DOI: 10.5061/dryad.wpzgmsbxd
title: Herpetological richness and diversity in an offshore archipelago of the Tropical Eastern Pacific

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: <strong>Herpetological Surveys</strong>
 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). <strong>Data
 Analysis</strong> 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 <em>vegan</em> 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 <em>BiodiversityR</em> (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 ± <em>SD </em>(range) unless otherwise indicated.
description: # Herpetological richness and diversity in an offshore archipelago of the
 Tropical Eastern Pacific This README file was generated on 2025-02-18 by
 Eric E. Flores. GENERAL INFORMATION Title of Dataset: Herpetological
 richness and diversity in an offshore archipelago of the Tropical Eastern
 Pacific 1. Author Information A. Principal Investigator Contact
 Information Name: Eric E. Flores Institution: Coiba Scientific Station
 (COIBA AIP) Address: Gustavo Lara street, building 145B, City of
 Knowledge, Clayton, PO Box 0843-01853, Panama, Republic of Panama 2.
 Email: [eflores@coiba.org.pa](mailto:eflores@coiba.org.pa) B. Associate or
 Co-investigator Contact Information Name: NA Institution: NA Address: NA
 Email: NA 3\. Date of data collection (single date, range, approximate
 date): 2019-2023 4\. Geographic location of data collection: Coiba
 National Park, Panama 5\. Information about funding sources that supported
 the collection of the data: Coiba Scientific Station (COIBA AIP), internal
 grant award SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on
 the data: CC0 1.0 Universal (CC0 1.0) Public Domain 2. Links to
 publications that cite or use the data: None 3. Links to other publicly
 accessible locations of the data: None 4. Links/relationships to ancillary
 data sets: None 5. Was data derived from another source? No A. If yes,
 list source(s): NA 6. Recommended citation for this dataset: Flores De
 Gracia, Eric Enrique (2025). Herpetological richness and diversity in an
 offshore archipelago of the Tropical Eastern Pacific [Dataset]. Dryad. 7.
 DATA & FILE OVERVIEW 8. File List: A) Mainland_rept_corr.txt B)
 Mainland_amph_corr.txt C) Canales_rept_corr.txt D) Rancheria_rept_corr.txt
 E) Rancheria_amph_corr.txt F) Coiba_PNC_rept_corr.txt G)
 Coiba_PNC_amph_corr.txt H) Jicaron_rept_corr.txt I) Jicaron_amph_corr.txt
 J) Dissimilarity_rept.txt K) Dissimilarity_amph.txt 9. Relationship
 between files, if important: None 10. Additional related data collected
 that was not included in the current data package: None 11. Are there
 multiple versions of the dataset? No A. If yes, name of file(s) that was
 updated: NA (not applicable) i. Why was the file updated? NA (not
 applicable) ii. When was the file updated? NA (not applicable)
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Mainland_rept_corr.txt 12. Number of
 variables: 25 13. Number of cases/rows: 30 14. Variable List: o Number of
 individuals of each reptile species (row) in each transect 15. Missing
 data codes: NA (not applicable) 16. Specialized formats or other
 abbreviations used: This format is to be used with EstimateS software to
 calculate species richness and diversity values.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Mainland_amph_corr.txt 17. Number of
 variables: 25 18. Number of cases/rows: 12 19. Variable List: o Number of
 individuals of each amphibian species (row) in each transect 20. Missing
 data codes: None 21. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Canales_rept_corr.txt 22. Number of
 variables: 4 23. Number of cases/rows: 30 24. Variable List: o Number of
 individuals of each reptile species (row) in each transect 25. Missing
 data codes: None 26. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Rancheria_rept_corr.txt 27. Number of
 variables: 4 28. Number of cases/rows: 30 29. Variable List: o Number of
 individuals of each reptile species (row) in each transect 30. Missing
 data codes: None 31. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Rancheria_amph_corr.txt 32. Number of
 variables: 4 33. Number of cases/rows: 12 34. Variable List: o Number of
 individuals of each amphibian species (row) in each transect 35. Missing
 data codes: NA (not applicable) 36. Specialized formats or other
 abbreviations used: This format is to be used with EstimateS software to
 calculate species richness and diversity values.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Coiba_PNC_rept_corr.txt 37. Number of
 variables: 30 38. Number of cases/rows: 30 39. Variable List: o Number of
 individuals of each reptile species (row) in each transect 40. Missing
 data codes: NA (not applicable) 41. Specialized formats or other
 abbreviations used: This format is to be used with EstimateS software to
 calculate species richness and diversity values.
 \#################################################### DATA-SPECIFIC
 INFORMATION FOR: Coiba_PNC_amph_corr.txt 42. Number of variables: 30 43.
 Number of cases/rows: 12 44. Variable List: o Number of individuals of
 each amphibian species (row) in each transect 45. Missing data codes: NA
 (not applicable) 46. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#################################################### DATA-SPECIFIC
 INFORMATION FOR: Jicaron_rept_corr.txt 1. Number of variables: 6 2. Number
 of cases/rows: 30 3. Variable List: o Number of individuals of each
 reptile species (row) in each transect 4. Missing data codes: NA (not
 applicable) 5. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#################################################### DATA-SPECIFIC
 INFORMATION FOR: Jicaron_amph_corr.txt 1. Number of variables: 6 2. Number
 of cases/rows: 12 3. Variable List: o Number of individuals of each
 amphibian species (row) in each transect 4. Missing data codes: NA (not
 applicable) 5. Specialized formats or other abbreviations used: This
 format is to be used with EstimateS software to calculate species richness
 and diversity values.
 \#################################################### DATA-SPECIFIC
 INFORMATION FOR: Dissimilarity_rept.txt 1. Number of variables: 37 2.
 Number of cases/rows: 5 3. Variable List: o Absence (0) presence (1) of
 each reptile species in every island. 4. Missing data codes: NA (not
 applicable) 5. Specialized formats or other abbreviations used: This
 format is to be used with the package vegan in R statistical software
 Jaccard dissimilarity values.
 \#################################################### DATA-SPECIFIC
 INFORMATION FOR: Dissimilarity_amph.txt 2\. Number of variables: 21 3\.
 Number of cases/rows: 4 4\. Variable List: o Absence (0) presence (1) of
 each amphibian species in every island. 5\. Missing data codes: NA (not
 applicable) 6\. Specialized formats or other abbreviations used: This
 format is to be used with the package vegan in R statistical software to
 calculate Jaccard dissimilarity values. Version changes 18-February-2025:
 Abstract section was updated. Method section was updated. Added new
 versions of files: Mainland_rept_corr.txt; Mainland_amph_corr.txt,
 Coiba_PCN_amph_corr.txt; Coiba_PCN_rept_corr.txt; Canales_rept_corr.txt;
 Rancheria_rept_corr.txt; Rancheria_amph_corr.txt; Coiba_PNC_rept_corr.txt;
 Coiba_PNC_amph_corr.txt; Jicaron_rept_corr.txt; Jicaron_amph_corr.txt;
 Dissimilarity_rept.txt. The word ‘venue’ was replaced by the word
 ´location´ to the Table_S1.docx and in Table_S2.docx. No change was made
 to Table_S3.docx and Table_S4.docx.