Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

Historical analysis of the recovery of physical functionality in a coral reef

community following the implementation of active restoration practices

Adahara Muñoz-Alfaro1, 2; https://orcid.org/0009-0006-1736-4670

Alma Paola Rodríguez-Troncoso3; https://orcid.org/0000-0001-6243-7679

Amílcar Levi Cupul-Magaña3; https://orcid.org/0000-0002-6455-1253

José de Jesús Adolfo Tortolero-Langarica4; https://orcid.org/0000-0001-8857-5789

Rafael Andrés Cabral-Tena5*; https://orcid.org/0000-0002-2836-2834

1. Posgrado en Ecología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja

California. Carretera Ensenada – Tijuana, No. 3918, Zona Playitas, 22860, Ensenada, B.C., México; adaharam_24@

alu.uabcs.mx

2. Doctorado en Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur. Boulevard Forjadores S/N,

Col. Universitario, La Paz, Baja California Sur, México.

3. Laboratorio de Ecología Marina, Centro Universitario de la Costa, Universidad de Guadalajara. Avenida Universidad

203, Delegación Ixtapa, Puerto Vallarta, Jalisco, 48280. México; alma.rtroncoso@academicos.udg.mx, levi.cupul@

academicos.udg.mx

4. Tecnológico Nacional de México, Instituto Tecnológico de Bahía de Banderas, Nayarit, México. Crucero a Punta de

Mita S/N, col. La Cruz de Huanacaxtle, Nayarit, 63734. México; adolfo.tl@bahia.tecnm.mx

5. Laboratorio de Arrecifes y Biodiversidad/Departamento de Ecología Marina, Centro de Investigación Científica y

de Educación Superior de Ensenada, Baja California. Carretera Ensenada – Tijuana, No. 3918, Zona Playitas, 22860,

Ensenada, B.C. México; rcabral@cicese.mx (*Correspondence)

Received 04-VII-2025. Corrected 09-XII-2025. Accepted 10-II-2026.

ABSTRACT

Introduction: The Reef Functional Index (RFI) is a tool used to analyze the physical functionality of coral assem-

blages based on morpho-functional traits that support their geo-ecological roles. This tool has been applied to

assess the effects of active restoration on coral reefs under varying levels of stress. However, to date, it has not

been used to analyze long-term assisted recovery through restoration activities.

Objective: This study evaluated the historical trajectory of physical functionality over the long term (2012–2023)

in six coral reef communities within the Islas Marietas National Park (PNIM), considering that active restoration

efforts have been in place since 2014, using the RFI as a metric.

Methods: The RFI was used as an indicator of physical functionality to assess temporal changes in reef condi-

tion throughout the analysis period. The percentage of natural change and change subsidized by restoration was

calculated for both RFI and live coral cover (LCC).

Results: RFI values revealed that although coral communities in the PNIM had, by 2023, regained LCC levels

exceeding those recorded in 1997, physical functionality had not yet been fully restored. Restoration activities

have contributed to approaching historical functional values, even under the impact of various natural stressors;

however, spatial analysis at the island and site level indicated that recovery has not been uniform.

Conclusions: The findings highlight the need to review and adapt restoration strategies, emphasizing greater

efforts in sites where coral functionality remains below pre-disturbance levels. Additionally, the results dem-

onstrate that the RFI is a valuable tool for evaluating the long-term success of coral restoration and identifying

potential areas of opportunity in degraded reef sites.

https://doi.org/10.15517/3s8sp047

SUPPLEMENT

2Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266883, abril 2026 (Publicado Abr. 22, 2026)

INTRODUCTION

Coral reefs are highly productive and bio-

diverse ecosystems (Burke et al., 2011), with

an estimated value of USD $352 000 ha-¹ yr-¹,

stemming from the social, economic, and eco-

logical functions they provide (Allemand &

Osborn, 2019; Woodhead et al., 2019). They

also fulfill essential geo-ecological functions

such as reef structure formation, the generation

of microhabitats, and sediment production (de

Groot et al., 2012; Perry & Álvarez-Filip, 2018).

Currently, coral reefs face both local and

global threats that are driving their degradation

(Souter et al., 2021), leading to declines in the

abundance of reef-building corals and causing

shifts in the composition and structure of asso-

ciated communities (Norström et al., 2009). To

mitigate reef degradation, restoration strategies

have been implemented over the past three

decades, aiming to support the recovery of both

foundational species and the ecosystem’s func-

tional capacity (Hein et al., 2021). However,

most interventions have focused on short-term

recovery (1–2 years), prioritizing indicators

such as coral survival and growth (Vaughan,

2021). As a result, it is now recommended to

implement long-term interventions (>5 years)

that allow for the evaluation of restoration

outcomes from both functional and geological

perspectives in a synergistic manner (Goergen

et al., 2020; Rinkevich, 2019).

Key words: physical functionality; Reef Functional Index (RFI); coral reef restoration, long-term recovery;

Marietas Islands National Park reefs.

RESUMEN

Análisis histórico de la recuperación de la funcionalidad física en una comunidad coralina

tras la implementación de prácticas de restauración activa

Introducción: El Índice de Función Arrecifal (RFI) es una herramienta que sirve para analizar la funcionalidad

física de los ensambles coralinos con base en rasgos morfofuncionales que sustentan sus roles geo-ecológicos. Esta

herramienta se ha aplicado para evaluar los efectos de la restauración activa en arrecifes coralinos bajo diferentes

niveles de estrés. Sin embargo, hasta la fecha, no se ha utilizado para analizar la recuperación asistida a largo plazo

mediante actividades de restauración.

Objetivo: Este estudio evaluó la trayectoria histórica de la funcionalidad física a largo plazo (2012-2023) en seis

comunidades arrecifales dentro del Parque Nacional Islas Marietas (PNIM), considerando que se han realizado

esfuerzos de restauración activa desde 2014, utilizando el RFI como métrica.

Métodos: El RFI se utilizó como un indicador de la funcionalidad física para evaluar cambios temporales en la

condición del arrecife a lo largo del período de análisis. El porcentaje de cambio natural y cambio subsidiado por

la restauración se calculó tanto para el RFI como para la cobertura de coral vivo (LCC).

Resultados: Los valores del RFI revelaron que, si bien las comunidades coralinas del PNIM habían recuperado,

para 2023, niveles de LCC superiores a los registrados en 1997, la funcionalidad física aún no se había restaurado

por completo. Las actividades de restauración han contribuido a aproximarse a los valores funcionales históricos,

incluso bajo el impacto de diversos estresores naturales; sin embargo, el análisis espacial a nivel de isla y de sitio

indicó que la recuperación no ha sido uniforme.

Conclusiones: Los hallazgos resaltan la necesidad de revisar y adaptar las estrategias de restauración, enfatizando

mayores esfuerzos en sitios donde la funcionalidad coralina se mantiene por debajo de los niveles previos a la

perturbación. Adicionalmente, los resultados demuestran que el RFI es una herramienta valiosa para evaluar el

éxito a largo plazo de la restauración coralina e identificar áreas de oportunidad potenciales en sitios arrecifales

degradados.

Palabras clave: funcionalidad física; Índice de Función Arrecifal (RFI); restauración de arrecifes de coral, recupe-

ración a largo plazo; arrecifes del Parque Nacional Islas Marietas.

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

One approach to functionally assess coral

reefs is the Reef Functional Index (RFI), which

evaluates the status of physical functionality

in coral communities based on morpho-func-

tional traits that underpin their geo-ecological

roles (González-Barrios & Álvarez-Filip, 2018).

In the Eastern Tropical Pacific (ETP), the RFI

has been applied to understand the role of coral

species in reef functioning, particularly in the

Mexican Pacific, and to assess the effects of

active restoration from a functional perspec-

tive across areas with varying anthropogenic

impacts (Cabral-Tena et al., 2020; Muñoz-Alfa-

ro et al., 2023; Navarrete-Torices et al., 2023). It

also enables the characterization of natural reef

recovery following exposure to both natural

and anthropogenic stressors (González-Barrios

et al., 2021; McWilliam et al., 2018), showing

that the physical functionality of coral reefs

is not restored solely by increasing live coral

cover (LCC). However, to date, no long-term

(>1 year) analysis of assisted recovery through

restoration activities has been conducted using

the physical functionality approach.

Coral reefs in the Mexican Pacific (MP)

are characterized by patchy distributions and

are composed of assemblages dominated by

the genera Pocillopora, Porites, Psammocora,

and Pavona (Reyes-Bonilla et al., 2005). In this

region, average RFI values vary among locali-

ties, with the southern MP showing the highest

values (0.71 ± 0.1; Cabral-Tena et al., 2020),

followed by northern communities (0.65 ± 0.15;

Navarrete-Torices et al., 2023), while the Cen-

tral Mexican Pacific (CMP) exhibits the lowest

values, ranging from 0.28 to 0.71 (Muñoz-Alfa-

ro et al., 2023). However, these values do not

reflect the current condition, as the recent

2023–2024 El Niño event (López-Pérez et al.,

2024) resulted in accumulated coral losses of

over 70 % in several MP localities. Further-

more, the CMP region is particularly affected by

local stressors such as coastal development and

increased tourism (Burroughs & Rodríguez-

Troncoso, 2024). In response to these adverse

conditions, passive restoration strategies—such

as the implementation of tourist load regula-

tions (Cupul-Magaña & Rodríguez-Troncoso,

2017)—and active coral reef restoration pro-

grams have been promoted. One such program

has been ongoing in the Islas Marietas National

Park (IMNP) since 2014 (Tortolero-Langarica

et al., 2014) and continues to this day. Within

this context, the present study assessed the

historical trajectory of physical functionality

over the long term (2012–2023) in the coral

communities of PNIM, under the influence of

active restoration, using the RFI as a tool for

functional analysis.

MATERIALS AND METHODS

Study area. The evaluation of physical func-

tionality was carried out at six sites within Islas

Marietas National Park (IMNP) (20°40’35”–

20°41’45” N, 105°33’30”–105°38’10” W). IMNP

comprises two volcanic islands, Isla Larga and

Isla Redonda, located approximately 7 km off

the coast of the Central Mexican Pacific (CMP).

Coral communities in this area are mainly dis-

tributed between 1 and 15 m in depth, with Isla

Larga harboring the highest coral species rich-

ness (Hernández-Zulueta et al., 2017) (Fig. 1).

This region is an oceanographic conver-

gence zone influenced by three major currents:

the California Current, which brings cold,

nutrient-rich waters; the Mexican Coastal Cur-

rent, which carries warm, nutrient-poor waters;

and the Gulf of California Current, character-

ized by warm, high-salinity waters. Sea surface

temperature in the region shows interannual

variation ranging from 23.3 to 30 °C (Kessler,

2006; Palacios-Hernández et al., 2010). The

area is also subject to decadal and interannual

thermal anomalies, including El Niño–South-

ern Oscillation (ENSO) events, with positive

phases reaching anomalies ≥ 3 °C and negative

phases (La Niña) ≤ –4 °C (Palacios-Hernández

et al., 2010).

Fieldwork. Six study sites were selected,

and starting in 2012, annual monitoring of live

coral cover (LCC, %) was conducted. At each

site, five semi-permanent 25 m transects were

laid parallel to the shoreline. LCC was assessed

using six 1 m² quadrats per transect, spaced

4Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266883, abril 2026 (Publicado Abr. 22, 2026)

approximately 4 m apart. Historical data from

1996–1997 were also incorporated, based on

previous monitoring by Rodríguez-Zaragoza

(2001), which used three 10 m permanent

transects parallel to the shore. The transect

average was used as the experimental unit

in this study. Coral species at each site were

identified based on morphological traits fol-

lowing taxonomic descriptions (Veron et al.,

2016). Between 2014 and 2023, active restora-

tion activities were implemented, involving

direct transplantation of opportunity fragments

from the genus Pocillopora, as described by

Tortolero-Langarica et al. (2019).

To calculate the RFI, in addition to LCC

data (%), 15 coral colonies per species (7 spp.)

were randomly selected along the transects at

each site. For each colony, the maximum and

minimum diameters, height, and linear length

along the colony’s major axis were measured.

The perimeter was also measured using a No.

9 bead chain (2–3 mm) from one end of the

colony to the other.

Data analysis. The Reef Functional Index

(RFI) was calculated based on LCC. To esti-

mate the calcification rate (kg m-² yr-¹), the

morphology of each coral species was con-

sidered, following the method proposed by

González-Barrios & Álvarez-Filip (2018).

Extension rate (cm yr-¹) and skeletal density (g

cm-³) were based on local values reported by

Tortolero-Langarica et al. (2016) and Tortolero-

Langarica et al. (2017). Structural complexity

was estimated using the rugosity index (RI)

at the colony level, calculated as the ratio

between the perimeter, linear length of the

major axis, and the maximum colony height

(Alvarez-Filip et al., 2009).

Calcification rate, rugosity, and colo-

ny height were standardized to values rang-

ing from 0 to 1 using the following formula

(González-Barrios & Álvarez-Filip, 2018):

where x is the observed value of each growth

parameter.

To compute the RFI (González-Barrios &

Álvarez-Filip, 2018), the Functional Coefficient

(FC) was first calculated for each species by

averaging the standardized values of calcifica-

tion, rugosity, and height. Then, the RFI for

each site and year was calculated by summing

Fig. 1. Map of the study area and sampling sites: Isla Larga (IL); Zona de Restauración (ZR); Zona de restauración Sur (ZRS);

Cueva del Muerto (CM); Isla Redonda (IR); Playa del Amor (PA); Pavonas Platform (PP); and Túnel Amarradero (TA).

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

the product of the LCC of each species present

at the site (expressed as a percentage), by its

respective CF value for each site and year.

To aid interpretation, a fourth root trans-

formation was applied to the RFI values, result-

ing in scores between 0 and 1, where values

closer to 0 represent low reef functionality

and values near 1 indicate high functional-

ity (González-Barrios & Álvarez-Filip, 2018)

(Table 1).

LCC and RFI were evaluated for each

transect. Both datasets were averaged annu-

ally at three spatial scales: park-wide (IMNP),

island-level (Isla Larga and Isla Redonda), and

site-level (Zona de Restauración: ZR, Zona de

Restauración Sur: ZRS, Cueva del Muerto: CM,

Playa del Amor: PA, Plataforma Pavonas: PP,

and Túnel Amarradero: TA). The percentage of

natural change and change supported by resto-

ration were calculated for both RFI and LCC.

Statistical analysis. To evaluate temporal

(2012-2023) and spatial patterns in coral cover

(LCC) and Reef Functional Index (RFI) across

the PNIM, Generalized Linear Mixed Models

(GLMM) were fitted. LCC was modeled using

beta-binomial distributions with a logit link.

This family was used because LCC data cor-

responded to proportions derived from counts

and exhibited over-dispersion. RFI was mod-

eled using beta-regression with a logit link.

This was selected because RFI is a continuous

variable bounded between 0 and 1. For each

metric, we first fitted a global model includ-

ing centered year as a fixed effect, followed by

models incorporating site or island as fixed

factors, and full interaction structures (Year

× Site, Year × Island) to test for spatial differ-

ences in temporal trends. Additionally, we fit-

ted independent models for each site and each

island to assess localized trajectories. Model fit

was evaluated using AIC and likelihood-based

diagnostics, and significance of fixed effects

was assessed using Type III Wald χ² tests. All

analyses were performed in R 4.2.2 using the

glmmTMB function of the glmmTMB package

for model fitting and Anova function from the

car package for inference. The model’s assump-

tions were validated through the generation of

residual plots using the simulateResiduals func-

tion in the DHARMa package.

RESULTS

The historical analysis of live coral cover

(LCC) in the Islas Marietas National Park

(IMNP) began with a baseline established in

1997, showing a park-wide LCC of 19.85 %,

with 18.1 % at Isla Larga and 21.6 % at Isla

Redonda (Fig. 2A, Fig. 2B, Fig. 2C). The aver-

age baseline for the Reef Functional Index

(RFI) at the PNIM scale was 0.6, with values

of 0.59 for Isla Larga and 0.61 for Isla Redonda

(Fig. 2D, Fig. 2E, Fig. 2F).

In 2012, at the start of the current monitor-

ing effort, the data showed a park-level LCC

decrease of -34.87 % (LCC = 12.93 ± 12.50 %),

Tabl e 1

Calcification rate, rugosity index, mean colony height, and functional coefficient for each coral species recorded in PNIM.

Species Calcification Rate (kg CaCO₃ m-² yr-¹) Rugosity Index SD Height (cm) SD FC

Porites panamensis 3.66 1.59 0.29 9 5 0.01

Pocillopora damicornis 24.97 3.43 0.24 23 0 0.57

Pocillopora verrucosa 25.70 5.13 2.00 17 9 0.67

Pocillopora capitata 23.28 5.41 0.93 21 7 0.68

Pocillopora grandis 25.44 5.75 0.95 21 7 0.74

Pavona clavus 12.79 1.88 0.47 25 10 0.28

SD = Standard deviation; FC = Functional coefficient.

6Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266883, abril 2026 (Publicado Abr. 22, 2026)

with a reduction of -3.87 % at Isla Larga (LCC =

17.40 ± 14.57 %) and -60.85 % at Isla Redonda

(LCC = 8.46 ± 8.28 %) (Appendix 1). This trend

was also reflected in the RFI, which showed a

park-level decline of -30.37 % (RFI = 0.42 ±

0.19), with decreases of -15.27 % at Isla Larga

(RFI = 0.50 ± 0.17) and -44.90 % at Isla Redon-

da (RFI = 0.34 ± 0.18) (Fig. 2; Appendix 1).

At the site level, the highest LCC values

in 2012 were recorded at all three sites on Isla

Larga, with the highest in Zona de Restauración

(32.40 ± 14.10 %), while the lowest values were

recorded at Isla Redonda, particularly at Túnel

Amarradero (7.00 ± 7.39%) (Table 2). For RFI,

no clear spatial pattern was observed, with the

highest value at Cueva del Muerto (0.48 ± 0.09)

and the lowest at Playa del Amor (0.30 ± 0.22)

(Table 2).

In 2014, the year restoration activities

began, LCC at the park scale was 12.57 ± 11.51

%, with an average of 18 ± 13.29 % at Isla Larga

and 7.14 ± 5.86 % at Isla Redonda (Fig. 2c).

These patterns were also reflected in RFI, with

a park-wide value of 0.44 ± 0.17, and values

of 0.53 ± 0.13 at Isla Larga and 0.34 ± 0.14 at

Isla Redonda (Fig. 2d, Fig. 2e, Fig. 2f). In gen-

eral, sites located on Isla Larga exhibited higher

average LCC and RFI values compared to those

on Isla Redonda (Table 2).

Temporal analysis showed an increase in

both LCC and RFI from 2014 to 2015, followed

by a decline associated with the 2016 El Niño

Fig. 2. Historical trends in live coral cover (LCC; A, B, C) and reef function index (RFI; D, E, F) across different spatial scales

(a and d: PNIM; b, c, e, f: Islands). RP = start of the restoration program.

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

event and Hurricane Roslyn in 2022 (Fig. 2,

Appendix 2, 3). In 2023, LCC increased to 20.69

± 14.24 % across PNIM, with 29.2 ± 13.73 % at

Isla Larga and 12.18 ± 8.75 % at Isla Redonda.

The site with the greatest increase was Cueva

del Muerto, while the lowest was Túnel Amar-

radero (Table 2; Appendix 1).

RFI also increased in 2023 compared to

values at the start of the restoration program,

reaching 0.54 ± 0.15 at the park scale (+22.59

%), 0.63 ± 0.12 at Isla Larga (+17.82 %), and

0.44 ± 0.13 at Isla Redonda (+30 %). At the site

level, the highest RFI increase was recorded at

Playa del Amor (+43.78 %), and the lowest at

Túnel Amarradero (RFI = 0.35) (Fig. 2, Table 2;

Appendix 1).

Over a period of more than 20 years, LCC

and RFI values surpassed the 1997 baseline

in 67 % and 44.44 % of the cases, respective-

ly. Zona de Restauración showed the highest

increase in both metrics (LCC +100.55 %, RFI

+15.40 %), followed by Isla Larga (LCC +61.36

%, RFI +6.64 %). The lowest increases were

observed at the park scale for LCC (+4.23 %)

and at Zona de Restauración Sur for RFI (+0.12

%). Notably, the sites located on Isla Redonda

did not surpass the historical LCC baseline

from 1997 (Table 2), a pattern that was also evi-

dent for RFI. On the island scale, Isla Redonda

showed a -27.24 % decrease in LCC relative to

the baseline, while IMNP showed a -10.62 %

decrease (Appendix 2–3).

When analyzing the GLMM models, we

found that the LCC showed a pattern of sus-

tained recovery in the PNIM between 2012 and

2023. The model (Appendix 4–5) indicated a

significant increase over time (β = 0.061, p <

0.001; χ² = 20.29, df = 1, p < 0.001), equivalent

to an average positive trend of approximately

6% per year. This result suggests that, on a

regional scale, the coral communities of the

PNIM have experienced continuous recovery

during the analyzed period. At the island scale,

the model (Appendix 6–7) showed a signifi-

cant increase over time (β = 0.084, p < 0.001,

χ² = 30.39, df = 1, p < 0.001) and differences

between Isla Larga and Isla Redonda (χ² =

146.14, df = 1, p < 0.001). Isla Larga exhibited a

significant positive slope (β = 0.084, p < 0.001),

while Isla Redonda maintained significantly

lower initial LCC values (β = −1.03, p < 0.001)

and a weaker trend that did not differ statisti-

cally from that observed on Isla Larga (Year

× Island interaction: p = 0.171). Overall, both

islands show signs of recovery, but Isla Larga

has higher values and greater rates of increase.

When analyzing site-level patterns, the models

(Appendix 8–10) revealed marked heterogene-

ity in recovery, showing differences between

sites (χ² = 243.82, df = 5, p < 0.001) and years

(χ² = 12.70, df = 1, p < 0.001). Four sites

showed positive and statistically significant

trends: Zona de Restauración (β = 0.104, p <

0.001), Cueva del Muerto (β = 0.090, p < 0.001),

Tabl e 2

Average live coral cover (LCC) and Reef Functional Index (RFI) values at the site level for the years 2012 (start of monitoring),

2014 (beginning of active restoration activities), and 2023 (end of the present study’s analysis).

Site 2012 2014 2023

LCC (%) RFI LCC (%) RFI LCC (%) RFI

ZR 32.40 ± 14.10 0.65 ± 0.10 27.70 ± 17.14 0.61 ± 0.11 36.30 ± 11.90 0.68 ± 0.07

ZRS 8.67 ± 8.31 0.38 ± 0.19 12.93 ± 7.63 0.50 ± 0.13 24.37 ± 13.20 0.59 ± 0.15

CM 11.13 ± 7.03 0.48 ± 0.09 13.37 ± 9.49 0.50 ± 0.13 26.93 ± 15.66 0.62 ± 0.12

PP 10.37 ± 8.37 0.41 ± 0.13 8.40 ± 5.57 0.37 ± 0.15 16.07 ± 4.67 0.52 ± 0.04

TA 7.00 ± 7.39 0.31 ± 0.20 6.20 ± 4.94 0.34 ± 0.14 7.20 ± 4.33 0.35 ± 0.18

PA 8.00 ± 10.39 0.30 ± 0.22 6.83 ± 7.85 0.32 ± 0.17 13.27 ± 13.26 0.47 ± 0.17

ZR = Zona de Restauración, ZRS = Zona de Restauración Sur, CM = Cueva del Muerto, PP = Plataforma Pavonas, TA = Túnel

Amarradero, PA = Playa del Amor.

8Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266883, abril 2026 (Publicado Abr. 22, 2026)

Plataforma Pavonas (β = 0.092, p < 0.001),

and Zona de Restauración Sur (β = 0.059, p =

0.042). These sites represent the areas with the

clearest recovery, with annual increases ranging

from 6% to 10% of the LCC. In contrast, Playa

del Amor showed a positive but not statisti-

cally significant trend (p = 0.109), while Túnel

Amarradero showed no evidence of recovery (p

= 0.625) during the analyzed period. The year

× site interaction model confirmed this spatial

pattern. Most sites presented significantly dif-

ferent intercepts (Appendix 8), reflecting the

contrast in initial conditions.

On the other hand, the GLMM models

performed with the RFI as the response variable

indicate that there is a general pattern of sig-

nificant increase in functionality in the PNIM

between 2012 and 2023. The global model

(Appendix 11–12) indicated a positive and sig-

nificant effect of the year on the change in RFI

(β = 0.058, p = 0.005; χ² = 7.89, df = 1, p < 0.01),

revealing a sustained improvement in reef func-

tioning at a regional scale during the study peri-

od. At the island scale, as with the LCC case, the

model (Appendix 13–14) showed a significant

temporal increase (β = 0.0548, p < 0.001, χ² =

18.09, df = 1, p < 0.01) and differences between

Isla Larga and Isla Redonda (χ² = 176.29, df = 1,

p < 0.01). Isla Redonda (β = −0.839, p < 0.001)

presented significantly lower initial values than

Isla Larga (β = 0.055, p < 0.001), reflecting more

degraded baseline conditions. However, both

islands showed positive trends that did not dif-

fer statistically between islands (Year × Island

interaction: p = 0.841), indicating that, despite

differences in initial state, the rate of reef func-

tion recovery is similar between the two islands.

Site-specific models (Appendix 11–12) revealed

marked spatial heterogeneity (χ² = 251.37, df =

5, p < 0.001) in the RFI trajectory. Five of the

six monitored sites showed significant increases

over time (Appendix 15): Zona de Restauración

(β = 0.062, p < 0.001), Cueva del Muerto (β

= 0.060, p < 0.001), Plataforma Pavonas (β =

0.075, p < 0.001), Playa del Amor (β = 0.085,

p = 0.004), and Zona de Restauración Sur (β

= 0.050, p = 0.016). In contrast, Túnel Amar-

radero did not show a significant temporal

effect (p = 0.577), suggesting the absence of a

clear recovery trajectory at this site during the

study period. The year × site interaction model

(Appendix 12) confirmed spatial differences in

initial RFI values but did not detect significant

differences in the rates of change between sites

(Year × Site: p = 0.166). Thus, although the

sites differ in their starting state (Appendix 15),

most follow parallel recovery trajectories, with

Túnel Amarradero being the only exception.

Overall, the LCC and RFI trajectory results

indicate that, from 2012 to 2023, the coral com-

munities in the PNIM were steadily recovering

their ecological functionality, although with

significant spatial variation. Zona de Restau-

ración, Zona de Restauración Sur and several

sites on Isla Larga show the clearest signs of

improvement, while the trend is lagging in

Túnel Amarradero. This suggests that local

factors—including restoration efforts, specific

environmental conditions, and historical dis-

turbances—play a decisive role in the dynamics

of reef function recovery within the PNIM.

DISCUSSION

Data showed that over a decade (2012–

2023), both live coral cover (LCC) and the

Reef Functional Index (RFI) increased in most

years and sites, indicating a trend of coral com-

munity recovery in the IMNP. Previous studies

have documented that coral communities in

the Eastern Tropical Pacific (ETP) exhibit high

resistance and recovery capacity in response to

positive thermal anomalies caused by El Niño

events, which can reach up to +3.5 °C mo–1,

as well as to other natural and anthropogenic

stressors (Martínez-Castillo et al., 2022; Rome-

ro-Torres et al., 2020). Therefore, the observed

increases in both indices reflect not only the

efforts of the restoration program (Hein et al.,

2019) but also the natural recovery capacity

developed by corals in the region (Martínez-

Castillo et al., 2022; Romero-Torres et al., 2020).

Considering historical data, the highest

LCC and RFI values were recorded in 1997,

prior to the 1997–98 El Niño event (Rodrí-

guez-Zaragoza, 2001), which caused one of

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

the greatest coral mortalities reported in the

last four decades, resulting in a 96 % loss of

coral cover in the Central Mexican Pacific

(Carriquiry et al., 2001). From that point until

2012, values continued to decline, driven by

the synergistic effects of subsequent thermal

anomalies such as the 2011 La Niña event

(Cruz-García et al., 2020) and the impacts of

coastal urbanization (Martínez-Castillo et al.,

2022). Notably, while the coral community has

recovered, its composition has changed. Earlier

studies reported that Redonda Island harbored

the highest live coral cover, primarily dominat-

ed by Porites panamensis (Rodríguez-Zaragoza,

2001). However, currently the highest coral

abundance is recorded at Larga Island, and as

in the rest of the ETP region, is dominated by

Pocillopora (Hernández-Zulueta et al., 2017;

Sotelo-Casas et al., 2016; Tortolero-Langarica

et al., 2014; Tortolero-Langarica et al., 2019).

In the Eastern Pacific, Pocillopora is the genus

with the lowest thermal stress resistance but

shows higher recovery capacity compared to

massive and sub-massive morphologies such as

Porites and Pavona (Cruz-García et al., 2020).

As a result, recovery has largely been driven

by the proliferation of Pocillopora, leading to

monospecific communities, similar to those in

the rest of the ETP (Romero-Torres et al., 2018;

Romero-Torres et al., 2020), with slower recov-

ery at Redonda Island and greater heterogeneity

in the system (Hernández-Zulueta et al., 2017;

Sotelo-Casas et al., 2016; Tortolero-Langarica et

al., 2014; Tortolero-Langarica et al., 2019).

Given that the restoration program began

in 2014, the declines observed at Redonda

Island and some sites at Larga Island from

2012 to 2014 reflect the natural dynamics of

the area and may be linked to increasing tour-

ism pressure. Since 2010, IMNP has grown

in popularity, with tourist influx increasing

from ~50 000 individuals in 2013 to 322 535

in 2015 (Burroughs & Rodríguez-Troncoso,

2024). This led to the implementation of regu-

lations and passive restoration actions such

as carrying capacity limits (Cupul-Magaña &

Rodríguez-Troncoso, 2017) to mitigate coral

cover loss. The negative impact of uncontrolled

tourism on coral cover and biodiversity loss has

been extensively documented (Cupul-Magaña

& Rodríguez-Troncoso, 2017; Harriott, 2004).

In contrast, data indicate that in sites classified

as restricted use areas, particularly in Zona de

Restauración Sur (Comisión Nacional de Áreas

Naturales Protegidas [CONANP], 2007), live

coral cover was maintained or even increased.

In our study, active restoration actions gen-

erated a gradual positive effect on the trajectory

of both LCC and RFI. Following implementa-

tion and over a decade, a sustained increase

was observed, though it was negatively affected

by the 2015–2016 El Niño event, considered

the first extreme ENSO of the 21st century

(Santoso et al., 2017). This event negatively

impacted both LCC and RFI not only at resto-

ration sites but throughout the entire Central

Mexican Pacific (Rodríguez-Troncoso et al.,

2023a). However, given that restoration efforts

continued, both indicators recovered on both

islands, demonstrating that restoration inter-

ventions can contribute to coral reef resilience

in the face of extreme climatic disturbances.

This pattern suggests that active restoration

favors the long-term recovery of physical func-

tionality, thereby reinstating key processes such

as habitat provision for multiple species.

Meteorological events such as hurricanes

have also been described as negative stressors

for coral reefs due to the mechanical damage

they can cause (Heron et al., 2008). Nonethe-

less, in the study area, Pocillopora spp. uses

asexual reproduction via fragmentation as a

primary strategy. Therefore, hurricane-induced

fragmentation may benefit coral communities

(Chávez-Romo et al., 2007; Rodríguez-Tron-

coso et al., 2023b). Nonetheless, considering

that after the impact of Hurricane Roslyn in

IMNP, a sharper decrease in LCC and RFI

was observed compared to the 2015–2016 El

Niño event, continued monitoring is essential

to identify recovery trajectories following such

meteorological events.

Although restoration consistently promot-

ed an increase in both LCC and RFI across all

cases, the magnitude of this increase was not

spatially homogeneous. Unlike the 2012–2014

10 Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266883, abril 2026 (Publicado Abr. 22, 2026)

period, when LCC and RFI were unaffected

by restoration efforts, a greater increase was

recorded at Redonda Island compared to Larga

Island. The larger increase at Redonda Island is

noteworthy, as Larga Island is generally consid-

ered more suitable for reef development due to

its broader continental shelf, greater distance

from the coast, and shallower depth (CONANP,

2007; Hernández-Zulueta et al., 2017; Sotelo-

Casas et al., 2016). In fact, the Túnel Amarrade-

ro site showed the lowest increase in both LCC

and RFI regardless of restoration efforts. This

underscores the importance of considering

site-specific characteristics when implementing

restoration programs. Túnel Amarradero has

limited available substrate compared to other

sites, which not only restricts active restoration

actions but also natural processes such as coral

recruitment (Hernández-Zulueta et al., 2017),

thereby limiting restoration success (Burroughs

& Rodríguez-Troncoso, 2024).

In 2023, RFI values in IMNP indicated

that the average physical functionality remains

lower than that of other Mexican Pacific reefs.

Moreover, reef sites to the north and south

of the study area, dominated mainly by Pocil-

lopora, show nearly twice the live coral cover

(Cabral-Tena et al., 2020; Navarrete-Torices et

al., 2023), suggesting that they likely have high-

er RFI values, given the strong contribution of

branching species to reef physical functionality.

The observed increases in LCC and RFI

from 1997 to 2023 support the notion of a

recovery trend for coral communities within

the park, partially driven by active restoration

efforts. The greater increase at Redonda Island,

despite Larga Island previously showing greater

natural gains without intervention, suggests that

restoration actions are supporting the recovery

of both coral cover and physical functionality.

Overall, RFI analysis in this study followed

a similar trend to LCC across spatial scales.

However, the main difference between LCC

and RFI emerged when comparing baseline

data with values observed after nine years of

active restoration. Starting from the concept

that restoration is an intervention that seeks

to recover a degraded, damaged or destroyed

ecosystem (Bayraktarov et al., 2020; Boström-

Einarsson et al., 2020), this distinction is rel-

evant because, based solely on LCC, one might

conclude that by 2023, restoration had fully

recovered the ecosystem to pre-disturbance

levels. However, physical functionality had not

been fully restored. Similar patterns have been

observed in the Mexican Caribbean, where

functional recovery progresses more slowly

than LCC due to continuous exposure to natu-

ral and anthropogenic stressors (González-

Barrios et al., 2021).

Based on the results of this study, it can

be inferred that a historical analysis of coral

reef recovery using functional metrics like RFI

provides a more comprehensive and accurate

perspective. This approach allows us to track

LCC trends and the recovery of key reef func-

tions, such as habitat provision, and assess the

effectiveness and long-term sustainability of

restoration interventions. However, it is impor-

tant to note that RFI focuses solely on physical

functionality, and future studies should explore

complementary ecosystem-level functional

indices. Historical analysis further revealed

that restoration efforts in PNIM have aided in

restoring coral reef physical functionality to

levels approaching pre-disturbance conditions.

Nevertheless, as recovery has not been spatially

uniform, we recommend reviewing and adjust-

ing strategies for sites that have not yet regained

their physical functionality.

Ethical statement: The authors declare

that they all agree with this publication and

made significant contributions; that there is no

conflict of interest of any kind; and that we fol-

lowed all pertinent ethical and legal procedures

and requirements. All financial sources are fully

and clearly stated in the acknowledgments sec-

tion. A signed document has been filed in the

journal archives.

ACKNOWLEDGMENTS

To the Postgraduate Program in Marine

Ecology at CICESE, to the LEMAC at UDG.

AMA received a Masters scholarship from

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266883, marzo 2026 (Publicado Abr. 22, 2026)

Secretaría de Ciencia, Humanidades, Tec-

nología e Innovación (Secihti) while conduct-

ing the study and writing the manuscript (CVU

135762). The present research was funded

by National Geographic Society Grant NGS-

55349R-19 and NGS-100354 C-23 to APRT,

Ciencia de Frontera CONAHCYT CF 2019–

86397 “Evaluación de la función geo-ecológica

de los arrecifes coralinas del Pacífico mexicano”

to RACT, and by the project CONANP (PRO-

CER/CCER/DROPC/09/2016) and P0014-

DCB-2020 to ALCM.

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