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Damiani G, Sebastiano M, Dell'Omo G, Costantini D. Blood transcriptome analysis of common kestrel nestlings living in urban and non-urban environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172585. [PMID: 38641099 DOI: 10.1016/j.scitotenv.2024.172585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
Urbanisation is one of the main anthropogenic forms of land cover affecting an ever-increasing number of wild animals and their habitats. Physiological plasticity represents an important process through which animals can adjust to the novel conditions of anthropogenic environments. Relying on the analysis of gene expression, it is possible to identify the molecular responses to the habitat conditions and infer possible environmental factors that affect the organismal physiology. We have quantified for the first time the blood transcriptome of common kestrel (Falco tinnunculus) nestlings living in urban sites and compared it to the transcriptome of kestrel nestlings inhabiting rural and natural environments. We found mild differences in the expression of genes among sites, indicating adaptability or acclimation of the birds to the urban habitat. We identified 58 differentially expressed genes between urban and natural kestrels, and 12 differentially expressed genes between urban and rural kestrels. The most striking differences among sites involved inflammatory-immunological, metabolic, apoptosis, DNA repair and development genes. In particular, we found that (i) urban kestrel nestlings had higher expression of genes linked to inflammation, repair of DNA damage, or apoptosis than natural kestrel nestlings, and (ii) natural and rural kestrel nestlings had higher expression of genes linked to the development and activation of immune cells, type I interferon response, or major histocompatibility complex than urban kestrel nestlings. Finally, the KEGG enrichment analysis identified the insulin signalling as the main pathway that differed between natural and urban kestrel nestlings. This is one of a limited number of studies on vertebrates that revealed habitat-associated differences in the transcriptome. It paves the way for further in-depth studies on the links between physiological variation and habitat structure at different spatial and temporal scales.
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Affiliation(s)
- Gianluca Damiani
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy; Ornis italica, Piazza Crati 15, 00199 Rome, Italy.
| | - Manrico Sebastiano
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | | | - David Costantini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università, 01100 Viterbo, Italy; Ornis italica, Piazza Crati 15, 00199 Rome, Italy; Unité Physiologie Moléculaire et Adaptation, UMR7221-Muséum National d'Histoire Naturelle-CNRS, 75005 Paris, France.
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Rannaud-Bartaire P, Demeneix BA, Fini JB. Pressures of the urban environment on the endocrine system: Adverse effects and adaptation. Mol Cell Endocrinol 2024; 583:112125. [PMID: 38147952 DOI: 10.1016/j.mce.2023.112125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 12/28/2023]
Abstract
With an increasing collective awareness of the rapid environmental changes, questions and theories regarding the adaptability of organisms are emerging. Global warming as well as chemical and non-chemical pollution have been identified as triggers of these adaptative changes, but can we link different kinds of stressors to certain phenotypic traits? The physiological adaptation, and particularly endocrine system adaptation, of living beings to urban environments is a fascinating way of studying urban endocrinology, which has emerged as a research field in 2007. In this paper, we stress how endocrine disruption in humans and environment can be studied in the urban environment by measuring the levels of pollution, endocrine activities or adversity. We broaden the focus to include not only exposure to the chemicals that have invaded our private spheres and their effects on wild and domestic species but also non-chemical effectors such as light, noise and climate change. We argue that taking into account the various urban stress factors and their effects on the endocrine system would enable the adoption of new approaches to protect living organisms.
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Affiliation(s)
- Patricia Rannaud-Bartaire
- PhyMa Unit, CNRS UMR 7221, Muséum National d'Histoire Naturelle, F-75005, Paris, France; Université Catholique de Lille, l'hôpital Saint-Vincent-De-Paul, Boulevard de Belfort, 59000, Lille, France
| | - Barbara A Demeneix
- PhyMa Unit, CNRS UMR 7221, Muséum National d'Histoire Naturelle, F-75005, Paris, France
| | - Jean-Baptiste Fini
- PhyMa Unit, CNRS UMR 7221, Muséum National d'Histoire Naturelle, F-75005, Paris, France.
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Caizergues AE, Le Luyer J, Grégoire A, Szulkin M, Senar J, Charmantier A, Perrier C. Epigenetics and the city: Non-parallel DNA methylation modifications across pairs of urban-forest Great tit populations. Evol Appl 2022; 15:149-165. [PMID: 35126653 PMCID: PMC8792475 DOI: 10.1111/eva.13334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Identifying the molecular mechanisms involved in rapid adaptation to novel environments and determining their predictability are central questions in evolutionary biology and pressing issues due to rapid global changes. Complementary to genetic responses to selection, faster epigenetic variations such as modifications of DNA methylation may play a substantial role in rapid adaptation. In the context of rampant urbanization, joint examinations of genomic and epigenomic mechanisms are still lacking. Here, we investigated genomic (SNP) and epigenomic (CpG methylation) responses to urban life in a passerine bird, the Great tit (Parus major). To test whether urban evolution is predictable (i.e. parallel) or involves mostly nonparallel molecular processes among cities, we analysed both SNP and CpG methylation variations across three distinct pairs of city and forest Great tit populations in Europe. Our analyses reveal a polygenic response to urban life, with both many genes putatively under weak divergent selection and multiple differentially methylated regions (DMRs) between forest and city great tits. DMRs mainly overlapped transcription start sites and promotor regions, suggesting their importance in modulating gene expression. Both genomic and epigenomic outliers were found in genomic regions enriched for genes with biological functions related to the nervous system, immunity, or behavioural, hormonal and stress responses. Interestingly, comparisons across the three pairs of city-forest populations suggested little parallelism in both genetic and epigenetic responses. Our results confirm, at both the genetic and epigenetic levels, hypotheses of polygenic and largely nonparallel mechanisms of rapid adaptation in novel environments such as urbanized areas.
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Affiliation(s)
| | - Jeremy Le Luyer
- Ifremer, IRD, Institut Louis‐MalardéUniv Polynésie Française, EIOTaravaoFrench Polynesia
| | | | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | | | | | - Charles Perrier
- CBGP, INRAe, CIRAD, IRD, Montpellier SupAgroUniv. MontpellierMontpellierFrance
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Smith SH, Hessong-Brown J, Lipshutz SE, Phillips JN, Rochefort C, Derryberry EP, Luther DA. Long-term changes of plumage between urban and rural populations of white-crowned sparrows ( Zonotrichia leucophrys). JOURNAL OF URBAN ECOLOGY 2021. [DOI: 10.1093/jue/juaa038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Urbanization is one of the most extreme forms of land transformation and results in changes to ecosystems and species compositions. As a result, there are strong directional selection pressures compared to nearby rural areas. Despite a surge in research on the different selection pressures on acoustic communication in urban and rural areas, there has been comparatively little investigation into traits involved with visual communication. We measured the plumage of museum specimens of white-crowned sparrows (Zonotrichia leucophrys) from urban and adjacent rural habitats in San Francisco, CA, to assess the effects of divergent habitats on plumage. We found significant differences in dorsal plumage, but not crown plumage, between urban and rural populations that have been diverging over the past 100 years. Urban birds have increasingly darker and duller dorsal plumage, whereas rural birds in adjacent areas have plumage with richer hues and more color complexity. Our findings suggest a newly observed adaptation to urban environments by native species and suggest that many traits, in addition to acoustic signals, may be changing in response to urban selection pressures. Additional collections in urban areas are needed to explore likely divergences in plumage coloration between urban and rural environments.
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Affiliation(s)
- Shawn H Smith
- Environmental Science and Policy Department, George Mason University, Fairfax, VA, USA
| | | | - Sara E Lipshutz
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jennifer N Phillips
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, USA
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, USA
| | | | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - David A Luther
- Biology Department, George Mason University, Fairfax, VA, USA
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Mueller JC, Carrete M, Boerno S, Kuhl H, Tella JL, Kempenaers B. Genes acting in synapses and neuron projections are early targets of selection during urban colonization. Mol Ecol 2020; 29:3403-3412. [DOI: 10.1111/mec.15451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jakob C. Mueller
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
| | - Martina Carrete
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
- Department of Physical, Chemical and Natural Systems University Pablo de Olavide Sevilla Spain
| | - Stefan Boerno
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
| | - Heiner Kuhl
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
- Department of Ecophysiology and Aquaculture Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - José L. Tella
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
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Close encounters of the urban kind: predators influence prey body size variation in an urban landscape. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10008-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ouyang JQ, Isaksson C, Schmidt C, Hutton P, Bonier F, Dominoni D. A New Framework for Urban Ecology: An Integration of Proximate and Ultimate Responses to Anthropogenic Change. Integr Comp Biol 2019; 58:915-928. [PMID: 30376106 DOI: 10.1093/icb/icy110] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
As urban areas continue to grow, understanding how species respond and adapt to urban habitats is becoming increasingly important. Knowledge of the mechanisms behind observed phenotypic changes of urban-dwelling animals will enable us to better evaluate the impact of urbanization on current and future generations of wildlife and predict how animals respond to novel environments. Recently, urban ecology has emerged not only as a means of understanding organismal adaptation but also as a framework for exploring mechanisms mediating evolutionary phenomena. Here, we have identified four important research topics that will advance the field of urban ecology and shed light on the proximate and ultimate causes of the phenotypic differences commonly seen among species and populations that vary in their responses to urbanization. First, we address the ecological and socio-economic factors that characterize cities, how they might interact with each other, and how they affect urban species. Second, we ask which are the proximate mechanisms underlying the emergence over time of novel traits in urban organisms, focusing on developmental effects. Third, we emphasize the importance of understanding the ultimate causations that link phenotypic shifts to function. This question highlights the need to quantify the strength and direction of selection that urban individuals are exposed to, and whether the phenotypic shifts associated with life in the city are adaptive. Lastly, we stress the need to translate how individual-level responses scale up to population dynamics. Understanding the mechanistic underpinnings of variation among populations and species in their responses to urbanization will unravel species resilience to environmental perturbation, which will facilitate predictive models for sustainability and development of green cities that maintain or even increase urban biodiversity and wildlife health and wellbeing.
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Affiliation(s)
- Jenny Q Ouyang
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, USA
| | | | - Chloé Schmidt
- Department of Biological Sciences, University of Manitoba, Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Pierce Hutton
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Frances Bonier
- Biology Department, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Davide Dominoni
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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Riyahi S, Björklund M, Mateos-Gonzalez F, Senar JC. Personality and urbanization: behavioural traits and DRD4 SNP830 polymorphisms in great tits in Barcelona city. J ETHOL 2016. [DOI: 10.1007/s10164-016-0496-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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10
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Mak C, Scholz M, James P. Sustainable drainage system site assessment method using urban ecosystem services. Urban Ecosyst 2016. [DOI: 10.1007/s11252-016-0593-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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McDonnell MJ, Hahs AK. Adaptation and Adaptedness of Organisms to Urban Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054258] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mark J. McDonnell
- Australian Research Center for Urban Ecology, Royal Botanic Gardens Victoria and University of Melbourne, Victoria 3010, Australia;
| | - Amy K. Hahs
- Australian Research Center for Urban Ecology, Royal Botanic Gardens Victoria and University of Melbourne, Victoria 3010, Australia;
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