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Becklin KM, Betancourt JL, Braasch J, Dézerald O, Díaz FP, González AL, Harbert R, Holmgren CA, Hornsby AD, Latorre C, Matocq MD, Smith FA. New uses for ancient middens: bridging ecological and evolutionary perspectives. Trends Ecol Evol 2024; 39:479-493. [PMID: 38553315 DOI: 10.1016/j.tree.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 11/30/2023] [Accepted: 12/08/2023] [Indexed: 05/12/2024]
Abstract
Rodent middens provide a fine-scale spatiotemporal record of plant and animal communities over the late Quaternary. In the Americas, middens have offered insight into biotic responses to past environmental changes and historical factors influencing the distribution and diversity of species. However, few studies have used middens to investigate genetic or ecosystem level responses. Integrating midden studies with neoecology and experimental evolution can help address these gaps and test mechanisms underlying eco-evolutionary patterns across biological and spatiotemporal scales. Fully realizing the potential of middens to answer cross-cutting ecological and evolutionary questions and inform conservation goals in the Anthropocene will require a collaborative research community to exploit existing midden archives and mount new campaigns to leverage midden records globally.
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Affiliation(s)
- Katie M Becklin
- Biology Department, Syracuse University, Syracuse, NY 13244, USA.
| | - Julio L Betancourt
- US Geological Survey, Science and Decisions Center, Reston, VA 20192, USA
| | - Joseph Braasch
- Department of Biology, Rutgers University, Camden, NJ 08103, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Olivier Dézerald
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Francisca P Díaz
- Instituto de Geografía, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile; Institute of Ecology and Biodiversity (IEB), Santiago, Chile; Millennium Nucleus of Applied Historical Ecology for Arid Forests (AFOREST), Santiago, Chile
| | - Angélica L González
- Department of Biology, Rutgers University, Camden, NJ 08103, USA; Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08103, USA
| | - Robert Harbert
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Camille A Holmgren
- Department of Geosciences, SUNY Buffalo State University, Buffalo, NY 14222, USA
| | - Angela D Hornsby
- Philip L. Wright Zoological Museum, Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Claudio Latorre
- Institute of Ecology and Biodiversity (IEB), Santiago, Chile; Centro UC Desierto de Atacama, Pontificia Universidad Católica de Chile, Santiago, Chile; Department of Ecology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, Department of Natural Resources and Environmental Science, University of Nevada, Reno, NV 89557, USA
| | - Felisa A Smith
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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2
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Zhang S, Song F, Wang J, Li X, Zhang Y, Zhou W, Xu L. Gut microbiota facilitate adaptation of invasive moths to new host plants. THE ISME JOURNAL 2024; 18:wrae031. [PMID: 38423525 PMCID: PMC10980833 DOI: 10.1093/ismejo/wrae031] [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: 11/10/2023] [Revised: 01/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Gut microbiota are important in the adaptation of phytophagous insects to their plant hosts. However, the interaction between gut microbiomes and pioneering populations of invasive insects during their adaptation to new hosts, particularly in the initial phases of invasion, has been less studied. We studied the contribution of the gut microbiome to host adaptation in the globally recognized invasive pest, Hyphantria cunea, as it expands its range into southern China. The southern population of H. cunea shows effective adaptation to Metasequoia glyptostroboides and exhibits greater larval survival on Metasequoia than the original population. Genome resequencing revealed no significant differences in functions related to host adaptation between the two populations. The compatibility between southern H. cunea populations and M. glyptostroboides revealed a correlation between the abundance of several gut bacteria genera (Bacteroides, Blautia, and Coprococcus) and H. cunea survival. Transplanting the larval gut microbiome from southern to northern populations enhanced the adaptability of the latter to the previously unsuitable plant M. glyptostroboides. This research provides evidence that the gut microbiome of pioneering populations can enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.
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Affiliation(s)
- Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Feng Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jie Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiayu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yuxin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenwu Zhou
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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de Jong M, van Rensburg AJ, Whiteford S, Yung CJ, Beaumont M, Jiggins C, Bridle J. Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range. Mol Ecol 2023; 32:5742-5756. [PMID: 37800849 DOI: 10.1111/mec.17138] [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: 05/16/2022] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 10/07/2023]
Abstract
Understanding the rate and extent to which populations can adapt to novel environments at their ecological margins is fundamental to predicting the persistence of biological communities during ongoing and rapid global change. Recent range expansion in response to climate change in the UK butterfly Aricia agestis is associated with the evolution of novel interactions with a larval food plant, and the loss of its ability to use an ancestral host species. Using ddRAD analysis of 61,210 variable SNPs from 261 females from throughout the UK range of this species, we identify genomic regions at multiple chromosomes that are associated with evolutionary responses, and their association with demographic history and ecological variation. Gene flow appears widespread throughout the range, despite the apparently fragmented nature of the habitats used by this species. Patterns of haplotype variation between selected and neutral genomic regions suggest that evolution associated with climate adaptation is polygenic, resulting from the independent spread of alleles throughout the established range of this species, rather than the colonization of pre-adapted genotypes from coastal populations. These data suggest that rapid responses to climate change do not depend on the availability of pre-adapted genotypes. Instead, the evolution of novel forms of biotic interaction in A. agestis has occurred during range expansion, through the assembly of novel genotypes from alleles from multiple localities.
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Affiliation(s)
- Maaike de Jong
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alexandra Jansen van Rensburg
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Samuel Whiteford
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Carl J Yung
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Chris Jiggins
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Jon Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
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Walter GM, Clark J, Terranova D, Cozzolino S, Cristaudo A, Hiscock SJ, Bridle J. Hidden genetic variation in plasticity provides the potential for rapid adaptation to novel environments. THE NEW PHYTOLOGIST 2023; 239:374-387. [PMID: 36651081 DOI: 10.1111/nph.18744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/02/2023] [Indexed: 06/02/2023]
Abstract
Rapid environmental change is forcing populations into environments where plasticity will no longer maintain fitness. When populations are exposed to novel environments, evolutionary theory predicts that genetic variation in fitness will increase and should be associated with genetic differences in plasticity. If true, then genetic variation in plasticity can increase adaptive potential in novel environments, and population persistence via evolutionary rescue is more likely. To test whether genetic variation in fitness increases in novel environments and is associated with plasticity, we transplanted 8149 clones of 314 genotypes of a Sicilian daisy (Senecio chrysanthemifolius) within and outside its native range, and quantified genetic variation in fitness, and plasticity in leaf traits and gene expression. Although mean fitness declined by 87% in the novel environment, genetic variance in fitness increased threefold and was correlated with plasticity in leaf traits. High fitness genotypes showed greater plasticity in gene expression, but lower plasticity in most leaf traits. Interestingly, genotypes with the highest fitness in the novel environment had the lowest fitness at the native site. These results suggest that standing genetic variation in plasticity could help populations to persist and adapt to novel environments, despite remaining hidden in native environments.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - James Clark
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Delia Terranova
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, 95128, Italy
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Naples, 80126, Italy
| | - Antonia Cristaudo
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, 95128, Italy
| | - Simon J Hiscock
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jon Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK
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Pigot AL. Biodiversity: What makes a city bird? Curr Biol 2023; 33:R369-R371. [PMID: 37160097 DOI: 10.1016/j.cub.2023.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The impacts of urbanisation on biodiversity varies greatly across species. A new study shows how the intrinsic species properties underlying urban tolerance vary globally according to environmental context. This has important implications for conserving biodiversity in a rapidly urbanising world.
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Affiliation(s)
- Alex L Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK.
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Hoffmann AA, Bridle J. Plasticity and the costs of incorrect responses. Trends Ecol Evol 2023; 38:219-220. [PMID: 36528412 DOI: 10.1016/j.tree.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/26/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Ary A Hoffmann
- Pest and Environmental Research Group, Bio21 Institute, University of Melbourne, Melbourne, Vic 3010, Australia.
| | - Jon Bridle
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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The importance of spatial and temporal structure in determining the interplay between plasticity and evolution. Trends Ecol Evol 2023; 38:221-223. [PMID: 36610919 DOI: 10.1016/j.tree.2022.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023]
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Harris NC, Murphy A, Green AR, Gámez S, Mwamidi DM, Nunez-Mir GC. Socio-ecological gap analysis to forecast species range contractions for conservation. Proc Natl Acad Sci U S A 2022; 120:e2201942119. [PMID: 36165442 PMCID: PMC9962987 DOI: 10.1073/pnas.2201942119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Conservation requires both a needs assessment and prioritization scheme for planning and implementation. Range maps are critical for understanding and conserving biodiversity, but current range maps often omit content, negating important metrics of variation in populations and places. Here, we integrate a myriad of conditions that are spatially explicit across distributions of carnivores to identify gaps in capacity necessary for their conservation. Expanding on traditional gap analyses that focus almost exclusively on quantifying discordance in protected area coverage across a species' range, our work aggregates threat layers (e.g., drought, human pressures) with resources layers (e.g., protected areas, cultural diversity) to identify gaps in available conservation capacity (ACC) across ranges for 91 African carnivores. Our model indicated that all species have some portion of their range at risk of contraction, with an average of 15 percentage range loss. We found that the ACC differed based on body size and taxonomy. Results deviated from current perceptions of extinction risks for species with an International Union for Conservation of Nature (IUCN) threat status of Least Concern and yielded insights for species categorized as Data Deficient. Our socio-ecological gap analysis presents a geospatial approach to inform decision-making and resource allocation in conservation. Ultimately, our work advances forecasting dynamics of species' ranges that are increasingly vital in an era of great socio-ecological change to mitigate human-wildlife conflict and promote inclusive carnivore conservation across geographies.
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Affiliation(s)
- Nyeema C. Harris
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University, New Haven, CT06511
| | - Asia Murphy
- Department of Environmental Studies, University of California, Santa Cruz, CA95064
| | - Aalayna R. Green
- Department of Natural Resources and the Environment, Cornell University, Ithaca, NY14853
| | - Siria Gámez
- Applied Wildlife Ecology Lab, Yale School of the Environment, Yale University, New Haven, CT06511
| | - Daniel M. Mwamidi
- Laboratory for Analysis of Socio-ecological Systems in a Global World, Institute of Environmental Science and Technology, Autonomous University of Barcelona, 08193 Barcelona, Spain
| | - Gabriela C. Nunez-Mir
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL60607
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Yang X, Ni X, Fu C. Phylogeographical Analysis of the Freshwater Gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) in Southern China. Life (Basel) 2022; 12:1024. [PMID: 35888112 PMCID: PMC9318155 DOI: 10.3390/life12071024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/17/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023] Open
Abstract
The freshwater gudgeon Huigobio chenhsienensis (Cypriniformes: Gobionidae) is a small fish endemic to southern China. In this study, we used mitochondrial cytochrome b gene (Cytb), from wide-ranging samplings of H. chenhsienensis from the Ou River (the central of southern China) to the Yangtze River Basin (the northernmost part of southern China) to explore genetic variations and the evolutionary history of H. chenhsienensis in southern China. In total, 66 haplotypes were identified from Cytb sequences of 142 H. chenhsienensis individuals, which could be divided into lineages A, B, and C with divergence times of ~4.24 Ma and ~3.03 Ma. Lineage A was distributed in the lower reaches of the Yangtze River, the Oujiang River, and the Jiao River, lineage B was distributed in the Qiantang River and the Cao'e River, whereas lineage C was restricted to the Poyang Lake drainage from the middle reaches of the Yangtze River. Lineage A could be subdivided into sub-lineages A-I, A-II, A-III, and A-IV, with divergence times of 1.30, 0.97, and 0.44 Ma. Lineage C could be subdivided into sub-lineages C-I and C-II, with a divergence time of 0.85 Ma. Our findings indicate that climate change during the Pliocene and Pleistocene eras, as well as the limited dispersal ability of H. chenhsienensis, have been major drivers for shaping the phylogeographical patterns of H. chenhsienensis.
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Rafajlović M, Alexander JM, Butlin RK, Johannesson K. Introduction to the theme issue 'Species' ranges in the face of changing environments'. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210002. [PMID: 35184596 PMCID: PMC8859519 DOI: 10.1098/rstb.2021.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding where, when and how species’ ranges will be modified is both a fundamental problem and essential to predicting how spatio-temporal environmental changes in abiotic and biotic factors impact biodiversity. Notably, different species may respond disparately to similar environmental changes: some species may overcome an environmental change only with difficulty or not at all, while other species may readily overcome the same change. Ranges may contract, expand or move. The drivers and consequences of this variability in species' responses remain puzzling. Importantly, changes in a species’ range creates feedbacks to the environmental conditions, populations and communities in its previous and current range, rendering population genetic, population dynamic and community processes inextricably linked. Understanding these links is critical in guiding biodiversity management and conservation efforts. This theme issue presents current thinking about the factors and mechanisms that limit and/or modify species' ranges. It also outlines different approaches to detect changes in species’ distributions, and illustrates cases of range modifications in several taxa. Overall, this theme issue highlights the urgency of understanding species' ranges but shows that we are only just beginning to disentangle the processes involved. One way forward is to unite ecology with evolutionary biology and empirical with modelling approaches. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.
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Affiliation(s)
- Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden.,Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jake M Alexander
- Department of Environmental Systems Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Roger K Butlin
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.,Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK.,Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, 452 96 Strömstad, Sweden
| | - Kerstin Johannesson
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden.,Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, 452 96 Strömstad, Sweden
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