Hughes, T. P. et al. Global warming and recurrent mass bleaching of corals. Nature 543, 373–377 (2017).
Bellwood, D. R., Hughes, T. P., Folke, C. & Nyström, M. Confronting the coral reef crisis. Nature 429, 827–833 (2004).
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).
Van Hooidonk, R., Maynard, J. A. & Planes, S. Temporary refugia for coral reefs in a warming world. Nat. Clim. Chang. 3, 508–511 (2013).
Costanza, R. et al. Changes in the global value of ecosystem services. Glob. Environ. Chang. 26, 152–158 (2014).
Moberg, F. & Folke, C. Ecological goods and services of coral reef ecosystems. Ecol. Econ. 29, 215–233 (1999).
Hughes, T. P. et al. Ecological memory modifies the cumulative impact of recurrent climate extremes. Nat. Clim. Change 9, 40–43 (2019).
Krueger, T. et al. Common reef-building coral in the northern red sea resistant to elevated temperature and acidification. R. Soc. Open Sci. 4, 170038 (2017).
Penin, L., Vidal-Dupiol, J. & Adjeroud, M. Response of coral assemblages to thermal stress: are bleaching intensity and spatial patterns consistent between events?. Environ. Monit. Assess. 185, 5031–5042 (2013).
Thompson, D. M. & van Woesik, R. Corals escape bleaching in regions that recently and historically experienced frequent thermal stress. Proc. Biol. Sci. 276, 2893–2901 (2009).
Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. Nat. Commun. 10, 1–5 (2019).
Thomas, L. et al. Mechanisms of thermal tolerance in reef-building corals across a fine-grained environmental mosaic: lessons from Ofu, American Samoa. Front. Mar. Sci. 4, 434 (2018).
Bay, R. A. & Palumbi, S. R. Multilocus adaptation associated with heat resistance in reef-building corals. Curr. Biol. 24, 2952–2956 (2014).
Wilson, K. L., Tittensor, D. P., Worm, B. & Lotze, H. K. Incorporating climate change adaptation into marine protected area planning. Glob. Chang. Biol. 26, 3251–3267 (2020).
Baums, I. B. et al. Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic. Ecol. Appl. 29, (2019).
Matz, M. V., Treml, E. & Haller, B. C. Predicting coral adaptation to global warming in the Indo-West-Pacific. BioRxiv https://doi.org/10.1101/722314 (2019).
Selmoni, O., Rochat, E., Lecellier, G., Berteaux-Lecellier, V. & Joost, S. Seascape genomics as a new tool to empower coral reef conservation strategies: an example on north-western Pacific Acropora digitifera. Evol. Appl. https://doi.org/10.1101/588228 (2020).
Riginos, C., Crandall, E. D., Liggins, L., Bongaerts, P. & Treml, E. A. Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr. Zool. https://doi.org/10.1093/cz/zow067 (2016).
Maina, J., Venus, V., McClanahan, T. R. & Ateweberhan, M. Modelling susceptibility of coral reefs to environmental stress using remote sensing data and GIS models. Ecol. Modell. 212, 180–199 (2008).
Liu, G., Strong, A. E. & Skirving, W. Remote sensing of sea surface temperatures during 2002 Barrier Reef coral bleaching. Eos Trans. Am. Geophys. Union 84, 137–141 (2003).
Rochat, E. & Joost, S. Spatial areas of genotype probability (SPAG): predicting the spatial distribution of adaptive genetic variants under future climatic conditions. BioRxiv. https://doi.org/10.1101/2019.12.20.884114 (2019).
Boulanger, E., Dalongeville, A., Andrello, M., Mouillot, D. & Manel, S. Spatial graphs highlight how multi-generational dispersal shapes landscape genetic patterns. Ecography (Cop) https://doi.org/10.1111/ecog.05024 (2020).
Selmoni, O. et al. Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species. BioRxiv. https://doi.org/10.1101/2020.05.12.090050 (2020).
Job, S. New Caledonia network of coral reef observation (RORC) – Field campaign report 2017–2018. (French title: Réseau d’observation des récifs coralliens (RORC) de Nouvelle-Calédonie. Campagne 2017–2018. Rapport Pays. Rapport CORTEX. Pour le compte de : Conservatoire d’espaces naturels de Nouvelle-Calédonie – Province des îles Loyauté – Observatoire de l’environnement). (CORTEX, New Caledonia, 2018).
Lefèvre, J., Marchesiello, P., Jourdain, N. C., Menkes, C. & Leroy, A. Weather regimes and orographic circulation around New Caledonia. Mar. Pollut. Bull. 61, 413–431 (2010).
Marchesiello, P., Lefèvre, J., Vega, A., Couvelard, X. & Menkes, C. Coastal upwelling, circulation and heat balance around New Caledonia’s barrier reef. Mar. Pollut. Bull. 61, 432–448 (2010).
Berkelmans, R., Weeks, S. J. & Steinberga, C. R. Upwelling linked to warm summers and bleaching on the Great Barrier Reef. Limnol. Oceanogr. 55, 2634–2644 (2010).
Cravatte, S. et al. Regional circulation around New Caledonia from two decades of observations. J. Mar. Syst. 148, 249–271 (2015).
Hénin, C., Guillerm, J. & Chabert, L. Circulation superficielle autour de la Nouvelle-Calédonie. Océanographie Trop. 19, 113–126 (1984).
Magris, R. A., Pressey, R. L., Weeks, R. & Ban, N. C. Integrating connectivity and climate change into marine conservation planning. Biol. Cons. 170, 207–221 (2014).
Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).
Welle, P. D., Small, M. J., Doney, S. C. & Azevedo, I. L. Estimating the effect of multiple environmental stressors on coral bleaching and mortality. PLoS ONE 12, e0175018 (2017).
Kenkel, C. D., Almanza, A. T. & Matz, M. V. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 96, 3197–3212 (2015).
Palumbi, S. R. Population genetics, demographic connectivity, and the design of marine reserves. Ecol. Appl. 13, 146–158 (2003).
Hock, K. et al. Connectivity and systemic resilience of the Great Barrier Reef. PLoS Biol. 15, (2017).
Robinson, J. P. W., Wilson, S. K. & Graham, N. A. J. Abiotic and biotic controls on coral recovery 16 years after mass bleaching. Coral Reefs 38, 1255–1265 (2019).
Kawecki, T. J. Adaptation to marginal habitats. Annu. Rev. Ecol. Evol. Syst. 39, 321–342 (2008).
Treml, E. A. et al. Reproductive output and duration of the pelagic larval stage determine seascape-wide connectivity of marine populations. Integr. Comp. Biol. 52, 525–537 (2012).
Storlazzi, C. D., van Ormondt, M., Chen, Y.-L. & Elias, E. P. L. Modeling fine-scale coral larval dispersal and interisland connectivity to help designate mutually-supporting coral reef marine protected areas: insights from Maui Nui, Hawaii. Front. Mar. Sci. 4, 381 (2017).
Colberg, F., Brassington, G. B., Sandery, P., Sakov, P. & Aijaz, S. High and medium resolution ocean models for the Great Barrier Reef. Ocean Model. 145, 101507 (2020).
Andréfouët, S., Cabioch, G., Flamand, B. & Pelletier, B. A reappraisal of the diversity of geomorphological and genetic processes of New Caledonian coral reefs: A synthesis from optical remote sensing, coring and acoustic multibeam observations. Coral Reefs 28, 691–707 (2009).
Dalleau, M. et al. Use of habitats as surrogates of biodiversity for efficient coral reef conservation planning in Pacific Ocean islands. Conserv. Biol. 24, 541–552 (2010).
Loya, Y. et al. Coral bleaching: the winners and the losers. Ecol. Lett. 4, 122–131 (2001).
Darling, E. S., Alvarez-Filip, L., Oliver, T. A., McClanahan, T. R. & Côté, I. M. Evaluating life-history strategies of reef corals from species traits. Ecol. Lett. 15, 1378–1386 (2012).
Ayre, D. J. & Hughes, T. P. Genotypic diversity and gene flow in brooding and spawning corals along the great barrier reef, Australia. Evolution (NY) 54, 1590–1605 (2000).
Kawecki, T. J. & Ebert, D. Conceptual issues in local adaptation. Ecol. Lett. 7, 1225–1241 (2004).
Selmoni, O., Vajana, E., Guillaume, A., Rochat, E. & Joost, S. Sampling strategy optimization to increase statistical power in landscape genomics: A simulation-based approach. Mol. Ecol. Resour. 20, (2020).
EU Copernicus Marine Service. Global Ocean – In-Situ-Near-Real-Time Observations. (2017). Available at: https://marine.copernicus.eu. Accessed: 2nd February 2017
Merchant, C. J. et al. Satellite-based time-series of sea-surface temperature since 1981 for climate applications. Sci. data 6, 223 (2019).
UNEP-WCMC, WorldFish-Center, WRI & TNC. Global distribution of warm-water coral reefs, compiled from multiple sources including the Millennium Coral Reef Mapping Project. Version 1.3. (2010). Available at: https://data.unep-wcmc.org/datasets/1. Accessed: 9th May 2017
QGIS development team. QGIS Geographic Information System. Open Source Geospatial Foundation Project. (2009).
Hijmans, R. J. raster: Geographic Data Analysis and Modeling. (2016).
R Core Team. R: A Language and Environment for Statistical Computing. (2016).
Ryan, W. B. F. et al. Global multi-resolution topography synthesis. Geochemistry, Geophys. Geosystems 10, (2009).
van Etten, J. gdistance: Distances and Routes on Geographical Grids. (2018). Available at: https://cran.r-project.org/package=gdistance.
Kilian, A. et al. Diversity arrays technology: A generic genome profiling technology on open platforms. Methods Mol. Biol. 888, 67–89 (2012).
Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326–3328 (2012).
Frichot, E., Schoville, S. D., Bouchard, G. & François, O. Testing for associations between loci and environmental gradients using latent factor mixed models. Mol. Biol. Evol. 30, 1687–1699 (2013).
Joost, S. et al. A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Mol. Ecol. 16, 3955–3969 (2007).
Brooks, M. E. et al. glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. R J. 9, 378–400 (2017).
Breheny, P. & Burchett, W. Visualization of regression models using visreg. R J. 9, 56–71 (2017).
Xuereb, A., Kimber, C. M., Curtis, J. M. R., Bernatchez, L. & Fortin, M. Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction-site associated DNA sequencing data. Mol. Ecol. 27, 5035–5048 (2018).
Benestan, L. et al. Seascape genomics provides evidence for thermal adaptation and current-mediated population structure in American lobster (Homarus americanus). Mol. Ecol. 25, 5073–5092 (2016).
Legendre, P. & Gallagher, E. D. Ecologically meaningful transformations for ordination of species data. Oecologia 129, 271–280 (2001).
Borcard, D. & Legendre, P. All-scale spatial analysis of ecological data by means of principal coordinates of neighbour matrices. Ecol. Modell. 153, 51–68 (2002).
Dixon, P. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14, 927–930 (2003).
Ferrari, S. L. P. & Cribari-Neto, F. Beta regression for modelling rates and proportions. J. Appl. Stat. 31, 799–815 (2004).
Verbeke, G., Molenberghs, G. & Rizopoulos, D. Random effects models for longitudinal data. In Longitudinal Research with Latent Variables 37–96 (Springer, Berlin, 2010). https://doi.org/10.1007/978-3-642-11760-2_2
Garcia, T. P. & Marder, K. Statistical approaches to longitudinal data analysis in neurodegenerative diseases: Huntington’s disease as a model. Curr. Neurol. Neurosci. Rep. 17, 14 (2017).
Bozdogan, H. Model selection and Akaike’s Information Criterion (AIC): the general theory and its analytical extensions. Psychometrika 52, 345–370 (1987).
Source: Ecology - nature.com
