**1. Introduction**

Invertebrates are frequently associated with scleractinian corals of the genus *Pocillopora* [1]. Macrocrustaceans are the most representative coral-associated fauna. Among these, diverse assemblages find shelter among the *Pocillopora* branches [2,3]. Different taxa, including shrimps, crabs, isopods, and copepods, have been described as coral symbionts [4], presenting different degrees of specialization in form and function [5]. Several of these species are obligate symbionts, always and permanently associated with specific hosts, while other species are facultative symbionts that can also survive outside their host, usually on non-living substrates [1,5]. As a general trend, the coral-associated fauna

**Citation:** Alonso-Domínguez, A.; Ayón-Parente, M.; Hendrickx, M.E.; Ríos-Jara, E.; Vargas-Ponce, O.; Esqueda-González, M.d.C.; Rodríguez-Zaragoza, F.A. Taxonomic Diversity of Decapod and Stomatopod Crustaceans Associated with Pocilloporid Corals in the Central Mexican Pacific. *Diversity* **2022**, *14*, 72. https://doi.org/ 10.3390/d14020072

**\*** Academic Editors: Michael Wink and Simone Montano

Received: 15 December 2021 Accepted: 18 January 2022 Published: 21 January 2022

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**Copyright:** © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/).

depends on the host for feeding and refuge [6,7]. In addition, coral-associated crustaceans help to maintain coral health by performing cleaning activities, such as removing sediment and parasites [8,9]. Some species also have an active role in their defense against predators. For example, species of *Trapezia* defend the coral from predators, such as the crown star (*Acanthaster planci*) [10,11], and the shrimp *Alpheus lottini* protects the coral from coralivorous mollusks of the genus *Drupella* [12]. Crustaceans represent up to 80% of the coral-associated fauna [1,13], playing multiple ecological roles. They are part of different trophic relationships: acting as predators, parasites, herbivores, scavengers, and detritivores. Most obligate symbionts are mucus, suspension, or deposit feeders [1,5]. Thus, they link primary producers with high-level consumers [14–16]. This strong relationship between corals and crustaceans can be affected by the changes induced by anthropogenic activities or climate change [1,7].

The coral ecosystems of the Central Mexican Pacific (CMP) are dominated by several species of *Pocillopora* [17,18]. The most common is *P. verrucosa*, but other species, such as *P. damicornis*, *P. capitata*, *P. eydouxi*, *P. effusus*, *P. inflata*, and *P. meandrina*, have also been recorded [18]. Pocilloporid corals are structurally complex, generating many microhabitats for crustaceans [1]. However, few studies have focused on the crustacean diversity associated with pocilloporid corals in this area. Earlier studies in the Mexican Pacific by Pereyra-Ortega [19] and Hernández [20] described the decapods associated with *Pocillopora* corals in Isla Espíritu Santo and the southern area of the Baja California peninsula. Ramírez-Luna et al. [21] studied the temporal variation of the xanthid crabs in Huatulco Bay, Oaxaca, and found the largest diversity and abundance during the dry season. Hernández et al. [22,23] analyzed the impact of coral bleaching and hurricanes on the diversity and abundance of decapods from La Paz and Loreto Bay, Baja California Sur. They concluded that these phenomena changed the species richness considerably, decreasing the abundance of coral-associated decapod species. Two studies have evaluated the diversity of coral-associated crustaceans in the CMP, including the coastal region from Nayarit to Michoacan. Hernández et al. [24] performed a visual census of the decapods in coral ecosystems and found 36 species, with most individuals in or near corals. Ayón-Parente et al. [25] formulated an inventory of 19 species of caridean shrimps associated with the *Pocillopora* from Chamela Bay, Jalisco. Although both studies contributed to the inventories of the crustaceans associated with pocilloporid corals of the CMP, they did not offer evidence of possible spatio–temporal changes in their species richness and abundance, nor did they evaluate the contribution of the different taxonomic categories to diversity.

The average taxonomic distinctness ( Δ+) index has been used to assess biodiversity [26]. Environmental variability, sampling effort, and sampling size can affect most classical indices based on species richness and evenness [27]. However, the Δ+ and its variation ( Λ+) are good ecological indicators, because they reflect the taxonomic relatedness of species within assemblages [28,29]. These indices allow for comparing different studies because they are independent of sample size and effort and provide a test for the significance of departure from expectation by chance if no other studies are available for comparison [30]. This analysis determines how certain taxa contribute to the total taxonomic diversity [26]. The taxonomic distinctness and its variation have mainly been used to evaluate biodiversity in time and space scales in different assemblages such as freshwater fishes [31,32], marine invertebrates [29,33,34], and insects [35,36].

In this study, the main objective was to use the species richness and taxonomic distinctness to assess the spatio–temporal variation of the decapods and stomatopods associated with the coral *Pocillopora* in the CMP. Knowing this information could help us understand the potential effects of coral reef degradation [7]. This area harbors the highest richness and coral coverage of the Mexican Pacific [17,18]; its coral ecosystems are dominated by the *Pocillopora* genus, which includes up to 80% of coral-associated fauna [1,13]. The CMP has suffered from a significant human impact and, although some areas are protected, most of the coral ecosystems are not [18]. Corals are very susceptible to environmental changes and natural and anthropogenic impacts. These changes affect associated fauna,

especially symbiotic species. Evidence has shown that the *Pocillopora*-associated fauna has a spatio–temporal variation due to environmental drivers [3,6,21,37]. We hypothesized that the sites with the most discontinuous coral cover and highest human intervention (local tourism, fishing, etc.) would have the lowest richness and taxonomic distinctness, along with a high abundance of coral-associated fauna due to the low coverage and greater isolation of the host coral colonies.

#### **2. Materials and Methods**

#### *2.1. Study Area*

The study area included four coral ecosystems in the Central Mexican Pacific (CMP): (i) Chamela and (ii) Cuastecomate-Punta Melaque in southern Jalisco, and (iii) Carrizales and (iv) Punto B in Colima (Figure 1). The CMP is part of the eastern tropical Pacific ecoregion spanning from Baja California to northern Peru and the Galapagos Islands, Ecuador [38]. In the summer, the CMP is influenced by the California Current, the Cabo Corrientes Upwelling, the Mexican Warm Pool, and the Costa Rica Coastal Current. However, these currents have a weaker effect during the winter and spring due to the cold water from the California Current and the warm water from the Cortés Current [39]. Furthermore, the Mexican Warm Pool is part of the Western Hemisphere Warm Pool, which induces an important annual climatic variation in the water temperature to develop the El Niño-Southern Oscillation (ENSO) [40,41]. These currents provide the CMP with species from different biogeographic provinces [38]. Hurricanes, tropical storms, and upwellings also significantly impact the coral colony structure and associated fauna [18].

**Figure 1.** Study area in the CMP. Site codes: (**a**) CH, Chamela; (**b**) CT, Cuastecomate-Punta Melaque, Jalisco; (**c**) CA, Carrizales; and (**d**) PB, Punto B, Colima.

Some of the general characteristics of the sampled sites are as follows: (1) Chamela (CH) is formed by different small islands and islets; its coral ecosystems are patchy and isolated, and the benthos has a high coverage of rubble, sand, and dead coral. This site

is important for fishing and local tourism. (2) Cuastecomate-Punta Melaque (CT) has a discontinuously distributed high coral cover, characterized by small reef patches with fleshy macroalgae stands, sand, and rocks. (3) Carrizales (CA) is located in Ceniceros Bay; it is a short beach defined by two small and fringing coral reefs on each side of the shore with ~100% live coral cover. (4) Punto B (PB) is located in Santiago Bay near the Julualpan Lagoon's mouth and is considered a highly touristic area. Its coral community has scarce, isolated coral colonies but grea<sup>t</sup> coverage of sponges, calcareous algae, and sandy and rocky substrates.

Three samples of live *Pocillopora* corals were collected in each coral ecosystem using randomly placed 0.25 m<sup>2</sup> quadrants. Each sample position was marked using a global positioning system (GPS). A total of 48 samples were collected during September 2017, January and September 2018, and January 2019. All samplings were obtained by scuba diving at a 10 m depth. Each coral sample was covered with a plastic bag to avoid losing organisms and detached using a hammer and chisel. Subsequently, the coral was carefully fragmented to collect all the organisms between and within the *Pocillopora* branches. All live decapods and stomatopods were fixed with 70% ethylic alcohol. Samples were identified to the most precise taxonomic level possible in the Molecular Ecology, Microbiology, and Taxonomy Laboratory (LEMITAX), Universidad de Guadalajara. The specialized literature for identification included Rathbun [42], Haig [43], Abele and Kim [44], Castro [45], Anker et al. [46], Hendrickx et al. [47], Ayón-Parente [48], García-Madrigal and Andréu-Sánchez [49], Hermoso-Salazar [50], Salgado-Barragán and Hendrickx [51], and Hiller and Lessios [52]. A presence/absence matrix was constructed to perform the ecological analysis.

#### *2.2. Data Analysis*

The spatial and temporal variation of the taxonomic diversity was evaluated with a three-way experimental design with crossed factors expressed as:

$$\mathbf{Y} = \mu + \mathbf{Y}\mathbf{e}\_i + \mathbf{S}\mathbf{e}\_j + \mathbf{S}\mathbf{i}\_k + \mathbf{Y}\mathbf{e}\_i\mathbf{x}\mathbf{S}\mathbf{e}\_j + \mathbf{Y}\mathbf{e}\_i\mathbf{x}\mathbf{S}\mathbf{i}\_k + \mathbf{S}\mathbf{e}\_j\mathbf{x}\mathbf{S}\mathbf{i}\_k + \mathbf{Y}\mathbf{e}\_i\mathbf{x}\mathbf{S}\mathbf{e}\_j\mathbf{x}\mathbf{S}\mathbf{i}\_k + \varepsilon\_{ijk} \tag{1}$$

where Y is the variable under analysis (taxonomic diversity), and μ is the mean of the analyzed variable. The year factor (Ye*i*) had two levels (years), and each year was composed of two seasons (dry and wet seasons), so the first year included September 2017 and January 2018, and the second included September 2018 and January 2019. The season factor (Se*j*) had two levels: wet (September 2017 and 2018) and dry (January 2018 and 2019). The site factor (Si*k*) had four levels corresponding to the studied coral ecosystems. Finally, <sup>ε</sup>*ijk* represented the accumulated error. All factors were considered as fixed effects (model type I).

The sampling effort was evaluated using sample-based rarefactions at three levels (i.e., site, season, and year) with the observed species richness and the expected richness estimated using non-parametric estimators Chao 1, Chao 2, Jackknife 1, Jackknife 2, ICE, and ACE. These estimators were based on rare species; they estimated the number of potential species considering the incidence and abundance data recorded in the samplings [53]. The total observed richness (SObs) was calculated for each ecosystem with the Mao Tao function. Then, the coral ecosystems were compared in pairs with individual-based rarefactions and 95% confidence intervals. All rarefaction curves were built with 10,000 randomizations without replacement. Species rarity was also calculated (singletons, doubletons, unique, and duplicate species), and the species were identified. These analyses were performed in the software EstimateS 9.1 [54]. The absolute density of each species (represented as the number of individuals per m2) and their absolute frequency were also estimated.

The taxonomic diversity analysis considered each site's taxonomic differences and singularities regarding the seasonal variation and the years analyzed. Thus, the average taxonomic distinctness ( Δ+) analysis was performed to evaluate the species' distribution and incidence as well as their taxonomic relations [28]. This analysis also measured the taxonomic distance between two species and its variation (Λ+), according to the following equations:

$$\Delta^{+} = \left[\sum\_{i$$

$$\Lambda^{+} = \left[\sum\_{i \neq j} \sum\_{j \neq j} \omega\_{ij - \phi} \cdot 2\right] / \left[\mathbb{S}(\mathbb{S} - 1) / \right] \tag{3}$$

where S represents the number of species, and <sup>ω</sup>*ij* denotes the assigned weight of each supraspecific taxonomic level. An eight-level taxonomic aggregation matrix was built, including species, genus, family, subfamily, suborder, order, subclass, and class. According to Warwick and Clarke [55], the taxa were weighted as follows: ω = 1, species within the same genus; ω = 2, species within the same family but different genus; ω = 3, species within the same subfamily but in a different family; and so on. The Δ+ and Λ+ were estimated for each site, season, and year. The models were created with a 95% confidence interval, and the statistical significance was tested with 10,000 permutations.

The Δ+ analysis was followed by a taxonomic dissimilarity analysis (Γ+), which is described as: 

$$\Gamma^{+} = \frac{\left(\sum\_{i=1}^{\mathbb{S}\_1} \min\_{\{\boldsymbol{\cdot}\}} \{\boldsymbol{\omega}\_{i\boldsymbol{j}}\} + \sum\_{j=1}^{\mathbb{S}\_2} \min\_{\{\boldsymbol{\cdot}\}} \{\boldsymbol{\omega}\_{i\boldsymbol{j}}\}\right)}{\left(\mathbb{S}\_1 + \mathbb{S}\_2\right)}\tag{4}$$

where Γ+ denotes the gamma<sup>+</sup> taxonomic dissimilarity, S1 represents the number of species in the first sample, S2 is the number of species in the second sample, and <sup>ω</sup>*ij* denotes the path length between species *i* and *j*.

A non-parametric multidimensional scaling (nMDS) and a cluster analysis were performed using the taxonomic dissimilarity (Γ+) matrix to explore the crustacean taxonomic differentiation patterns across the spatio–temporal experimental design (site, season, and year). The cluster analysis was built with the average group linking method and similarity profile analysis (SIMPROF) to assess group formation using 10,000 permutations. Therefore, nMDS ordination was coupled with the cluster analysis outputs. All analyses (i.e., Δ+, Λ+, Γ+, nMDS, and cluster analysis) were performed in PRIMER 7.0.21 and PERMANOVA +1 [56].
