1
|
Sin SYW, Ke F, Chen G, Huang PY, Enbody ED, Karubian J, Webster MS, Edwards SV. Genetic Basis and Evolution of Structural Color Polymorphism in an Australian Songbird. Mol Biol Evol 2024; 41:msae046. [PMID: 38415852 PMCID: PMC10962638 DOI: 10.1093/molbev/msae046] [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: 11/13/2023] [Revised: 02/02/2024] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Island organisms often evolve phenotypes divergent from their mainland counterparts, providing a useful system for studying adaptation under differential selection. In the white-winged fairywren (Malurus leucopterus), subspecies on two islands have a black nuptial plumage whereas the subspecies on the Australian mainland has a blue nuptial plumage. The black subspecies have a feather nanostructure that could in principle produce a blue structural color, suggesting a blue ancestor. An earlier study proposed independent evolution of melanism on the islands based on the history of subspecies divergence. However, the genetic basis of melanism and the origin of color differentiation in this group are still unknown. Here, we used whole-genome resequencing to investigate the genetic basis of melanism by comparing the blue and black M. leucopterus subspecies to identify highly divergent genomic regions. We identified a well-known pigmentation gene ASIP and four candidate genes that may contribute to feather nanostructure development. Contrary to the prediction of convergent evolution of island melanism, we detected signatures of a selective sweep in genomic regions containing ASIP and SCUBE2 not in the black subspecies but in the blue subspecies, which possesses many derived SNPs in these regions, suggesting that the mainland subspecies has re-evolved a blue plumage from a black ancestor. This proposed re-evolution was likely driven by a preexisting female preference. Our findings provide new insight into the evolution of plumage coloration in island versus continental populations, and, importantly, we identify candidate genes that likely play roles in the development and evolution of feather structural coloration.
Collapse
Affiliation(s)
- Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fushi Ke
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Guoling Chen
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Pei-Yu Huang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Erik D Enbody
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, USA
| | - Michael S Webster
- Cornell Lab of Ornithology and Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| |
Collapse
|
2
|
Jiang B, Zhang J, Bai X, Zhang Y, Yao Y, Li J, Yu G, He S, Sun Y, Mikolajewski DJ. Genetic variation and population structure of a widely distributed damselfly (Ischnura senegalensis). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-14. [PMID: 37032456 DOI: 10.1002/arch.22015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Ischnura senegalensis Rambur, 1842 is among the most widespread damselfly species in the world. Unlike dragonflies with strong migration abilities, I. senegalensis have limited dispersing abilities. Gene flow among I. senegalensis populations may be greatly influenced by anthropogenic disturbance, fragmented suitable habitats, sea straits, or even global warming. In this study, to investigate the genetic diversity of I. senegalensis populations, we sequenced and collected 498 cytochrome oxidase I sequences across the Old World. Haplotype network analysis showed 51 haplotypes and I. senegalensis could be grouped into four regions (Afrotropical region, Oriental region, main Islands of Japan, and the Ryukyu Islands), each of which contains different dominant haplotypes. Based on molecular variance analysis, we found that populations from the Afrotropical region have quite a low gene flow with the Asian populations (except Yemen). Furthermore, rice cultivation may aid the dispersion of I. senegalensis in the oriental region. Populations from the Ryukyu Islands show the highest genetic diversity, which may be due to the geological separation among islands. Our results prove that I. senegalensis has great genetic diversity among different populations across the world.
Collapse
Affiliation(s)
- Bin Jiang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jiang Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Xinrui Bai
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yongmei Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yu Yao
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jia Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Guozhi Yu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Shulin He
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yang Sun
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
| | | |
Collapse
|
3
|
Campagna L, Mo Z, Siepel A, Uy JAC. Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species. PLoS Genet 2022; 18:e1010474. [PMID: 36318577 PMCID: PMC9624418 DOI: 10.1371/journal.pgen.1010474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies. Chestnut-bellied Monarchs (Monarcha castaneiventris ugiensis) from two archipelagos in the Solomon Islands have evolved entirely black plumage from a chestnut ancestor (Monarcha castaneiventris megarhynchus), a phenomenon known as island melanism. We obtain and analyze whole genome sequences using traditional summary statistics and new methods that combine inference of the ancestral recombination graph with machine learning. We find multiple lines of evidence for independent selective sweeps on the MC1R and ASIP genes, a receptor/ligand pair which regulates the production of melanin. Melanism on each archipelago is mediated by mutations in one of these two genes. Mutations in and around MC1R underwent a recent soft sweep experiencing strong selection on the islands of Santa Ana and Santa Catalina, whereas selection was also strong but comparatively older for ASIP on the island of Ugi. We show how melanism originated under positive selection on independent molecular targets, evolving convergently in taxa where coloration mediates reproductive isolation.
Collapse
Affiliation(s)
- Leonardo Campagna
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, United States of America
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (LC); (JACU)
| | - Ziyi Mo
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - J. Albert C. Uy
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (LC); (JACU)
| |
Collapse
|
4
|
Enbody ED, Sin SYW, Boersma J, Edwards SV, Ketaloya S, Schwabl H, Webster MS, Karubian J. The evolutionary history and mechanistic basis of female ornamentation in a tropical songbird. Evolution 2022; 76:1720-1736. [PMID: 35748580 PMCID: PMC9543242 DOI: 10.1111/evo.14545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 01/22/2023]
Abstract
Ornamentation, such as the showy plumage of birds, is widespread among female vertebrates, yet the evolutionary pressures shaping female ornamentation remain uncertain. In part this is due to a poor understanding of the mechanistic route to ornamentation in females. To address this issue, we evaluated the evolutionary history of ornament expression in a tropical passerine bird, the White-shouldered Fairywren, whose females, but not males, strongly vary between populations in occurrence of ornamented black-and-white plumage. We first use phylogenomic analysis to demonstrate that female ornamentation is derived and that female ornamentation evolves independently of changes in male plumage. We then use exogenous testosterone in a field experiment to induce partial ornamentation in naturally unornamented females. By sequencing the transcriptome of experimentally induced ornamented and natural feathers, we identify genes expressed during ornament production and evaluate the degree to which female ornamentation in this system is associated with elevated testosterone, as is common in males. We reveal that some ornamentation in females is linked to testosterone and that sexes differ in ornament-linked gene expression. Lastly, using genomic outlier analysis we identify a candidate melanogenesis gene that lies in a region of high genomic divergence among populations that is also differentially expressed in feather follicles of different female plumages. Taken together, these findings are consistent with sex-specific selection favoring the evolution of female ornaments and demonstrate a key role for testosterone in generating population divergence in female ornamentation through gene regulation. More broadly, our work highlights similarities and differences in how ornamentation evolves in the sexes.
Collapse
Affiliation(s)
- Erik D. Enbody
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana70118,Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSE‐75123Sweden
| | - Simon Y. W. Sin
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusetts02138,School of Biological SciencesThe University of Hong KongPok Fu Lam RoadHong Kong
| | - Jordan Boersma
- School of Biological Sciences, Center for Reproductive BiologyWashington State UniversityPullmanWashington99164,Department of Neurobiology and BehaviorCornell UniversityIthacaNew York14853,Macaulay LibraryCornell Lab of OrnithologyIthacaNew York14850
| | - Scott V. Edwards
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusetts02138
| | - Serena Ketaloya
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana70118
| | - Hubert Schwabl
- School of Biological Sciences, Center for Reproductive BiologyWashington State UniversityPullmanWashington99164
| | - Michael S. Webster
- Department of Neurobiology and BehaviorCornell UniversityIthacaNew York14853,Macaulay LibraryCornell Lab of OrnithologyIthacaNew York14850
| | - Jordan Karubian
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLouisiana70118
| |
Collapse
|
5
|
Robert A, Peona V, Ottenburghs J. Digest: Population genomics reveals convergence toward melanism in different island populations. Evolution 2021; 75:1582-1584. [PMID: 33905142 DOI: 10.1111/evo.14242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/19/2021] [Indexed: 11/28/2022]
Abstract
Distinct traits between mainland and island populations provide an excellent opportunity to study the evolution and genetic basis of these traits. In this issue, Walsh et al. unraveled the evolution of black plumage color that arose independently in two island populations of the white-winged fairywren. They also described the first steps in understanding the genetic underpinnings of this trait.
Collapse
Affiliation(s)
- Aloïs Robert
- Department of Ecology and Evolutionary Biology, Environmental Science, Center (ESC), Yale University, New Haven, Connecticut, 06511
| | - Valentina Peona
- Department of Ecology and Genetics-Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden.,Department of Organismal Biology-Systematic Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Jente Ottenburghs
- Department of Ecology and Genetics-Evolutionary Biology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Karolinska Institute, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| |
Collapse
|