Herpetological richness and diversity in an offshore archipelago of the Tropical Eastern Pacific
Creators: name: Flores De Gracia, Eric Enrique
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Coiba island
Eastern Tropical Pacific
Herpetology
Panama

description: Coiba National Park (CNP) comprises an offshore archipelago of around 35 islands and islets of different areas off the coast of the Panama Pacific that separated from Mainland around 12,000 ya. In this study, Visual Encounter Surveys and pitfall traps assembled with occurrence data from GBIF and other sources were employed to assess the herpetological richness, and community assemblages along four different islands of CNP and compared these to Mainland. Amphibian richness was lower in the islands (maximum 5 spp.) compared to the Mainland (11 spp.); meanwhile, reptile richness was similar between the Mainland and Coiba island (19 spp.) and were higher compared to the other islands. The higher species estimates for amphibian and reptiles in CNP were five and 27 respectively and were lower compared with those reported in the CNP´s management plan. The Mexican White-lipped Frog (Leptodactylus fragilis) was identified which constitutes the first formal record of the species in CNP. The amphibian communities were more similar between the larger islands of CNP, possibly reflecting the importance of the island´s area and similar environments. As for reptile assemblages the smaller islands were more similar, perhaps related to its relative isolation, local adaptation and a small-islands effect. CNP may harbour a unique herpetofauna with local adaptations to the habitat but also influenced by other elements and past anthropogenic factors that need to be investigated in more detail.
description: Funding provided by: Coiba Scientific Station (COIBA AIP)Crossref Funder Registry ID: Award Number:
description: Herpetological Surveys

Surveys were conducted between July 2019 and August 2023 along 69 transects distributed in 18 sites and five locations (Figure 1) from the Mainland in front of CNP (25 transects) and on four islands of CNP archipelago: Canales de Afuera (4 transects), Rancheria (4 transects), Coiba (30 transects), and Jicaron (6 transects) (Table 1, Table 2). Several field trips occurred each year except for 2020 when only one site in one location was visited.

Visual encounter surveys (VES) (Crump & Norman, 1994; Rodda, Campbell, Fritts, & Clark, 2007) were used to identify metamorphic amphibians and terrestrial reptiles. VES were conducted along one to six randomly deployed 2 m wide and 100 m long transects at each site during day and night without time constraints, and each transect was visited between one to five times. Each transect was separated at least 20 m from each other, and two people constantly surveyed the transects. Search effort (in person-hr) was calculated by multiplying the total search time at each site by the number of observers (Maritz & Alexander, 2012), excluding time allocated to manipulate captured individuals. Manipulation was necessary to ensure a clearer identification of the species, moreover at night, as it has been occurred during other surveys using VES (Metcalf, Marsh, Torres, Graham, & Gunnels, 2020; Quilumbaquin, Carrera-Gonzalez, Van der heyden, & Ortega-Andrade, 2023; Vences et al., 2008). Assuming that some species cannot be detected, pitfall traps were used (Kenneth Dodd Jr., 2010; Todd, Winne, Willson, & Whitfield Gibbons, 2007). When possible, one or two pitfall traps were deployed at each site and were separated at least 100 m from transects to provide independent sampling units. Each pitfall trap consisted of five 19 L plastic buckets buried so the rim was flush with the ground and separated among them ca. 3 m. Each pitfall was deployed using a cross design and connected with drift fences made of black tick plastic sheets. Individuals were identified in the field at the species level and compared with dichotomic keys (Köhler, 2008, 2011). Updated species scientific names follow those in AmphibiaWeb (AmphibiaWeb, 2023) and Reptile Database (Uetz, Freed, & Hošek, 2023).

Data Analysis

Surveyed transects were assigned to a location according to the following order, transects in sites one to six to Mainland, transects in site seven to Canales de Afuera island, transects in site eight to Rancheria island, transects in sites nine to 17 to Coiba island and those from site 18 to Jicaron island (Figure 1). Prior to analysis, the number of individual specimens registered in each transect was averaged across all visits because each transects was visited between one and five times. Introduced species were excluded from the diversity analyses because as mentioned earlier, unlike native species there are major anthropogenic factors influencing introduced species richness in islands that were not the focus of this study.

Because differences in search effort may affect the overall richness estimates, a correction factor was applied to the abundances data in each transect, by multiplying the result of dividing the maximum search effort (42.40 persons-hr) by each other search effort value (see Table 2).

For α diversity, species richness was considered as representative of the level of diversity (Magurran, 2021). Individual-based rarefaction curves of observed species richness (Sobs) were plotted for each location with 95% confidence intervals based on the Mao-tau analytical function (Colwell et al., 2012) with the software Estimates v9.1.0 (Colwell, 2006). Estimated species richness (Sest) resulted from the average of the nonparametric Chao1 classic or unbiased (Chao, 1984, 1987) and the ACE (Chao & Lee, 1992) estimators also computed with Estimates v9.1.0 (Colwell, 2006). These estimators have been widely used in diversity studies as a measure of expected total species richness of amphibians and reptiles (Edwards et al., 2023; Hernández-Salinas, Ramírez-Bautista, & Mata-Silva, 2014; Johari et al., 2021).

To determine β diversity the Jaccard dissimilarity index with the presence–absence of species was calculated using the vegan package (Oksanen et al., 2022). For a visual representation, clusters were produced using the hierarchical clustering algorithm using the hclust function and the unweighted pair group method with arithmetic mean to create dendrograms using the package BiodiversityR (Kindt & Coe, 2005).

An updated biodiversity repository for CNP does not exist and specimen collections are difficult to access. Hence, the surveys were further supplemented with new published records and occurrences and counts of amphibians and terrestrial reptiles from 2018 to 2023 downloaded from the Global Biodiversity Information Facility (GBIF) website (www.gbif.org). These occurrences were added for the α and β diversity analyses. GBIF is an open access platform that integrates data resulting from specimen surveys and collections worldwide (Heberling, Miller, Noesgaard, Weingart, & Schigel, 2021) and is being used in herpetological biodiversity assessments (Sillero et al., 2014; T. S. Vasconcelos & Nascimento, 2014). The point-occurrence records were obtained using the draw area tool encircling the study islands in CNP and a section along the Mainland coast where the study sites were located. Data curation before analysis included the deletion of those: without geographic coordinate, without specific year, and without a clear description of location. Scientific names were also validated to check for synonyms and to abide to actual scientific nomenclature. In total, 45 reptiles belonging to 14 species and 6 amphibians belonging to 3 species, were included and assigned to the corresponding location. Presence–absence data of additional species of amphibians and terrestrial reptiles reported by De la Riva (1997a, 1997b), and Pérez-Santos and Martínez (1997) for some islands of CNP and by Martinez and Rodríguez (2003) for Mainland, were also included in the β diversity analyses assuming these species are extant species (Table S1, Table S2). Data on vegetation classes of the study sites was obtained from the Ministry of Environment of Panama GeoPortal (https://geoportal.miambiente.gob.pa/server/rest/services/Nodo_Suelos/MapServer). Statistical analyses were conducted using the software R v4.2.2 (R Core Team, 2023). Data presented here are mean ± SD (range) unless otherwise indicated.