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Basset Y, Hajibabaei M, Wright MTG, Castillo AM, Donoso DA, Segar ST, Souto-Vilarós D, Soliman DY, Roslin T, Smith MA, Lamarre GPA, De León LF, Decaëns T, Palacios-Vargas JG, Castaño-Meneses G, Scheffrahn RH, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez Silva JA, Cruz MM, Galván AA, Barrios H. Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Sci Rep 2022; 12:10762. [PMID: 35750774 PMCID: PMC9232565 DOI: 10.1038/s41598-022-14915-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/15/2022] [Indexed: 11/09/2022] Open
Abstract
The soil fauna of the tropics remains one of the least known components of the biosphere. Long-term monitoring of this fauna is hampered by the lack of taxonomic expertise and funding. These obstacles may potentially be lifted with DNA metabarcoding. To validate this approach, we studied the ants, springtails and termites of 100 paired soil samples from Barro Colorado Island, Panama. The fauna was extracted with Berlese-Tullgren funnels and then either sorted with traditional taxonomy and known, individual DNA barcodes ("traditional samples") or processed with metabarcoding ("metabarcoding samples"). We detected 49 ant, 37 springtail and 34 termite species with 3.46 million reads of the COI gene, at a mean sequence length of 233 bp. Traditional identification yielded 80, 111 and 15 species of ants, springtails and termites, respectively; 98%, 37% and 100% of these species had a Barcode Index Number (BIN) allowing for direct comparison with metabarcoding. Ants were best surveyed through traditional methods, termites were better detected by metabarcoding, and springtails were equally well detected by both techniques. Species richness was underestimated, and faunal composition was different in metabarcoding samples, mostly because 37% of ant species were not detected. The prevalence of species in metabarcoding samples increased with their abundance in traditional samples, and seasonal shifts in species prevalence and faunal composition were similar between traditional and metabarcoding samples. Probable false positive and negative species records were reasonably low (13-18% of common species). We conclude that metabarcoding of samples extracted with Berlese-Tullgren funnels appear suitable for the long-term monitoring of termites and springtails in tropical rainforests. For ants, metabarcoding schemes should be complemented by additional samples of alates from Malaise or light traps.
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Affiliation(s)
- Yves Basset
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama.
- Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic.
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic.
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama.
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Michael T G Wright
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Anakena M Castillo
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Andhra Pradesh, 522 510, India
| | - David A Donoso
- Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Simon T Segar
- Agriculture and Environment Department, Harper Adams University, Newport, TF10 8NB, Shropshire, UK
| | - Daniel Souto-Vilarós
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague, Czech Republic
| | - Dina Y Soliman
- Centre for Biodiversity Genomics, Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G2W1, Canada
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - M Alex Smith
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - Greg P A Lamarre
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, 370 05, Ceske Budejovice, Czech Republic
| | - Luis F De León
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), P.O. Box 0843-01103, Panamá 5, Panama
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd., Boston, MA, 02125, USA
| | - Thibaud Decaëns
- CEFE, University of Montpellier, CNRS, EPHE, IRD, University Paul Valéry, Montpellier 3, Montpellier, France
| | - José G Palacios-Vargas
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Gabriela Castaño-Meneses
- Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Universidad Nacional Autónoma de México, Campus Juriquilla, Juriquilla 76230, Querétaro, Mexico
| | - Rudolf H Scheffrahn
- Fort Lauderdale Research & Education Center, 3205 College Avenue, Davie, FL, 33314, USA
| | - Marleny Rivera
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Filonila Perez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Ricardo Bobadilla
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | - Yacksecari Lopez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá, Panama
| | | | - Maira Montejo Cruz
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Angela Arango Galván
- Laboratorio de Ecología y Sistemática de Microartrópodos, Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Héctor Barrios
- Maestría de Entomología, Universidad de Panamá, 080814, Panama City, Republic of Panama
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Lamarre GPA, Pardikes NA, Segar S, Hackforth CN, Laguerre M, Vincent B, Lopez Y, Perez F, Bobadilla R, Silva JAR, Basset Y. More winners than losers over 12 years of monitoring tiger moths (Erebidae: Arctiinae) on Barro Colorado Island, Panama. Biol Lett 2022; 18:20210519. [PMID: 35382585 PMCID: PMC8984363 DOI: 10.1098/rsbl.2021.0519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Understanding the causes and consequences of insect declines has become an important goal in ecology, particularly in the tropics, where most terrestrial diversity exists. Over the past 12 years, the ForestGEO Arthropod Initiative has systematically monitored multiple insect groups on Barro Colorado Island (BCI), Panama, providing baseline data for assessing long-term population trends. Here, we estimate the rates of change in abundance among 96 tiger moth species on BCI. Population trends of most species were stable (n = 20) or increasing (n = 62), with few (n = 14) declining species. Our analysis of morphological and climatic sensitivity traits associated with population trends shows that species-specific responses to climate were most strongly linked with trends. Specifically, tiger moth species that are more abundant in warmer and wetter years are more likely to show population increases. Our study contrasts with recent findings indicating insect decline in tropical and temperate regions. These results highlight the significant role of biotic responses to climate in determining long-term population trends and suggest that future climate changes are likely to impact tropical insect communities.
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Affiliation(s)
- Greg P A Lamarre
- Department of Ecology, Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic.,Faculty of Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic.,ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá
| | - Nicholas A Pardikes
- Department of Ecology, Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic.,Department of Life and Earth Sciences, Perimeter College, Georgia State University, Atlanta, USA
| | - Simon Segar
- Agriculture and Environment Department, Harper Adams University, Newport, Shropshire TF10 8NB, UK
| | - Charles N Hackforth
- Department of Geography, University College London, Gower Street, London WC1E 6BT, UK
| | - Michel Laguerre
- Muséum National d'Histoire Naturelle, Département Systématique et Évolution, Entomologie, 57 rue Cuvier, Paris, France
| | - Benoît Vincent
- Muséum National d'Histoire Naturelle, Département Systématique et Évolution, Entomologie, 57 rue Cuvier, Paris, France
| | - Yacksecari Lopez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá
| | - Filonila Perez
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá
| | - Ricardo Bobadilla
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá
| | - José Alejandro Ramírez Silva
- ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá
| | - Yves Basset
- Department of Ecology, Institute of Entomology, Biology Centre, Czech Academy of Sciences, Ceske Budejovice 37005, Czech Republic.,Faculty of Sciences, University of South Bohemia, Ceske Budejovice, Czech Republic.,ForestGEO, Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panamá City, Republic of Panamá.,Maestria de Entomologia, Universidad de Panamá, Apartado 3366, Panamá 4, Panamá
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Roubik DW, Basset Y, Lopez Y, Bobadilla R, Perez F, Ramírez S. JA. Long‐term (1979–2019) dynamics of protected orchid bees in Panama. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- David W. Roubik
- Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Yves Basset
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
- Faculty of Science University of South Bohemia Budejovice Czech Republic
- Institute of Entomology Biology Centre of the Czech Academy of Sciences Budejovice Czech Republic
- Maestría de Entomología Universidad de Panamá Panama City Republic of Panama
| | - Yacksecari Lopez
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Ricardo Bobadilla
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - Filonila Perez
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
| | - José Alejandro Ramírez S.
- ForestGEO; Smithsonian Tropical Research Institute Balboa Republic of Panama
- Maestría de Entomología Universidad de Panamá Panama City Republic of Panama
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Basset Y, Donoso DA, Hajibabaei M, Wright MTG, Perez KHJ, Lamarre GPA, De León LF, Palacios-Vargas JG, Castaño-Meneses G, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Barrios H. Methodological considerations for monitoring soil/litter arthropods in tropical rainforests using DNA metabarcoding, with a special emphasis on ants, springtails and termites. MBMG 2020. [DOI: 10.3897/mbmg.4.58572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Robust data to refute or support claims of global insect decline are currently lacking, particularly for the soil fauna in the tropics. DNA metabarcoding represents a powerful approach for rigorous spatial and temporal monitoring of the taxonomically challenging soil fauna. Here, we provide a detailed field protocol, which was successfully applied in Barro Colorado Island (BCI) in Panama, to collect soil samples and arthropods in a tropical rainforest, to be later processed with metabarcoding. We also estimate the proportion of soil/litter ant, springtail and termite species from the local fauna that can be detected by metabarcoding samples obtained either from Berlese-Tullgren (soil samples), Malaise or light traps. Each collecting method detected a rather distinct fauna. Soil and Malaise trap samples detected 213 species (73%) of all target species. Malaise trap samples detected many ant species, whereas soil samples were more efficient at detecting springtail and termite species. With respect to long-term monitoring of soil-dwelling and common species (more amenable to statistical trends), the best combination of two methods were soil and light trap samples, detecting 94% of the total of common species. A protocol including 100 soil, 40 Malaise and 80 light trap samples annually processed by metabarcoding would allow the long-term monitoring of at least 11%, 18% and 16% of species of soil/litter ants, springtails and termites, respectively, present on BCI, and a high proportion of the total abundance (up to 80% of all individuals) represented by these taxa.
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Basset Y, Lamarre GP, Ratz T, Segar ST, Decaëns T, Rougerie R, Miller SE, Perez F, Bobadilla R, Lopez Y, Ramirez JA, Aiello A, Barrios H. The Saturniidae of Barro Colorado Island, Panama: A model taxon for studying the long-term effects of climate change? Ecol Evol 2017; 7:9991-10004. [PMID: 29238531 PMCID: PMC5723595 DOI: 10.1002/ece3.3515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/01/2017] [Accepted: 09/16/2017] [Indexed: 02/04/2023] Open
Abstract
We have little knowledge of the response of invertebrate assemblages to climate change in tropical ecosystems, and few studies have compiled long-term data on invertebrates from tropical rainforests. We provide an updated list of the 72 species of Saturniidae moths collected on Barro Colorado Island (BCI), Panama, during the period 1958-2016. This list will serve as baseline data for assessing long-term changes of saturniids on BCI in the future, as 81% of the species can be identified by their unique DNA Barcode Index Number, including four cryptic species not yet formally described. A local species pool of 60 + species breeding on BCI appears plausible, but more cryptic species may be discovered in the future. We use monitoring data obtained by light trapping to analyze recent population trends on BCI for saturniid species that were relatively common during 2009-2016, a period representing >30 saturniid generations. The abundances of 11 species, of 14 tested, could be fitted to significant time-series models. While the direction of change in abundance was uncertain for most species, two species showed a significant increase over time, and forecast models also suggested continuing increases for most species during 2017-2018, as compared to the 2009 base year. Peaks in saturniid abundance were most conspicuous during El Niño and La Niña years. In addition to a species-specific approach, we propose a reproducible functional classification based on five functional traits to analyze the responses of species sharing similar functional attributes in a fluctuating climate. Our results suggest that the abundances of larger body-size species with good dispersal abilities may increase concomitantly with rising air temperature in the future, because short-lived adults may allocate less time to increasing body temperature for flight, leaving more time available for searching for mating partners or suitable oviposition sites.
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Affiliation(s)
- Yves Basset
- Smithsonian Tropical Research InstituteAnconPanamá
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
- Maestria de EntomologiaUniversidad de PanamáPanama CityPanama
| | - Greg P.A. Lamarre
- Institute of Entomology, Biology CentreCzech Academy of ScienceCeske BudejoviceCzech Republic
| | - Tom Ratz
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Simon T. Segar
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
- Institute of Entomology, Biology CentreCzech Academy of ScienceCeske BudejoviceCzech Republic
| | - Thibaud Decaëns
- Centre d'Ecologie Fonctionnelle et EvolutiveUMR 5175, CNRS–Université Montpellier–Univesrsité Paul‐Valéry–EPHE–SupAgroMontpellier–INRA–IRDMontpellierFrance
| | - Rodolphe Rougerie
- Institut de Systématique Evolution, BiodiversitéUMR 7205, CNRS–MNHN–UPMC–EPHE–Sorbonne UniversitésParisFrance
| | - Scott E. Miller
- National Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
| | | | | | | | | | | | - Héctor Barrios
- Maestria de EntomologiaUniversidad de PanamáPanama CityPanama
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Basset Y, Barrios H, Segar S, Srygley RB, Aiello A, Warren AD, Delgado F, Coronado J, Lezcano J, Arizala S, Rivera M, Perez F, Bobadilla R, Lopez Y, Ramirez JA. The Butterflies of Barro Colorado Island, Panama: Local Extinction since the 1930s. PLoS One 2015; 10:e0136623. [PMID: 26305111 PMCID: PMC4549329 DOI: 10.1371/journal.pone.0136623] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022] Open
Abstract
Few data are available about the regional or local extinction of tropical butterfly species. When confirmed, local extinction was often due to the loss of host-plant species. We used published lists and recent monitoring programs to evaluate changes in butterfly composition on Barro Colorado Island (BCI, Panama) between an old (1923-1943) and a recent (1993-2013) period. Although 601 butterfly species have been recorded from BCI during the 1923-2013 period, we estimate that 390 species are currently breeding on the island, including 34 cryptic species, currently only known by their DNA Barcode Index Number. Twenty-three butterfly species that were considered abundant during the old period could not be collected during the recent period, despite a much higher sampling effort in recent times. We consider these species locally extinct from BCI and they conservatively represent 6% of the estimated local pool of resident species. Extinct species represent distant phylogenetic branches and several families. The butterfly traits most likely to influence the probability of extinction were host growth form, wing size and host specificity, independently of the phylogenetic relationships among butterfly species. On BCI, most likely candidates for extinction were small hesperiids feeding on herbs (35% of extinct species). However, contrary to our working hypothesis, extinction of these species on BCI cannot be attributed to loss of host plants. In most cases these host plants remain extant, but they probably subsist at lower or more fragmented densities. Coupled with low dispersal power, this reduced availability of host plants has probably caused the local extinction of some butterfly species. Many more bird than butterfly species have been lost from BCI recently, confirming that small preserves may be far more effective at conserving invertebrates than vertebrates and, therefore, should not necessarily be neglected from a conservation viewpoint.
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Affiliation(s)
- Yves Basset
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
- Faculty of Science, University of South Bohemia and Institute of Entomology, Biology Centre of Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
- Universidad de Panamá, Maestria de Entomologia, 080814, Panama City, Republic of Panama
- * E-mail:
| | - Héctor Barrios
- Universidad de Panamá, Maestria de Entomologia, 080814, Panama City, Republic of Panama
| | - Simon Segar
- Faculty of Science, University of South Bohemia and Institute of Entomology, Biology Centre of Czech Academy of Sciences, Branišovská 31, 370 05, České Budějovice, Czech Republic
| | - Robert B. Srygley
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
- Northern Plains Agricultural Lab, USDA-Agricultural Research Service, 1500 N. Central Ave., Sidney, Montana, 59270, United States of America
| | - Annette Aiello
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Andrew D. Warren
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, 3215 Hull Rd., P.O. Box 112710, Gainesville, Florida, 32611–2710, United States of America
| | - Francisco Delgado
- Universidad de Panamá, Centro Regional Universitario de Veraguas, Santiago, Republic of Panama
| | - James Coronado
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Jorge Lezcano
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Stephany Arizala
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Marleny Rivera
- Universidad de Panamá, Maestria de Entomologia, 080814, Panama City, Republic of Panama
| | - Filonila Perez
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Ricardo Bobadilla
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - Yacksecari Lopez
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
| | - José Alejandro Ramirez
- Smithsonian Tropical Research Institute, Apartado 0843–03092, Panama City, Republic of Panama
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