1
|
Xu X, Wang C, Xu C, Yuan J, Wang G, Wu Y, Huang C, Jing H, Yang P, Xu L, Peng S, Shan F, Xia X, Jin F, Hou F, Wang J, Mi D, Ren Y, Liu Y, Irwin DM, Li X, Chen W, Li G. Genomic evolution of island birds from the view of the Swinhoe's pheasant (Lophura swinhoii). Mol Ecol Resour 2024; 24:e13896. [PMID: 37955396 DOI: 10.1111/1755-0998.13896] [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: 07/05/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/14/2023]
Abstract
Island endemic birds account for the majority of extinct vertebrates in the past few centuries. To date, the evolutionary characteristics of island endemic bird's is poorly known. In this research, we de novo assembled a high-quality chromosome-level reference genome for the Swinhoe's pheasant, which is a typical endemic island bird. Results of collinearity tests suggest rapid ancient chromosome rearrangement that may have contributed to the initial species radiation within Phasianidae, and a role for the insertions of CR1 transposable elements in rearranging chromosomes in Phasianidae. During the evolution of the Swinhoe's pheasant, natural selection positively selected genes involved in fecundity and body size functions, at both the species and population levels, which reflect genetic variation associated with island adaptation. We further tested for variation in population genomic traits between the Swinhoe's pheasant and its phylogenetically closely related mainland relative the silver pheasant, and found higher levels of genetic drift and inbreeding in the Swinhoe's pheasant genome. Divergent demographic histories of insular and mainland bird species during the last glacial period may reflect the differing impact of insular and continental climates on the evolution of species. Our research interprets the natural history and population genetic characteristics of the insular endemic bird the Swinhoe's pheasant, at a genome-wide scale, provides a broader perspective on insular speciation, and adaptive evolution and contributes to the genetic conservation of island endemic birds.
Collapse
Affiliation(s)
- Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yajiang Wu
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Haohao Jing
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Shiming Peng
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Fen Shan
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Xiaochao Xia
- Guangdong Wildlife Monitoring, Rescue and Conservation Center, Guangzhou, China
| | - Fuyuan Jin
- Guangdong Maoming Forest Park Administrative Office, Maoming, China
| | - Fanghui Hou
- Shanghai Wild Animal Park Development Co., Ltd, Shanghai, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Da Mi
- Xi'an Haorui Genomics Technology Co., Ltd, Xi'an, China
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yandong Ren
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou, China
- Guangzhou Collaborative Innovation Center on Science-Tech of Ecology and Landscape, Guangzhou, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
- Guangzhou Zoo, Guangzhou, China
| |
Collapse
|
2
|
Sherpa S, Paris JR, Silva‐Rocha I, Di Canio V, Carretero MA, Ficetola GF, Salvi D. Genetic depletion does not prevent rapid evolution in island-introduced lizards. Ecol Evol 2023; 13:e10721. [PMID: 38034325 PMCID: PMC10682264 DOI: 10.1002/ece3.10721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, and Pod Mrčaru), including the islet of Pod Mrčaru, where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated with a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.
Collapse
Affiliation(s)
- Stéphanie Sherpa
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Josephine R. Paris
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| | - Iolanda Silva‐Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
| | - Viola Di Canio
- Dipartimento di Scienze e Politiche AmbientaliUniversità degli Studi di MilanoMilanoItaly
| | - Miguel Angel Carretero
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- BIOPOLIS Program in Genomics, Biodiversity and Land PlanningCIBIOVairãoPortugal
- Departamento de Biologia, Faculdade de CiênciasUniversidade do PortoPortoPortugal
| | | | - Daniele Salvi
- Dipartimento di Medicina Clinica, Sanità Pubblica, Scienze della Vita e dell'AmbienteUniversità degli Studi dell'AquilaL'Aquila‐CoppitoItaly
| |
Collapse
|
4
|
McCullough JM, Oliveros C, Benz BW, Zenil-Ferguson R, Cracraft J, Moyle RG, Andersen MJ. Wallacean and Melanesian Islands Promote Higher Rates of Diversification within the Global Passerine radiation Corvides. Syst Biol 2022; 71:1423-1439. [PMID: 35703981 DOI: 10.1093/sysbio/syac044] [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: 11/12/2021] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/14/2022] Open
Abstract
The complex island archipelagoes of Wallacea and Melanesia have provided empirical data behind integral theories in evolutionary biology, including allopatric speciation and island biogeography. Yet, questions regarding the relative impact of the layered biogeographic barriers, such as deep-water trenches and isolated island systems, on faunal diversification remain underexplored. One such barrier is Wallace's Line, a significant biogeographic boundary that largely separates Australian and Asian biodiversity. To assess the relative roles of biogeographic barriers-specifically isolated island systems and Wallace's Line-we investigated the tempo and mode of diversification in a diverse avian radiation, Corvides (Crows and Jays, Birds-of-paradise, Vangas, and allies). We combined a genus-level dataset of thousands of ultraconserved elements (UCEs) and a species-level, 12-gene Sanger sequence matrix to produce a well-resolved supermatrix tree that we leveraged to explore the group's historical biogeography and effects of biogeographic barriers on their macroevolutionary dynamics. The tree is well-resolved and differs substantially from what has been used extensively for past comparative analyses within this group. We confirmed that Corvides, and its major constituent clades, arose in Australia and that a burst of dispersals west across Wallace's Line occurred after the uplift of Wallacea during the mid-Miocene. We found that dispersal across this biogeographic barrier were generally rare, though westward dispersals were two times more frequent than eastward dispersals. Wallacea's central position between Sundaland and Sahul no doubt acted as a bridge for island-hopping dispersal out of Australia, across Wallace's Line, to colonize the rest of Earth. In addition, we found that the complex island archipelagoes east of Wallace's Line harbor the highest rates of net diversification and are a substantial source of colonists to continental systems on both sides of this biogeographic barrier. Our results support emerging evidence that island systems, particularly the geologically complex archipelagoes of the Indo-pacific, are drivers of species diversification.
Collapse
Affiliation(s)
- Jenna M McCullough
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Carl Oliveros
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Brett W Benz
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Joel Cracraft
- Department of Ornithology, American Museum of Natural History, New York, NY, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | - Michael J Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
5
|
Lapiedra O, Sayol F, Garcia-Porta J, Sol D. Niche shifts after island colonization spurred adaptive diversification and speciation in a cosmopolitan bird clade. Proc Biol Sci 2021; 288:20211022. [PMID: 34465237 PMCID: PMC8437225 DOI: 10.1098/rspb.2021.1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/05/2021] [Indexed: 01/14/2023] Open
Abstract
Islands have long been recognized as key contributors to biodiversity because they facilitate geographic isolation and ecological divergence from mainland ancestors. However, island colonization has traditionally been considered an evolutionary dead-end process, and its consequences for continental biodiversity remain understudied. Here, we use the evolutionary radiation of Columbiformes (i.e. pigeons and doves) to examine if ecological niche shifts on islands shaped biological diversification and community composition on continents. We show that the colonization of islands by continental, terrestrial-foraging lineages led to the exploitation of a new ecological niche (i.e. arboreal foraging). This transition towards arboreal foraging was associated with evolutionary adaptation towards a new morphological optimum. In addition, arboreal-foraging lineages of islands experienced an increase in speciation rates, which was associated with successful range expansions to other islands as well as back colonization of continents. Our results provide empirical evidence that diversification on continents can only be fully understood when studying the diversification processes that took place on islands, challenging the view of islands as mere sinks of evolutionary diversity.
Collapse
Affiliation(s)
| | - Ferran Sayol
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Joan Garcia-Porta
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Daniel Sol
- CREAF, Cerdanyola del Vallès, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Catalonia, Spain
| |
Collapse
|