Pioneer generation shapes long-term recovery of coral populations

Pioneer generation shapes long-term recovery of coral populations | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Pioneer generation shapes long-term recovery of coral populations Aziz J. Mulla, Vianney Denis, Yoko Nozawa This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6548265/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 10 Nov, 2025 Read the published version in Coral Reefs → Version 1 posted 10 You are reading this latest preprint version Abstract Reef recovery following a disturbance largely depends on successful coral recruitment and the absence of chronic stressors. However, recent recovery events show increasing homogenization, with dominant coral species replacing the high diversity that once characterized these ecosystems. In this study, we analysed a nine-year dataset (2012–2020) describing the recovery of a reef towards a Pocillopora -dominated state in Taiwan following a devastating typhoon. Tracking eight coral cohorts, we assessed growth, survival and reproduction. Pocillopora recruitment peaked during the first three years, but mortality surged in the fourth year. The initial generation had the highest survival rates, while by the fifth year, newly settled individuals failed to survive beyond two years. By 2020, 83% of the reef consisted of corals from 2012–2016, with 38% originating from the first generation alone (2012). This pioneer generation was the primary contributor to growth and reproduction, emphasizing the reef's reliance on early settlers, leading to an ageing coral community. While pioneer generations were critical to recovery, their dominance may have driven a gradual loss of biodiversity. Our findings highlight the importance of early recruitment in reef development but underscores the risk of reliance on only a few species during and after recovery. Recruitment Cohort effect Dominance Pocillopora paradox Resilience Coral reefs Figures Figure 1 Figure 2 Figure 3 Figure 4 Introduction Marine ecosystems face a wide range of disturbances, with negative impacts exacerbated by human-induced climate change and pollution (Henson et al. 2017). Whilst no ecosystem appears immune (Ratajczak et al. 2018), tropical coral reefs are particularly at risk of local extinction due to their extreme sensitivity to environmental fluctuations (Romero-Torres et al. 2020). Coral bleaching i.e. the breakdown of the symbiotic relationship between corals and their photosynthetic algal endosymbionts (van Woesik et al. 2022), represents a particular major threat. Rising sea surface temperatures, reaching record highs (McManus et al. 2019; Cheng et al. 2021), have driven recurrent mass mortality events globally. However, recent studies suggest some reefs show resilience, with populations recovering from surviving individuals that may have developed tolerance to heat stress (Humanes et al. 2022; Howells et al. 2021). However, unlike bleaching, destructive events such as typhoons directly lead to physical damage and the removal of coral skeletons, particularly those of adult branching colonies, leaving the reef structurally compromised. Coral recovery following a typhoon relies heavily on annual recruitment rates from nearby (Holbrook et al. 2018) and distant sources (Mulla et al. 2021), as well as the growth of surviving and newly settled individuals (Connell et al. 2004; Mulla et al. 2024a). Similar to plant forests (França et al. 2020; Barlow et al. 2018), coral reef recovery involves species replacement (Ricklefs 1990), with initial stages marked by high diversity (Hughes et al. 1999). Over time, species more tolerant of environmental conditions outcompete and dominate earlier settlers (Connell and Slatyer 1977). Recovery, however, can be hindered by factors affecting reproduction (Doropoulos et al. 2015), recruitment (Lachs et al. 2024), population density (Morais et al. 2023), as well as recurrent disturbances that disrupt successional processes (Tebbett et al. 2022). Where disturbance persists, reefs have often shifted to a dominance of algal turf (Lin et al. 2024) or alternative taxa (Reverter et al. 2020). However, in the Indo-Pacific, an increasing number of coral assemblages have been observed to transition to Pocillopora -dominated communities (Adjeroud et al. 2018). Pocillopora -dominated reefs have been reported from the eastern (Edmunds et al. 2019) and southern Pacific (López-Pérez et al. 2012), the Red Sea (Riegl et al. 2013), French Polynesia (Bramanti and Edmunds 2016; Adjeroud et al. 2018), the Andaman Sea (Fiesinger et al. 2023) and Taiwan (Mulla et al. 2024a). This phenomenon, coined here as the " Pocillopora paradox" highlights the systematic colonization and dominance of a single genus during and after recovery. The paradox entails a recovery which seemingly benefits reef development over the short term, yet a dominance of few resilient species, results in a reduction of diversity, which may limit reef functionality and adaptive capacity (McWilliam et al. 2020). Reefs dominated by Pocillopora appear resilient, with population stability maintained through survival and growth rather than transient dynamics (Mulla et al. 2024a). However, the mechanisms underlying this dominance remain unclear. Potential contributing factors include a higher abundance of Pocillopora recruits (Holbrook et al. 2018), greater survival rates of adult colonies (Schmidt-Roach et al. 2014; Speare et al. 2021) and increased mortality among competitors such as Acropora , Montipora and Porites (Edmunds 2018; Morais et al. 2023). Coral populations are thought to develop through individuals being replaced (Mora et al. 2016), typically skewed towards younger colonies (Hughes and Jackson 1985) with few surviving older individuals. The annual settlement of recruits occurs under similar abiotic conditions, which influence biotic success, creating an opportunity to examine how successive cohorts respond to environmental fluctuations. Compared to other biological models, such as fish, relatively little research has focused on tracking coral cohorts over time. However, such studies are highly informative for understanding the dynamics and long-term fate of coral populations (Rouyer et al. 2011; Botsford et al. 2014). In this study, we used long-term monitoring data to assess the recovery of a coral reef community dominated by genus Pocillopora , following a major typhoon disturbance in Taiwan (Mulla et al. 2024a). Through the use of permanent quadrats, we tracked the dynamics of 336 Pocillopora individuals and 1,150 individuals from 32 other coral genera over nine years. We hypothesize that Pocillopora -dominated reefs emerge via ecological mechanisms that promote the sustained dominance of Pocillopora species over time, rather than through individuals being replaced. Instead, cohort development is likely driven by temporal variations in vital rates that confer competitive advantages, ultimately shaping the structure and composition of the community. Materials and Methods Data set A 9-year dataset (2012–2020) describes the recovery of a reef after a severe typhoon disturbance in Orchid Island, Taiwan (Mulla et al. 2024b). A detailed description of the site, sampling method and data variables can be found in Mulla et al. 2024a. Briefly, three parallel 20 m transects were established in 2012, three years after a typhoon (Morakot) in 2009 removed most corals on the reef (Mulla et al. 2024c). Along each transect, 11 quadrats (0.5 × 0.5 m, n=33) were haphazardly placed and permanently demarcated for future monitoring. In this way, only four quadrats were lost during the course of the experiment. High-resolution benthic cover data (projected surface area) were extracted from the analysis of the photo-quadrats to track the growth, survival and recruitment of individual colonies. This method allowed the detection of coral recruits with an area as small as 0.4 cm 2 and was repeated annually between June and October. The contribution of Pocillopora to the coral assemblage was calculated each year as the number of individual Pocillopora colonies by the total number of colonies observed in the quadrats. Even if part of the colony grew outside of the quadrat boundary, it was also taken into consideration. All colonies were identified to genus level and for Pocillopora, DNA analysis from neighbouring Green Island confirmed membership to a species complex, dominated by P. verrucosa (~55%) followed by P. meandrina (~45%). In addition to these two dominant species, there were at least two other Pocillopora species present but rarely observed; P. eydouxi and other Pocillopora sp. (Mulla et al. 2024a). To quantify reproductive output (eggs per polyp), two nubbins (~5 cm branch length) from 40 colonies of different sizes (68.2–685.8 cm 2 in 3D size) were collected during the reproductive season at the neighbouring Green Island (April, 2017). An additional 20 nubbins (of the same size) were collected to determine at what size colonies are considered fertile or infertile (see Mulla et al. 2024a). The number of eggs per colony was estimated by multiplying the number of eggs per polyp by the number of polyps per colony. The final dataset tracks the size of individual colonies over a 9-year period, together with information of the cohort they belong to (year of initial recruitment i.e. 2012 to 2019) as well as survival (fully or partial) and estimated fertility status (fecundity and number of eggs per polyp). Pocillopora colonies were further categorized as recruits (newly appearing individuals), juveniles (≤ 100.0 cm 2 minus recruits) and adults (> 100.0 cm 2 , sexually mature individuals). Data analysis Depending on the year of settlement, Pocillopora individuals were grouped into initial year (2012), early years (2012-2015), later years (2016-2020) and final year (2020) cohorts. To minimize the influence of extreme outliers, colony size data were Winsorized by capping values below the 5th percentile and above the 95th percentile at their respective percentiles (Cheng and Young, 2023). The Shapiro-Wilk test was used to assess the normality of colony size data for both Pocillopora and other genera, indicating that size distributions are not normally distributed ( p < 0.05) . To evaluate changes in size between both groups, while accounting for repeated measures on the same individuals, we used a linear mixed-effects model (LMM) . The model included the 2012 cohort as a fixed effect and individual ID as a random effect to control for within-subject correlation. Significance was determined using Satterthwaite’s approximation for degrees of freedom to provide accurate p -values. Residuals were visually assessed and found to meet the assumptions of normality. Individual growth was calculated as relative growth per year by taking the difference of size between two consecutive years divided by the individual size in the former year and multiplying by 100. Relative growth (yr -1 ) is defined as: where size represent individual size (cm 2 ) and t a given year. Relative growth can be negative in the case of partial mortality and was averaged by cohort. Logically, relative growth cannot be calculated for the first year where new individual recruits settle. Survival was analysed for each cohort using the Kaplan-Meier method and compared between cohorts using the Hazard Ratio (HR) illustrating cohort mortality rate. In addition, the number of Surviving Colonies (SC) was calculated for each cohort as the number of colonies that survived until the final year of the experiment (2020). To further assess mortality rate distribution in each year, skewness of the number of mortality events for Pocillopora was calculated using the following formula: where n is the total number of all mortality events, x i is the number of mortality events in a given year, x̄ is the mean and s is the standard deviation. Differences in fecundity among cohorts (2012, 2013, 2014, 2015) were tested using the Kruskal-Wallis rank sum test , a non-parametric alternative selected due to violations of normality (Shapiro-Wilk test, p < 0.05). When significant differences were detected ( p < 0.05), Dunn’s post hoc test with Bonferroni correction was used to identify specific year-to-year differences. All statistical analyses were conducted in R (version 3.6.1), using packages emmeans (Lenth, 2021), FSA (Ogle and Barber, 2020) and survival (Therneau 2024). The full dataset is available from Mulla et al. (2024b). Results We tracked the fate of 1,486 colonies from 33 genera between 2012 and 2020 following a devastating typhoon in 2009. Our data illustrates how one genus came to dominate the reef compared to all other genera (Figure 1). Pocillopora accounts for almost a third of all colonies present, with proportion remaining relatively stable over time (26%-35% of total; Figure 1a and 1b). Both Pocillopora and other genera are characterized by an initial influx of new colonies in the first few years, which then decreases over time. Mortality was highest in both groups in the same year (2015-2016), with 51 documented events for Pocillopora (Figure 1a) in contrast to 237 for other genera (Figure 1b). Mortality is skewed (0.79) towards early-years (2013-2016), when ~65% of individuals are lost in both groups. The dominance of Pocillopora is most evident in its imposing size compared to other genera (Figure 1c; Figure S1), both in individual years and in all years combined (2015-2020; p < 0.001). From 2015 onwards, other genera are consistently smaller than the Pocillopora groupings with highly significant differences in each year (p < 0.001; Table S1). This size gap becomes more pronounced over time with other genera being considerably smaller in later years (2016-2020). The rapid growth of Pocillopora is not curtailed for 7 years until 2018, but remains higher than other genera throughout. Survival rates decrease over the monitoring period (Figure 2) with a clear difference between early (2012-2016; Figure 2a) and later years (2016-2020; Figure 2b). This is evidenced by the number of colonies which survived until the final year in 2020 (SC in Figure 2), recorded as 45 colonies from early years (2012-2016) and only 9 from later years (2016-2020). The highest rates of survival are recorded in the early years, in contrast to later years in which almost all newly settled individuals did not survive longer than two years. Over the monitoring period, the risk of mortality however decreases, with the highest probability being in the initial year of 2012 and mid-monitoring in 2016. This is reflected in the HR for both years, scoring highest throughout the monitoring period (1 for both years). HR was recorded at its lowest (0) in the final 2 years of monitoring (2018-2020) due to a lack of mortality events. Focusing on early year cohorts (2012-2015), relative growth rates are at their highest for all cohorts within the first 2 years of their settlement (Figure 3a). The first 3 cohorts (2012- 2014) experience high levels of growth which dramatically declines after 2015. The 2015 cohort itself follows a similar pattern with 2 years of high-level growth and a decline in 2017. All cohorts show signs of a small increase in growth between 2018-2019 until 2020, where growth is at its minimum. A snapshot of the final year (dashed line circle; Figure 3b), shows that the vast majority (~83%) of the final population consists of early year individuals in contrast to only ~17% from later years. The initial cohort of 2012 contributes the most to this (> 38%) in contrast to the 2017 cohort which contributes the least (< 2%). In terms of fecundity (eggs per colony), reproduction is highly concentrated in cohorts from early years (2012-2016) and is almost non-existent in cohorts from later years (2016-2020) due to a lack of growth and survival (Figure 4). Even so, when focusing on cohorts from early years, the vast majority of individuals contributing in terms of reproduction are from the initial year of 2012, with reproductive output steadily declining for subsequent cohorts. Pairwise comparisons (Table S2) showed all cohorts were significant different (p < 0.05) compared to the 2012 cohort. Discussion Recovery represents a fundamental process of ecosystem dynamics. It describes a pattern of change, towards a former state, following partial degradation or a significant shift in composition (Dudgeon et al. 2010). This study aimed to investigate the recovery towards the dominance of genus Pocillopora after a disturbance, a phenomenon increasingly observed across the Indo-Pacific (López-Pérez et al. 2012; Riegl, Berumen and Bruckner 2013; Bramanti and Edmunds 2016; Adjeroud et al. 2018; Mulla et al. 2024a). Our findings suggest that, rather than individual replacement, early generations of pioneer settlers dominate from the outset, shaping the reef’s structure until the next major disturbance. While recovery, often measured as an increase in coral cover or individual abundance, is generally seen as positive (Mumby and Harborne 2010; Manfrino et al. 2013; Nozawa et al. 2020), it is crucial to consider how such dominance impacts the broader ecosystem. The emergence of a Pocillopora -dominated reef highlights a pattern of community development where one genus—and in this case, a few specific cohorts—are disproportionately favoured. This dynamic is somewhat similar to mast seeding in trees, where synchronized and variable seed production leads to years of abundance followed by years of scarcity (Silvertown 2008). A further parallel can be drawn with the priority effect, where the timing of species arrival in a habitat significantly influences community structure and ecosystem dynamics (Meester et al. 2016). The persistence of Pocillopora dominance despite subsequent disturbances suggests that such dynamics could drive the formation of less diverse reef communities, with long-term implications for ecosystem resilience and function. The reef in Orchid Island experienced a fast and seemingly predictable recovery towards coral dominance following a disturbance which may lead to assumptions of resilience (Côté and Darling 2010). Here however, resilience depends on specific cohorts, with a population potentially relying on just a few cohorts for its survival. Pocillopora is often described as a "weedy" coral (McClanahan 2014), known for its rapid colonization and ability to quickly respond to environmental change. As such, it would be expected that the succession of other genera would follow the colonisation of Pocillopora , yet was not the case. Despite this apparent stability of Pocillopora survival, it may also mask underlying sensitivities to disturbance events, potentially leading to rapid collapse and impact on the entire ecosystem. Although cohorts from early years were able to withstand consecutive disturbances during recovery, their limits remain unknown, including how much environmental pressure they can endure. The reef in Orchid Island, relies heavily on early cohorts, as they contribute substantially to both cover and reproductive output. Therefore, any perturbation which exceeds their tolerance could result in tipping points being reached at a rapid rate. More frequent recovery events that lead to a dominance of Pocillopora could have significant implications for future reef dynamics having important implications for management, whether overseeing a natural recovery of degraded areas (Morais et al. 2023) or some form of intervention through restoration (Fox et al. 2019). Emergence of the Pocillopora-paradox Recruitment sources from surviving Pocillopora populations, whether nearby or from distant but well-connected populations, play a key role in founding events (Cruz et al. 2018; Soares et al. 2021). Following a disturbance, larval dispersal helps replenish areas where widespread colony removal has occurred. While the significance of dispersal mechanisms warrants further exploration, particle dispersal models suggest that some coral populations between the Philippines and East Taiwan are well-connected (Mercado-Vicentillo et al. 2024). For Pocillopora populations in particular, dispersal mechanisms like photo-movement (Mulla et al. 2021), provide larvae a competitive advantage, enabling them to quickly colonize available space and thrive. These recruitment events are often considered independent and stochastic (Gotelli 1988; Caley et al. 1996; Ricardo et al. 2017), yet an increase in Pocillopora reefs may lead future reef structure to be more deterministic. The dominance of early-year cohorts allows certain colonies to outcompete others for space, even within the same genus (Horwitz, Hoogenboom and Fine 2017), which explains the high levels of recruit mortality observed. Growth and survival rates of recruits are skewed towards founding cohorts (early years), where those that settle earlier experience faster growth and higher survival rates. Similar trends in early-life dynamics have been observed in terrestrial systems, such as forests (Swanson et al. 2011), where trees that arrive later exhibit reduced growth and lower survival overall. Additionally, early cohorts are more reproductively active during recovery, compared to those arriving in later years, which have limited reproductive potential and experience higher mortality. In this study, we demonstrate that newly settled, early-year cohorts are critical to recovery of the reef in Orchid Island. Coexistence theory explains that such demographic trends are driven by competition within sedentary communities that are limited by space (Johnson and Hastings 2023). This theory suggests that pioneer events are as significant as their demographic characteristics. However, these features have been shown to benefit only a few coral species (Edmunds et al. 2024) or the broader community (Mumby 2017). Early competitive exclusion is advantageous for future development, as space becomes a density-dependent factor later in life (Edmunds et al. 2018). In addition, inter-cohort cannibalism may play a role in reinforcing the dominance of early settlers. Although rarely documented, it is plausible that large, established individuals may consume or suppress the settlement of incoming larvae, further reducing competition (Pineda et al. 2010). This dynamic has been observed in other marine systems, where inter-cohort cannibalism is a major source of mortality at settlement (Moksnes et al. 1997; Sainte-Marie & Lafrance 2002; Moksnes 2004). Few studies have explicitly linked cannibalism to stabilizing population dynamics (Luppi et al. 2001), but its potential role in decoupling larval supply from successful recruitment warrants consideration, especially in systems structured by strong spatial constraints. If such interactions occur, they would advantage early cohorts not only through priority effects but also through active suppression of newcomers, suggesting that predictions of population structure should account for localized cannibalistic interactions among benthic broadcast spawners. Pocillopora is well-documented for its tolerance to harsh conditions (Haryanti et al. 2015; Rodriguez-Troncoso et al. 2016; Pratchett, McWilliam and Riegl 2020). The ability of adult colonies to a reach reproductive age/size is critical, as their increased resilience to disturbances like typhoons, enables them to lead the recovery process from the outset. Surviving colonies reach this stage relatively quickly, allowing them to withstand further major disturbances and solidify their dominance, while younger colonies struggle. As the Orchid Island population matures, density-dependent mechanisms help sustain the dominance of this single genus (Mulla et al. 2024a). Further, Pocillopora’s portfolio ofsurvival strategies such as unique dispersal mechanisms, skewed growth rates, inter-cohort competition and high tolerance all contribute to the paradox, where a seemingly apparent recovery masks a homogenized reef with reduced diversity. Challenges of the Pocillopora-paradox The existence of such a paradox poses a significant risk to the reef in Orchid Island in several ways, and more broadly for any taxa that might be selected and thrive on future reefs. Firstly, it raises concerns about barriers to ecosystem function, particularly with the predicted intensification of disturbance events (Hughes et al. 2021). While a general decline in diversity, associated with reef homogenization, may not be a major issue at the alpha scale, a rise of Pocillopora -dominated states across the region is troubling for the future (Dornelas et al. 2006). In our study, 83% of the reef in Orchid Island was composed of corals from early cohorts (2012–2016), which could jeopardize long-term reproductive success, as age is a key determinant of fertility (Rapuano et al. 2023). The establishment of Pocillopora-dominated reefs suggests that allochthonous larvae may impact reefs further north. While reproductive output is currently driven by early cohorts, it is unclear how many reproductive cycles a coral can undergo (Marchini et al. 2015) or how variability between early and later cohorts affects population dynamics (Shlesinger and Loya 2021). Early-life environmental conditions may cause lasting "cohort effects," influencing reproductive output at maturation (Stenseth et al. 2002). Although older colonies remain sexually active (Mezaki et al. 2013), some studies report declining fecundity with age due to reproductive senescence (Rinkevich and Loya 1986; Nozawa and Lin 2014). However, evidence remains limited (Bythell et al. 2017), and Mulla et al. 2024a found no sign of senescence, with larger colonies showing higher fertility. Still, long-term monitoring is needed, as cohort-specific infertility could threaten overall reef reproduction. Homogenization may also reduce genetic diversity within populations, leading to a decline in overall resilience. Analysis from neighbouring Green Island in Taiwan revealed that biological variation within Pocillopora populations was low at both shallow and mesophotic depths (De Palmas et al. 2018). Reduced diversity has been demonstrated in Mo'orea, French Polynesia, where following a mass bleaching event, 86% of Pocillopora individuals, all belonging to a single haplotype, suffered mortality (Burgess et al. 2021). This genetic bottleneck may result from few genotypes dispersing from the same location, populating the reef and facilitating further homogenization. Changes in environmental conditions may lead Pocillopora corals to exhibit a uniform response to disturbance. In our study, typhoons were the primary cause of coral decline, removing a significant number of individuals from the reef. Those left behind suffered partial mortality, increasing the risk of disease (Brandt et al. 2013). Outbreaks such as black band disease have caused major declines in Pocillopora populations (Plucer-Rosario 1987), particularly in Taiwan (Huang et al. 2021). In some cases, black band disease was found to affect Pocillopora specifically, while other genera remained unaffected (Thinesh et al. 2013). This blanket response within a population places immense pressure on early-year cohorts and the broader community, as a single event risks the loss of entire populations. As global temperatures continue to rise, including in Taiwan (Belkin and Lee 2014) and the wider Indo-Pacific (Matz et al. 2020), the risk of coral bleaching events also increases. Unlike typhoons, which remove entire coral skeletons and frees up space for recruitment, bleaching results in dead coral skeletons that can accumulate macroalgae (Liu et al. 2009), obstructing coral recruitment and hindering recovery. While typhoons and bleaching differ in their immediate impact, both pose a certain threat to homogeneous reefs, which may respond uniformly, leading to a wider decline in resilience. Implications for coral reef dynamics Tracking cohort progression helps reduce variability in population dynamics, often attributed to disparities in size or age (Hughes and Connell 1987). While this method is well-established in fish ecology (Rouyer et al. 2011), it is less commonly applied to corals, partly due to the lack of stable, long-term monitoring data or a preference for short-term population or community dynamics studies. As a result, density-dependent processes like cohort resonance (Bjørnstad and Grenfell 2001) are often overlooked. The cohort method offers a way to track spatial dynamics, with individual interactions documented over time, improving our understanding of density-dependent mechanisms in space-limited populations. For corals, it helps identify factors directly influencing growth, survival and reproduction at critical life stages. This approach highlights the vulnerabilities within a population, revealing that beyond Pocillopora dominance, a reef may be dominated by a few cohorts, potentially from the same source and genetically homogenous. This method has been overlooked in examining general patterns that significantly influence reef dynamics. Events like coral bleaching, typhoons and pollution can be tracked using this method, offering insights into how specific disturbances affect particular individuals within a certain grouping and how coral resilience and adaptability evolve in response to fluctuating conditions. Ultimately, this method facilitates in-depth comparative studies across regions, providing valuable data for conservation and management strategies. Conclusions Here we show that a Pocillopor a-dominated state arises from the survival and growth of the initial settlement of recruits following a disturbance, with the pioneer generation playing a disproportionately large role in recovery. Recognizing this phenomenon is key to understanding the Pocillopora -paradox and highlights the pivotal influence of early settlement (Edmunds et al. 2024) on coral population trajectories. In Orchid Island, not just a single genus, but a single generation, dictates future reef structure, suggesting that apparent recovery may mask declining diversity. The absence of later cohort survival reflects density-dependent processes rather than recruitment failure. Such recovery patterns may lead to broader disequilibrium under climate change, driving local extinctions and reef homogenization. While the impacts on diversity, ecosystem function and services remain uncertain, these findings stress the importance of post-settlement processes for reef restoration efforts. Declarations Acknowledgments We thank C-H Lin, C-L Fong, J-H Shiu, T-Y Lai, V. Dang for their assistance in the field. A.J.M is supported through UCAJEDI Investments in the Future Project managed by National Research Agency (ANR-15-IDEX-01). V.D. was supported by grants from National Science and Technology Council, Taiwan (NSTC, 111-2628-M-002-007-MY3) and National Taiwan University (NTU, CDP-114L7722). 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Biol J Linn Soc 14:235–250 Shlesinger T, Loya Y (2021) Depth-dependent parental effects create invisible barriers to coral dispersal. Commun Biol 4:202 Smallhorn-West PF, Garvin JB, Slayback DA, DeCarlo TM, Gordon SE, Fitzgerald SH, Halafihi T, Jones GP, Bridge TCL (2020) Coral reef annihilation, persistence and recovery at Earth’s youngest volcanic island. Coral Reefs 39:529–536 Soares MO, Rossi S, Gurgel AR, Lucas CC, Tavares TCL, Diniz B, Feitosa CV, Rabelo EF, Pereira PHC, Papa de Kikuchi RK et al (2021) Impacts of a changing environment on marginal coral reefs in the Tropical Southwestern Atlantic. Ocean Coast Manag 210:105692 Speare KE, Adam TC, Winslow EM, Lenihan HS, Burkepile DE (2021) Size-dependent mortality of corals during marine heatwave erodes recovery capacity of a coral reef. Glob Change Biol 28:1342–1358 Stenseth NC, Mysterud A, Otterson G, Hurrell JW, Chan KS, Lima M (2002) Ecological effects of climate fluctuations. Science 297:1292–1296 Swanson ME, Franklin JF, Beschta RL, Crisafulli CM, DellaSala DA, Hutto RL, Lindenmayer DB, Swanson FJ (2010) The forgotten stage of forest succession: early-successional ecosystems on forest sites. Front Ecol Environ 9:117–125 Tebbett SB, Morais J, Bellwood DR (2022) Spatial patchiness in change, recruitment, and recovery on coral reefs at Lizard Island following consecutive bleaching events. Mar Environ Res 173:105537 Therneau T (2015) A package for survival analysis in R: Version 3.7-0. Available at https://cran.r-project.org/web/packages/survival/index.html. Accessed 20 Sep 2023 Thinesh T, Raj KD, Matthews G, Edward JP (2013) Coral diseases are major contributors to coral mortality in Shingle Island, Gulf of Mannar, southeastern India. Dis Aquat Organ 106:68–77 van Woesik R, Shlesinger T, Grottoli AG, Toonen RJ, Thurber RV, Warner ME, Hulver AM, Chapron L, McLachlan RH, Albright R et al (2022) Coral-bleaching responses to climate change across biological scales. Glob Change Biol 28:4229–4250 Additional Declarations No competing interests reported. Supplementary Files MullaCRSUPP.docx Cite Share Download PDF Status: Published Journal Publication published 10 Nov, 2025 Read the published version in Coral Reefs → Version 1 posted Editorial decision: Revision requested 19 Jun, 2025 Reviews received at journal 04 Jun, 2025 Reviews received at journal 28 May, 2025 Reviewers agreed at journal 28 May, 2025 Reviewers agreed at journal 20 May, 2025 Reviewers agreed at journal 12 May, 2025 Reviewers invited by journal 06 May, 2025 Editor assigned by journal 03 May, 2025 Submission checks completed at journal 29 Apr, 2025 First submitted to journal 28 Apr, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6548265","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":454982048,"identity":"eb974bd5-c779-4a56-ac11-bbec70f9cef0","order_by":0,"name":"Aziz J. Mulla","email":"","orcid":"","institution":"Academia Sinica","correspondingAuthor":false,"prefix":"","firstName":"Aziz","middleName":"J.","lastName":"Mulla","suffix":""},{"id":454982049,"identity":"3fb26d64-5824-424e-9894-80627c46a84b","order_by":1,"name":"Vianney Denis","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9ElEQVRIiWNgGAWjYDACZgjF2ABCHyAcA+K1MM6AqAYSCYQtA2oBauchRovBceZnjwsqDsv2Szc3f7bd8Sexgb15mwTjj8O4tRxmMzeeceaw8cw5B9ukc88YJDbwHCuTYEjArUWymcFMmrftcOKGG4ltzLltQC0SOWZALbfxaGH/Js3773Di/huJzZ8tQVrk3+DXws/MA7SlAWiLRGKDNCPYFh6CWsqkeY6lG88AOkyyt83YuI0nrdgiIe0/Ti1s/Me3SfPUWMv2z0h//OFnm5xsP/vhjTc+2KTh1AIFzUiGgIgEQhoYGOoIKxkFo2AUjIKRCwDrAlD9pXVCFgAAAABJRU5ErkJggg==","orcid":"","institution":"National Taiwan University","correspondingAuthor":true,"prefix":"","firstName":"Vianney","middleName":"","lastName":"Denis","suffix":""},{"id":454982050,"identity":"897e5350-fd1a-4d62-8f46-2738678d4da7","order_by":2,"name":"Yoko Nozawa","email":"","orcid":"","institution":"Academia Sinica","correspondingAuthor":false,"prefix":"","firstName":"Yoko","middleName":"","lastName":"Nozawa","suffix":""}],"badges":[],"createdAt":"2025-04-28 13:23:10","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-6548265/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6548265/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00338-025-02769-9","type":"published","date":"2025-11-10T15:57:23+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":82486890,"identity":"6cb0b84a-657c-4af2-8de0-83d4f83497c2","added_by":"auto","created_at":"2025-05-12 05:40:10","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":883924,"visible":true,"origin":"","legend":"\u003cp\u003eCommunity data illustrating the recovery dynamics of \u003cem\u003ePocillopora\u003c/em\u003e (blue)\u003cem\u003e \u003c/em\u003eand other genera (green; \u003cem\u003en\u003c/em\u003e = 32) over 9 years in Orchid Island, Taiwan a) The number of \u003cem\u003ePocillopora\u003c/em\u003eindividuals observed between 2012 and 2020 highlighting both colonies already present in that year (dark blue) and those newly appearing (light blue). Black line indicates the number of mortality events b) The number of individuals of other genera observed between 2012 and 2020 separated between colonies already present on that year (dark green) and those newly appearing (light green). Black line indicates the number of mortality events c) Boxplot illustrating changes in size of \u003cem\u003ePocillopora \u003c/em\u003e(blue) and colonies of other genera (green) over time. Asterisks indicate significance levels (*** = p \u0026lt; 0.001).\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/b47dc12456d5382414bdf5dc.png"},{"id":82486353,"identity":"45af3232-b042-41f0-818c-6bf371c51a82","added_by":"auto","created_at":"2025-05-12 05:32:10","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":801582,"visible":true,"origin":"","legend":"\u003cp\u003eKaplan-Meier survival curves of newly appearing \u003cem\u003ePocillopora\u003c/em\u003e individuals from cohorts between 2012 and 2019. a) Early years (\u003cem\u003en \u003c/em\u003e= 283) including the highlighted initial year (2012 cohort) b) Later years (\u003cem\u003en \u003c/em\u003e= 42) including the highlighted final year (2019 cohort). Dashed lines indicate 95% confidence intervals. \u003cem\u003en\u003c/em\u003e indicates the number of colonies within the cohort and HR is the hazard ratio for each year. SC represents the number of surviving colonies for each cohort.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/f5227f92878b9b9cbe02fd8b.png"},{"id":82486358,"identity":"c0655dbc-7689-42cc-9184-f1efc5b09b68","added_by":"auto","created_at":"2025-05-12 05:32:10","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":1478264,"visible":true,"origin":"","legend":"\u003cp\u003eGrowth of the early-year \u003cem\u003ePocillopora\u003c/em\u003e cohort and their contribution to the final-year population a) Relative growth (%) of early year \u003cem\u003ePocillopora\u003c/em\u003e cohorts (2012-2015) illustrating a preliminary period of rapid growth which is then suppressed, to then experience a slight rebound in later years (2018-2019). Shaded areas represent 95% confidence intervals. b) A pie chart demonstrating the contribution of surviving individuals from each cohort to the final year of 2020. Cohorts from early years make up ~83% of the population with the remaining ~17% from later years.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/780406fec25c82bcaf1f9281.png"},{"id":82486357,"identity":"d90dacbc-3088-4c9d-95bd-ac044433b742","added_by":"auto","created_at":"2025-05-12 05:32:10","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":703908,"visible":true,"origin":"","legend":"\u003cp\u003eAnnual cumulative reproductive output (eggs per colony x10\u003csup\u003e6\u003c/sup\u003e) of individuals from early years (2012-2015) illustrating how reproduction is favoured in the earlier years.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/afee99134842d280ca05213b.png"},{"id":96104983,"identity":"92a48686-8234-4ff5-af29-a8d1fd1928c1","added_by":"auto","created_at":"2025-11-17 16:06:11","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":4301752,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/7fd335d7-8258-4f35-8849-95b5215b025f.pdf"},{"id":82486364,"identity":"913585fa-f681-403a-9efd-6cbc8198b915","added_by":"auto","created_at":"2025-05-12 05:32:10","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":3496080,"visible":true,"origin":"","legend":"","description":"","filename":"MullaCRSUPP.docx","url":"https://assets-eu.researchsquare.com/files/rs-6548265/v1/071201fb077a37ca115bc9e1.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Pioneer generation shapes long-term recovery of coral populations","fulltext":[{"header":"Introduction","content":"\u003cp\u003eMarine ecosystems face a wide range of disturbances, with negative impacts exacerbated by human-induced climate change and pollution (Henson et al. 2017). Whilst no ecosystem appears immune (Ratajczak et al. 2018), tropical coral reefs are particularly at risk of local extinction due to their extreme sensitivity to environmental fluctuations (Romero-Torres et al. 2020). Coral bleaching i.e. the breakdown of the symbiotic relationship between corals and their photosynthetic algal endosymbionts (van Woesik et al. 2022), represents a particular major threat. Rising sea surface temperatures, reaching record highs (McManus et al. 2019; Cheng et al. 2021), have driven recurrent mass mortality events globally. However, recent studies suggest some reefs show resilience, with populations recovering from surviving individuals that may have developed tolerance to heat stress (Humanes et al. 2022; Howells et al. 2021). However, unlike bleaching, destructive events such as typhoons directly lead to physical damage and the removal of coral skeletons, particularly those of adult branching colonies, leaving the reef structurally compromised.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eCoral recovery following a typhoon relies heavily on annual recruitment rates from nearby (Holbrook et al. 2018) and distant sources (Mulla et al. 2021), as well as the growth of surviving and newly settled individuals (Connell et al. 2004; Mulla et al. 2024a). Similar to plant forests (França et al. 2020; Barlow et al. 2018), coral reef recovery involves species replacement (Ricklefs 1990), with initial stages marked by high diversity (Hughes et al. 1999). Over time, species more tolerant of environmental conditions outcompete and dominate earlier settlers (Connell and Slatyer 1977). Recovery, however, can be hindered by factors affecting reproduction (Doropoulos et al. 2015), recruitment (Lachs et al. 2024), population density (Morais et al. 2023), as well as recurrent disturbances that disrupt successional processes (Tebbett et al. 2022). Where disturbance persists, reefs have often shifted to a dominance of algal turf (Lin et al. 2024) or alternative taxa (Reverter et al. 2020). However, in the Indo-Pacific, an increasing number of coral assemblages have been observed to transition to \u003cem\u003ePocillopora\u003c/em\u003e-dominated communities (Adjeroud et al. 2018).\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cem\u003ePocillopora\u003c/em\u003e-dominated reefs have been reported from the eastern (Edmunds et al. 2019) and southern Pacific (López-Pérez et al. 2012), the Red Sea (Riegl et al. 2013), French Polynesia (Bramanti and Edmunds 2016; Adjeroud et al. 2018), the Andaman Sea (Fiesinger et al. 2023) and Taiwan (Mulla et al. 2024a). This phenomenon, coined here as the \"\u003cem\u003ePocillopora\u003c/em\u003e paradox\" highlights the systematic colonization and dominance of a single genus during and after recovery. The paradox entails a recovery which seemingly benefits reef development over the short term, yet a dominance of few resilient species, results in a reduction of diversity, which may limit reef functionality and adaptive capacity (McWilliam et al. 2020). Reefs dominated by \u003cem\u003ePocillopora\u003c/em\u003e appear resilient, with population stability maintained through survival and growth rather than transient dynamics (Mulla et al. 2024a). However, the mechanisms underlying this dominance remain unclear. Potential contributing factors include a higher abundance of \u003cem\u003ePocillopora\u003c/em\u003e recruits (Holbrook et al. 2018), greater survival rates of adult colonies (Schmidt-Roach et al. 2014; Speare et al. 2021) and increased mortality among competitors such as \u003cem\u003eAcropora\u003c/em\u003e, \u003cem\u003eMontipora\u003c/em\u003e and \u003cem\u003ePorites\u003c/em\u003e (Edmunds 2018; Morais et al. 2023).\u003c/p\u003e\n\u003cp\u003eCoral populations are thought to develop through individuals being replaced (Mora et al. 2016), typically skewed towards younger colonies (Hughes and Jackson 1985) with few surviving older individuals. The annual settlement of recruits occurs under similar abiotic conditions, which influence biotic success, creating an opportunity to examine how successive cohorts respond to environmental fluctuations. Compared to other biological models, such as fish, relatively little research has focused on tracking coral cohorts over time. However, such studies are highly informative for understanding the dynamics and long-term fate of coral populations (Rouyer et al. 2011; Botsford et al. 2014).\u003c/p\u003e\n\u003cp\u003eIn this study, we used long-term monitoring data to assess the recovery of a coral reef community dominated by genus \u003cem\u003ePocillopora\u003c/em\u003e, following a major typhoon disturbance in Taiwan (Mulla et al. 2024a). Through the use of permanent quadrats, we tracked the dynamics of 336 \u003cem\u003ePocillopora\u003c/em\u003e individuals and 1,150 individuals from 32 other coral genera over nine years. We hypothesize that \u003cem\u003ePocillopora\u003c/em\u003e-dominated reefs emerge via ecological mechanisms that promote the sustained dominance of \u003cem\u003ePocillopora\u003c/em\u003e species over time, rather than through individuals being replaced. Instead, cohort development is likely driven by temporal variations in vital rates that confer competitive advantages, ultimately shaping the structure and composition of the community.\u003c/p\u003e"},{"header":"Materials and Methods","content":"\u003cp\u003e\u003cstrong\u003e\u003cem\u003eData set\u0026nbsp;\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eA 9-year dataset (2012\u0026ndash;2020) describes the recovery of a reef after a severe typhoon disturbance in Orchid Island, Taiwan (Mulla et al. 2024b). A detailed description of the site, sampling method and data variables can be found in Mulla et al. 2024a. Briefly, three parallel 20 m transects were established in 2012, three years after a typhoon (Morakot) in 2009 removed most corals on the reef (Mulla et al. 2024c). Along each transect, 11 quadrats (0.5 \u0026times; 0.5 m, n=33) were haphazardly placed and permanently demarcated for future monitoring. In this way, only four quadrats were lost during the course of the experiment. High-resolution benthic cover data (projected surface area) were extracted from the analysis of the photo-quadrats to track the growth, survival and recruitment of individual colonies. This method allowed the detection of coral recruits with an area as small as 0.4 cm\u003csup\u003e2\u003c/sup\u003e and was repeated annually between June and October. The contribution of \u003cem\u003ePocillopora\u003c/em\u003e to the coral assemblage was calculated each year as the number of individual \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003ecolonies by the total number of colonies observed in the quadrats. Even if part of the colony grew outside of the quadrat boundary, it was also taken into consideration. All colonies were identified to genus level and for \u003cem\u003ePocillopora,\u0026nbsp;\u003c/em\u003eDNA analysis from neighbouring Green Island confirmed membership to a species complex, dominated by \u003cem\u003eP. verrucosa\u003c/em\u003e (~55%) followed by \u003cem\u003eP. meandrina\u003c/em\u003e (~45%). In addition to these two dominant species, there were at least two other \u003cem\u003ePocillopora\u003c/em\u003e species present but rarely observed; \u003cem\u003eP.\u003c/em\u003e\u003cem\u003e\u0026nbsp;eydouxi\u003c/em\u003e and other \u003cem\u003ePocillopora sp.\u003c/em\u003e (Mulla et al. 2024a).\u003cem\u003e\u0026nbsp;\u003c/em\u003e\u003c/p\u003e\n\u003cp\u003eTo quantify reproductive output (eggs per polyp), two nubbins (~5 cm branch length) from 40 colonies of different sizes (68.2\u0026ndash;685.8 cm\u003csup\u003e2\u003c/sup\u003e in 3D size) were collected during the reproductive season at the neighbouring Green Island (April, 2017). An additional 20 nubbins (of the same size) were collected to determine at what size colonies are considered fertile or infertile (see Mulla et al. 2024a). The number of eggs per colony was estimated by multiplying the number of eggs per polyp by the number of polyps per colony. The final dataset tracks the size of individual colonies over a 9-year period, together with information of the cohort they belong to (year of initial recruitment i.e. 2012 to 2019) as well as survival (fully or partial) and estimated fertility status (fecundity and number of eggs per polyp). \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003ecolonies were further categorized as recruits (newly appearing individuals), juveniles (\u0026le; 100.0 cm\u003csup\u003e2\u003c/sup\u003e minus recruits) and adults (\u0026gt; 100.0 cm\u003csup\u003e2\u0026nbsp;\u003c/sup\u003e, sexually mature individuals).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eData analysis\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eDepending on the year of settlement, \u003cem\u003ePocillopora\u003c/em\u003e individuals were grouped into initial year (2012), early years (2012-2015), later years (2016-2020) and final year (2020) cohorts.\u0026nbsp;To minimize the influence of extreme outliers, colony size data were Winsorized by capping values below the 5th percentile and above the 95th percentile at their respective percentiles (Cheng and Young, 2023). The \u003cstrong\u003eShapiro-Wilk test\u003c/strong\u003e was used to assess the normality of colony size data for both \u003cem\u003ePocillopora\u003c/em\u003e and other genera, indicating that \u003cstrong\u003esize distributions are not normally distributed\u0026nbsp;\u003c/strong\u003e(\u003cem\u003ep\u003c/em\u003e \u0026lt; 0.05)\u003cstrong\u003e.\u0026nbsp;\u003c/strong\u003eTo evaluate changes in size between both groups, while accounting for repeated measures on the same individuals, we used a \u003cstrong\u003elinear mixed-effects model (LMM)\u003c/strong\u003e\u003cstrong\u003e.\u003c/strong\u003e The model included \u003cstrong\u003ethe 2012 cohort\u003c/strong\u003e as a fixed effect and \u003cstrong\u003eindividual ID\u003c/strong\u003e as a random effect to control for within-subject correlation.\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003eSignificance was determined using \u003cstrong\u003eSatterthwaite\u0026rsquo;s approximation\u003c/strong\u003e for degrees of freedom to provide accurate \u003cem\u003ep\u003c/em\u003e-values. Residuals were visually assessed and found to meet the assumptions of normality.\u003c/p\u003e\n\u003cp\u003eIndividual growth was calculated as relative growth per year by taking the difference of size between two consecutive years divided by the individual size in the former year and multiplying by 100. Relative growth (yr\u003csup\u003e-1\u003c/sup\u003e) is defined as:\u003c/p\u003e\n\u003cp\u003e\u003cimg 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\"\u003e\u003cbr\u003e\u003c/p\u003e\n\u003cp\u003ewhere \u003cem\u003esize\u003c/em\u003e represent individual size (cm\u003csup\u003e2\u003c/sup\u003e) and \u003cem\u003et\u003c/em\u003e a given year. Relative growth can be negative in the case of partial mortality and was averaged by cohort. Logically, relative growth cannot be calculated for the first year where new individual recruits settle.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eSurvival was analysed for each cohort using the\u0026nbsp;Kaplan-Meier method and compared between cohorts using the\u0026nbsp;Hazard Ratio (HR) illustrating cohort mortality rate. In addition, the number of Surviving Colonies (SC) was calculated for each cohort as the number of colonies that survived until the final year of the experiment (2020). To further assess mortality rate distribution in each year, skewness of the number of mortality events for \u003cem\u003ePocillopora\u003c/em\u003e was calculated using the following formula:\u003c/p\u003e\n\u003cp\u003e\u0026nbsp;\u003cimg 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\"\u003e\u003c/p\u003e\n\u003cp\u003ewhere \u003cem\u003en\u003c/em\u003e is the total number of all mortality events, \u003cem\u003ex\u003csub\u003ei\u0026nbsp;\u003c/sub\u003e\u003c/em\u003eis the number of mortality events in a given year, \u003cem\u003ex̄ is the mean and s is the standard deviation.\u0026nbsp;\u003c/em\u003eDifferences in \u003cstrong\u003efecundity\u003c/strong\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003eamong cohorts (2012, 2013, 2014, 2015) were tested using the \u003cstrong\u003eKruskal-Wallis rank sum test\u003c/strong\u003e, a non-parametric alternative selected due to violations of normality (Shapiro-Wilk test, \u003cem\u003ep\u003c/em\u003e \u0026lt; 0.05). When significant differences were detected (\u003cem\u003ep\u003c/em\u003e \u0026lt; 0.05), \u003cstrong\u003eDunn\u0026rsquo;s post hoc test\u003c/strong\u003e with \u003cstrong\u003eBonferroni correction\u003c/strong\u003e was used to identify specific year-to-year differences. All statistical analyses were conducted in \u003cstrong\u003eR\u003c/strong\u003e (version 3.6.1), using packages \u003cem\u003eemmeans\u003c/em\u003e (Lenth, 2021), \u003cem\u003eFSA\u003c/em\u003e (Ogle and Barber, 2020) and \u003cem\u003esurvival\u003c/em\u003e (Therneau 2024). The full dataset is available from Mulla et al. (2024b).\u003cstrong\u003e\u003cbr\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e"},{"header":"Results ","content":"\u003cp\u003eWe tracked the fate of 1,486 colonies from 33 genera between 2012 and 2020 following a devastating typhoon in 2009. Our data illustrates how one genus came to dominate the reef compared to all other genera (Figure 1). \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003eaccounts for almost a third of all colonies present, with proportion remaining relatively stable over time (26%-35% of total; Figure 1a and 1b). Both \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003eand other genera are characterized by an initial influx of new colonies in the first few years, which then decreases over time. Mortality was highest in both groups in the same year (2015-2016), with 51 documented events for \u003cem\u003ePocillopora\u003c/em\u003e (Figure 1a)\u003cem\u003e\u0026nbsp;\u003c/em\u003ein contrast to 237 for other genera (Figure 1b). Mortality is skewed (0.79) towards early-years (2013-2016), when ~65% of individuals are lost in both groups. The dominance of \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003eis most evident in its imposing size compared to other genera (Figure 1c; Figure S1), both in individual years and in all years combined (2015-2020; p \u0026lt; 0.001). From 2015 onwards, other genera are consistently smaller than the \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003egroupings with highly significant differences in each year (p \u0026lt; 0.001; Table S1). This size gap becomes more pronounced over time with other genera being considerably smaller in later years (2016-2020). The rapid growth of \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003eis not curtailed for 7 years until 2018, but remains higher than other genera throughout.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eSurvival rates decrease over the monitoring period (Figure 2) with a clear difference between early (2012-2016; Figure 2a) and later years (2016-2020; Figure 2b). This is evidenced by the number of colonies which survived until the final year in 2020 (SC in Figure 2), recorded as 45 colonies from early years (2012-2016) and only 9 from later years (2016-2020). The highest rates of survival are recorded in the early years, in contrast to later years in which almost all newly settled individuals did not survive longer than two years. Over the monitoring period, the risk of mortality however decreases, with the highest probability being in the initial year of 2012 and mid-monitoring in 2016. This is reflected in the HR for both years, scoring highest throughout the monitoring period (1 for both years). HR was recorded at its lowest (0) in the final 2 years of monitoring (2018-2020) due to a lack of mortality events.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eFocusing on early year cohorts (2012-2015), relative growth rates are at their highest for all cohorts within the first 2 years of their settlement (Figure 3a). The first 3 cohorts (2012- 2014) experience high levels of growth which dramatically declines after 2015. The 2015 cohort itself follows a similar pattern with 2 years of high-level growth and a decline in 2017. All cohorts show signs of a small increase in growth between 2018-2019 until 2020, where growth is at its minimum. A snapshot of the final year (dashed line circle; Figure 3b), shows that the vast majority (~83%) of the final population consists of early year individuals in contrast to only ~17% from later years. The initial cohort of 2012 contributes the most to this (\u0026gt; 38%) in contrast to the 2017 cohort which contributes the least (\u0026lt; 2%).\u003c/p\u003e\n\u003cp\u003eIn terms of fecundity (eggs per colony), reproduction is highly concentrated in cohorts from early years (2012-2016) and is almost non-existent in cohorts from later years (2016-2020) due to a lack of growth and survival (Figure 4). Even so, when focusing on cohorts from early years, the vast majority of individuals contributing in terms of reproduction are from the initial year of 2012, with reproductive output steadily declining for subsequent cohorts. Pairwise comparisons (Table S2) showed all cohorts were significant different (p \u0026lt; 0.05) compared to the 2012 cohort.\u0026nbsp;\u003c/p\u003e"},{"header":"Discussion ","content":"\u003cp\u003eRecovery represents a fundamental process of ecosystem dynamics. It describes a pattern of change, towards a former state, following partial degradation or a significant shift in composition (Dudgeon et al. 2010). This study aimed to investigate the recovery towards the dominance of genus \u003cem\u003ePocillopora\u003c/em\u003e after a disturbance, a phenomenon increasingly observed across the Indo-Pacific (López-Pérez et al. 2012; Riegl, Berumen and Bruckner 2013; Bramanti and Edmunds 2016; Adjeroud et al. 2018; Mulla et al. 2024a). Our findings suggest that, rather than individual replacement, early generations of pioneer settlers dominate from the outset, shaping the reef’s structure until the next major disturbance. While recovery, often measured as an increase in coral cover or individual abundance, is generally seen as positive (Mumby and Harborne 2010; Manfrino et al. 2013; Nozawa et al. 2020), it is crucial to consider how such dominance impacts the broader ecosystem. The emergence of a \u003cem\u003ePocillopora\u003c/em\u003e-dominated reef highlights a pattern of community development where one genus—and in this case, a few specific cohorts—are disproportionately favoured. This dynamic is somewhat similar to mast seeding in trees, where synchronized and variable seed production leads to years of abundance followed by years of scarcity (Silvertown 2008). A further parallel can be drawn with the priority effect, where the timing of species arrival in a habitat significantly influences community structure and ecosystem dynamics (Meester et al. 2016). The persistence of \u003cem\u003ePocillopora\u003c/em\u003e dominance despite subsequent disturbances suggests that such dynamics could drive the formation of less diverse reef communities, with long-term implications for ecosystem resilience and function.\u003c/p\u003e\n\u003cp\u003eThe reef in Orchid Island experienced a fast and seemingly predictable recovery towards coral dominance following a disturbance which may lead to assumptions of resilience (Côté and Darling 2010). Here however, resilience depends on specific cohorts, with a population potentially relying on just a few cohorts for its survival. \u003cem\u003ePocillopora\u003c/em\u003e is often described as a \"weedy\" coral (McClanahan 2014), known for its rapid colonization and ability to quickly respond to environmental change. As such, it would be expected that the succession of other genera would follow the colonisation of \u003cem\u003ePocillopora\u003c/em\u003e, yet was not the case. Despite this apparent stability of \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003esurvival, it may also mask underlying sensitivities to disturbance events, potentially leading to rapid collapse and impact on the entire ecosystem. Although cohorts from early years were able to withstand consecutive disturbances during recovery, their limits remain unknown, including how much environmental pressure they can endure. The reef in Orchid Island, relies heavily on early cohorts, as they contribute substantially to both cover and reproductive output. Therefore, any perturbation which exceeds their tolerance could result in tipping points being reached at a rapid rate. More frequent recovery events that lead to a dominance of \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003ecould have significant implications for future reef dynamics having important implications for management, whether overseeing a natural recovery of degraded areas (Morais et al. 2023) or some form of intervention through restoration (Fox et al. 2019).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eEmergence of the Pocillopora-paradox\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eRecruitment sources from surviving \u003cem\u003ePocillopora\u003c/em\u003e populations, whether nearby or from distant but well-connected populations, play a key role in founding events (Cruz et al. 2018; Soares et al. 2021). Following a disturbance, larval dispersal helps replenish areas where widespread colony removal has occurred. While the significance of dispersal mechanisms warrants further exploration, particle dispersal models suggest that some coral populations between the Philippines and East Taiwan are well-connected (Mercado-Vicentillo et al. 2024). For \u003cem\u003ePocillopora\u003c/em\u003e populations in particular, dispersal mechanisms like photo-movement (Mulla et al. 2021), provide larvae a competitive advantage, enabling them to quickly colonize available space and thrive. These recruitment events are often considered independent and stochastic (Gotelli 1988; Caley et al. 1996; Ricardo et al. 2017), yet an increase in \u003cem\u003ePocillopora\u0026nbsp;\u003c/em\u003ereefs may lead future reef structure to be more deterministic.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eThe dominance of early-year cohorts allows certain colonies to outcompete others for space, even within the same genus (Horwitz, Hoogenboom and Fine 2017), which explains the high levels of recruit mortality observed. Growth and survival rates of recruits are skewed towards founding cohorts (early years), where those that settle earlier experience faster growth and higher survival rates. Similar trends in early-life dynamics have been observed in terrestrial systems, such as forests (Swanson et al. 2011), where trees that arrive later exhibit reduced growth and lower survival overall. Additionally, early cohorts are more reproductively active during recovery, compared to those arriving in later years, which have limited reproductive potential and experience higher mortality.\u003c/p\u003e\n\u003cp\u003eIn this study, we demonstrate that newly settled, early-year cohorts are critical to recovery of the reef in Orchid Island. Coexistence theory explains that such demographic trends are driven by competition within sedentary communities that are limited by space (Johnson and Hastings 2023). This theory suggests that pioneer events are as significant as their demographic characteristics. However, these features have been shown to benefit only a few coral species (Edmunds et al. 2024) or the broader community (Mumby 2017). Early competitive exclusion is advantageous for future development, as space becomes a density-dependent factor later in life (Edmunds et al. 2018).\u0026nbsp;In addition, inter-cohort cannibalism may play a role in reinforcing the dominance of early settlers. Although rarely documented, it is plausible that large, established individuals may consume or suppress the settlement of incoming larvae, further reducing competition (Pineda et al. 2010). This dynamic has been observed in other marine systems, where inter-cohort cannibalism is a major source of mortality at settlement (Moksnes et al. 1997; Sainte-Marie \u0026amp; Lafrance 2002; Moksnes 2004). Few studies have explicitly linked cannibalism to stabilizing population dynamics (Luppi et al. 2001), but its potential role in decoupling larval supply from successful recruitment warrants consideration, especially in systems structured by strong spatial constraints. If such interactions occur, they would advantage early cohorts not only through priority effects but also through active suppression of newcomers, suggesting that predictions of population structure should account for localized cannibalistic interactions among benthic broadcast spawners.\u003c/p\u003e\n\u003cp\u003e\u003cem\u003ePocillopora\u003c/em\u003e is well-documented for its tolerance to harsh conditions (Haryanti et al. 2015; Rodriguez-Troncoso et al. 2016; Pratchett, McWilliam and Riegl 2020). The ability of adult colonies to a reach reproductive age/size is critical, as their increased resilience to disturbances like typhoons, enables them to lead the recovery process from the outset. Surviving colonies reach this stage relatively quickly, allowing them to withstand further major disturbances and solidify their dominance, while younger colonies struggle. As the Orchid Island population matures, density-dependent mechanisms help sustain the dominance of this single genus (Mulla et al. 2024a). Further, \u003cem\u003ePocillopora’s\u0026nbsp;\u003c/em\u003eportfolio ofsurvival strategies such as unique dispersal mechanisms, skewed growth rates, inter-cohort competition and high tolerance all contribute to the paradox,\u0026nbsp;where a seemingly apparent recovery masks a homogenized reef with reduced diversity.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eChallenges of the Pocillopora-paradox\u0026nbsp;\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe existence of such a paradox poses a significant risk to the reef in Orchid Island in several ways, and more broadly for any taxa that might be selected and thrive on future reefs. Firstly, it raises concerns about barriers to ecosystem function, particularly with the predicted intensification of disturbance events (Hughes et al. 2021). While a general decline in diversity, associated with reef homogenization, may not be a major issue at the alpha scale, a rise of \u003cem\u003ePocillopora\u003c/em\u003e-dominated states across the region is troubling for the future (Dornelas et al. 2006).\u003c/p\u003e\n\u003cp\u003eIn our study, 83% of the reef in Orchid Island was composed of corals from early cohorts (2012–2016), which could jeopardize long-term reproductive success, as age is a key determinant of fertility (Rapuano et al. 2023). The establishment of Pocillopora-dominated reefs suggests that allochthonous larvae may impact reefs further north. While reproductive output is currently driven by early cohorts, it is unclear how many reproductive cycles a coral can undergo (Marchini et al. 2015) or how variability between early and later cohorts affects population dynamics (Shlesinger and Loya 2021). Early-life environmental conditions may cause lasting \"cohort effects,\" influencing reproductive output at maturation (Stenseth et al. 2002). Although older colonies remain sexually active (Mezaki et al. 2013), some studies report declining fecundity with age due to reproductive senescence (Rinkevich and Loya 1986; Nozawa and Lin 2014). However, evidence remains limited (Bythell et al. 2017), and Mulla et al. 2024a found no sign of senescence, with larger colonies showing higher fertility. Still, long-term monitoring is needed, as cohort-specific infertility could threaten overall reef reproduction.\u003c/p\u003e\n\u003cp\u003eHomogenization may also reduce genetic diversity within populations, leading to a decline in overall resilience. Analysis from neighbouring Green Island in Taiwan revealed that biological variation within \u003cem\u003ePocillopora\u003c/em\u003e populations was low at both shallow and mesophotic depths (De Palmas et al. 2018). Reduced diversity has been demonstrated in Mo'orea, French Polynesia, where following a mass bleaching event, 86% of \u003cem\u003ePocillopora\u003c/em\u003e individuals, all belonging to a single haplotype, suffered mortality (Burgess et al. 2021). This genetic bottleneck may result from few genotypes dispersing from the same location, populating the reef and facilitating further homogenization.\u003c/p\u003e\n\u003cp\u003eChanges in environmental conditions may lead \u003cem\u003ePocillopora\u003c/em\u003e corals to exhibit a uniform response to disturbance. In our study, typhoons were the primary cause of coral decline, removing a significant number of individuals from the reef. Those left behind suffered partial mortality, increasing the risk of disease (Brandt et al. 2013). Outbreaks such as black band disease have caused major declines in \u003cem\u003ePocillopora\u003c/em\u003e populations (Plucer-Rosario 1987), particularly in Taiwan (Huang et al. 2021). In some cases, black band disease was found to affect \u003cem\u003ePocillopora\u003c/em\u003e specifically, while other genera remained unaffected (Thinesh et al. 2013). This blanket response within a population places immense pressure on early-year cohorts and the broader community, as a single event risks the loss of entire populations.\u003c/p\u003e\n\u003cp\u003eAs global temperatures continue to rise, including in Taiwan (Belkin and Lee 2014) and the wider Indo-Pacific (Matz et al. 2020), the risk of coral bleaching events also increases. Unlike typhoons, which remove entire coral skeletons and frees up space for recruitment, bleaching results in dead coral skeletons that can accumulate macroalgae (Liu et al. 2009), obstructing coral recruitment and hindering recovery. While typhoons and bleaching differ in their immediate impact, both pose a certain threat to homogeneous reefs, which may respond uniformly, leading to a wider decline in resilience.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eImplications for coral reef dynamics\u0026nbsp;\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eTracking cohort progression helps reduce variability in population dynamics, often attributed to disparities in size or age (Hughes and Connell 1987). While this method is well-established in fish ecology (Rouyer et al. 2011), it is less commonly applied to corals, partly due to the lack of stable, long-term monitoring data or a preference for short-term population or community dynamics studies. As a result, density-dependent processes like cohort resonance (Bjørnstad and Grenfell 2001) are often overlooked. The cohort method offers a way to track spatial dynamics, with individual interactions documented over time, improving our understanding of density-dependent mechanisms in space-limited populations. For corals, it helps identify factors directly influencing growth, survival and reproduction at critical life stages. This approach highlights the vulnerabilities within a population, revealing that beyond \u003cem\u003ePocillopora\u003c/em\u003e dominance, a reef may be dominated by a few cohorts, potentially from the same source and genetically homogenous. This method has been overlooked in examining general patterns that significantly influence reef dynamics. Events like coral bleaching, typhoons and pollution can be tracked using this method, offering insights into how specific disturbances affect particular individuals within a certain grouping and how coral resilience and adaptability evolve in response to fluctuating conditions. Ultimately, this method facilitates in-depth comparative studies across regions, providing valuable data for conservation and management strategies.\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eHere we show that a \u003cem\u003ePocillopor\u003c/em\u003ea-dominated state arises from the survival and growth of the initial settlement of recruits following a disturbance, with the pioneer generation playing a disproportionately large role in recovery. Recognizing this phenomenon is key to understanding the \u003cem\u003ePocillopora\u003c/em\u003e-paradox and highlights the pivotal influence of early settlement (Edmunds et al. 2024) on coral population trajectories. In Orchid Island, not just a single genus, but a single generation, dictates future reef structure, suggesting that apparent recovery may mask declining diversity. The absence of later cohort survival reflects density-dependent processes rather than recruitment failure. Such recovery patterns may lead to broader disequilibrium under climate change, driving local extinctions and reef homogenization. While the impacts on diversity, ecosystem function and services remain uncertain, these findings stress the importance of post-settlement processes for reef restoration efforts.\u003cstrong\u003e\u003cbr\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eAcknowledgments\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe thank C-H Lin, C-L Fong, J-H Shiu, T-Y Lai, V. Dang for their assistance in the field. A.J.M is supported through UCAJEDI Investments in the Future Project managed by National Research Agency (ANR-15-IDEX-01). V.D. was supported by grants from National Science and Technology Council, Taiwan (NSTC, 111-2628-M-002-007-MY3) and National Taiwan University (NTU, CDP-114L7722). This study was funded by an internal research grant of Biodiversity Research Center, Academia Sinica to Y.N. We also thank R. Chang for providing the translation of the abstract.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eOpen Research Statement\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe dataset used in the present study is available in Dryad at: https://doi.org/10.5061/dryad.msbcc2g5n\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAJM and YN designed the study and collected the data. AJM analysed the data. AJM and VD led the writing of the manuscript.\u0026nbsp;\u003cstrong\u003e\u003cbr\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n \u003cli\u003eAdjeroud M, Kayal M, Iborra-Cantonnet C, Vercelloni J, Bosserelle P, Liao V, Chancerelle Y, Claudet J, Penin L (2018) Recovery of coral assemblages despite acute and recurrent disturbances on a South-Central Pacific reef. \u003cem\u003eSci Rep \u003c/em\u003e8(1): 9680\u003c/li\u003e\n \u003cli\u003eBarlow J, França FM, Gardner TA, Hicks CC, Lennox GD, Berenguer E, Castello L, Economo EP, Ferreira J, Guénard B, et al. 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Dis Aquat Organ 106:68–77\u003c/li\u003e\n \u003cli\u003evan Woesik R, Shlesinger T, Grottoli AG, Toonen RJ, Thurber RV, Warner ME, Hulver AM, Chapron L, McLachlan RH, Albright R et al (2022) Coral-bleaching responses to climate change across biological scales. Glob Change Biol 28:4229–4250\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"coral-reefs","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"core","sideBox":"Learn more about [Coral Reefs](http://link.springer.com/journal/338)","snPcode":"338","submissionUrl":"https://submission.nature.com/new-submission/338/3","title":"Coral Reefs","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Recruitment, Cohort effect, Dominance, Pocillopora paradox, Resilience, Coral reefs","lastPublishedDoi":"10.21203/rs.3.rs-6548265/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6548265/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eReef recovery following a disturbance largely depends on successful coral recruitment and the absence of chronic stressors. However, recent recovery events show increasing homogenization, with dominant coral species replacing the high diversity that once characterized these ecosystems. In this study, we analysed a nine-year dataset (2012–2020) describing the recovery of a reef towards a \u003cem\u003ePocillopora\u003c/em\u003e-dominated state in Taiwan following a devastating typhoon. Tracking eight coral cohorts, we assessed growth, survival and reproduction. \u003cem\u003ePocillopora\u003c/em\u003e recruitment peaked during the first three years, but mortality surged in the fourth year. The initial generation had the highest survival rates, while by the fifth year, newly settled individuals failed to survive beyond two years. By 2020, 83% of the reef consisted of corals from 2012–2016, with 38% originating from the first generation alone (2012). This pioneer generation was the primary contributor to growth and reproduction, emphasizing the reef's reliance on early settlers, leading to an ageing coral community. While pioneer generations were critical to recovery, their dominance may have driven a gradual loss of biodiversity. Our findings highlight the importance of early recruitment in reef development but underscores the risk of reliance on only a few species during and after recovery.\u003c/p\u003e","manuscriptTitle":"Pioneer generation shapes long-term recovery of coral populations","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-05-12 05:32:05","doi":"10.21203/rs.3.rs-6548265/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-06-19T12:38:23+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-06-04T15:18:33+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-05-29T02:12:06+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"45092997497322057854347291026309455656","date":"2025-05-28T13:16:30+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"95776409756851375740871413086747811095","date":"2025-05-20T16:05:04+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"88597178802192031163783355036038180221","date":"2025-05-12T10:35:44+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-05-07T01:04:03+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-05-03T04:57:22+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-04-29T04:57:22+00:00","index":"","fulltext":""},{"type":"submitted","content":"Coral Reefs","date":"2025-04-28T13:08:43+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"coral-reefs","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"core","sideBox":"Learn more about [Coral Reefs](http://link.springer.com/journal/338)","snPcode":"338","submissionUrl":"https://submission.nature.com/new-submission/338/3","title":"Coral Reefs","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"75faa8d0-136d-47ed-8262-7040c95d1f1f","owner":[],"postedDate":"May 12th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2025-11-17T16:00:19+00:00","versionOfRecord":{"articleIdentity":"rs-6548265","link":"https://doi.org/10.1007/s00338-025-02769-9","journal":{"identity":"coral-reefs","isVorOnly":false,"title":"Coral Reefs"},"publishedOn":"2025-11-10 15:57:23","publishedOnDateReadable":"November 10th, 2025"},"versionCreatedAt":"2025-05-12 05:32:05","video":"","vorDoi":"10.1007/s00338-025-02769-9","vorDoiUrl":"https://doi.org/10.1007/s00338-025-02769-9","workflowStages":[]},"version":"v1","identity":"rs-6548265","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6548265","identity":"rs-6548265","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}