3000-456, Coimbra, Portugal
- CIBIO, Centro de Investigação Em Biodiversidade E Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade Do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
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Abstract
The process by which new complex traits evolve has been a persistent conundrum throughout the history of evolutionary inquiry. How multiple physiological changes at the organism level and genetic changes at the molecular level combine is still unclear for many traits. Here, we studied the displays of manakins, who beat their wings together at nearly twice the speed of other songbirds to produce a loud “snap” that attracts mates. We simultaneously analyzed evolution of gene expression levels and gene sequences to identify key genes related to muscle contractions and tissue regeneration after stress. Our results show how innovative behavioral traits evolve as a layered process where recent molecular shifts build on ancestral genetic evolutionary changes. Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized “superfast” muscles to generate a “snap” that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.
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White ND, Batz ZA, Braun EL, Braun MJ, Carleton KL, Kimball RT, Swaroop A. A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution. Mol Ecol Resour 2021; 22:587-601. [PMID: 34652059 DOI: 10.1111/1755-0998.13496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 11/27/2022]
Abstract
The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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Affiliation(s)
- Noor D White
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA
| | - Zachary A Batz
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA.,Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Karen L Carleton
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, Maryland, USA.,Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Anand Swaroop
- Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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Alfonso C, Jones BC, Vernasco BJ, Moore IT. Integrative Studies of Sexual Selection in Manakins, a Clade of Charismatic Tropical Birds. Integr Comp Biol 2021; 61:1267-1280. [PMID: 34251421 DOI: 10.1093/icb/icab158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/07/2021] [Accepted: 07/07/2021] [Indexed: 11/14/2022] Open
Abstract
The neotropical manakins (family Pipridae) provide a great opportunity for integrative studies of sexual selection as nearly all of the 51 species are lek-breeding, an extreme form of polygyny, and highly sexually dimorphic both in appearance and behavior. Male courtship displays are often elaborate and include auditory cues, both vocal and mechanical, as well as visual elements. In addition, the displays are often extremely rapid, highly acrobatic, and, in some species, multiple males perform coordinated displays that form the basis of long-term coalitions. Male manakins also exhibit unique neuroendocrine, physiological, and anatomical adaptations to support the performance of these complex displays and the maintenance of their intricate social systems. The Manakin Genomics Research Coordination Network (Manakin RCN, https://www.manakinsrcn.org) has brought together researchers (many in this symposium and this issue) from across disciplines to address the implications of sexual selection on evolution, ecology, behavior, and physiology in manakins. The objective of this paper is to present some of the most pertinent and integrative manakin research as well as introducing the papers presented in this issue. The results discussed at the manakin symposium, part of the 2021 Society for Integrative and Comparative Biology Conference, highlight the remarkable genomic, behavioral, and physiological adaptations as well as the evolutionary causes and consequences of strong sexual selection pressures that are evident in manakins.
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Affiliation(s)
- Camilo Alfonso
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Blake C Jones
- Science and Mathematics, Bennington College, 1 College Dr., Bennington, VT 05201, USA
| | - Ben J Vernasco
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Ignacio T Moore
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA
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Bennett KFP, Lim HC, Braun MJ. Sexual selection and introgression in avian hybrid zones: Spotlight on Manacus. Integr Comp Biol 2021; 61:1291-1309. [PMID: 34128981 DOI: 10.1093/icb/icab135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.
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Affiliation(s)
- Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University, Manassas, VA, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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