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Padilla Perez DJ. Geographic and seasonal variation of the for gene reveal signatures of local adaptation in Drosophila melanogaster. J Evol Biol 2024; 37:201-211. [PMID: 38301664 DOI: 10.1093/jeb/voad018] [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: 07/03/2023] [Revised: 11/18/2023] [Accepted: 12/16/2023] [Indexed: 02/03/2024]
Abstract
In the early 1980s, the observation that Drosophila melanogaster larvae differed in their foraging behaviour laid the foundation for the work that would later lead to the discovery of the foraging gene (for) and its associated foraging phenotypes, rover and sitter. Since then, the molecular characterization of the for gene and our understanding of the mechanisms that maintain its phenotypic variants in the laboratory have progressed enormously. However, the significance and dynamics of such variation are yet to be investigated in nature. With the advent of next-generation sequencing, it is now possible to identify loci underlying the adaptation of populations in response to environmental variation. Here, I present the results of a genotype-environment association analysis that quantifies variation at the for gene among samples of D. melanogaster structured across space and time. These samples consist of published genomes of adult flies collected worldwide, and at least twice per site of collection (during spring and fall). Both an analysis of genetic differentiation based on Fst values and an analysis of population structure revealed an east-west gradient in allele frequency. This gradient may be the result of spatially varying selection driven by the seasonality of precipitation. These results support the hypothesis that different patterns of gene flow as expected under models of isolation by distance and potentially isolation by environment are driving genetic differentiation among populations. Overall, this study is essential for understanding the mechanisms underlying the evolution of foraging behaviour in D. melanogaster.
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2
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Britton D, Layton C, Mundy CN, Brewer EA, Gaitán-Espitia JD, Beardall J, Raven JA, Hurd CL. Cool-edge populations of the kelp Ecklonia radiata under global ocean change scenarios: strong sensitivity to ocean warming but little effect of ocean acidification. Proc Biol Sci 2024; 291:20232253. [PMID: 38228502 DOI: 10.1098/rspb.2023.2253] [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: 10/04/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024] Open
Abstract
Kelp forests are threatened by ocean warming, yet effects of co-occurring drivers such as CO2 are rarely considered when predicting their performance in the future. In Australia, the kelp Ecklonia radiata forms extensive forests across seawater temperatures of approximately 7-26°C. Cool-edge populations are typically considered more thermally tolerant than their warm-edge counterparts but this ignores the possibility of local adaptation. Moreover, it is unknown whether elevated CO2 can mitigate negative effects of warming. To identify whether elevated CO2 could improve thermal performance of a cool-edge population of E. radiata, we constructed thermal performance curves for growth and photosynthesis, under both current and elevated CO2 (approx. 400 and 1000 µatm). We then modelled annual performance under warming scenarios to highlight thermal susceptibility. Elevated CO2 had minimal effect on growth but increased photosynthesis around the thermal optimum. Thermal optima were approximately 16°C for growth and approximately 18°C for photosynthesis, and modelled performance indicated cool-edge populations may be vulnerable in the future. Our findings demonstrate that elevated CO2 is unlikely to offset negative effects of ocean warming on the kelp E. radiata and highlight the potential susceptibility of cool-edge populations to ocean warming.
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Affiliation(s)
- Damon Britton
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, Tasmania 7004, Australia
| | - Cayne Layton
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, Tasmania 7004, Australia
| | - Craig N Mundy
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, Tasmania 7004, Australia
| | | | - Juan Diego Gaitán-Espitia
- School of Biological Sciences and the SWIRE Institute of Marine Sciences, The University of Hong-Kong, Hong Kong, People's Republic of China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biological Sciences, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, New South Wales 2007, Australia
| | - Catriona L Hurd
- Institute for Marine and Antarctic Studies, University of Tasmania, 20 Castray Esplanade, Battery Point, Hobart, Tasmania 7004, Australia
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3
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Cid-Alda FP, Montecinos AE, Guillemin ML. A temporal and spatial study of genetic structure in four species of bladed Bangiales (Rhodophyta) from the southeastern Pacific coast of Chile. JOURNAL OF PHYCOLOGY 2023; 59:712-724. [PMID: 37166446 DOI: 10.1111/jpy.13343] [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: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/12/2023]
Abstract
The coastline is a heterogeneous and highly dynamic environment influenced by abiotic and biotic variables affecting the temporal stability of genetic diversity and structure of marine organisms. The aim of this study was to determine how much the genetic structure of four species of marine Bangiales vary in time and space. Partial sequences of the cytochrome oxidase I (COI) gene obtained from two Pyropia (Py. sp. CHJ and Py. orbicularis) and two Porphyra (P. mumfordii and P. sp. FIH) species were used to compare the effect of the 40° S/41° S biogeographic break (spatial-regional scale) and the one of the Valdivia River discharges (spatial-local scale) and determine their temporal stability. Four seasonal samplings were taken during 1 year at five sites, one site located in Melinka (Magallanes province) and four sites along the coast of Valdivia (Intermediate area), on both sides of the river mouth. Results showed a strong genetic spatial structure at regional scale (ΦST > 0.4) in Py. sp. CHJ, Py. orbicularis, and P. mumfordii, congruent with the 41° S/42° S biogeographic break. A potential barrier to gene flow, related to the Valdivia River discharge, was detected only in P. mumfordii. In P. sp. FIH, spatial genetic structure was not detected at any scale. The genetic structure of all four species is stable throughout the year. The potential effect of main currents and river discharge in limiting the transport of Bangiales spores are discussed. We propose that both a restricted propagule dispersal and the formation potential for persistent banks of microscopic stages could lead to a temporally stable spatial partitioning of genetic variation in bladed Bangiales.
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Affiliation(s)
- Fernanda P Cid-Alda
- Post-doctoral researcher in Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco, Chile
| | - Alejandro E Montecinos
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Marie Laure Guillemin
- Núcleo Milenio MASH, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, Roscoff, France
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
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4
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Asadi Aghbolaghi M, Keyghobadi N, Azarakhsh Z, Dadizadeh M, Asadi Aghbolaghi S, Zamani N. An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel ( Sciurus anomalus) in the Zagros forests of Iran. Ecol Evol 2023; 13:e10225. [PMID: 37408621 PMCID: PMC10318582 DOI: 10.1002/ece3.10225] [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: 12/08/2022] [Revised: 05/27/2023] [Accepted: 06/11/2023] [Indexed: 07/07/2023] Open
Abstract
For the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.
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Affiliation(s)
- Marzieh Asadi Aghbolaghi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti UniversityTehranIran
| | - Nusha Keyghobadi
- Department of BiologyThe University of Western OntarioLondonCanada
| | - Zeinab Azarakhsh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Marzieh Dadizadeh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Shahab Asadi Aghbolaghi
- Department of Education of Chaharmahal and Bakhtiari Province (Ministry of Education)ShahrekordIran
| | - Navid Zamani
- Department of Environmental Science, Faculty of Natural ResourceUniversity of KurdistanSanandajIran
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5
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Gallegos C, Hodgins KA, Monro K. Climate adaptation and vulnerability of foundation species in a global change hotspot. Mol Ecol 2023; 32:1990-2004. [PMID: 36645732 DOI: 10.1111/mec.16848] [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: 04/05/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023]
Abstract
Climate change is altering species ranges, and relative abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Understanding present species ranges, whether species harbour and exchange adaptive variants, and how variants are distributed across landscapes undergoing rapid change, is therefore crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We assess genomic patterns of neutral variation, climate adaptation and climate vulnerability (offsets in predicted distributions of putatively adaptive variants across present and future landscapes) for sister foundation species, the marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, in a sentinel region for climate change impacts. We find that species are genetically isolated despite uncovering sympatry in their ranges, show parallel and nonparallel signals of thermal adaptation on spatial scales smaller than gene flow across their ranges, and are predicted to face different risks of maladaptation under future temperatures across their ranges. Our findings have implications for understanding local adaptation in the face of gene flow, and generate spatially explicit predictions for climatic disruption of adaptation and species distributions in coastal ecosystems that could guide experimental validation and conservation planning.
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Affiliation(s)
- Cristóbal Gallegos
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Keyne Monro
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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6
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Young MA, Critchell K, Miller AD, Treml EA, Sams M, Carvalho R, Ierodiaconou D. Mapping the impacts of multiple stressors on the decline in kelps along the coast of Victoria, Australia. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mary A. Young
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
| | - Kay Critchell
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Queenscliff Vic. Australia
| | - Adam D. Miller
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
| | - Eric A. Treml
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Queenscliff Vic. Australia
| | - Michael Sams
- Parks Victoria, Marine and Coastal Science and Programs Melbourne Vic. Australia
| | - Rafael Carvalho
- School of Earth, Atmosphere and Environment Monash University Melbourne Vic. Australia
| | - Daniel Ierodiaconou
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Warrnambool Vic. Australia
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7
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Holland OJ, Young MA, Sherman CDH, Tan MH, Gorfine H, Matthews T, Miller AD. Ocean warming threatens key trophic interactions supporting a commercial fishery in a climate change hotspot. GLOBAL CHANGE BIOLOGY 2021; 27:6498-6511. [PMID: 34529873 DOI: 10.1111/gcb.15889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/09/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Worldwide, rising ocean temperatures are causing declines and range shifts in marine species. The direct effects of climate change on the biology of marine organisms are often well documented; yet, knowledge on the indirect effects, particularly through trophic interactions, is largely lacking. We provide evidence of ocean warming decoupling critical trophic interactions supporting a commercially important mollusc in a climate change hotspot. Dietary assessments of the Australian blacklip abalone (Haliotis rubra) indicate primary dependency on a widespread macroalgal species (Phyllospora comosa) which we show to be in state of decline due to ocean warming, resulting in abalone biomass reductions. Niche models suggest further declines in P. comosa over the coming decades and ongoing risks to H. rubra. This study highlights the importance of studies from climate change hotspots and understanding the interplay between climate and trophic interactions when determining the likely response of marine species to environmental changes.
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Affiliation(s)
- Owen J Holland
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Mary A Young
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Craig D H Sherman
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
| | - Mun Hua Tan
- School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Harry Gorfine
- School of Biosciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Ty Matthews
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Adam D Miller
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia
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8
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Cameron H, Amor MD, Bellgrove A. Barriers to restoration: Pollution alters nurse effects for an ecosystem engineer. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Hayley Cameron
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Warrnambool Victoria Australia
- Centre for Geometric Biology School of Biological Sciences Monash University Clayton Victoria Australia
| | - Michael D. Amor
- Royal Botanic Gardens Victoria South Yarra Victoria Australia
- Department of Aquatic Zoology Western Australian Museum Welshpool Western Australia Australia
| | - Alecia Bellgrove
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Warrnambool Victoria Australia
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9
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Combined Effects of Temperature and Salinity on Polyps and Ephyrae of Aurelia solida (Cnidaria: Scyphozoa). DIVERSITY 2021. [DOI: 10.3390/d13110573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Jellyfish outbreaks are conspicuous natural events in marine ecosystems that have a substantial impact on the structure and dynamics of marine ecosystems and different economic sectors of human activities. Understanding the life cycle strategies of jellyfish species is therefore critical to mitigate the impacts these organisms may have. In this context, the present study investigated the effect of different temperature and salinity regimes on the rearing success of the jellyfish Aurelia solida in microcosm experiments on two different life stages: polyps and ephyrae. Polyps showed high survival rates across the different conditions (except at 28 °C/20 psu) and reproduced asexually in all combinations, with the highest budding activity at 20 °C and 30 psu. Strobilation occurred mainly at 16 °C and 35 psu. Although ephyra survival was highest at low salinities (20 psu) and lower temperatures (10 and 15 °C), the highest growth rates were reached at intermediate temperatures (20 °C). The comparison to other Aurelia species underlines the differences between even closely related species. Given the high tolerance capacity that A. solida presented in the experiments, the species has the potential to cope well under current climate change scenarios and possibly adapt successfully to other regions and ecosystems.
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10
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Vranken S, Wernberg T, Scheben A, Severn-Ellis AA, Batley J, Bayer PE, Edwards D, Wheeler D, Coleman MA. Genotype-Environment mismatch of kelp forests under climate change. Mol Ecol 2021; 30:3730-3746. [PMID: 34018645 DOI: 10.1111/mec.15993] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/23/2023]
Abstract
Climate change is increasingly impacting ecosystems globally. Understanding adaptive genetic diversity and whether it will keep pace with projected climatic change is necessary to assess species' vulnerability and design efficient mitigation strategies such as assisted adaptation. Kelp forests are the foundations of temperate reefs globally but are declining in many regions due to climate stress. A lack of knowledge of kelp's adaptive genetic diversity hinders assessment of vulnerability under extant and future climates. Using 4245 single nucleotide polymorphisms (SNPs), we characterized patterns of neutral and putative adaptive genetic diversity for the dominant kelp in the southern hemisphere (Ecklonia radiata) from ~1000 km of coastline off Western Australia. Strong population structure and isolation-by-distance was underpinned by significant signatures of selection related to temperature and light. Gradient forest analysis of temperature-linked SNPs under selection revealed a strong association with mean annual temperature range, suggesting adaptation to local thermal environments. Critically, modelling revealed that predicted climate-mediated temperature changes will probably result in high genomic vulnerability via a mismatch between current and future predicted genotype-environment relationships such that kelp forests off Western Australia will need to significantly adapt to keep pace with projected climate change. Proactive management techniques such as assisted adaptation to boost resilience may be required to secure the future of these kelp forests and the immense ecological and economic values they support.
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Affiliation(s)
- Sofie Vranken
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Thomas Wernberg
- UWA Oceans Institute, Crawley, WA, Australia
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Institute of Marine Research, His, Norway
| | - Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Philipp Emanuel Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - David Wheeler
- New South Wales Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, Australia
| | - Melinda Ann Coleman
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- New South Wales Fisheries, National Marine Science Centre, Coffs Harbour, NSW, Australia
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, Australia
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11
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Mamo LT, Wood G, Wheeler D, Kelaher BP, Coleman MA. Conservation genomics of a critically endangered brown seaweed. JOURNAL OF PHYCOLOGY 2021; 57:1345-1355. [PMID: 33908033 DOI: 10.1111/jpy.13177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/27/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Seaweeds provide valuable ecosystem services, but many are undergoing global decline due to climate and anthropogenic stressors. The brown macroalga, Nereia lophocladia (hereafter called Nereia), is among only a handful of seaweeds globally to be listed as critically endangered and is only described from two known locations, but there exists little knowledge about this species. Here, we combine field surveys to verify the distribution of Nereia, with cutting-edge genomics to determine genetic diversity and population structure, and inform ongoing conservation actions. We expand Nereia's known distribution from one to seven locations along a 70-km long coastal stretch in New South Wales but reveal small population sizes at some sites (as few as 8 individuals despite extensive searching). A total of 1,261 genome-wide SNPs were retained from 70 individuals after filtering, and 304 outlier loci under putative selection were detected by one of three methods. Populations showed low genetic diversity (mean expected heterozygosity HE = 0.055 ± 0.014) and high levels of inbreeding within populations (mean FIS = 0.721 ± 0.085), along with high genetic differentiation among sites (mean FST = 0.276), which may increase susceptibility to future environmental change and decrease the species' ability to recover after loss. Given these findings, we recommend the consideration of both in situ and ex situ conservation measures for Nereia, as well as further research into the species' ecology and biology. Nereia remains of conservation concern and its listing as critically endangered is justified until further investigation elucidates the full distribution and adaptive capacity of the species.
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Affiliation(s)
- Lea T Mamo
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, 2450, Australia
| | - Georgina Wood
- School of Life and Environmental Sciences, Coastal and Marine Ecosystems, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange, New South Wales, 2800, Australia
| | - Brendan P Kelaher
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, 2450, Australia
| | - Melinda A Coleman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, 2450, Australia
- Department of Primary Industries, NSW Fisheries, Coffs Harbour, New South Wales, 2450, Australia
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12
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Hays CG, Hanley TC, Hughes AR, Truskey SB, Zerebecki RA, Sotka EE. Local Adaptation in Marine Foundation Species at Microgeographic Scales. THE BIOLOGICAL BULLETIN 2021; 241:16-29. [PMID: 34436968 DOI: 10.1086/714821] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AbstractNearshore foundation species in coastal and estuarine systems (e.g., salt marsh grasses, mangroves, seagrasses, corals) drive the ecological functions of ecosystems and entire biomes by creating physical structure that alters local abiotic conditions and influences species interactions and composition. The resilience of foundation species and the ecosystem functions they provide depends on their phenotypic and genetic responses to spatial and temporal shifts in environmental conditions. In this review, we explore what is known about the causes and consequences of adaptive genetic differentiation in marine foundation species over spatial scales shorter than dispersal capabilities (i.e., microgeographic scales). We describe the strength of coupling field and laboratory experiments with population genetic techniques to illuminate patterns of local adaptation, and we illustrate this approach by using several foundation species. Among the major themes that emerge from our review include (1) adaptive differentiation of marine foundation species repeatedly evolves along vertical (i.e., elevation or depth) gradients, and (2) mating system and phenology may facilitate this differentiation. Microgeographic adaptation is an understudied mechanism potentially underpinning the resilience of many sessile marine species, and this evolutionary mechanism likely has particularly important consequences for the ecosystem functions provided by foundation species.
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13
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Krug PJ, Shimer E, Rodriguez VA. Differential Tolerance and Seasonal Adaptation to Temperature and Salinity Stress at a Dynamic Range Boundary Between Estuarine Gastropods. THE BIOLOGICAL BULLETIN 2021; 241:105-122. [PMID: 34436970 DOI: 10.1086/715845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
AbstractInsight into how coastal organisms will respond to changing temperature and salinity regimes may be derived from studies of adaptation to fluctuating estuarine environments, especially under stressful range-edge conditions. We characterized a dynamic range boundary between two estuarine sea slugs, Alderia modesta (distributed across the North Pacific and North Atlantic) and Alderia willowi, known from southern and central California. The species overlap from Bodega Bay to San Francisco Bay, where populations are dominated by A. modesta after winter rains but by A. willowi after peak summer temperatures. Laboratory assays confirmed superior tolerance to low salinity for the northern species, A. modesta: encapsulated embryos developed at 8 ppt, larvae survived at 4-6 ppt, and adults survived repeated exposure to 2 ppt, salinities that reduced development or survival for the same stages of A. willowi. Adults did not appreciably differ in their high-temperature threshold, however. Each species showed increased tolerance to either temperature or salinity stress at its range margin, indicating plasticity or local adaptation, but at the cost of reduced tolerance to the other stressor. At its northern limit, A. willowi became more tolerant of low salinity during the winter rainy season, but also less heat tolerant. Conversely, A. modesta became more heat resistant from spring to summer at its southern limit, but less tolerant of low salinity. Trade-offs in stress tolerance may generally constrain adaptation and limit biotic response to a rapidly changing environment, as well as differentiating species niches.
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14
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Stelling‐Wood TP, Poore AGB, Gribben PE. Shifts in biomass and structure of habitat-formers across a latitudinal gradient. Ecol Evol 2021; 11:8831-8842. [PMID: 34257931 PMCID: PMC8258212 DOI: 10.1002/ece3.7714] [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: 01/25/2021] [Revised: 04/21/2021] [Accepted: 04/29/2021] [Indexed: 11/10/2022] Open
Abstract
Global patterns of plant biomass drive the distribution of much of the marine and terrestrial life on Earth. This is because their biomass and physical structure have important consequences for the communities they support by providing food and habitat. In terrestrial ecosystems, temperature is one of the major determinants of plant biomass and can influence plant and leaf morphology. In temperate marine systems, macroalgae are major habitat-formers and commonly display highly variable morphology in response to local environmental conditions. Variation in their morphology, and thus habitat structure on temperate reefs, however, is poorly understood across large scales. In this study, we used a trait-based approach to quantify morphological variability in subtidal rocky reefs dominated by the algal genus Sargassum along a latitudinal gradient, in southeastern Australia (~900 km). We tested whether large-scale variation in sea surface temperature (SST), site exposure, and nutrient availability can predict algal biomass and individual morphology. We found Sargassum biomass declined with increasing maximum SST. We also found that individual morphology varied with abiotic ocean variables. Frond size and intraindividual variability in frond size decreased with increasing with distance from the equator, as SST decreased and nitrate concentration increased. The shape of fronds displayed no clear relationship with any of the abiotic variables measured. These results suggest climate change will cause significant changes to the structure of Sargassum habitats along the southeastern coast of Australia, resulting in an overall reduction in biomass and increase in the prevalence of thalli with large, highly variable fronds. Using a space-for-time approach means shifts in morphological trait values can be used as early warning signs of impending species declines and regime shifts. Consequently, by studying traits and how they change across large scales we can potentially predict and anticipate the impacts of environmental change on these communities.
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Affiliation(s)
- Talia Peta Stelling‐Wood
- Evolution & Ecology Research CentreUNSW SydneySydneyNSWAustralia
- Centre of Marine Science and InnovationUNSW SydneySydneyNSWAustralia
| | - Alistair G. B. Poore
- Evolution & Ecology Research CentreUNSW SydneySydneyNSWAustralia
- Centre of Marine Science and InnovationUNSW SydneySydneyNSWAustralia
| | - Paul E. Gribben
- Centre of Marine Science and InnovationUNSW SydneySydneyNSWAustralia
- Sydney Institute of Marine ScienceMosmanNSWAustralia
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15
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Clark RD, Aardema ML, Andolfatto P, Barber PH, Hattori A, Hoey JA, Montes HR, Pinsky ML. Genomic signatures of spatially divergent selection at clownfish range margins. Proc Biol Sci 2021; 288:20210407. [PMID: 34102891 PMCID: PMC8187997 DOI: 10.1098/rspb.2021.0407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.
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Affiliation(s)
- René D. Clark
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Matthew L. Aardema
- Department of Biology, Montclair State University, 1 Normal Avenue, Montclair, NJ 07043, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 200 Central Park West, New York, NY 10024-5102, USA
| | - Peter Andolfatto
- Department of Biological Sciences, Columbia University, New York, NY 10026, USA
| | - Paul H. Barber
- Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Akihisa Hattori
- Faculty of Liberal Arts and Education, Shiga University, 2-5-1 Hiratsu, Otsu, Shiga 520-0862, Japan
| | - Jennifer A. Hoey
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
- Department of Ecology and Evolutionary Biology, University of California-Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | | | - Malin L. Pinsky
- Department of Ecology, Evolution and Natural Resources, Rutgers University, 14 College Farm Road, New Brunswick, NJ 08901, USA
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16
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Thomson AI, Archer FI, Coleman MA, Gajardo G, Goodall‐Copestake WP, Hoban S, Laikre L, Miller AD, O’Brien D, Pérez‐Espona S, Segelbacher G, Serrão EA, Sjøtun K, Stanley MS. Charting a course for genetic diversity in the UN Decade of Ocean Science. Evol Appl 2021; 14:1497-1518. [PMID: 34178100 PMCID: PMC8210796 DOI: 10.1111/eva.13224] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.
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Affiliation(s)
| | | | - Melinda A. Coleman
- New South Wales FisheriesNational Marine Science CentreCoffs HarbourNSWAustralia
- National Marine Science CentreSouthern Cross UniversityCoffs HarbourNSWAustralia
- Oceans Institute and School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Gonzalo Gajardo
- Laboratory of Genetics, Aquaculture & BiodiversityUniversidad de Los LagosOsornoChile
| | | | - Sean Hoban
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
| | - Linda Laikre
- Centre for Tree ScienceThe Morton ArboretumLisleILUSA
- The Wildlife Analysis UnitThe Swedish Environmental Protection AgencyStockholmSweden
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | | | - Sílvia Pérez‐Espona
- The Royal (Dick) School of Veterinary Studies and The Roslin InstituteMidlothianUK
| | - Gernot Segelbacher
- Chair of Wildlife Ecology and ManagementUniversity FreiburgFreiburgGermany
| | - Ester A. Serrão
- CCMARCentre of Marine SciencesFaculty of Sciences and TechnologyUniversity of AlgarveFaroPortugal
| | - Kjersti Sjøtun
- Department of Biological SciencesUniversity of BergenBergenNorway
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17
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Yue L, Cao LJ, Chen JC, Gong YJ, Lin YH, Hoffmann AA, Wei SJ. Low levels of genetic differentiation with isolation by geography and environment in populations of Drosophila melanogaster from across China. Heredity (Edinb) 2021; 126:942-954. [PMID: 33686193 PMCID: PMC8178374 DOI: 10.1038/s41437-021-00419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 01/31/2023] Open
Abstract
The fruit fly, Drosophila melanogaster, is a model species in evolutionary studies. However, population processes of this species in East Asia are poorly studied. Here we examined the population genetic structure of D. melanogaster across China. There were 14 mitochondrial haplotypes with 10 unique ones out of 23 known from around the globe. Pairwise FST values estimated from 15 novel microsatellites ranged from 0 to 0.11, with geographically isolated populations showing the highest level of genetic uniqueness. STRUCTURE analysis identified high levels of admixture at both the individual and population levels. Mantel tests indicated a strong association between genetic distance and geographical distance as well as environmental distance. Full redundancy analysis (RDA) showed that independent effects of environmental conditions and geography accounted for 62.10% and 31.58% of the total explained genetic variance, respectively. When geographic variables were constrained in a partial RDA analysis, the environmental variables bio2 (mean diurnal air temperature range), bio13 (precipitation of the wettest month), and bio15 (precipitation seasonality) were correlated with genetic distance. Our study suggests that demographic history, geographical isolation, and environmental factors have together shaped the population genetic structure of D. melanogaster after its introduction into China.
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Affiliation(s)
- Lei Yue
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Li-Jun Cao
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jin-Cui Chen
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ya-Jun Gong
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yan-Hao Lin
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China ,International Department of Beijing No. 80 High School, Beijing, China
| | - Ary Anthony Hoffmann
- grid.1008.90000 0001 2179 088XBio21 Institute, School of BioSciences, The University of Melbourne, Victoria, Australia
| | - Shu-Jun Wei
- grid.418260.90000 0004 0646 9053Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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18
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Wood G, Marzinelli EM, Campbell AH, Steinberg PD, Vergés A, Coleman MA. Genomic vulnerability of a dominant seaweed points to future-proofing pathways for Australia's underwater forests. GLOBAL CHANGE BIOLOGY 2021; 27:2200-2212. [PMID: 33511779 DOI: 10.1111/gcb.15534] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Globally, critical habitats are in decline, threatening ecological, economic and social values and prompting calls for 'future proofing' efforts that enhance resilience to climate change. Such efforts rely on predicting how neutral and adaptive genomic patterns across a species' distribution will change under future climate scenarios, but data is scant for most species of conservation concern. Here, we use seascape genomics to characterise genetic diversity, structure and gene-environmental associations in a dominant forest-forming seaweed, Phyllospora comosa, along its entire latitudinal (12° latitude), and thermal (~14°C) range. Phyllospora showed high connectivity throughout its central range, with evidence of genetic structure and potential selection associated with sea surface temperatures (SSTs) at its rear and leading edges. Rear and leading-edge populations harboured only half the genetic diversity of central populations. By modelling genetic turnover as a function of SST, we assessed the genomic vulnerability across Phyllospora's distributional range under climate change scenarios. Despite low diversity, range-edge populations were predicted to harbour beneficial adaptations to marginal conditions and overall adaptability of the species may be compromised by their loss. Assisted gene flow from range edge populations may be required to enhance adaptation and increase resilience of central and leading-edge populations under warming oceans. Understanding genomic vulnerability can inform proactive restoration and future-proofing strategies for underwater forests and ensure their persistence in changing oceans.
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Affiliation(s)
- Georgina Wood
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Alexandra H Campbell
- USC Seaweed Research Group, University of the Sunshine Coast, Sunshine Coast, Qld, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
- Sydney Institute of Marine Science, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Adriana Vergés
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Melinda A Coleman
- Department of Primary Industries, National Marine Science Centre, Coffs Harbour, NSW, Australia
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19
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Lewis RD, Johnson CR, Wright JT. Demography of the Intertidal Fucoid Hormosira banksii: Importance of Recruitment to Local Abundance. JOURNAL OF PHYCOLOGY 2021; 57:664-676. [PMID: 33406291 DOI: 10.1111/jpy.13124] [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: 12/04/2019] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Canopy-forming macroalgae form the basis of diverse coastal ecosystems globally. The fucoid Hormosira banksii is often the dominant canopy-forming macroalga in the temperate intertidal of southern Australia and New Zealand, where it is commonly associated with an understory of coralline turf. Hormosira banksii is susceptible to both natural and anthropogenic disturbance and despite its abundance, few studies have examined the demography of this important species. This study determined the demographic response of H. banksii to different gradients of disturbance to both its canopy and to the understory coralline turf. We established plots in which the density of H. banksii and/or understory coralline turf was manipulated in a pulse perturbation to simulate a disturbance event. The manipulated plots contained eight treatments ranging from 100% removal of H. banksii to 100% removal of the understory coralline turf. We then measured recruitment and followed individual recruits for up to 18 months to determine growth and survivorship. We found that H. banksii recruitment was seasonally variable throughout the experiment and highest over summer, survivorship of recruits was generally high, and the species was slow-growing and long-lived. Moreover, the level of disturbance did not seem to affect recruitment, growth, or survivorship and post-recruitment mortality was independent of H. banksii density. In this system, it appears that H. banksii is a relatively long-lived perennial species whose demography is density-independent which appears to allow recovery from disturbance.
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Affiliation(s)
- Ryan D Lewis
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 129, Hobart, Tasmania, 7001, Australia
| | - Craig R Johnson
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 129, Hobart, Tasmania, 7001, Australia
| | - Jeffrey T Wright
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 129, Hobart, Tasmania, 7001, Australia
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20
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Hoffmann AA, Miller AD, Weeks AR. Genetic mixing for population management: From genetic rescue to provenancing. Evol Appl 2021; 14:634-652. [PMID: 33767740 PMCID: PMC7980264 DOI: 10.1111/eva.13154] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/10/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.
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Affiliation(s)
- Ary A. Hoffmann
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
| | - Adam D. Miller
- School of Life and Environmental SciencesCentre for Integrative EcologyDeakin UniversityWarrnamboolVic.Australia
- Deakin Genomics CentreDeakin UniversityGeelongVic.Australia
| | - Andrew R. Weeks
- School of BioSciencesBio21 InstituteThe University of MelbourneParkvilleVic.Australia
- cesar Pty LtdParkvilleVic.Australia
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21
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Cortés AJ, López-Hernández F, Osorio-Rodriguez D. Predicting Thermal Adaptation by Looking Into Populations' Genomic Past. Front Genet 2020; 11:564515. [PMID: 33101385 PMCID: PMC7545011 DOI: 10.3389/fgene.2020.564515] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/24/2020] [Indexed: 12/18/2022] Open
Abstract
Molecular evolution offers an insightful theory to interpret the genomic consequences of thermal adaptation to previous events of climate change beyond range shifts. However, disentangling often mixed footprints of selective and demographic processes from those due to lineage sorting, recombination rate variation, and genomic constrains is not trivial. Therefore, here we condense current and historical population genomic tools to study thermal adaptation and outline key developments (genomic prediction, machine learning) that might assist their utilization for improving forecasts of populations' responses to thermal variation. We start by summarizing how recent thermal-driven selective and demographic responses can be inferred by coalescent methods and in turn how quantitative genetic theory offers suitable multi-trait predictions over a few generations via the breeder's equation. We later assume that enough generations have passed as to display genomic signatures of divergent selection to thermal variation and describe how these footprints can be reconstructed using genome-wide association and selection scans or, alternatively, may be used for forward prediction over multiple generations under an infinitesimal genomic prediction model. Finally, we move deeper in time to comprehend the genomic consequences of thermal shifts at an evolutionary time scale by relying on phylogeographic approaches that allow for reticulate evolution and ecological parapatric speciation, and end by envisioning the potential of modern machine learning techniques to better inform long-term predictions. We conclude that foreseeing future thermal adaptive responses requires bridging the multiple spatial scales of historical and predictive environmental change research under modern cohesive approaches such as genomic prediction and machine learning frameworks.
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Affiliation(s)
- Andrés J Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia.,Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia - Sede Medellín, Medellín, Colombia
| | - Felipe López-Hernández
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Daniela Osorio-Rodriguez
- Division of Geological and Planetary Sciences, California Institute of Technology (Caltech), Pasadena, CA, United States
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22
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Miller AD, Nitschke C, Weeks AR, Weatherly WL, Heyes SD, Sinclair SJ, Holland OJ, Stevenson A, Broadhurst L, Hoebee SE, Sherman CDH, Morgan JW. Genetic data and climate niche suitability models highlight the vulnerability of a functionally important plant species from south-eastern Australia. Evol Appl 2020; 13:2014-2029. [PMID: 32908601 PMCID: PMC7463319 DOI: 10.1111/eva.12958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/23/2020] [Accepted: 03/02/2020] [Indexed: 11/28/2022] Open
Abstract
Habitat fragmentation imperils the persistence of many functionally important species, with climate change a new threat to local persistence due to climate niche mismatching. Predicting the evolutionary trajectory of species essential to ecosystem function under future climates is challenging but necessary for prioritizing conservation investments. We use a combination of population genetics and niche suitability models to assess the trajectory of a functionally important, but highly fragmented, plant species from south-eastern Australia (Banksia marginata, Proteaceae). We demonstrate significant genetic structuring among, and high level of relatedness within, fragmented remnant populations, highlighting imminent risks of inbreeding. Population simulations, controlling for effective population size (N e), suggest that many remnant populations will suffer rapid declines in genetic diversity due to drift in the absence of intervention. Simulations were used to demonstrate how inbreeding and drift processes might be suppressed by assisted migration and population mixing approaches that enhance the size and connectivity of remnant populations. These analyses were complemented by niche suitability models that predicted substantial reductions of suitable habitat by 2080; ~30% of the current distribution of the species climate niche overlaps with the projected distribution of the species climate niche in the geographic region by the 2080s. Our study highlights the importance of conserving remnant populations and establishing new populations in areas likely to support B. marginata in the future, and adopting seed sourcing strategies that can help populations overcome the risks of inbreeding and maladaptation. We also argue that ecological replacement of B. marginata using climatically suited plant species might be needed in the future to maintain ecosystem processes where B. marginata cannot persist. We recommend the need for progressive revegetation policies and practices to prevent further deterioration of species such as B. marginata and the ecosystems they support.
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Affiliation(s)
- Adam D. Miller
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVicAustralia
| | - Craig Nitschke
- School of Ecosystem and Forest SciencesThe University of MelbourneRichmondVicAustralia
| | - Andrew R. Weeks
- School of BioSciencesThe University of MelbourneParkvilleVicAustralia
| | | | - Simon D. Heyes
- Department of Ecology, Environment and EvolutionLa Trobe UniversityBundooraVicAustralia
| | - Steve J. Sinclair
- Department of Environment, Land, Water and PlanningArthur Rylah InstituteHeidelbergVicAustralia
| | - Owen J. Holland
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVicAustralia
| | - Aggie Stevenson
- Glenelg Hopkins Catchment Management AuthorityHamiltonVicAustralia
| | - Linda Broadhurst
- Centre for Australian National Biodiversity ResearchCSIRO National Research CollectionsCanberraACTAustralia
| | - Susan E. Hoebee
- Department of Ecology, Environment and EvolutionLa Trobe UniversityBundooraVicAustralia
| | - Craig D. H. Sherman
- Centre for Integrative EcologySchool of Life and Environmental SciencesDeakin UniversityGeelongVicAustralia
- Deakin Genomics CentreDeakin UniversityGeelongVicAustralia
| | - John W. Morgan
- Department of Ecology, Environment and EvolutionLa Trobe UniversityBundooraVicAustralia
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23
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Liesner D, Fouqueau L, Valero M, Roleda MY, Pearson GA, Bischof K, Valentin K, Bartsch I. Heat stress responses and population genetics of the kelp Laminaria digitata (Phaeophyceae) across latitudes reveal differentiation among North Atlantic populations. Ecol Evol 2020; 10:9144-9177. [PMID: 32953052 PMCID: PMC7487260 DOI: 10.1002/ece3.6569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 12/26/2022] Open
Abstract
To understand the thermal plasticity of a coastal foundation species across its latitudinal distribution, we assess physiological responses to high temperature stress in the kelp Laminaria digitata in combination with population genetic characteristics and relate heat resilience to genetic features and phylogeography. We hypothesize that populations from Arctic and cold-temperate locations are less heat resilient than populations from warm distributional edges. Using meristems of natural L. digitata populations from six locations ranging between Kongsfjorden, Spitsbergen (79°N), and Quiberon, France (47°N), we performed a common-garden heat stress experiment applying 15°C to 23°C over eight days. We assessed growth, photosynthetic quantum yield, carbon and nitrogen storage, and xanthophyll pigment contents as response traits. Population connectivity and genetic diversity were analyzed with microsatellite markers. Results from the heat stress experiment suggest that the upper temperature limit of L. digitata is nearly identical across its distribution range, but subtle differences in growth and stress responses were revealed for three populations from the species' ecological range margins. Two populations at the species' warm distribution limit showed higher temperature tolerance compared to other populations in growth at 19°C and recovery from 21°C (Quiberon, France), and photosynthetic quantum yield and xanthophyll pigment responses at 23°C (Helgoland, Germany). In L. digitata from the northernmost population (Spitsbergen, Norway), quantum yield indicated the highest heat sensitivity. Microsatellite genotyping revealed all sampled populations to be genetically distinct, with a strong hierarchical structure between southern and northern clades. Genetic diversity was lowest in the isolated population of the North Sea island of Helgoland and highest in Roscoff in the English Channel. All together, these results support the hypothesis of moderate local differentiation across L. digitata's European distribution, whereas effects are likely too weak to ameliorate the species' capacity to withstand ocean warming and marine heatwaves at the southern range edge.
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Affiliation(s)
- Daniel Liesner
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Louise Fouqueau
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, UC, UACH, Station Biologique de RoscoffRoscoff CedexFrance
| | - Myriam Valero
- UMI EBEA 3614, Evolutionary Biology and Ecology of Algae, CNRSSorbonne Université, UC, UACH, Station Biologique de RoscoffRoscoff CedexFrance
| | - Michael Y. Roleda
- Norwegian Institute of Bioeconomy ResearchBodøNorway
- The Marine Science Institute, College of ScienceUniversity of the Philippines, DilimanQuezon CityPhilippines
| | | | - Kai Bischof
- Marine BotanyUniversity of BremenBremenGermany
| | - Klaus Valentin
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
| | - Inka Bartsch
- Alfred Wegener InstituteHelmholtz Centre for Polar and Marine ResearchBremerhavenGermany
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