Abstract
Marine protected areas are an important tool to recover and protect coral reef biodiversity. Connected networks of individual marine protected areas enhance system-wide resilience and persistence via the exchange of individuals, supporting greater population sizes and functional genetic diversity. Conservation area networks are typically designed with a systematic spatial planning process. New perspectives and emerging methods enable the long-standing goal to incorporate connectivity as a conservation feature with the aim of maximizing larval flow within the network. Additionally, there is growing recognition that protected area networks that support adaptive evolutionary change make the long-term survival of coral reefs more likely. Genetic data and evolutionary principles can feed into the planning process by providing measures of dispersal connectivity and adaptation potential. Here, we review genetic and genomic approaches to estimate dispersal connectivity and the geography of adaptation for corals. We outline key conservation objectives that can be informed by genetic data, propose surrogates for connectivity and adaptation features, and recommend future pathways to improve the uptake of genetic information for reef conservation such that management actions that prioritize connectivity and adaptation can be realized.
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References
Abesamis RA, Saenz-Agudelo P, Berumen ML, Bode M, Jadloc CRL, Solera LA, Villanoy CL, Bernardo LPC, Alcala AC, Russ GR (2017) Reef-fish larval dispersal patterns validate no-take marine reserve network connectivity that links human communities. Coral Reefs 36:791–801. https://doi.org/10.1007/s00338-017-1570-0
Almany GR, Berumen ML, Thorrold SR, Planes S, Jones GP (2007) Local replenishment of coral reef fish populations in a marine reserve. Science 316:742–744. https://doi.org/10.1126/science.1140597
Almany GR, Planes S, Thorrold SR, Berumen ML, Bode M, Saenz-Agudelo P, Bonin MC, Frisch AJ, Harrison HB, Messmer V, Nanninga GB, Priest MA, Srinivasan M, Sinclair-Taylor T, Williamson DH, Jones GP (2017) Larval fish dispersal in a coral-reef seascape. Nat Ecol Evol 1:0148–0148. https://doi.org/10.1038/s41559-017-0148
Álvarez-Romero JG, Munguia-Vega A, Beger M, Mar Mancha Cisneros M, Suárez Castillo AN, Gurney GG, Pressey RL, Gerber LR, Morzaria Luna HN, Reyes Bonilla H, Adams VM, Kolb M, Graham EM, VanDerWal J, Castillo López A, Hinojosa Arango G, Petatán Ramírez D, Moreno-Baez M, Godínez Reyes CR, Torre J (2017) Designing connected marine reserves in the face of global warming. Glob Chang Biol 24:e671–e691. https://doi.org/10.1111/gcb.13989
Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229
Anthony KRN, Helmstedt KJ, Bay LK, Fidelman P, Hussey KE, Lundgren P, Mead D, McLeod IM, Mumby PJ, Newlands M, Schaffelke B, Wilson KA, Hardisty PE (2020) Interventions to help coral reefs under global change-a complex decision challenge. PLoS One 15:e0236399. https://doi.org/10.1371/journal.pone.0236399
Arnaud-Haond S, Duarte CM, Alberto F, Serrao EA (2007) Standardizing methods to address clonality in population studies. Mol Ecol 16:5115–5139. https://doi.org/10.1111/j.1365-294X.2007.03535.x
Bailleul D, Stoeckel S, Arnaud-Haond S, Poisot T (2016) RClone: a package to identify MultiLocus clonal lineages and handle clonal data sets in R. Methods Ecol Evol 7:966–970. https://doi.org/10.1111/2041-210x.12550
Baird AH, Guest JR, Willis BL (2009) Systematic and biogeographical patterns in the reproductive biology of scleractinian corals. Annu Rev Ecol Evol Syst 40:551–571. https://doi.org/10.1146/annurev.ecolsys.110308.120220
Bairos-Novak KR, Hoogenboom MO, van Oppen MJH, Connolly SR (2021) Coral adaptation to climate change: meta-analysis reveals high heritability across multiple traits. Glob Chang Biol 27:5694–5710. https://doi.org/10.1111/gcb.15829
Baker N, Beger M, McClennen C, Ishoda A, Edwards F (2011) Reimaanlok: a national framework for conservation area planning in the Marshall Islands. J Mar Biol 2011
Balbar AC, Metaxas A (2019) The current application of ecological connectivity in the design of marine protected areas. Global Ecology and Conservation 17:e00569
Ball IR, Possingham HP, Watts M (2009) Marxan and relatives: software for spatial conservation prioritisation. In: Moilanen A, Wilson KA, Possingham HP (eds) Spatial conservation prioritisation: quantitative methods and computational tools. Oxford University Press, Oxford, UK, pp 185–195
Balloux F, Lehmann L, de Meeüs T (2003) The population genetics of clonal and partially clonal diploids. Genetics 164:1635–1644. https://doi.org/10.1093/genetics/164.4.1635
Baums IB, Boulay JN, Polato NR, Hellberg ME (2012) No gene flow across the eastern Pacific barrier in the reef-building coral Porites lobata. Mol Ecol 21:5418–5433. https://doi.org/10.1111/j.1365-294X.2012.05733.x
Baums IB, Miller MW (2006) Geographic variation in clonal structure in a reef-building Caribbean coral, Acropora palmata. Ecol Monogr 76:503–519. https://doi.org/10.1890/0012-9615(2006)076[0503:GVICSI]2.0.CO;2
Bayraktarov E, Stewart-Sinclair PJ, Brisbane S, Boström-Einarsson L, Saunders MI, Lovelock CE, Possingham HP, Mumby PJ, Wilson KA (2019) Motivations, success, and cost of coral reef restoration. Restor Ecol 27:981–991
Becheler R, Cassone A-L, Noël P, Mouchel O, Morrison CL, Arnaud-Haond S (2017) Low incidence of clonality in cold water corals revealed through the novel use of a standardized protocol adapted to deep sea sampling. Deep-Sea Res II Top Stud Oceanogr 145:120–130. https://doi.org/10.1016/j.dsr2.2015.11.013
Beerli P, Mashayekhi S, Sadeghi M, Khodaei M, Shaw K (2019) Population genetic inference with MIGRATE. Curr Protoc Bioinformatics 68:e87. https://doi.org/10.1002/cpbi.87
Beger M, Linke S, Watts M, Game E, Treml EA, Ball I, Possingham HP (2010) Incorporating asymmetric connectivity into spatial decision making for conservation. Cons Lett 3:359–368. https://doi.org/10.1111/j.1755-263X.2010.00123.x
Beger M, McGowan J, Treml EA, Green AL, White AT, Wolff NH, Klein CJ, Mumby PJ, Possingham HP (2015) Integrating regional conservation priorities for multiple objectives into national policy. Nat Commun 6:8208. https://doi.org/10.1038/ncomms9208
Beger M, Selkoe KA, Treml EA, Barber PH, von der Heyden S, Crandall ED, Toonen RJ, Riginos C (2014) Evolving coral reef conservation with genetic information. Bull Mar Sci 90:159–185. https://doi.org/10.5343/bms.2012.1106
Beyer HL, Kennedy EV, Beger M, Chen CA, Cinner JE, Darling ES, Eakin CM, Gates RD, Heron SF, Knowlton N, Obura DO, Palumbi SR, Possingham HP, Puotinen M, Runting RK, Skirving WJ, Spalding M, Wilson KA, Wood S, Veron JE, Hoegh-Guldberg O (2018) Risk-sensitive planning for conserving coral reefs under rapid climate change. Cons Lett 11:e12587. https://doi.org/10.1111/conl.12587
Bierne N, Gagnaire P-A, David P (2013) The geography of introgression in a patchy environment and the thorn in the side of ecological speciation. Curr Zool 59:72–86. https://doi.org/10.1093/czoolo/59.1.72
Bode M, Leis JM, Mason LB, Williamson DH, Harrison HB, Choukroun S, Jones GP (2019) Successful validation of a larval dispersal model using genetic parentage data. PLoS Biol 17:e3000380. https://doi.org/10.1371/journal.pbio.3000380
Bode M, Williamson DH, Harrison HB, Outram N, Jones GP (2017) Estimating dispersal kernels using genetic parentage data. Methods Ecol Evol 9:490–501. https://doi.org/10.1111/2041-210x.12922
Bode M, Williamson DH, Weeks R, Jones GP, Almany GR, Harrison HB, Hopf JK, Pressey RL (2016) Planning marine reserve networks for both feature representation and demographic persistence using connectivity patterns. PLoS One 11:e0154272. https://doi.org/10.1371/journal.pone.0154272
Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015) Prevalent endosymbiont zonation shapes the depth distributions of scleractinian coral species. R Soc Open Sci 2:140297. https://doi.org/10.1098/rsos.140297
Bongaerts P, Cooke IR, Ying H, Wels D, den Haan S, Hernandez-Agreda A, Brunner CA, Dove S, Englebert N, Eyal G, Foret S, Grinblat M, Hay KB, Harii S, Hayward DC, Lin Y, Mihaljevic M, Moya A, Muir P, Sinniger F, Smallhorn-West P, Torda G, Ragan MA, van Oppen MJH, Hoegh-Guldberg O (2021) Morphological stasis masks ecologically divergent coral species on tropical reefs. Curr Biol 31(2286–2298):e2288. https://doi.org/10.1016/j.cub.2021.03.028
Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJA, Bak RPM, Visser PM, Hoegh-Guldberg O (2013) Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evol Biol 13:1–1. https://doi.org/10.1186/1471-2148-13-205
Bongaerts P, Riginos C, Brunner R, Englebert N, Smith SR, Hoegh-Guldberg O (2017) Deep reefs are not universal refuges: reseeding potential varies among coral species. Sci Adv 3:e1602373. https://doi.org/10.1126/sciadv.1602373
Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O (2010) Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. PLoS One 5:e10871. https://doi.org/10.1371/journal.pone.0010871
Boscari E, Abbiati M, Badalamenti F, Bavestrello G, Benedetti-Cecchi L, Cannas R, Cau A, Cerrano C, Chimienti G, Costantini F, Fraschetti S, Ingrosso G, Marino IAM, Mastrototaro F, Papetti C, Paterno M, Ponti M, Zane L, Congiu L, Zhan A (2019) A population genomics insight by 2b-RAD reveals populations' uniqueness along the Italian coastline in Leptopsammia pruvoti (Scleractinia, Dendrophylliidae). Divers Distrib 25:1101–1117. https://doi.org/10.1111/ddi.12918
Bostrom-Einarsson L, Babcock RC, Bayraktarov E, Ceccarelli D, Cook N, Ferse SCA, Hancock B, Harrison P, Hein M, Shaver E, Smith A, Suggett D, Stewart-Sinclair PJ, Vardi T, McLeod IM (2020) Coral restoration - a systematic review of current methods, successes, failures and future directions. PLoS One 15:e0226631. https://doi.org/10.1371/journal.pone.0226631
Botsford LW, White JW, Coffroth MA, Paris CB, Planes S, Shearer TL, Thorrold SR (2009) Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs. Coral Reefs 28:327–337. https://doi.org/10.1007/s00338-009-0466-z
Broquet T, Petit EJ (2009) Molecular estimation of dispersal for ecology and population genetics. Annu Rev Ecol Evol Syst 40:193–216. https://doi.org/10.1146/annurev.ecolsys.110308.120324
Brown CJ, Harborne AR, Paris CB, Mumby PJ (2016) Uniting paradigms of connectivity in marine ecology. Ecology 97:2447–2457. https://doi.org/10.1002/ecy.1463
Bryan-Brown DN, Brown CJ, Hughes JM, Connolly RM (2017) Patterns and trends in marine population connectivity research. Mar Ecol Prog Ser 585:243–256
Budd AF, Pandolfi JM (2010) Evolutionary novelty is concentrated at the edge of coral species distributions. Science 328:1558–1561. https://doi.org/10.1126/science.1188947
Capdevila P, Stott I, Beger M, Salguero-Gómez R (2020) Towards a comparative framework of demographic resilience. Trends Ecol Evol 35:776–786
Cayuela H, Rougemont Q, Prunier JG, Moore JS, Clobert J, Besnard A, Bernatchez L (2018) Demographic and genetic approaches to study dispersal in wild animal populations: a methodological review. Mol Ecol 27:3976–4010. https://doi.org/10.1111/mec.14848
Chan AN, Lewis CL, Neely KL, Baums IB (2019) Fallen pillars: the past, present, and future population dynamics of a rare, specialist coral–algal symbiosis. Front Mar Sci 6:218. https://doi.org/10.3389/fmars.2019.00218
Chan WY, Peplow LM, Menéndez P, Hoffmann AA, van Oppen MJH (2018) Interspecific hybridization may provide novel opportunities for coral reef restoration. Front Mar Sci 5:161. https://doi.org/10.3389/fmars.2018.00160
Charlesworth B, Jensen JD (2021) Effects of selection at linked sites on patterns of genetic variability. Annu Rev Ecol Evol Syst 52:177–197. https://doi.org/10.1146/annurev-ecolsys-010621-044528
Cheung MWM, Hock K, Skirving WJ, Mumby PJ (2021) Cumulative bleaching undermines systemic resilience of the great barrier reef. Curr Biol 31:5385–5392
Chollett I, Garavelli L, O'Farrell S, Cherubin L, Matthews TR, Mumby PJ, Box SJ (2017) A genuine win-win: resolving the “conserve or catch” conflict in marine reserve network design. Cons Lett 10:555–563
Cooke I, Ying H, Forêt S, Bongaerts P, Strugnell J, Simakov O, Zhang J, Field MA, Rodriguez-Lanetty M, Bell SC, Bourne DG, van Oppen MJH, Ragan MA, Miller DJ (2020) Signatures of selection in the coral holobiont reveal complex adaptations to inshore environments driven by Holocene climate change. Science. Advances 6:eabc6318. https://doi.org/10.1101/2020.02.25.951905
Cooper TF, Berkelmans R, Ulstrup KE, Weeks S, Radford B, Jones AM, Doyle J, Canto M, O'Leary RA, van Oppen MJ (2011) Environmental factors controlling the distribution of Symbiodinium harboured by the coral Acropora millepora on the great barrier reef. PLoS One 6:e25536. https://doi.org/10.1371/journal.pone.0025536
Crandall ED, Toonen RJ, ToBo L, Selkoe KA (2019) A coalescent sampler successfully detects biologically meaningful population structure overlooked by F-statistics. Evol App 12:255–265. https://doi.org/10.1111/eva.12712
Crandall KA, Bininda-Emonds OR, Mace GM, Wayne RK (2000) Considering evolutionary processes in conservation biology. Trend Ecol Evol 15:290–295. https://doi.org/10.1016/S0169-5347(00)01876-0
D'Aloia CC, Daigle RM, Côté IM, Curtis JMR, Guichard F, Fortin PDM-J (2017) A multiple-species framework for integrating movement processes across life stages into the design of marine protected areas. Biol Conserv 216:93–100. https://doi.org/10.1016/j.biocon.2017.10.012
Daigle RM, Metaxas A, Balbar AC, McGowan J, Treml EA, Kuempel CD, Possingham HP, Beger M (2020) Operationalizing ecological connectivity in spatial conservation planning with Marxan connect. Methods Ecol Evol 11:570–579. https://doi.org/10.1111/2041-210x.13349
Davies SW, Moreland KN, Wham DC, Kanke MR, Matz MV (2020) Cladocopium community divergence in two Acropora coral hosts across multiple spatial scales. Mol Ecol 29:4559–4572
de Villemereuil P, Frichot E, Bazin E, François O, Gaggiotti OE (2014) Genome scan methods against more complex models: when and how much should we trust them? Mol Ecol 23:2006–2019. https://doi.org/10.1111/mec.12705
Dietzel A, Bode M, Connolly SR, Hughes TP (2021) The population sizes and global extinction risk of reef-building coral species at biogeographic scales. Nat Ecol Evol 5:663–669. https://doi.org/10.1038/s41559-021-01393-4
Dixon AM, Forster PM, Heron SF, Stoner AMK, Beger M (2022) Local-scale oceanographic features are unlikely to provide future thermal refugia for coral reefs. PLoS Climate Change in press
Dixon GB, Davies SW, Aglyamova GA, Meyer E, Bay LK, Matz MV (2015) Genomic determinants of coral heat tolerance across latitudes. Science 348:1460–1462. https://doi.org/10.1126/science.1261224
Dubé CE, Boissin E, Mercière A, Planes S (2020) Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate. Mol Ecol 29:1508–1522. https://doi.org/10.1111/mec.15418
Fernandes L, Day J, Lewis A, Slegers S, Kerrigan B, Breen D, Cameron D, Jago B, Hall J, Lowe D (2005) Establishing representative no-take areas in the great barrier reef: large-scale implementation of theory on marine protected areas. Cons Biol 19:1733–1744
Foley MM, Halpern BS, Micheli F, Armsby MH, Caldwell MR, Crain CM, Prahler E, Rohr N, Sivas D, Beck MW, Carr MH, Crowder LB, Emmett Duffy J, Hacker SD, McLeod KL, Palumbi SR, Peterson CH, Regan HM, Ruckelshaus MH, Sandifer PA, Steneck RS (2010) Guiding ecological principles for marine spatial planning. Mar Policy 34:955–966. https://doi.org/10.1016/j.marpol.2010.02.001
Fontoura L, D’Agata S, Gamoyo M, Barneche DR, Luiz OJ, Madin EMP, Eggertsen L, Maina JM (2021) Protecting connectivity promotes successful biodiversity and fisheries conservation. Science 375:336–340
Forester BR, Lasky JR, Wagner HH, Urban DL (2018) Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations. Mol Ecol 27:2215–2233. https://doi.org/10.1111/mec.14584
Fuller ZL, Mocellin VJL, Morris LA, Cantin N, Shepherd J, Sarre L, Peng J, Liao Y, Pickrell J, Andolfatto P, Matz M, Bay LK, Przeworski M (2020) Population genetics of the coral Acropora millepora: toward genomic prediction of bleaching. Science 369:eaba4674. https://doi.org/10.1126/science.aba4674
Gagnaire P-A, Gaggiotti OE (2016) Detecting polygenic selection in marine populations by combining population genomics and quantitative genetics approaches. Curr Zool 62:603–616. https://doi.org/10.1093/cz/zow088
Gaines SD, White C, Carr MH, Palumbi SR (2010) Designing marine reserve networks for both conservation and fisheries management. Proceedings of the National Academy of Sciences USA 107:18286–18293. https://doi.org/10.1073/pnas.0906473107
Gazulla CR, López-Sendino P, Antunes A, Aurelle D, Montero-Serra I, Dominici J-M, Linares C, Garrabou J, Ledoux J-B (2021) Demo-genetic approach for the conservation and restoration of a habitat-forming octocoral: the case of red coral, Corallium rubrum, in the Réserve Naturelle de Scandola. Front Mar Sci 8:633057. https://doi.org/10.3389/fmars.2021.633057
Gomez-Corrales M, Prada C (2020) Cryptic lineages respond differently to coral bleaching. Mol Ecol 29:4265–4273. https://doi.org/10.1111/mec.15631
González-Pech RA, Ragan MA, Chan C-X (2017) Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. Sci Rep 7:15021. https://doi.org/10.1038/s41598-017-15029-w
Groves CR, Game ET (2016) Conservation planning: informed decisions for a healthier planet. Roberts and Company Publishers, Greenwood Village, Colorado, USA
Guillot G, Renaud S, Ledevin R, Michaux J, Claude J (2012) A unifying model for the analysis of phenotypic, genetic, and geographic data. Syst Biol 61:897–911. https://doi.org/10.1093/sysbio/sys038
Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD (2009) Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet 5:e1000695. https://doi.org/10.1371/journal.pgen.1000695
Hanson JO, Rhodes JR, Riginos C, Fuller RA (2017) Environmental and geographic variables are effective surrogates for genetic variation in conservation planning. Proc Natl Acad Sci U S A 114:12755–12760. https://doi.org/10.1073/pnas.1711009114
Hanson JO, Schuster R, Morrell N, Strimas-Mackey M, Watts ME, Arcese P, Bennett JR, Possingham HP (2020) prioritizR: systematic conservation prioritization in R. R Package Version 4(1):5
Hardy OJ, Vekemans X (1999) Isolation by distance in a continuous population: reconciliation between spatial autocorrelation analysis and population genetics models. Heredity 83(Pt 2):145–154. https://doi.org/10.1046/j.1365-2540.1999.00558.x
Harrison HB, Bode M, Williamson DH, Berumen ML, Jones GP (2020) A connectivity portfolio effect stabilizes marine reserve performance. Proceedings of the National Academy of Sciences USA 117:25595–25600. https://doi.org/10.1073/pnas.1920580117
Hartfield M (2021) Approximating the coalescent under facultative sex. J Hered 112:145–154. https://doi.org/10.1093/jhered/esaa036
Hey J, Chung Y, Sethuraman A, Lachance J, Tishkoff S, Sousa VC, Wang Y (2018) Phylogeny estimation by integration over isolation with migration models. Mol Biol Evol 35:2805–2818. https://doi.org/10.1093/molbev/msy162
Hock K, Wolff NH, Ortiz JC, Condie SA, Anthony KRN, Blackwell PG, Mumby PJ (2017) Connectivity and systemic resilience of the great barrier reef. PLoS Biol 15:e2003355–e2003323. https://doi.org/10.1371/journal.pbio.2003355
Hoffmann AA, Griffin PC, Dillon S, Catullo RA, Rane R, Byrne M, Jordan R, Oakeshott J, Weeks AR, Joseph L, Lockhart P, Borevitz J, Sgrò CM (2015) A framework for incorporating evolutionary genomics into biodiversity conservation and management. Clim Chang Responses 2:1–24. https://doi.org/10.1186/s40665-014-0009-x
Hoffmann AA, Miller AD, Weeks AR (2021) Genetic mixing for population management: from genetic rescue to provenancing. Evol App 14:634–652. https://doi.org/10.1111/eva.13154
Howells EJ, Abrego D, Liew YJ, Burt JA, Meyer E, Aranda M (2021) Enhancing the heat tolerance of reef-building corals to future warming. Science. Advances 7:eabg6070
Howells EJ, van Oppen MJH, Willis BL (2009) High genetic differentiation and cross-shelf patterns of genetic diversity among great barrier reef populations of Symbiodinium. Coral Reefs 28:215–225. https://doi.org/10.1007/s00338-008-0450-z
Howells EJ, Willis BL, Bay LK, van Oppen MJH (2013) Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the great barrier reef. Mol Ecol 22:3693–3708. https://doi.org/10.1111/mec.12342
Huerta-Sánchez E, Jin X, Asan BZ, Peter BM, Vinckenbosch N, Liang Y, Yi X, He M, Somel M, Ni P, Wang B, Ou X, Huasang LJ, Cuo ZXP, Li K, Gao G, Yin Y, Wang W, Zhang X, Xu X, Yang H, Li Y, Wang J, Wang J, Nielsen R (2015) Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512:194–197. https://doi.org/10.1038/nature13408
Hughes TP, Kerry JT, Baird AH, Connolly SR, Dietzel A, Eakin CM, Heron SF, Hoey AS, Hoogenboom MO, Liu G, McWilliam MJ, Pears RJ, Pratchett MS, Skirving WJ, Stella JS, Torda G (2018) Global warming transforms coral reef assemblages. Nature 556:492–496. https://doi.org/10.1038/s41586-018-0041-2
Humanes A, Beauchamp EA, Bythell JC, Carl MK, Craggs JR, Edwards AJ, Golbuu Y, Lachs L, Martinez HM, Palmowski P (2021) An experimental framework for selectively breeding corals for assisted evolution. Front Mar Sci 8:626
Hume BCC, Smith EG, Ziegler M, Warrington HJM, Burt JA, LaJeunesse TC, Wiedenmann J, Voolstra CR (2019) SymPortal: a novel analytical framework and platform for coral algal symbiont next-generation sequencing ITS2 profiling. Mol Ecol Resour 19:1063–1080. https://doi.org/10.1111/1755-0998.13004
Jin YK, Lundgren P, Lutz A, Raina JB, Howells EJ, Paley AS, Willis BL, van Oppen MJH (2016) Genetic markers for antioxidant capacity in a reef-building coral. Sci Adv 2:e1500842–e1500842. https://doi.org/10.1126/sciadv.1500842
Johnston EC, Forsman ZH, Flot J-F, Schmidt-Roach S, Pinzón JH, Knapp ISS, Toonen RJ (2017) A genomic glance through the fog of plasticity and diversification in Pocillopora. Sci Rep 7:1595–1511. https://doi.org/10.1038/s41598-017-06085-3
Jones GP (2015) Mission impossible: unlocking the secrets of coral reef fish dispersal ecology of fishes on coral reefs. Cambridge University Press, Cambridge, pp 16–27
Jones GP, Almany GR, Russ GR, Sale PF, Steneck RS, van Oppen MJH, Willis BL (2009) Larval retention and connectivity among populations of corals and reef fishes: history, advances and challenges. Coral Reefs 28:307–325. https://doi.org/10.1007/s00338-009-0469-9
Jones GP, Srinivasan M, Almany GR (2007) Population connectivity and conservation of marine biodiversity. Oceanography 20:100–111
Jones KR, Maina JM, Kark S, McClanahan TR, Klein CJ, Beger M (2018) Incorporating feasibility and collaboration into large-scale planning for regional recovery of coral reef fisheries. Mar Ecol Prog Ser 604:211–222
Kalmus P, Ekanayaka A, Kang EL, Baird ME, Gierach MM (2022) Past the precipice? Projected coral habitability under global heating. Earth and Space Science Open Archive https://doi.org/10.1002/essoar1051020110510201
Kardos M, Armstrong EE, Fitzpatrick SW, Hauser S, Hedrick PW, Miller JM, Tallmon DA, Funk WC (2021) The crucial role of genome-wide genetic variation in conservation. Proc Natl Acad Sci U S A 118:e2104642118. https://doi.org/10.1073/pnas.2104642118
Kardos M, Shafer ABA (2018) The peril of gene-targeted conservation. Trend Ecol Evol 33:827–839. https://doi.org/10.1016/j.tree.2018.08.011
Kinnimonth S, Beger M, Bode M, Peterson E, Adams VM, Dorfman D, Brumbaugh DR, Possingham HP (2011) Dispersal connectivity and reserve selection for marine conservation. Ecol Model 222:1272–1282. https://doi.org/10.1016/j.ecolmodel.2011.01.012
Kirk NL, Howells EJ, Abrego D, Burt JA, Meyer E (2018) Genomic and transcriptomic signals of thermal tolerance in heat-tolerant corals (Platygyra daedalea) of the Arabian/Persian gulf. Mol Ecol 27:5180–5194
Kool JT, Moilanen A, Treml EA (2013) Population connectivity: recent advances and new perspectives. Landsc Ecol 28:165–185. https://doi.org/10.1007/s10980-012-9819-z
Krueck NC, Ahmadia GN, Green A, Jones GP, Possingham HP, Riginos C, Treml EA, Mumby PJ (2017) Incorporating larval dispersal into MPA design for both conservation and fisheries. Ecol Appl 27:925–941. https://doi.org/10.1002/eap.1495
Ladner JT, Palumbi SR (2012) Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes. Mol Ecol 21:2224–2238. https://doi.org/10.1111/j.1365-294X.2012.05528.x
Láruson ÁJ, Fitzpatrick MC, Keller SR, Haller BC, Lotterhos KE (2021) Seeing the forest for the trees: assessing genetic offset predictions with gradient forest. bioRxiv https://doi.org/10.1101/2021.09.20.461151
Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP (2015) Genome-environment associations in sorghum landraces predict adaptive traits. Sci Adv 1:e1400218–e1400218. https://doi.org/10.1126/sciadv.1400218
Ledoux JB, Mokhtar-Jamai K, Roby C, Feral JP, Garrabou J, Aurelle D (2010) Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation. Mol Ecol 19:675–690. https://doi.org/10.1111/j.1365-294X.2009.04516.x
Leitwein M, Duranton M, Rougemont Q, Gagnaire PA, Bernatchez L (2020) Using haplotype information for conservation genomics. Trend Ecol Evol 35:245–258. https://doi.org/10.1016/j.tree.2019.10.012
Liggins L, Treml EA, Riginos C (2019) Seascape genomics: contextualizing adaptive and neutral genomic variation in the ocean environment. In: Oleksiak MF, Rajora OP (eds) Population genomics: marine organisms. Springer International Publishing, Cham, pp 327–349
Logan CA, Dunne JP, Ryan JS, Baskett ML, Donner SD (2021) Quantifying global potential for coral evolutionary response to climate change. Nat Clim Chang 11:537–542. https://doi.org/10.1038/s41558-021-01037-2
Lotterhos KE, Whitlock MC (2015) The relative power of genome scans to detect local adaptation depends on sampling design and statistical method. Mol Ecol 24:1031–1046. https://doi.org/10.1111/mec.13100
Lowe WH, Allendorf FW (2010) What can genetics tell us about population connectivity? Mol Ecol 19:3038–3051. https://doi.org/10.1111/j.1365-294X.2010.04688.x
Lukoschek V, Riginos C, van Oppen MJH (2016) Congruent patterns of connectivity can inform management for broadcast spawning corals on the great barrier reef. Mol Ecol 25:3065–3080. https://doi.org/10.1111/mec.13649
Magalon H, Adjeroud M, Veuille M (2005) Patterns of genetic variation do not correlate with geographical distance in the reef-building coral Pocillopora meandrina in the South Pacific. Mol Ecol 14:1861–1868. https://doi.org/10.1111/j.1365-294X.2004.02430.x
Magris RA, Andrello M, Pressey RL, Mouillot D, Dalongeville A, Jacobi MN, Manel S (2018) Biologically representative and well-connected marine reserves enhance biodiversity persistence in conservation planning. Cons Lett 11:e12439
Magris RA, Treml EA, Pressey RL, Weeks R (2015) Integrating multiple species connectivity and habitat quality into conservation planning for coral reefs. Ecography 39:649–664. https://doi.org/10.1111/ecog.01507
Maina JM, Gamoyo M, Adams VM, D'agata S, Bosire J, Francis J, Waruinge D (2020) Aligning marine spatial conservation priorities with functional connectivity across maritime jurisdictions. Conservation Science and Practice 2:e156
Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trend Ecol Evol 20:136–142. https://doi.org/10.1016/j.tree.2004.12.004
Manzello DP, Matz MV, Enochs IC, Valentino L, Carlton RD, Kolodziej G, Serrano XM, Towle EK, Jankulak M (2019) Role of host genetics and heat-tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida keys with ocean warming. Glob Chang Biol 25:1016–1031. https://doi.org/10.1111/gcb.14545
Mao Y, Economo EP, Satoh N (2018) The roles of introgression and climate change in the rise to dominance of Acropora corals. Curr Biol 28:3373–3382.e3375. https://doi.org/10.1016/j.cub.2018.08.061
Mao Y, Satoh N (2019) A likely ancient genome duplication in the speciose reef-building coral genus, Acropora. ISCIENCE 13:20–32. https://doi.org/10.1016/j.isci.2019.02.001
Marhoefer SR, Zenger KR, Strugnell JM, Logan M, van Oppen MJH, Kenkel CD, Bay LK (2021) Signatures of adaptation and acclimatization to reef flat and slope habitats in the coral Pocillopora damicornis. Front Mar Sci 8:704709. https://doi.org/10.3389/fmars.2021.704709
Matz MV (2018) Fantastic beasts and how to sequence them: ecological genomics for obscure model organisms. Trends Genet 34:121–132. https://doi.org/10.1016/j.tig.2017.11.002
Matz MV, Treml EA, Aglyamova GV, Bay LK (2018) Potential and limits for rapid genetic adaptation to warming in a great barrier reef coral. PLoS Genet 14:e1007220–e1007219. https://doi.org/10.1371/journal.pgen.1007220
Matz MV, Treml EA, Haller BC (2020) Estimating the potential for coral adaptation to global warming across the indo-West Pacific. Glob Chang Biol 26:3473–3481. https://doi.org/10.1111/gcb.15060
Maxwell SL, Milner-Gulland EJ, Jones JPG, Knight AT, Bunnefeld N, Nuno A, Bal P, Earle S, Watson JEM, Rhodes JR (2015) Being SMART about SMART environmental targets. Science 347:1075–1076
Mazor T, Beger M, McGowan J, Possingham HP, Kark S (2016) The value of migration information for conservation prioritization of sea turtles in the Mediterranean. Glob Ecol Biogeogr 25:540–552
Mittell EA, Nakagawa S, Hadfield JD (2015) Are molecular markers useful predictors of adaptive potential? Ecol Lett 18:772–778. https://doi.org/10.1111/ele.12454
Moilanen A, Kujala H, Leathwick JR (2009) The zonation framework and software for conservation prioritization. In: Moilanen A, Wilson KA, Possingham HP (eds) Spatial conservation prioritisation: quantitative methods and computational tools. Oxford University Press, Oxford, UK, pp 196–210
Mokodongan DF, Taninaka H, Sara L, Kikuchi T, Yuasa H, Suyama Y, Yasuda N (2021) Spatial autocorrelation analysis using mig-seq data indirectly estimated the gamete and larval dispersal range of the blue coral, Heliopora coerulea, within reefs. Front Mar Sci 8:702977. https://doi.org/10.3389/fmars.2021.702977
Morikawa MK, Palumbi SR (2019) Using naturally occurring climate resilient corals to construct bleaching-resistant nurseries. Proceedings of the National Academy of Sciences USA 116:10586–10591. https://doi.org/10.1073/pnas.1721415116
Moritz CC (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst Biol 51:238–254. https://doi.org/10.1080/10635150252899752
Mumby PJ, Elliott IA, Eakin CM, Skirving W, Paris CB, Edwards HJ, Enríquez S, Iglesias-Prieto R, Cherubin LM, Stevens JR (2010) Reserve design for uncertain responses of coral reefs to climate change. Ecol Lett 14:132–140. https://doi.org/10.1111/j.1461-0248.2010.01562.x
Nielsen ES, Beger M, Henriques R, Selkoe KA, von der Heyden S (2017) Multispecies genetic objectives in spatial conservation planning. Cons Biol 31:872–882. https://doi.org/10.1111/cobi.12875
Nielsen ES, Beger M, Henriques R, von der Heyden S (2020) A comparison of genetic and genomic approaches to represent evolutionary potential in conservation planning. Biol Conserv 251:108770. https://doi.org/10.1016/j.biocon.2020.108770
Nielsen ES, Henriques R, Toonen RJ, Knapp ISS, Guo B, von der Heyden S (2018) Complex signatures of genomic variation of two non-model marine species in a homogeneous environment. BMC Genomics 19:1–16. https://doi.org/10.1186/s12864-018-4721-y
Noreen AME, Harrison PL, van Oppen MJH (2009) Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution. Proc R Soc B 276:3927–3935. https://doi.org/10.1098/rspb.2009.1050
Orive ME, Barfield M, Fernandez C, Holt RD (2017) Effects of clonal reproduction on evolutionary lag and evolutionary rescue. Am Nat 190:469–490. https://doi.org/10.1086/693006
Oury N, Gélin P, Magalon H (2021) High connectivity within restricted distribution range in Pocillopora corals. J Biogeogr 48:1679–1692. https://doi.org/10.1111/jbi.14104
Pearse DE (2016) Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. J Fish Biol 89:2697–2716. https://doi.org/10.1111/jfb.13168
Pickrell JK, Pritchard JK (2012) Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet 8:e1002967. https://doi.org/10.1371/journal.pgen.1002967.s016
Pinsky ML, Saenz-Agudelo P, Salles OC, Almany GR, Bode M, Berumen ML, Andréfouët S, Thorrold SR, Jones GP, Planes S (2017) Marine dispersal scales are congruent over evolutionary and ecological time. Curr Biol 27:149–154. https://doi.org/10.1016/j.cub.2016.10.053
Pinzón JH, LaJeunesse TC (2010) Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics and symbiosis ecology. Mol Ecol 20:311–325. https://doi.org/10.1111/j.1365-294X.2010.04939.x
Polis GA, Anderson WB, Holt RD (1997) Toward an integration of landscape and food web ecology: the dynamics of spatially subsidized food webs. Annu Rev Ecol Syst 28:289–316
Prata KE, Riginos C, Gutenkunst RN, Latijnhouwers K, Sánchez JA, Englebert N, Hay K, Bongaerts P (2022) Deep connections: divergence histories with gene flow in mesophotic Agaricia corals. in review
Quigley KM, Bay LK, Oppen MJH (2019) The active spread of adaptive variation for reef resilience. Ecol Evol 27:1342–1314. https://doi.org/10.1002/ece3.5616
Quigley KM, Bay LK, Willis BL (2017) Temperature and water quality-related patterns in sediment-associated Symbiodinium communities impact symbiont uptake and fitness of juveniles in the genus Acropora. Front Mar Sci 4:401. https://doi.org/10.3389/fmars.2017.00401
Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB (2021) Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts. Mol Ecol 30:3500–3514
Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370. https://doi.org/10.1111/mec.13322
Riginos C, Crandall ED, Liggins L, Bongaerts P, Treml EA (2016) Navigating the currents of seascape genomics: how spatial analyses can augment population genomic studies. Curr Zool 62:581–601. https://doi.org/10.1093/cz/zow067
Riginos C, Hock K, Matias AM, Mumby PJ, Oppen MJH, Lukoschek V (2019) Asymmetric dispersal is a critical element of concordance between biophysical dispersal models and spatial genetic structure in great barrier reef corals. Divers Distrib 25:1684–1696. https://doi.org/10.1111/ddi.12969
Ringbauer H, Coop G, Barton NH (2017) Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics 205:1335–1351. https://doi.org/10.1534/genetics.116.196220
Rippe JP, Dixon G, Fuller ZL, Liao Y, Matz M (2021) Environmental specialization and cryptic genetic divergence in two massive coral species from the Florida keys reef tract. Mol Ecol 30:3468–3484
Robinson JD, Coffman AJ, Hickerson MJ, Gutenkunst RN (2014) Sampling strategies for frequency spectrum-based population genomic inference. BMC Evol Biol 14:254. https://doi.org/10.1186/s12862-014-0254-4
Rose NH, Bay RA, Morikawa MK, Palumbi SR (2018) Polygenic evolution drives species divergence and climate adaptation in corals. Evolution 72:82–94. https://doi.org/10.1111/evo.13385
Rose NH, Bay RA, Morikawa MK, Thomas L, Sheets EA, Palumbi SR (2021) Genomic analysis of distinct bleaching tolerances among cryptic coral species. Proc R Soc B 288:20210678
Rousset F (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 145:1219–1228. https://doi.org/10.1093/genetics/145.4.1219
Rousset F (2000) Genetic differentiation between individuals. J Evol Biol 13:58–62. https://doi.org/10.1046/j.1420-9101.2000.00137.x
Rousset F, Leblois R (2012) Likelihood-based inferences under isolation by distance: two-dimensional habitats and confidence intervals. Mol Biol Evol 29:957–973. https://doi.org/10.1093/molbev/msr262
Saghand GP, Haider Z, Charkhgard H, Eaton M, Martin J, Yurek S, Udell BJ (2021) SiteOpt: an open-source R-package for site selection and portfolio optimization. Ecography 44:1678–1685
Sawall Y, Al-Sofyani A, Banguera-Hinestroza E, Voolstra CR (2014) Spatio-temporal analyses of Symbiodinium physiology of the coral Pocillopora verrucosa along large-scale nutrient and temperature gradients in the Red Sea. PLoS One 9:e103179. https://doi.org/10.1371/journal.pone.0103179
Selkoe KA, Gaggiotti OE, Treml EA, Wren JL, Donovan MK, Consortium HiRC, Toonen RJ (2016) The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages. Proc R Soc B 283:20160354
Selmoni O, Rochat E, Lecellier G, Berteaux-Lecellier V, Joost S (2020) Seascape genomics as a new tool to empower coral reef conservation strategies: an example on North-Western Pacific Acropora digitifera. Evol App 13:1923–1938. https://doi.org/10.1111/eva.12944
Sgrò CM, Lowe AJ, Hoffmann AA (2011) Building evolutionary resilience for conserving biodiversity under climate change. Evol App 4:326–337. https://doi.org/10.1111/j.1752-4571.2010.00157.x
Sheets EA, Warner PA, Palumbi SR (2018) Accurate population genetic measurements require cryptic species identification in corals. Coral Reefs 37:549–563. https://doi.org/10.1007/s00338-018-1679-9
Slatkin M (1987) Gene flow and the geographic structure of natural populations. Science 236:787–792. https://doi.org/10.1126/science.3576198
Slatkin M (1993) Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47:264. https://doi.org/10.2307/2410134
Stoeckel S, Porro B, Arnaud-Haond S (2019) The discernible and hidden effects of clonality on the genotypic and genetic states of populations: improving our estimation of clonal rates. Mol Ecol Resour 21:1068–1084
Sturm AB, Eckert RJ, Mendez JG, Gonzalez-Diaz P, Voss JD (2020) Population genetic structure of the great star coral, Montastraea cavernosa, across the Cuban archipelago with comparisons between microsatellite and SNP markers. Sci Rep 10:15432. https://doi.org/10.1038/s41598-020-72112-5
Tear TH, Kareiva P, Angermeier PL, Comer P, Czech B, Kautz R, Landon L, Mehlman D, Murphy K, Ruckelshaus M (2005) How much is enough? The recurrent problem of setting measurable objectives in conservation. Bioscience 55:835–849
Teixeira JC, Huber CD (2021) The inflated significance of neutral genetic diversity in conservation genetics. Proceedings of the National Academy of Sciences USA 118:e2015096118. https://doi.org/10.1073/pnas.2015096118
Thomas L, Rose NH, Bay RA, López EH, Morikawa MK, Ruiz-Jones L, Palumbi SR (2018) Mechanisms of thermal tolerance in reef-building corals across a fine-grained environmental mosaic: lessons from Ofu, American Samoa. Front Mar Sci 4:434. https://doi.org/10.3389/fmars.2017.00434
Thornhill DJ, Howells EJ, Wham DC, Steury TD, Santos SR (2017) Population genetics of reef coral endosymbionts (Symbiodinium, Dinophyceae). Mol Ecol 26:2640–2659. https://doi.org/10.1111/mec.14055
Toczydlowski RH, Liggins L, Gaither MR, Anderson TJ, Barton RL, Berg JT, Beskid SG, Davis B, Delgado A, Farrell E, Ghoojaei M, Himmelsbach N, Holmes AE, Queeno SR, Trinh T, Weyand CA, Bradburd GS, Riginos C, Toonen RJ, Crandall ED (2021) Poor data stewardship will hinder global genetic diversity surveillance. Proc Natl Acad Sci U S A 118:e2107934118. https://doi.org/10.1073/pnas.2107934118
Torda G, Donelson JM, Aranda M, Barshis DJ, Bay LK, Berumen ML, Bourne DG, Cantin N, Foret S, Matz MV, Miller DJ, Moya A, Putnam HM, Ravasi T, van Oppen MJH, Thurber RV, Vidal-Dupiol J, Voolstra CR, Watson S-A, Whitelaw E, Willis BL, Munday PL (2017) Rapid adaptive responses to climate change in corals. Nat Clim Chang 7:627–636. https://doi.org/10.1038/nclimate3374
Torda G, Lundgren P, Willis BL, van Oppen MJH (2013) Genetic assignment of recruits reveals short- and long-distance larval dispersal in Pocillopora damicornis on the great barrier reef. Mol Ecol 22:5821–5834. https://doi.org/10.1111/mec.12539
Torres AF, Forsman ZH, Ravago-Gotanco R (2020) Shifts in coral clonality along a gradient of disturbance: insights on reproduction and dispersal of Pocillopora acuta. Mar Biol 167. https://doi.org/10.1007/s00227-020-03777-9
Treml EA, Halpin PN (2012) Marine population connectivity identifies ecological neighbors for conservation planning in the coral triangle. Cons Lett 5:441–449. https://doi.org/10.1111/j.1755-263X.2012.00260.x
Treml EA, Roberts JJ, Chao Y, Halpin PN, Possingham HP, Riginos C (2012) Reproductive output and duration of the pelagic larval stage determine seascape-wide connectivity of marine populations. Integr Comp Biol 52:525–537. https://doi.org/10.1093/icb/ics101
Treml EA, Roberts JJ, Halpin PN, Possingham HP, Riginos C (2015) The emergent geography of biophysical dispersal barriers across the indo-West Pacific. Divers Distrib 21:465–476. https://doi.org/10.1111/ddi.12307
Tulloch VJ, Tulloch AI, Visconti P, Halpern BS, Watson JE, Evans MC, Auerbach NA, Barnes M, Beger M, Chadès I (2015) Why do we map threats? Linking threat mapping with actions to make better conservation decisions. Front Ecol Environ 13:91–99
Underwood JN, Richards Z, Berry O, Oades D, Howard A, Gilmour JP (2020) Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote north-West Australia. Evol App 13:2404–2421. https://doi.org/10.1111/eva.13033
van Oppen MJH, Bongaerts P (2011) The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and East Australia. Mol Ecol 20:1647–1660. https://doi.org/10.1111/j.1365-294X.2011.05050.x
van Oppen MJH, Bongaerts P, Frade PR, Peplow LM, Boyd SE, Nim HT, Bay LK (2018) Adaptation to reef habitats through selection on the coral animal and its associated microbiome. Mol Ecol 27:2956–2971. https://doi.org/10.1111/mec.14763
van Oppen MJH, Gates RD, Blackall LL, Cantin N, Chakravarti LJ, Chan WY, Cormick C, Crean A, Damjanovic K, Epstein H, Harrison PL, Jones TA, Miller MW, Pears RJ, Peplow LM, Raftos DA, Schaffelke B, Stewart K, Torda G, Wachenfeld D, Weeks AR, Putnam HM (2017) Shifting paradigms in restoration of the world's coral reefs. Glob Chang Biol 23:3437–3448. https://doi.org/10.1111/gcb.13647
van Oppen MJH, Peplow LM, Kinnimonth S, Berkelmans R (2011) Historical and contemporary factors shape the population genetic structure of the broadcast spawning coral, Acropora millepora, on the great barrier reef. Mol Ecol 20:4899–4914. https://doi.org/10.1111/j.1365-294X.2011.05328.x
Vekemans X, Hardy OJ (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol 13:921–935. https://doi.org/10.1046/j.1365-294X.2004.02076.x
von der Heyden S, Beger M, Toonen RJ, van Herwerden L, Juinio-Menez MA, Ravago-Gotanco R, Fauvelot C, Bernardi G (2014) The application of genetics to marine management and conservation: examples from the indo-Pacific. Bull Mar Sci 90:123–158. https://doi.org/10.5343/bms.2012.1079
Voolstra CR, Quigley KM, Davies SW, Parkinson JE, Peixoto RS, Aranda M, Baker AC, Barno AR, Barshis DJ, Benzoni F, Bonito V, Bourne DG, Buitrago-López C, Bridge TCL, Chan CX, Combosch DJ, Craggs J, Frommlet JC, Herrera S, Quattrini AM, Röthig T, Reimer JD, Rubio-Portillo E, Suggett DJ, Villela H, Ziegler M, Sweet M (2021) Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Front Mar Sci 8:701784. https://doi.org/10.3389/fmars.2021.701784
Walsworth TE, Schindler DE, Colton MA, Webster MS, Palumbi SR, Mumby PJ, Essington TE, Pinsky ML (2019) Management for network diversity speeds evolutionary adaptation to climate change. Nat Clim Chang 9:632–636. https://doi.org/10.1038/s41558-019-0518-5
Waples RS, Gaggiotti OE (2006) What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419–1439. https://doi.org/10.1111/j.1365-294X.2006.02890.x
Weeks R (2017) Incorporating seascape connectivity in conservation prioritisation. PLoS One 12:e0182396. https://doi.org/10.1371/journal.pone.0182396
Weeks R, Green AL, Joseph E, Peterson N, Terk E (2017) Using reef fish movement to inform marine reserve design. J Appl Ecol 54:145–152
Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: FST not equal to 1/(4Nm + 1). Heredity 82:117–125. https://doi.org/10.1038/sj.hdy.6884960
Wilson KA, Cabeza M, Klein CJ (2009) Fundamental concepts of spatial conservation prioritization. In: Moilanen A, Wilson KA, Possingham HP (eds) Spatial conservation prioritisation: quantitative methods and computational tools. Oxford University Press, Oxford, UK, pp 16–27
Wilson KL, Tittensor DP, Worm B, Lotze HK (2020) Incorporating climate change adaptation into marine protected area planning. Glob Chang Biol 26:3251–3267
Wright S (1931) Evolution in Mendelian populations. Genetics 16:97–159
Wright S (1946) Isolation by distance under diverse systems of mating. Genetics 31:39–59
Wu Q, Huang W, Chen B, Yang E, Meng L, Chen Y, Li J, Huang X, Liang J, Yap TK, Yu K (2021) Genetic structure of Turbinaria peltata in the northern South China Sea suggest insufficient genetic adaptability of relatively high-latitude scleractinian corals to environment stress. Science and the Total Environment 775:145775. https://doi.org/10.1016/j.scitotenv.2021.145775
Zayasu Y, Takeuchi T, Nagata T, Kanai M, Fujie M, Kawamitsu M, Chinen W, Shinzato C, Satoh N (2021) Genome-wide SNP genotyping reveals hidden population structure of an acroporid species at a subtropical coral island: implications for coral restoration. Aquatic Conserv: Mar Freshw Ecosyst 31:2429–2439. https://doi.org/10.1002/aqc.3626
Ziegler M, Roder C, Büchel C, Voolstra CR (2015) Niche acclimatization in Red Sea corals is dependent on flexibility of host-symbiont association. Mar Ecol Prog Ser 533:149–161. https://doi.org/10.3354/meps11365
Acknowledgments
This work was supported by the Reef Restoration and Adaptation Program, funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation, to Cynthia Riginos. The authors benefited from past conversations with colleagues, especially ED Crandall, P Bongaerts, MV Matz, I Popovic, T Richards, JC Ortiz, LK Bay, S vd Heyden, KM Quigley, and EJ Howells, and comments from two anonymous reviewers.
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Riginos, C., Beger, M. (2022). Incorporating Genetic Measures of Connectivity and Adaptation in Marine Spatial Planning for Corals. In: van Oppen, M.J.H., Aranda Lastra, M. (eds) Coral Reef Conservation and Restoration in the Omics Age. Coral Reefs of the World, vol 15. Springer, Cham. https://doi.org/10.1007/978-3-031-07055-6_2
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