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Benham PM, Walsh J, Bowie RCK. Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird. GLOBAL CHANGE BIOLOGY 2024; 30:e17126. [PMID: 38273486 DOI: 10.1111/gcb.17126] [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: 07/06/2023] [Revised: 11/22/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024]
Abstract
Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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Ramírez-Castañeda V, Westeen EP, Frederick J, Amini S, Wait DR, Achmadi AS, Andayani N, Arida E, Arifin U, Bernal MA, Bonaccorso E, Bonachita Sanguila M, Brown RM, Che J, Condori FP, Hartiningtias D, Hiller AE, Iskandar DT, Jiménez RA, Khelifa R, Márquez R, Martínez-Fonseca JG, Parra JL, Peñalba JV, Pinto-García L, Razafindratsima OH, Ron SR, Souza S, Supriatna J, Bowie RCK, Cicero C, McGuire JA, Tarvin RD. A set of principles and practical suggestions for equitable fieldwork in biology. Proc Natl Acad Sci U S A 2022; 119:e2122667119. [PMID: 35972961 PMCID: PMC9407469 DOI: 10.1073/pnas.2122667119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.
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Affiliation(s)
- Valeria Ramírez-Castañeda
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Erin P. Westeen
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Environmental, Science, Policy, and Management, University of California, Berkeley, CA, 94720
| | - Jeffrey Frederick
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Sina Amini
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Daniel R. Wait
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Anang S. Achmadi
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Noviar Andayani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Evy Arida
- Research Center for Applied Zoology, National Research and Innovation Agency, Jawa Barat 16911, Indonesia
| | - Umilaela Arifin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Centre for Taxonomy and Morphology, Leibniz Institute for the Analysis of Biodiversity Change, Hamburg 20146 Germany
| | - Moisés A. Bernal
- Department of Biological Sciences, Auburn University, Auburn, AL 36849
| | - Elisa Bonaccorso
- Laboratorio de Biología Evolutiva, Colegio de Ciencias Biológicas y Ambientales e Instituto Biósfera, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Marites Bonachita Sanguila
- Biodiversity Informatics and Research Center, Father Saturnino Urios University, Butuan City 8600, Philippines
| | - Rafe M. Brown
- Biodiversity Institute, University of Kansas, Lawrence, KS 66044
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66044
| | - Jing Che
- State Key Laboratory of Genetic Resource and Evolution and Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - F. Peter Condori
- Museo de Biodiversidad del Perú, Cusco 08003, Perú
- Museo de Historia Natural de la Universidad Nacional de San Antonio Abad del Cusco, Cusco 08002, Perú
| | | | - Anna E. Hiller
- Museum of Natural Science, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803
| | - Djoko T. Iskandar
- Basic Sciences Commision, Indonesian Academy of Sciences, Jakarta 10110, Indonesia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung 40132, Indonesia
| | - Rosa Alicia Jiménez
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Escuela de Biología, Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Ciudad de Guatemala 01012, Guatemala
| | - Rassim Khelifa
- Institute for Resources, Environment and Sustainability, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Biology Department, Condordia University, Montreal, Quebec H4B 1R6, Canada
| | - Roberto Márquez
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Michigan Society of Fellows, University of Michigan, Ann Arbor, MI 48109
| | - José G. Martínez-Fonseca
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011
- Nicaraguan Bat Conservation Program, Carazo, Nicaragua
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados, Instituto de Biología, Universidad de Antioquia, Medellín 050010, Colombia
| | - Joshua V. Peñalba
- Center for Integrative Biodiversity Discovery, Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin 10115, Germany
| | - Lina Pinto-García
- Centro Interdisciplinario de Estudios sobre el Desarrollo, Universidad de los Andes, Bogotá 111711, Colombia
- Institute for Science, Innovation and Society, University of Oxford, Oxford OX2 6PN, United Kingdom
| | - Onja H. Razafindratsima
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
- Mention Zoologie et Biodiversité Animale, Université d'Antananarivo, Antananarivo 101, Madagascar
| | - Santiago R. Ron
- Museo de Zoología, Escuela de Biología, Pontificia Universidad Católica del Ecuador, Quito 170525, Ecuador
| | - Sara Souza
- Environment, Health & Safety, University of California, Berkeley, CA 94720
| | - Jatna Supriatna
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Kampus UI Depok, Depok 16424, Indonesia
- Research Center for Climate Change, Gedung Laboratorium Multidisiplin, Faculty of Mathematics and Natural Sciences, Universitas Indonesia, Depok 16424, Indonesia
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
| | - Jimmy A. McGuire
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
| | - Rebecca D. Tarvin
- Museum of Vertebrate Zoology, University of California, Berkeley, CA, 94720
- Department of Integrative Biology, University of California, Berkeley, CA, 94720
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Ryding S, Klaassen M, Tattersall GJ, Gardner JL, Symonds MRE. Shape-shifting: changing animal morphologies as a response to climatic warming. Trends Ecol Evol 2021; 36:1036-1048. [PMID: 34507845 DOI: 10.1016/j.tree.2021.07.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022]
Abstract
Many animal appendages, such as avian beaks and mammalian ears, can be used to dissipate excess body heat. Allen's rule, wherein animals in warmer climates have larger appendages to facilitate more efficient heat exchange, reflects this. We find that there is widespread evidence of 'shape-shifting' (changes in appendage size) in endotherms in response to climate change and its associated climatic warming. We re-examine studies of morphological change over time within a thermoregulatory context, finding evidence that temperature can be a strong predictor of morphological change independently of, or combined with, other environmental changes. Last, we discuss how Allen's rule, the degree of temperature change, and other ecological factors facilitate morphological change and make predictions about what animals will show shape-shifting.
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Affiliation(s)
- Sara Ryding
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia.
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Glenn J Tattersall
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, Saint Catharines, Ontario L2S 3A1, Canada
| | - Janet L Gardner
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Matthew R E Symonds
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
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