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Duchêne DA, Chowdhury AA, Yang J, Iglesias-Carrasco M, Stiller J, Feng S, Bhatt S, Gilbert MTP, Zhang G, Tobias JA, Ho SYW. Drivers of avian genomic change revealed by evolutionary rate decomposition. Nature 2025; 641:1208-1216. [PMID: 40108459 PMCID: PMC12119353 DOI: 10.1038/s41586-025-08777-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/12/2025] [Indexed: 03/22/2025]
Abstract
Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change1-4, but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds5,6, we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.
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Affiliation(s)
- David A Duchêne
- Section of Health Data Science and AI, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Al-Aabid Chowdhury
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Jingyi Yang
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Maider Iglesias-Carrasco
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Doñana Biological Station-Spanish Research Council CSIC, Seville, Spain
| | - Josefin Stiller
- Centre for Biodiversity Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- Center for Evolutionary and Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China
| | - Samir Bhatt
- Section of Health Data Science and AI, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- MRC Centre for Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College London, London, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Guojie Zhang
- Center for Evolutionary and Organismal Biology, Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Hangzhou, China
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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2
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Romano A, Ambrosini R, Caprioli M, Costanzo A, Novelli A, Rubolini D. Shrinking body size under climate warming is not associated with selection for smaller individuals in a migratory bird. J Anim Ecol 2025; 94:958-970. [PMID: 40176260 PMCID: PMC12056357 DOI: 10.1111/1365-2656.70027] [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: 02/06/2024] [Accepted: 02/04/2025] [Indexed: 04/04/2025]
Abstract
How species are responding to climate change is a key topic in evolutionary ecology. Increasing temperatures are expected to affect phenotypic traits involved in thermoregulation, thus decreasing body size and/or increasing body appendages associated with heat exchange, as predicted by Bergmann's and Allen's rules. Results from long-term studies of variation in morphology over time have generally provided results supporting these predictions. However, two outstanding questions are frequently raised in studies relating changes in phenotypes to increasing temperatures: (1) whether such changes involve a shift in animal shape through the non-proportional variation of different body parts; and (2) whether they result from adaptive evolutionary responses. Relying on capture-recapture histories of almost 9000 breeding individuals from a declining Italian population of an Afro-Palearctic migratory bird, the barn swallow (Hirundo rustica), we documented a decrease in some body size traits (body mass, keel and wing length) over a 31-year period (1993-2023), with body mass declining the most (up to 4.0% in males). However, this was not the case for bill and partly tarsus length. Intra-individual lifelong changes in morphological traits of sexually mature birds showed only a limited contribution to trends over time in phenotypically plastic morphological traits. Viability and fecundity selection analyses revealed that smaller individuals did not enjoy greater success compared to larger ones. For some traits, the opposite was actually the case. The shifts in body size and, partly, shape over time we observed were coherent with predictions deriving from Bergmann's and Allen's rules. Yet, natural selection did not consistently favour smaller individuals. We thus call for caution in interpreting recent decreases in body size as adaptive evolutionary responses to climate warming, as they may rather reflect phenotypically plastic responses to changing climatic/environmental conditions occurring during early ontogenetic stages.
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Affiliation(s)
- Andrea Romano
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
| | - Roberto Ambrosini
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
| | - Manuela Caprioli
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
| | | | - Andrea Novelli
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
| | - Diego Rubolini
- Department of Environmental Science and PolicyUniversity of MilanMilanItaly
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Zhang M, Wang Y, Yang X, Yang Y, Yu F, Yi X. Global Avian Frugivore-Fruit Trait Matching Decreases Toward the Tropics. GLOBAL CHANGE BIOLOGY 2025; 31:e70180. [PMID: 40202823 DOI: 10.1111/gcb.70180] [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: 09/04/2024] [Revised: 02/15/2025] [Accepted: 03/21/2025] [Indexed: 04/11/2025]
Abstract
Trait matching, the phenomenon where ecological interactions are mediated by compatibility, constitutes a cornerstone of frugivore-fruit interaction network dynamics. Given that biotic interactions have long been hypothesized to be more intense or specialized in the tropics, the intensity of trait matching patterns might likewise exhibit a latitudinal gradient in frugivory networks, yet this remains unverified. Here, we established a dataset encompassing 200 avian frugivorous networks to explore the relationships between the body mass and gape size of frugivore birds and fruit traits (size and color) on a global scale. Our results indicated that frugivore traits were closely associated with fruit traits regardless of the climate, demonstrating a biotic match between the two counterparts. We detected a significant decrease in frugivore-fruit trait matching toward the tropics, which challenges prevailing concepts considering the high biodiversity therein. Our structural equation modeling clarified that latitude and temperature exert an indirect influence on trait matching by affecting gape size and fruit traits. These discoveries emphasize the impact of the latitudinal gradient of temperature in driving the observed patterns of trait matching. The weaker trait matching in tropical regions may suggest more complex interactions therein and also highlights the potential for altered network structures amid global climate change.
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Affiliation(s)
- Mingming Zhang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
- Henan Dabieshan National Field Observation and Research Station of Forest Ecosystem, Henan University, Zhengzhou, China
| | - Yang Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xifu Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Yueqin Yang
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Fei Yu
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Xianfeng Yi
- School of Life Sciences, Qufu Normal University, Qufu, China
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Aarif K, Zouhar J, Musilova Z, Musil P, Nefla A, Muzaffar S, Rubeena K. Bill Length of Non-breeding Shorebirds Influences the Water Depth Preferences for Foraging in the West Coast of India. Ecol Evol 2024; 14:e70396. [PMID: 39440208 PMCID: PMC11494249 DOI: 10.1002/ece3.70396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 10/25/2024] Open
Abstract
Body size, bill length and shape determine foraging techniques, habitat selection and diet among shorebirds. In this study, water depth preferences of different shorebirds with different bill sizes in various habitats including mudflats, mangroves at Kadalundi-Vallikkunnu Community Reserve (KVCR) (19 shorebird species) and adjacent agroecosystems at Vazhakkad (12 species) were studied between 2017 and 2020. The bill length of the shorebirds was significantly and positively associated with the average water depth, where shorebirds were observed to forage. Shorebirds with shorter bill lengths preferred shallow waters and those with longer bills preferred deep waters for their foraging activities. Habitat type also had a significant effect on the shorebird occurrence. Eurasian Curlews in both mangroves and mudflats were observed in areas with a higher water depth compared to other species. This is due to the fact that shorebirds tend to specialise in feeding habitats or in prey items to reduce intraspecific competition and distribute themselves in space and time in accordance with the availability of their resources. The occurrence of some species in agroecosystems is attributed to the reduced food availability, habitat quality and other disturbances for shorebirds on tidal flats, which are critical for sustaining migratory phenology. The differences in bill morphology are crucial in determining diet, water depth, niche preferences and segregation. Morphological characters and hydrological rhythms determine specialisation in diet and habitat preference in shorebirds.
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Affiliation(s)
- K. M. Aarif
- Department of Ecology, Faculty of Environmental SciencesCzech University of Life SciencesPraguePraha SuchdolCzechia
| | - Jan Zouhar
- Department of Ecology, Faculty of Environmental SciencesCzech University of Life SciencesPraguePraha SuchdolCzechia
| | - Zuzana Musilova
- Department of Ecology, Faculty of Environmental SciencesCzech University of Life SciencesPraguePraha SuchdolCzechia
| | - Petr Musil
- Department of Ecology, Faculty of Environmental SciencesCzech University of Life SciencesPraguePraha SuchdolCzechia
| | - Aymen Nefla
- Department of Biology, Faculty of Sciences of TunisUniversity of Tunis El Manar IITunisTunisia
| | - Sabir Bin Muzaffar
- Department of BiologyUnited Arab Emirates UniversityAl AinUAE
- Department of ScienceThe Natural History MuseumLondonUK
| | - K. A. Rubeena
- Centre for Environment and Marine Studies, Research & InnovationKing Fahd University of Petroleum & MineralsDhahranSaudi Arabia
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5
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Xu Y, Price M, Que P, Zhang K, Sheng S, He X, Wen Z, Wang B. Ecological predictors of interspecific variation in bird bill and leg lengths on a global scale. Proc Biol Sci 2023; 290:20231387. [PMID: 37491963 PMCID: PMC10369025 DOI: 10.1098/rspb.2023.1387] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
Bills and legs are two vital appendages for birds, and they exhibit huge interspecific variation in form and function, yet no study has examined the global predictors of this variation. This study examined global gradients in the relative lengths of bird bills and tarsi (i.e. exposed leg parts) to body size across non-migratory birds, while accounting for phylogeny. We found that relative bill length and tarsus length were related to diet, habitat density, latitude, annual mean temperature, temperature variability and hand-wing index (HWI), a proxy for birds' flight efficiency. Among these factors, diet played a primary role in predicting bill length, with nectar-feeding pollinators, vertivores, invertivores and omnivores having longer bills; HWI emerged as the predominant predictor of tarsus length, wherein species with higher HWI had shorter tarsi. However, the effects of these factors differed between passerines and non-passerines, with some temperature-related effects exhibiting opposite trends between these two groups. Our findings highlight the compromise in adaptations for feeding, thermoregulation and flight performance between the two distinct appendages.
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Affiliation(s)
- Yu Xu
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang 550001, People's Republic of China
| | - Megan Price
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Pinjia Que
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, People's Republic of China
| | - Kai Zhang
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang 550001, People's Republic of China
| | - Shang Sheng
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, School of Life Sciences, Guizhou Normal University, Guiyang 550001, People's Republic of China
| | - Xingcheng He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Bin Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637002, People's Republic of China
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