Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

Identifying resilient individuals of Pocillopora verrucosa

(Ellis & Solander, 1786): insights from diversity assessments

for coral restoration

María Teresa Macedo Rodríguez1; https://orcid.org/0009-0004-0210-4273

Eric Bautista-Guerrero1; https://orcid.org/0000-0002-4975-1767

Jeimy Denisse Santiago-Valentín2; https://orcid.org/0000-0003-2152-7875

Amílcar Leví Cupul-Magaña1; https://orcid.org/0000-0002-6455-1253

Alma Paola Rodríguez Troncoso1*; https://orcid.org/0000-0003-3958-6283

1. Laboratorio de Ecología Marina, Centro Universitario de la Costa, Universidad de Guadalajara, México; teresa.

macedo@alumnos.udg.mx, eric.bautista0177@academicos.udg.mx, levi.cupul@academicos.udg.mx, alma.rtroncoso@

academicos.udg.mx (*Correspondence)

2. Departamento de Estudios para el Desarrollo Sustentable de Zonas Costeras, Universidad de Guadalajara, México,

denisse.santiago@academicos.udg.mx

Received 30-X-2025. Corrected 05-III-2026. Accepted 13-IV-2026.

ABSTRACT

Introduction: The genus Pocillopora comprises coral species distributed throughout tropical and subtropi-

cal regions. In the Central Mexican Pacific region, Pocillopora verrucosa is the main reef-building species. In

response to the recent decline in coral coverage, restoration protocols have been implemented over the past

decade. However, to date, no genetic diversity records are available as potential markers to evaluate the effect of

assisted recruitment on site dynamics in the area.

Objective: Determine the genetic diversity of P. verrucosa in an insular (Islas Marietas National Park) and a

coastal (Punta de Mita) restoration site within the Central Mexican Pacific.

Methods: A 2 cm2 fragment from 15 colonies per site was collected. Mitochondrial markers for the COI and

ATP6 genes were amplified. A total of 40 sequences of the COI (n = 19) and ATP6 (n = 21) genes were obtained,

and the haplotype and nucleotide diversity were determined.

Results: For the COI gene, two haplotypes shared between the sites were identified, with H1 being the most

abundant. For the ATP6 gene, one exclusive haplotype was detected in Islas Marietas National Park, and one

more abundant haplotype was shared between the two sites. The AMOVA results revealed a homogeneous pat-

tern with Fst values of 0.21603 (p < 0.10655) for COI and Fst = 0.04174 (p < 0.3753) for ATP6.

Conclusions: The low genetic diversity suggests that, as previously reported, asexual reproduction has been the

predominant mode throughout the site’s history, and that the assisted propagation implemented may promote

the maintenance of the individuals that have historically shown resistance to thermal stressors. However, it is

essential to explore alternative propagation techniques in future restoration initiatives, as the long-term success

of restoration also relies on reducing the vulnerability of these ecosystems to future environmental stressors.

Key words: haplotype; branching coral; Eastern Tropical Pacific; molecular markers; resistance.

https://doi.org/10.15517/h7pzq822

SUPPLEMENT

2Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

INTRODUCTION

Coral reefs are considered ecosystems with

high ecological and economic value (Souter

et al., 2020). Their ecological importance lies

in their role as one of the largest reservoirs

of marine biodiversity (Sheppard et al., 2010;

Suggett & Van Oppen, 2022). Additionally,

they are economically important as a source of

livelihood for local communities, in activities

such as coastal fisheries and tourism (Alque-

zar & Boyd, 2007). Each coral colony can be

considered an individual, and as a result of its

growth, the polyps clone into identical genetic

organisms that build the biogenic foundation

of the entire ecosystem (Knowlton & Jack-

son, 2001; Sheppard et al., 2010) and, what

characterizes a coral community or reef is the

live coral cover, as well as its abundance and

even the geo-ecological development of the

ecosystem (González-Barrios et al., 2021; Sug-

gett et al., 2023). Within the Eastern Tropical

Pacific (ETP) region, coral communities are

characterized as monospecific, being domi-

nated by branching corals belonging to the

genus Pocillopora Lamarck, 1816 (Glynn &

Ault, 2000), with changes in the percentage of

live coral cover in each locality or region but

maintaining a benthic structure in the key spe-

cies along the ETP (González-Barrios et al.,

2021). Given their high abundance, pocillopo-

rids represent a key component of coral com-

munities and have shown differential response

to stressors considered natural, such as thermal

anomalies known as ENSO (El Niño Southern

Oscillation), as well as climate change, and

anthropogenic stressors, most of which are

local in scale (Glynn et al., 2017; Knowlton &

Jackson, 2001). That said, a high capacity for

recovery after disturbance has been observed in

the ETP (Romero-Torres et al., 2020). Even in

sites with massive coral loss, there are records

of recovery attributed to both natural pro-

cesses and the implementation of restoration

techniques, also known as assisted propagation

(Martínez-Castillo et al., 2022a).

RESUMEN

Identificación de individuos resilientes de Pocillopora verrucosa (Ellis y Solander, 1786):

perspectivas de las evaluaciones de la diversidad para la restauración de corales

Introducción: El género Pocillopora comprende especies de coral distribuidas en regiones tropicales y subtro-

picales. En la región del Pacífico central mexicano, Pocillopora verrucosa es la principal especie constructora de

arrecifes. En respuesta a la reciente disminución de la cobertura coralina, se han implementado protocolos de

restauración en la última década. Sin embargo, hasta la fecha, no se dispone de registros de diversidad genética

como marcadores potenciales para evaluar el efecto del reclutamiento asistido en la dinámica del sitio en el área.

Objetivo: Determinar la diversidad genética de P. verrucosa en un sitio de restauración insular (Parque Nacional

Islas Marietas) y en uno costero (Punta de Mita) dentro del Pacífico central mexicano.

Métodos: Se recolectó un fragmento de 2 cm² de 15 colonias por sitio. Se amplificaron los marcadores mitocon-

driales de los genes COI y ATP6. Se obtuvo un total de 40 secuencias de los genes COI (n = 19) y ATP6 (n = 21),

y se determinó la diversidad de haplotipos y nucleótidos.

Resultados: Para el gen COI, se identificaron dos haplotipos compartidos entre los sitios, siendo H1 el más abun-

dante. Para el gen ATP6, se detectó un haplotipo exclusivo en el Parque Nacional Islas Marietas y un haplotipo

más abundante compartido entre ambos sitios. Los resultados del AMOVA revelaron un patrón homogéneo con

valores de Fst de 0.21603 (p < 0.10655) para COI y Fst = 0.04174 (p < 0.3753) para ATP6.

Conclusiones: La baja diversidad genética sugiere que, como se informó previamente, la reproducción asexual ha

sido el modo predominante a lo largo de la historia del sitio, y que la propagación asistida implementada puede

promover el mantenimiento de los individuos que históricamente han mostrado resistencia a estresores térmicos.

Sin embargo, es esencial explorar técnicas de propagación alternativas en futuras iniciativas de restauración, ya

que el éxito a largo plazo de la restauración también depende de reducir la vulnerabilidad de estos ecosistemas

frente a futuros factores de estrés ambiental.

Palabras clave: haplotipo; restauración; coral ramificado; Pacífico Tropical Oriental; marcadores moleculares;

resistencia.

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Mitochondrial markers are commonly used

due to their maternal inheritance, low recombi-

nation rates, and the fact that their mutations

represent the unique genetic diversity observed

within the population (Avise, 2009). Particu-

larly, the use of mitochondrial DNA (mtDNA)

sequence data, as the cytochrome c oxidase

subunit I (COI) gene, has proven to be a robust

and widely applied approach for inferring

recent evolutionary history, including founder

events, population bottlenecks, and phylogeo-

graphic patterns in marine organisms (Liu et

al., 2020; Moussa et al., 2022; Park et al., 2020).

In the study of coral reef systems, this approach

may provide a tool to characterize not only the

genetic pool of a particular area, but have the

potential to reveal new mechanisms of adapta-

tion and asses the vulnerability of a particular

location, which is currently highly relevant as

a tool to contribute to implementing conserva-

tion and management actions, particularly for,

coral restoration programs (Suggett et al., 2023;

Van Oppen & Gates, 2006).

Previous studies have shown that Pocillo-

pora populations with low genetic diversity can

be considered demographically unique (Chi-

azzari et al., 2019; Oury et al., 2021). This is

particularly relevant in marginal regions, such

as the ETP, where high genetic diversity within

reefs has been recorded, but significant genetic

structure among regions and even within meters

of reefs, with the potential for local acclimatiza-

tion responses along environmental gradients

considered non-optimal (Combosch & Vollmer,

2011). A different scenario in the same region

may be observed, in which entire sites can be a

single clone, resulting in low genetic diversity in

sites with high coverage of live coral (Baums et

al., 2014). Therefore, Pocillopora can be struc-

tured by eco-regions, with exclusive genotypes

in northern and southern populations, indicat-

ing restricted gene flow and localized genetic

clusters (Dennis et al., 2024). Across the region,

barriers created by ocean currents prevent con-

nections between different populations, but

changes in oceanographic conditions during

El Niño Southern Oscillation (ENSO) events

intermittently promote the exchange of propa-

gules (Paz-García et al., 2012).

In the Central Mexican Pacific (CMP),

mass coral bleaching events have been primar-

ily associated with thermal anomalies driven

by ENSO events. However, differential mortal-

ity has been documented, with elevated tem-

peratures during El Niño events resulting in

catastrophic mass mortality, up to a 90% loss

of live coral cover during the 1997-98 event

(Carriquiry et al., 2001; Reyes-Bonilla et al.,

2002). In this scenario, it is also important to

consider La Niña events, which induce anoma-

lous decreases in seawater temperature, trigger

bleaching responses, and are usually followed

by substantial recovery, with observed mor-

tality as low as 1% (Cruz-García et al., 2020).

Additionally, anthropogenic pressures have fur-

ther negative effects, with urban development

among the primary threats (Martínez-Castillo

et al., 2020), but also non-regulated tourism

has also been shown to be detrimental for the

coralline areas (Burroughs & Rodríguez-Tron-

coso, 2024), promoting differential recovery

response even among nearby sites (Carriquiry

et al., 2001; Martínez-Castillo et al., 2022a).

In response to tackle the loss of coral cover-

age, a science-based coral restoration program

has been implemented over the past decade

along the CMP, utilizing direct asexual propa-

gation of coral fragments with positive results,

increasing live coral cover and survival, with

bleaching but not mortalities even during the

2014-2016 El Niño event (Tortolero-Langarica

et al., 2025). Along the years, the restoration

program have use as a toolbox to determine

the success, the colonies survival, growth and

increase in live coral cover (Tortolero-Lan-

garica et al., 2019); also, the sexual reproduc-

tion capacity of the translocated colonies has

been assessed by demonstrating the presence of

gametes in adults resulting from both natural

and assisted recruitment (Martínez-Castillo et

al., 2023). However, the use of molecular tools

as part of the restoration markers has not been

implemented in the CMP nor in any restora-

tion protocol along the ETP. Therefore, in

order to increase the toolbox, the present study

4Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

represents a first approach to assess the genetic

structure and haplotypic diversity of Pocillo-

pora verrucosa (Ellis & Solander, 1786) in two

survivor communities that have been subjected

to historical mass coral bleaching events and

recurrent restoration efforts: an insular site,

Islas Marietas National Park, with restricted but

constant touristic pressure, and a nearby coastal

site, Punta de Mita, which is a highly impacted

area with the presence of high-end hotels and

golf courses. Given that both sites have shown

positive results with the asexual propagation

technique (Tortolero-Langarica et al., 2019),

our goal is to include genetic diversity as an

additional marker to assess the possible impli-

cations of asexual propagation on the structure

of the restored community.

MATERIALS AND METHODS

Study site: The Mexican Central Pacific is

a region characterized by an average salinity of

35 psu and a pH range of 7.72 to 8.03 (Comis-

ión Nacional de Áreas Naturales Protegidas

[CONANP], 2007; Cupul-Cortés et al., 2018).

The average sea surface temperature (SST) is

26.4°C, with a minimum of 23°C in March

and a maximum of 30°C in September. These

conditions are annually influenced by three

currents: the California Current, the Gulf of

California Current, and the Costa Rica Cur-

rent, which converge with the North Equato-

rial Current (CONANP, 2007; Wyrtki, 1966).

In addition, local processes such as the pres-

ence of internal waves (Plata-Rosas & Filonov,

2007) and water transport processes caused by

upwellings, which occur periodically and sea-

sonally, promote vertical movements of deep,

cold-water masses, enriching the water column

with inorganic nutrients (Portela et al., 2016;

Wyrtki, 1966).

Pocillopora verrucosa samples were collect-

ed from two sites within the Mexican Central

Pacific: Islas Marietas National Park (IMNP),

an insular area (20°41’56” N, 105°35’06” W),

and Punta de Mita (PM), a continental site

(20°41’51.9” N, 105°34’07.9” W), both sepa-

rated by 8 km (Fig. 1). The IMNP is categorized

Fig. 1. Study area location. An insular restoration site: Islas Marietas National Park (IMNP), and a coastal restoration site:

Punta de Mita (PM), located in the Central Mexican Pacific Region.

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

as a Natural Protected Area (NPA) comprised

by Isla Redonda, Isla Larga, and two islets,

with a benthic structure composed primar-

ily of hermatypic corals, but also of rocky and

sandy bottoms ranging in depth from 6 to 30

m (CONANP, 2007). The coral community has

been characterized as a biodiversity hotspot at

the regional level (Glynn & Ault, 2000), and due

to their value for the local population, regulated

tourism and recreational activities are permit-

ted, the most popular being SCUBA diving or

free diving, which exerts moderate pressure on

the park’s natural resources (Cupul-Magaña &

Rodríguez-Troncoso, 2017).

The Punta de Mita site has experienced

minimal direct pressure from tourism uses in

its marine area; however, its terrestrial area has

experienced high anthropogenic pressure from

tourism derived from the development of the

Nuevo Vallarta-Punta de Mita tourist corridor,

with an important urbanization due to the

construction of hotels and golf courses (ECO-

PLAMB, S.A. DE C.V., 2004). Despite this, a

patch-shaped coral community is found along

the coast, home to corals of the genus Pocillo-

pora, which have demonstrated a high capacity

for resilience and recovery in the face of both

natural and anthropogenic stressors (Martínez-

Castillo et al., 2022a).

Sample Collection and Processing: At

each location, fragments of the P. verrucosa col-

onies were collected by SCUBA diving. A sam-

ple of approximately 2 cm² was obtained from

each colony using a chisel and hammer, with

a total of 15 colonies sampled at each site. To

mitigate the collection of clones, each sampled

colony was separated by at least 5 m. The col-

lected samples were preserved in 96 % alcohol

and stored at -20 °C until further processing.

Tissue was extracted individually from

each coral fragment using a needle and forceps,

and a Zeiss® Stemi 508 stereomicroscope for

visualization. The resulting tissue was stored in

1.5 ml tubes with 500 μl of 96 % ethanol. Sub-

sequently, genomic DNA was extracted using

the salt-out method (Aljanabi & Martínez,

1997). Partial sequences of the mitochondrial

genes cytochrome oxidase subunit 1 (COI) and

ATP synthase subunit 6 (ATP6) were ampli-

fied by polymerase chain reaction (PCR). The

use of these molecular markers stems from

the fact that COI and ATP6 are generally

considered complementary and therefore pri-

mary mitochondrial markers, owing to their

strong species-level resolution, and, particu-

larly for Pocillopora, both genes have extensive

reference databases. Primers were designed

based on the Pocillopora verrucosa reference

genome project (PRJNA551401) available at the

National Center for Biotechnology Information

(NCBI). The COI fragment (~1500 bp) was

amplified using FCOIPv: 5’-CCCCGTCTA-

AATGCTTTCTG-3’ and RCOIPv: 3’-CGG-

TATATAAACCCGGCACT-5’, while the

primers FATP6Pv: 5- GAGGCCTTAGGGCA-

GATTTT-3’ and RATP6Pv: 3’-ACAT-

GAGCCATCATCCCTTC-5’ were used for

amplification of the ATP6 (~678 bp). Each

PCR reaction included 7.23 μl of nuclease-free

H2O, 0.75 μl of MgCl2, 0.66 μl of dNTPs, 2.5 μl

of 10x buffer, 0.13 μl of each primer, 0.10 μl of

Taq polymerase (Promega®), and 1 μl of DNA.

Amplification for the sequences was car-

ried out in an Applied Biosystems® thermal

cycler using the following conditions: an ini-

tial denaturation step at 95 °C for 2 minutes,

35 cycles comprising 50 seconds at 95 °C, 50

seconds at 58 °C, and 1 minute at 72°C, and a

final extension cycle at 72 °C for 10 minutes.

PCR products were visualized on a 2 % aga-

rose gel in TAE buffer (Tris-acetate-EDTA;

40 mM Tris base, 20 mM glacial acetic acid, 2

mM EDTA, pH 8.3). Reactions were classified

as positive amplification (single band on the

agarose gel) or negative (no apparent band).

Only positive reactions were purified using a

commercial DNA purification kit (Promega®)

and then sent to Macrogen Inc.® in Seoul,

Korea for sequencing.

Bioinformatic and Statistical Analy-

sis: The sequences were manually edited in

Geneious Prime®, and multiple alignments were

performed with ClustalW in Mega11®. To con-

firm species identity, consensus sequences were

6Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

queried against the National Center for Bio-

technology Information (NCBI; https://www.

ncbi.nlm.nih.gov/nuccore) database using the

Basic Local Alignment Search Tool (BLAST).

Also, the COI and ATP6 sequences obtained

from the two sites were deposited in the Gene-

Bank database, and the accession numbers are

included as supplementary material (Table S1).

For each location, genetic diversity levels

were calculated using estimates of haplotype

diversity (Hd) and nucleotide diversity (Pi).

This estimate was performed using the DnaSP

software v. 6 to analyze DNA sequence poly-

morphisms (Rozas et al., 2003). Genetic dif-

ferentiation between sites was assessed using an

analysis of molecular variance (AMOVA), and

comparisons were made based on estimates of

the fixation index Fst with 10 000 permutations

using the Arlequin® v3.5.2 software (Excoffier

& Lischer, 2010).

A haplotype network was created for each

molecular marker using the algorithm imple-

mented by Templeton et al. (1992), which

employs statistical parsimony (TCS), with

a 95 % confidence interval (Clement et al.,

2000). The calculations were carried out using

the Population Analysis with Reticulate Trees

PopArt® software, as described by Leigh & Bry-

ant (2015).

RESULTS

A total of 13 IMNP colonies and 8 PM

colonies were successfully processed. In total,

40 sequences of the COI (n = 19) and ATP6 (n

= 21) genes were obtained due to difficulties

during amplification. For the IMNP site, 12

COI gene sequences were obtained, and two

haplotypes were detected. Regarding the ATP6

gene, 13 sequences were obtained, with two

haplotypes. At the Punta de Mita site, seven

COI gene sequences with two haplotypes were

detected, whereas at the same site, eight ATP6

gene sequences were obtained, with only one

haplotype detected (Table 1).

In the COI gene sequences analyzed, only

one polymorphic site was found in position

437, corresponding to two haplotypes. Also,

for the ATP6 gene, only one polymorphic site

in position 374 was identified, and represented

by two distinct haplotypes. Haplotype diversity

values were low for both genes from both local-

ities. In IMNP, the haplotype diversity values

were 0.167 for COI and 0.153 for ATP6, where-

as at the coastal site of PM, they were 0.571

(COI) and 0.000 (ATP6). Nucleotide diversity

was also evaluated, with values of 0.00011 for

the COI gene and 0.00022 for ATP6 at IMNP.

Meanwhile, for the coastal site, Punta de Mita,

the values were 0.00039 for the COI gene and

0.00000 for the ATP6 gene (Table 1).

The COI gene analysis allowed the con-

struction of a haplotype network revealing

a main group composed of two haplotypes

connected by a single mutational step. Both

haplotypes were present in the two sampled

locations, with the COI H1 haplotype being the

most abundant in each locality (Fig. 2a). Simi-

larly, the ATP6 gene network comprised two

haplotypes separated by one mutational step.

The ATP6 H1 haplotype was the most frequent

and occurred in both locations, whereas the

Table 1

Haplotype and nucleotide diversity in the coral Pocillopora verrucosa.

Site Gene n H Hd Pi

IMNP COI 12 2 0.167 ± 0.134 0.00011 ± 0.00009

IMNP ATP6 13 2 0.153 ± 0.126 0.00022 ±  0.00037

PM COI 7 2 0.571 ± 0.119 0.00039 ± 0.00008

PM ATP6 8 1 0.000 0.000000

Sample size- colonies successfully amplified (n), number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity

(Pi). Sites: Islas Marietas National Park (IMNP) and Punta de Mita (PM).

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

ATP6 H2 haplotype was detected exclusively in

IMNP and was represented by a single individ-

ual (Fig. 2b). Finally, the Analysis of Molecular

Variance (AMOVA) revealed a homogeneous

pattern across both gene loci, with overall Fst

values of 0.21603 (p < 0.10655) for COI and

Fst = 0.04174 (p < 0.3753) for ATP6, indicating

no significant genetic differences between the

studied sites.

DISCUSSION

Pocillopora is the most widespread reef-

building coral, but also considered a highly vul-

nerable species complex, as historical records

have shown massive bleaching and mortality

events during extreme heat waves caused by

ENSO events (Carriquiry et al., 2001), with

contrasting ability to recover in the ETP region

(Romero-Torres et al., 2020). The high restora-

tion potential of this coral genus, particularly

in the Mexican Pacific, can be attributed to its

capacity for acclimatization and resilience, as

well as to its rapid growth rates and branching

morphology, which may enhance habitat avail-

ability and structural complexity over short

temporal scales (García-Medrano et al., 2023;

Tortolero-Langarica et al., 2019; Tortolero-Lan-

garica et al., 2025). In this context, our evalu-

ation of the genetic structure and haplotypic

diversity of two coral sites that have historically

experienced mass mortality events provides

valuable insights into the mechanisms underly-

ing resilience to environmental stress. These

findings contribute to assessing the long-term

feasibility of restoration strategies and support

informed decisions on incorporating this genus

into coral reef restoration toolkits.

In this context, mitochondrial DNA

(mtDNA) analyses provide critical insights

into recent evolutionary dynamics, including

founder events and population bottlenecks (Liu

et al. 2020; Moussa et al., 2022; Park et al., 2020)

and have been previously proven in marine

invertebrates (Hellberg et al., 2002; Muller et

al., 2003). The mitochondrial genome plays a

fundamental role in cellular energy metabolism

and is therefore closely associated with organis-

mal responses to ecological pressures; accord-

ingly, genetic variation is reflected not only in

the nuclear genome but also in mitochondrial

genes, which may contribute to observed pat-

terns of population persistence and resilience

(Xing et al., 2025). For the management and

Fig. 2. TCS haplotype network of the A) COI and B) ATP6 gene in Pocillopora verrucosa. The locations are represented by

colors; IMNP = Islas Marietas National Park (green) and Punta de Mita (white). Horizontal segments connecting the network

nodes represent nucleotide substitutions. Numbers in parentheses indicate the abundance of individuals (n) associated with

each haplotype.

8Revista de Biología Tropical, ISSN: 2215-2075 Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

conservation of coralline areas, this information

is particularly relevant under contemporary

scenarios marked by recurrent mass mortality

events, as it helps to identify genetic signatures

associated with persistence and recovery in

reefs that have remained resilient despite ongo-

ing local stressors (Souter et al., 2020).

Nucleotide and haplotype diversity anal-

yses of both molecular markers (COI and

ATP6) showed low genetic diversity. It has

been observed that, unlike other marine inver-

tebrates, cnidarian mtDNA evolves up to 20

times more slowly than in most metazoans

(France & Hoover, 2002; Shearer et al., 2002);

still, our results reveal a diagnostically informa-

tive pattern. Specifically, we detected extremely

low haplotypic diversity and negligible genetic

differentiation between localities. While the

comparatively slow evolutionary rate of mito-

chondrial markers in anthozoans has often

been cited as a limitation for resolving fine-scale

genetic structure, in this context, such con-

servatism constitutes a key diagnostic advan-

tage. Rather than reflecting insufficient marker

resolution, the observed genetic homogeneity

provides strong evidence of a pronounced his-

torical genetic bottleneck and suggests that a

metapopulation dynamic shaped by sustained

connectivity among local coral communities,

along with other traits (e.g., reproduction plas-

ticity), must be considered to understand the

high resilience of this group.

Branching corals, particularly the genus

Pocillopora, are distinguished by a prevalence

of asexual reproduction through fragmenta-

tion (Chávez-Romo & Reyes-Bonilla, 2007;

Whitaker, 2006), which generates clones that

recruit in proximity to the progenitor colonies.

This could explain the low haplotypic diversity

observed between the two genes across both

studied locations and the high frequency of

the H1 haplotype in both locations, resulting

in genetic homogeneity at the site level and

suggesting that all individuals are genetically

identical. This could be considered as nega-

tive, as low genetic diversity is often associated

with low fitness; however, it has been shown

to be a successful strategy that increases cover

at a faster rate, while also maintaining and

stabilizing species populations and maintains

within the population the genotypes that cur-

rently prove to be the most resistant (Adjer-

oud & Tsuchiya, 1999; Miller & Ayre, 2008;

Stoddart, 1984). However, it should not be

overlooked that, although asexual reproduc-

tion has been a successful strategy thus far, one

of its consequences is the prevalence of clonal

organisms, resulting in genetic homogeneity

within the population. Interestingly, the H1

haplotype was shared at both locations, indicat-

ing that at some point there was a connection

or exchange of propagules between the sites.

However, unique haplotypes were also evi-

dent, indicating that P. verrucosa can reproduce

both sexually and asexually at both locations,

as has been observed throughout the region

(Santiago-Valentín et al., 2020), with an evi-

dent high rate of self-recruitment and sporadic

subsidiary recruitment.

Although the results showed no significant

genetic differentiation between P. verrucosa col-

onies from both locations, this does not indi-

cate the absence of genetic diversity in other

parts of the genome. The conceptualization that

low diversity is synonymous with poor health

should be taken with caution, since, in pocil-

loporids, as in the rest of the hermatypic corals,

their capacity for resistance and resilience is

not only attributed to the genetic diversity of

the coral but to the entire holobiont (Berkel-

mans & Van Oppen, 2006; Howells et al.,

2012). Corals are characterized by their sym-

biotic relationships with other groups, such as

their endosymbiont dinoflagellates of the fam-

ily Symbiodineacea, as well as assemblages of

bacteria, fungi, and other viruses (Herre et al.,

1999); therefore, the coral physiology, and their

susceptibility or tolerance, is the response to the

whole holobiont (Rowan et al., 1997; Warner et

al., 1996). In particular, P. verrucosa in the study

region harbors only Durusdinium glynni algal

endosymbiont (Martínez-Castillo et al., 2022b),

which is considered a high-thermo tolerant

dinoflagellate (Baker et al., 2017; Berkelmans

& Van Oppen, 2006). In addition, its bacterial

assemblage (microbiome) has been found to

Revista de Biología Tropical, ISSN: 2215-2075, Vol. 74 (S1): e20266961, abril 2026 (Publicado Abr. 22, 2026)

respond to changes in local conditions, primar-

ily high concentrations of inorganic nutrients

(Ostria-Hernández et al., 2022). Therefore, the

response, as well as the persistence of P. v e r-

rucosa genotypes in the region, results from the

holobiont, not just from the cnidarian’s genetic

identity (Van Oppen & Gates, 2006).

This approach leads to the need to imple-

ment and conduct new comprehensive studies

that allow us to determine the composition

and dynamics of the holobiont, as the theo-

ry establishes that effective coral restoration

depends on preserving genetic diversity by

using multiple, genetically distinct local donor

colonies and ongoing genetic monitoring as an

approach to enhance resilience and support

long-term reef recovery (Banaszak et al., 2023;

Blanco-Pimentel et al. 2023; Chan et al., 2018;

Rios et al., 2024; Van Oppen & Gates, 2006).

The observed genetic homogeneity reflects low

genetic variability and minimal differentiation

among sites. This pattern suggests that the

surviving coral colonies exhibiting resistance

to thermal stress do not represent a random

subset of the population but rather belong to

a shared evolutionary lineage. Consequently,

this genetic coherence may reduce the risk of

outbreeding depression when such colonies

are considered for restoration or propagation

efforts, and therefore, assisted asexual propaga-

tion has promoted the maintenance of haplo-

types that have historically shown resistance to

thermal stressors. Additionally, it has provided

us with other initial insights, such as that the

genetic resources available for natural recovery

may be limited and unstable. Consequently,

reduced genetic diversity could constrain the

capacity for natural recovery, supporting the

need for timely implementation of active resto-

ration strategies.

In this context, our findings provide a

rationale for considering assisted gene flow and

the translocation of coral fragments among

localities as potential measures to enhance

fertilization success while maintaining adap-

tive potential in these vulnerable assemblages.

Nevertheless, further research incorporating

both mitochondrial and nuclear markers (e.g.,

internal transcribed spacers or microsatellites)

is necessary to achieve a more comprehensive

understanding of the underlying evolutionary

processes and to more accurately assess popula-

tion structure in this species.

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

The present study was funded by the

National Geographic grant NGS-100354C-23.

We thank the authorities of Islas Marietas

National Park for the logistical support pro-

vided during the field trips and sampling. The

collection was conducted under the permit

PPF/DGOPA-88/22.

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