Addison JA, Hart MW (2005) Spawning, copulation and inbreeding coefficients in marine invertebrates. Biol Lett 1:450–453
Aguillon SM, Fitzpatrick JW, Bowman R, Schoech SJ, Clark AG, Coop G et al. (2017) Deconstructing isolation-by-distance: the genomic consequences of limited dispersal. PLoS Genet 13:1–27
Almany GR, Connolly SR, Heath DD, Hogan JD, Jones GP, McCook LJ et al. (2009) Connectivity, biodiversity conservation and the design of marine reserve networks for coral reefs. Coral Reefs 28:339–351
Bates D, Mächler M, Bolke B, Walker S (2015) Fitting linear mixed-effects models using lme4. J Stat Softw 67:1–48
Baums IB (2008) A restoration genetics guide for coral reef conservation. Mol Ecol 17:2796–2811
Bell JJ, Smith D, Hannan D, Haris A, Jompa J, Thomas L (2014) Resilience to disturbance despite limited dispersal and self-recruitment in tropical barrel sponges: implications for conservation and management. PLoS ONE 9:e91635
Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165–1188
Bertelsen RD, Butler MJ, Herrnkind WF, Hunt JH (2009) Regional characterisation of hard‐bottom nursery habitat for juvenile Caribbean spiny lobster (Panulirus argus) using rapid assessment techniques. N. Zeal J Mar Freshw Res 43:299–312
Blanquer A, Uriz M, Caujapé-Castells J (2009) Small-scale spatial genetic structure in Scopalina lophyropoda, an encrusting sponge with philopatric larval dispersal and frequent fission and fusion events. Mar Ecol Prog Ser 380:95–102
Butler MJ, Hunt JH, Herrnkind WF, Childress MJ, Bertelsen R, Sharp W et al. (1995) Cascading disturbances in Florida Bay, USA: cyanobacteria blooms, sponge mortality, and implications for juvenile spiny lobsters Panulirus argus. Mar Ecol Prog Ser 129:119–125
Butler J, Stanley JA, Butler MJ (2016) Underwater soundscapes in near-shore tropical habitats and the effects of environmental degradation and habitat restoration. J Exp Mar Bio Ecol 479:89–96
Butler IV MJ, Behringer DC, Valentine MM (2017) Commercial sponge fishery impacts on the population dynamics of sponges in the Florida Keys, FL (USA). Fish Res 190:113–121
Calderón I, Ortega N, Duran S, Becerro M, Pascual M, Turon X (2007) Finding the relevant scale: clonality and genetic structure in a marine invertebrate (Crambe crambe, Porifera). Mol Ecol 16:1799–1810
Carrillo L, Johns EM, Smith RH, Lamkin JT, Largier JL (2015) Pathways and hydrography in the Mesoamerican Barrier Reef System Part 1: Circulation. Cont Shelf Res 109:164–176
Castorani MCN, Reed DC, Raimondi PT, Alberto F, Bell TW, Cavanaugh KC et al. (2017) Fluctuations in population fecundity drive variation in demographic connectivity and metapopulation dynamics. Proc R Soc B Biol Sci 284:20162086.
Chapuis M-P, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–31
Chaves-Fonnegra A, Feldheim KA, Secord J, Lopez JV (2015) Population structure and dispersal of the coral-excavating sponge Cliona delitrix. Mol Ecol 24:1447–66
Chybicki IJ, Burczyk J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. J Hered 100:106–13
D’Aloia CC, Bogdanowicz SM, Harrison RG, Buston PM (2017) Cryptic genetic diversity and spatial patterns of admixture within Belizean marine reserves. Conserv Genet 18:211–223
Dailianis T, Tsigenopoulos CS, Dounas C, Voultsiadou E (2011) Genetic diversity of the imperilled bath sponge Spongia officinalis Linnaeus, 1759 across the Mediterranean Sea: patterns of population differentiation and implications for taxonomy and conservation. Mol Ecol 20:3757–72
de Bakker DM, Meesters EHWG, van Bleijswijk JDL, Luttikhuizen PC, Breeuwer HJAJ, Becking LE (2016) Population genetic structure, abundance, and health status of two dominant benthic species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta. PLoS ONE 11:e0155969
DeBiasse MB, Richards VP, Shivji MS (2010) Genetic assessment of connectivity in the common reef sponge, Callyspongia vaginalis (Demospongiae: Haplosclerida) reveals high population structure along the Florida reef tract. Coral Reefs 29:47–55
DeBiasse MB, Richards VP, Shivji MS, Hellberg ME (2016) Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals. J Biogeogr 43:2136–2146
Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B 39:1–38
Diaz M, Rutzler K (2001) Sponges: an essential component of Caribbean coral reefs. Bull Mar Sci 69:535–546
Drury C, Paris CB, Kourafalou VH, Lirman D (2018) Dispersal capacity and genetic relatedness in Acropora cervicornis on the Florida Reef Tract. Coral Reefs 37:585–596
Eldon B, Riquet F, Yearsley J, Jollivet D, Broquet T (2016) Current hypotheses to explain genetic chaos under the sea. Curr Zool 62:551–566
Ereskovsky AV, Tokina DB (2004) Morphology and fine structure of the swimming larvae of Ircinia oros (Porifera, Demospongiae, Dictyoceratida). Invertebr Reprod Dev 45:137–150
Estoup A, Jarne P, Cornuet J-M (2002) Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis. Mol Ecol 11:1591–1604
Ezer T, Thattai DV, Kjerfve B, Heyman WD (2005) On the variability of the flow along the Meso-American Barrier Reef system: A numerical model study of the influence of the Caribbean current and eddies. Ocean Dyn 55:458–475
Foster NL, Paris CB, Kool JT, Baums IB, Stevens JR, Sanchez JA et al. (2012) Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow. Mol Ecol 21:1143–1157
Garza JC, Williamson EG (2001) Detection of reduction in population size using data from microsatellite loci. Mol Ecol 10:305–18
Giles EC, Saenz-Agudelo P, Hussey NE, Ravasi T, Berumen ML (2015) Exploring seascape genetics and kinship in the reef sponge Stylissa carteri in the Red Sea. Ecol Evol 5:2487–502
Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ et al. (2019) Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 88:1984–1695
Griffiths SM, Taylor-Cox ED, Behringer DC, Butler MJ, Preziosi RF (2020) Using genetics to inform restoration and predict resilience in declining populations of a keystone marine sponge. Biodivers Conserv 29:1383–1410
Guardiola M, Frotscher J, Uriz M-J (2016) High genetic diversity, phenotypic plasticity, and invasive potential of a recently introduced calcareous sponge, fast spreading across the Atlanto-Mediterranean basin. Mar Biol 163:123
Guillot G, Estoup A, Mortier F, Cosson JF (2005) A spatial statistical model for landscape genetics. Genetics 170:1261–1280
Guillot G, Santos F, Estoup A (2008) Analysing georeferenced population genetics data with Geneland: a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics 24:1406–1407
Hedgecock D, Pudovkin AI (2011) Sweepstakes reproductive success in highly fecund marine fish and shellfish: a review and commentary. Bull Mar Sci 87:971–1002
Herrnkind WF, Butler IV MJ, Hunt JH, Childress M (1997) Role of physical refugia: implications from a mass sponge die-off in a lobster nursery in Florida. Mar Freshw Res 48:759
Hoffman JI, Peck LS, Linse K, Clarke A (2011) Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate. J Hered 102:55–66
Hothorn T, Bretz F, Westfall P (2008) Simultaneous inference in general parametric models. Biometrical J 50:346–363
Janes JK, Miller JM, Dupuis JR, Malenfant RM, Gorrell JC, Cullingham CI et al. (2017) The K = 2 conundrum. Mol Ecol 26:3594–3602
Japaud A, Bouchon C, Magalon H, Fauvelot C (2019) Geographic distances and ocean currents influence Caribbean Acropora palmata population connectivity in the Lesser Antilles. Conserv Genet 20:447–466
Johnson MS, Black R (1982) Chaotic genetic patchiness in an intertidal limpet, Siphonaria sp. Mar Biol 70:157–164
Jolly MT, Thiébaut E, Guyard P, Gentil F, Jollivet D (2014) Meso-scale hydrodynamic and reproductive asynchrony affects the source-sink metapopulation structure of the coastal polychaete Pectinaria koreni. Mar Biol 161:367–382
Jombart T (2008) Adegenet: A R package for the multivariate analysis of genetic markers. Bioinformatics 24:1403–1405
Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11:94
Jost L (2008) G ST and its relatives do not measure differentiation. Mol Ecol 17:4015–4026
Knutsen H, Jorde PE, Andre C, Stenseth NC (2003) Fine-scaled geographical population structuring in a highly mobile marine species: the Atlantic cod. Mol Ecol 12:385–394
Lazure P, Salomon JC, Breton M (1996) Subtidal circulation in Fort-de-France Bay. In: Maul GA (ed) Small Islands: Marine Science and Sustainable Development, Volume 51. American Geophysical Union, Washington DC
López-Legentil S, Pawlik JR (2009) Genetic structure of the Caribbean giant barrel sponge Xestospongia muta using the I3-M11 partition of COI. Coral Reefs 28:157–165
Maebe K, Golsteyn L, Nunes-Silva P, Blochtein B, Smagghe G (2018) Temporal changes in genetic variability in three bumblebee species from Rio Grande do Sul, South Brazil. Apidologie 49:415–429
Maldonado M, Riesgo A (2008) Reproduction in Porifera: a synoptic overview. Treb la SCB 59:29–49
Maldonado M, Sánchez-Tocino L, Navarro C (2010) Recurrent disease outbreaks in corneous demosponges of the genus Ircinia: Epidemic incidence and defense mechanisms. Mar Biol 157:1577–1590
Maldonado M, Uriz M (1999) Sexual propagation by sponge fragments. Nature 398:1999
Mariani S, Uriz MJ, Turon X, Alcoverro T (2006) Dispersal strategies in sponge larvae: Integrating the life history of larvae and the hydrologic component. Oecologia 149:174–184
Martínez S, Carrillo L, Marinone SG (2019) Potential connectivity between marine protected areas in the Mesoamerican Reef for two species of virtual fish larvae: Lutjanus analis and Epinephelus striatus. Ecol Indic 102:10–20
Meirmans PG, Van Tienderen PH (2004) Genotype and Genodive: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794
Morin PA, Leduc RG, Archer FI, Martien KK, Huebinger R, Bickham JW et al. (2009) Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Mol Ecol Resour 9:498–504
Muhling BA, Smith RH, Vásquez-Yeomans L, Lamkin JT, Johns EM, Carrillo L et al. (2013) Larval fish assemblages and mesoscale oceanographic structure along the Mesoamerican Barrier Reef System. Fish Oceanogr 22:409–428
Norderhaug KM, Anglès d’Auriac MB, Fagerli CW, Gundersen H, Christie H, Dahl K et al. (2016) Genetic diversity of the NE Atlantic sea urchin Strongylocentrotus droebachiensis unveils chaotic genetic patchiness possibly linked to local selective pressure. Mar Biol 163:1–13
Pante E, Simon-Bouhet B (2013) marmap: a package for importing, plotting and analyzing bathymetric and topographic data in R. PLoS One 8:e73051
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research- an update. Bioinformatics 28:2537–2539
Peery MZ, Kirby R, Reid BN, Stoelting R, Douchet-Beer E, Robinson S et al. (2012) Reliability of genetic bottleneck tests for detecting recent population declines. Mol Ecol 21:3403–3418
Pérez-Portela R, Noyer C, Becerro MA (2015) Genetic structure and diversity of the endangered bath sponge Spongia lamella. Aquat Conserv Mar Freshw Ecosyst 25:365–379
Perez T, Garrabou J, Sartoretto S, Harmelin JG, Francour P, Vacelet J (2000) Massive mortality of marine invertebrates: an unprecedented event in northwestern Mediterranean. C R Acad Sci III 323:853–65
Piry S, Luikart G, Cornuet J-M (1999) Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. J Hered 90:502–503
R Core Team (2017) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/
Raymond M, Rousset F (1995) GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Richards VP, Bernard AM, Feldheim KA, Shivji MS (2016) Patterns of population structure and dispersal in the long-lived “redwood” of the coral reef, the giant barrel sponge (Xestospongia muta). Coral Reefs 35:1097–1107
Riesgo A, Pérez-Portela R, Pita L, Blasco G, Erwin PM, López-Legentil S (2016) Population structure and connectivity in the Mediterranean sponge Ircinia fasciculata are affected by mass mortalities and hybridization. Heredity 117:427–439
Riesgo A, Taboada S, Pérez-Portela R, Melis P, Xavier JR, Blasco G et al. (2019) Genetic diversity, connectivity and gene flow along the distribution of the emblematic Atlanto-Mediterranean sponge Petrosia ficiformis (Haplosclerida, Demospongiae). BMC Evol Biol 19:1–18
Rippe JP, Matz MV, Green EA, Medina M, Khawaja NZ, Pongwarin T et al. (2017) Population structure and connectivity of the mountainous star coral, Orbicella faveolata, throughout the wider Caribbean region. Ecol Evol 7:9234–9246
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
Schunter C, Pascual M, Raventos N, Garriga J, Garza JC, Bartumeus F et al. (2019) A novel integrative approach elucidates fine-scale dispersal patchiness in marine populations. Sci Rep 9:1–10
Schwartz MK, Luikart G, Waples RS (2007) Genetic monitoring as a promising tool for conservation and management. Trends Ecol Evol 22:25–33
Shanks AL (2009) Pelagic larval duration and dispersal distance revisited. Biol Bull 216:373–85
Siegel DA, Mitarai S, Costello CJ, Gaines SD, Kendall BE, Warner RR et al. (2008) The stochastic nature of larval connectivity among nearshore marine populations. Proc Natl Acad Sci 105:8974–9
Sole-Cava AM, Klautau M, Boury-Esnault N, Borojecic R, Thorpe JP (1991) Genetic evidence for cryptic speciation in allopatric populations of two cosmopolitan species of the calcareous sponge genus Clathrina. Mar Biol 111:381–386
Soro A, Quezada-Euan JJG, Theodorou P, Moritz RFA, Paxton RJ (2017) The population genetics of two orchid bees suggests high dispersal, low diploid male production and only an effect of island isolation in lowering genetic diversity. Conserv Genet 18:607–619
Soto I, Andréfouët S, Hu C, Muller-Karger FE, Wall CC, Sheng J et al. (2009) Physical connectivity in the Mesoamerican Barrier Reef System inferred from 9 years of ocean color observations. Coral Reefs 28:415–425
Stabili L, Cardone F, Alifano P, Tredici SM, Piraino S, Corriero G et al. (2012) Epidemic mortality of the sponge Ircinia variabilis (Schmidt, 1862) associated to proliferation of a Vibrio bacterium. Micro Ecol 64:802–813
Stevely JM, Sweat DE, Bert TM, Sim-Smith C, Kelly M (2010) Sponge mortality at Marathon and Long Key, Florida: patterns of species response and population recovery. Proc 63rd Gulf Caribb Fish Inst 63:384–400
Szpiech ZA, Jakobsson M, Rosenberg NA (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24:2498–2504
Taboada S, Riesgo A, Wiklund H, Paterson GLJ, Koutsouveli V, Santodomingo N et al. (2018) Implications of population connectivity studies for the design of marine protected areas in the deep sea: an example of a demosponge from the Clarion-Clipperton Zone. Mol Ecol 27:4657–4679
Tesson SVM, Montresor M, Procaccini G, Kooistra WHCF (2014) Temporal changes in population structure of a marine planktonic diatom. PLoS One 9:e114984
Truelove NK, Griffiths S, Ley-Cooper K, Azueta J, Majil I, Box SJ et al. (2014) Genetic evidence from the spiny lobster fishery supports international cooperation among Central American marine protected areas. Conserv Genet 16:347–358
Uriz MJ, Turon X, Mariani S (2008) Ultrastructure and dispersal potential of sponge larvae: tufted versus evenly ciliated parenchymellae. Mar Ecol 29:280–297
Vacelet J (1999) Planktonic armoured propagules of the excavating sponge Alectona (Porifera: Demospongiae) are larvae: evidence from Alectona wallichii and A. mesatlantica sp. nov. Mem Queensl Mus 44:627–642
Vaha J-P, Erkinaro J, Niemela E, Primmer CR (2007) Life-history and habitat features influence the within-river genetic structure of Atlantic salmon. Mol Ecol 16:2638–2654
Valentine MM, Butler MJ IV (2019) Sponges structure water-column characteristics in shallow tropical coastal ecosystems. Mar Ecol Prog Ser 608:133–147
Wernberg T, Coleman MA, Bennett S, Thomsen MS, Tuya F, Kelaher BP (2018) Genetic diversity and kelp forest vulnerability to climatic stress. Sci Rep 8:1851
Wright S (1943) Isolation by distance. Genetics 28:114–38
Wulff JL (1991) Asexual fragmentation, genotype success, and population dynamics of erect branching sponges. J Exp Mar Bio Ecol 149:227–247
Wulff J (2006) Rapid diversity and abundance decline in a Caribbean coral reef sponge community. Biol Conserv 127:167–176
Xavier JR, Rachello-Dolmen PG, Parra-Velandia F, Schönberg CHL, Breeuwer JAJ, van Soest RWM (2010) Molecular evidence of cryptic speciation in the ‘cosmopolitan’ excavating sponge Cliona celata (Porifera, Clionaidae). Mol Phylogenet Evol 56:13–20
Source: Ecology - nature.com
