Amphibians on the hotspot: Molecular biology and conservation in the South American Atlantic Rainforest
Autoři:
Cesar R. L. Amaral aff001; Anna C. S. Chaves aff001; Vitor N. T. Borges Júnior aff001; Filipe Pereira aff002; Bruna M. Silva aff001; Dayse A. Silva aff001; António Amorim aff003; Elizeu F. Carvalho aff001; Carlos F. D. Rocha aff001
Působiště autorů:
Departamento de Ecologia, Instituto de Biologia Roberto Alcantara Gomes, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
aff001; Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
aff002; Instituto de Patologia Molecular e Imunologia (IPATIMUP) / Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
aff003; Faculdade de Ciências, Universidade do Porto, Porto, Portugal
aff004
Vyšlo v časopise:
PLoS ONE 14(10)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0224320
Souhrn
Amphibians are the focus of a recent debate and public attention owing to the global decline in their populations worldwide. Amphibians are one of the most threatened and poorly known groups of vertebrates in several geographic areas, even though they play a central role in their own ecosystems. At different levels, amphibians make their contribution to proper ecosystem functioning. They act as regulators of the food web and nutrient cycling, and they also provide several valuable ecosystem services, e.g., as a food source and as animal models for lab research. In this sense, it seems clear that the maintenance of amphibian diversity should be one of the major goals for the several countries where their population decline is observed. However, we are still struggling with the very first step of this process, i.e., the correct identification of the amphibian species diversity. Over the past few decades, research on molecular identification of amphibians using DNA barcoding has encountered some difficulties related to high variability in the mitochondrial genome of amphibians, and a research gap is noticeable in the literature. We herein evaluated both COI and 16S rRNA mitochondrial genes for the molecular identification of frogs and tadpoles in a large fragment of the South American Atlantic Rainforest in Rio de Janeiro, Brazil. Our results suggest that both COI and 16S rRNA are informative markers for the molecular identification of the amphibian specimens with all specimens unambiguously identified at the species level. We also made publicly available 12 new sequences of Atlantic Rainforest amphibian species for the first time, and we discussed some conservation issues related to amphibians within the Atlantic Rainforest domains in the state of Rio de Janeiro, Brazil.
Klíčová slova:
Species diversity – Amphibians – Frogs – Conservation science – Ribosomal RNA – DNA barcoding – Tadpoles – Rainforests
Zdroje
1. Amphibiaweb (2019) Amphibiaweb: information on amphibian biology and conservation. Berkeley, California. Amphibiaweb—http://amphibiaweb.org/. (Accessed: April 19, 2019).
2. Segalla MV, Caramaschi U, Cruz CAG, Grant T, Haddad CFB, Garcia PCA, Berneck BVM, Langone JA (2016) Brazilian amphibians: list of species. Herpetologia Brasileira, 5, 34–46.
3. SBH (2010) Brazilian amphibians–list of species. http://www.sbherpetologia.org.br. (accessed: April 19, 2019).
4. Haddad CFB, Toledo LF, Prado CPA, Loebmann D, Gasparini L, Sazima I (2013) Guia dos anfíbios da Mata Atlantica–Diversidade e Biologia. São Paulo, Anolis Books.
5. Ribeiro MC, Metzger JP, Martensen AC, Ponzoni FJ, Hirota MM (2009) The Brazilian Atlantic Forest: How much is left, and how is the remaining forest distributed? Implication for conservation. Biological Conservation, 142, 1144–1156.
6. Mittermeier RA, Gil RP, Hoffman M, Pilgrim J, Brooks T, Mittermeier CG, Lamoreux J, Fonseca GAB (2005) Hotspots revisited: earth’s biologically richest and most endangered terrestrial ecoregions. Chicago, University of Chicago Press.
7. Bergallo HG, Uzêda MC, Fidalgo ECC, Alves MAS, Rocha CFD, van Sluys M, Correa e Castro TC, Bebianno MC, Santos MA & Cozzolino ACR (2009) Conservação da biodiversidade da Mata Atlântica no estado do Rio de Janeiro: uma nova abordagem. In: Bergallo HG, Uzêda MC, Fidalgo ECC, Alves MAS, Rocha CFD, van Sluys M, Correa e Castro TC, Bebianno MC, Santos MA & Cozzolino ACR (eds.) Estratégias e ações para a conservação da biodiversidade no Estado do Rio de Janeiro. Rio de Janeiro, Instituto Biomas, 23–32.
8. Jenkins CN, Pimm SL (2006) Definindo prioridades de conservação em um hotspot de biodiversidade global. In: Rocha CFD, Bergallo HG, van Sluys M, Alves MAS (eds.) Biologia da conservação: essências. São Carlos, RiMa. 41–52.
9. Nascimento JL, Campos IB (2011) Atlas da fauna brasileira ameaçada de extinção em unidades de conservação federais. Brasília, ICMBIO.
10. Rocha CFD, Bergallo HG, Alves MAS, van Sluys M (2005) Endemic and threatened tetrapods in the restingas of the biodiversity corridors of Serra do Mar and of the central of Mata Atlântica in eastern Brazil. Brazilian Journal of Biology, 65, 159–168.
11. Cruz CAG & Feio RN (2007) Endemismos em anfíbios em áreas de altitude na Mata Atlântica no sudeste do Brasil. In: Nascimento LB & Oliveira ME (eds.) Herpetologia no Brasil II. Belo Horizonte, Sociedade Brasileira de Herpetologia, 117–126.
12. van Sluys M, Cruz CAG, Vrcibradic D, Silva HR, Almeida-Gomes M, Rocha CFD (2009) Anfíbios nos remanescentes florestais de Mata Atlântica no Estado do Rio de Janeiro. In: Bergallo HG, Fidalgo ECC, Rocha CFD, Uzêda MC, Bebianno MC, Alves MAS, van Sluys M, Santos MA, Correa e Castro TC, Cozzolino ACR (eds.) Estratégias e ações para a conservação da biodiversidade no Estado do Rio de Janeiro. Rio de Janeiro, Instituto Biomas, 175–182.
13. Dorigo TA, Vrcbradic D, Rocha CFD (2018) The amphibians of the state of Rio de Janeiro, Brazil: an updated and commented list. Papéis Avulsos de Zoologia, 58, e20185805. doi: 10.11606/1807-0205/2018.58.05
14. Wilkie D, Shaw E, Rotberg F, Morelli G, Auzel P (2000) Roads, development, and conservation in the Congo Basin. Conservation Biology, 14, 1614–1622. doi: 10.1111/j.1523-1739.2000.99102.x
15. Gibbs HK, Ruesch AS, Achard F, Clayton MK, Holmgren P, Ramankutty N, et al. (2010) Tropical forests were the primary sources of new agricultural land in the 1980s and 1990s. Proceedings of the National Academy of Sciences of the Unites States of America, 107, 16732–16737. doi: 10.1073/pnas.0910275107 20807750
16. Osti M, Coad L, Fisher J, Bomhard B, Hutton J (2011) Oil and gas development in the World Heritage and wider protected area network in sub-Saharan Africa. Biodiversity and Conservation, 20, 1863–1877. doi: 10.1007/s10531-011-0056-6
17. Hof C, Araujo MB, Jetz W, Rahbek C (2011) Additive threats from pathogens, climate and land-use change for global amphibian diversity. Nature, 480, 516–519. doi: 10.1038/nature10650 22089134
18. Stuart SN, Chanson JS, Cox NA, Young BE, Rodrigues ASL, Fischman DL, Waller RW (2004) Status and trends of amphibian declines and extinctions worldwide. Science, 306, 1783–1786. doi: 10.1126/science.1103538 15486254
19. IUCN (2015) The IUCN Red List of Threatened Species <http://www.iucnredlist.org>. Downloaded on 19 November2015.
20. Cortés-Gomez AM, Ruiz-Agudelo CA, Valencia-Aguilar A, Ladle RJ (2015) Ecological functions of neotropical amphibians and reptiles: a review. Universitas Scientiarum, 20, 229–245.
21. Hocking DJ, Babbitt KJ (2014) Amphibian contributions to ecosystem services. Herpetological Conservation and Biology, 9, 1–17.
22. Warkentin IG, Bickford D, Sodhi NS, Bradshaw CJA (2009) Eating frogs to extinction. Conservation Biology, 23, 1056–1059. doi: 10.1111/j.1523-1739.2008.01165.x 19210303
23. Deichmann JL, Mulcahy DG, Vanthomme H, Tobi E, Wynn AH, Zimkus BM, et al. (2017) How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation. PLoSONE, 12, e0187283. doi: 10.1371/journal.pone.0187283 29131846
24. Duellman WE, Trueb L (1994) Biology of Amphibians. Baltimore and London. McGraw-Hill.
25. Becker CG, Fonseca CR, Haddad CFB, Batista RF, Prado PI (2007) Habitat split and the global decline of amphibians. Science, 318, 1775–1777. doi: 10.1126/science.1149374 18079402
26. Almeida-Gomes M, Rocha CFD (2014) Landscape connectivity may explain anuran species distribution in an Atlantic forest fragmented area. Landscape Ecology, 29, 29–40.
27. Welsh HH, Ollivier LM (1998) Stream amphibians as indicators of ecosystem stress: a case study from California’s redwoods. Ecological Applications, 8, 1118–1132.
28. Alford RA, Richards SJ (1999) Global amphibian declines: a problem in applied ecology. Annual Review of Ecology and Systematics. 30, 133–165. doi: 10.1146/annurev.ecolsys.30.1.133
29. Welsh HH, Droege S (2001) A case for using plethodontid salamanders for monitoring biodiversity and ecosystem integrity of North American forests. Conservation Biology, 15, 558–569.
30. Davic RD, Welsh HH (2004) On the ecological role of salamanders. Annual Review of Ecology and Systematics, 35, 405–434. doi: 10.1146/annurev.ecolsys.35.112202.130116
31. Vences M, Van der Meijden A, Chiari Y, Vieites DR (2005a) Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians. Frontiers in Zoology, 2.
32. Larson PM, de Sá RO (1998) Chondrocranial morphology of Leptodactylus larvae (Leptodactylidae: Leptodactylinae): its utility in phylogenetic reconstruction. Journal of Morpholology, 238, 287–305.
33. Provete DB, Garey MV, Da Silva FR, Jordani MX (2012) Knowledge gaps and bibliographical revision about descriptions of free-swimming anuran larvae from Brazil. North-Western Journal of Zoology, 8, 283–286.
34. Lips KR, Savage JM (1996) Key to known Tadpoles (Amphibia: Anura) of Costa Rica. Studies on Neotropical Fauna and Environments, 31, 17–26.
35. Altig R, McDiarmid RW (1999) Diversity: Familial and Generic Characterizations. In Tadpoles. In: McDiarmid RW & Altig R (eds.) The Biology of Anuran Larvae. University of Chicago Press, Chicago and London, 295–337.
36. Rossa-Feres DC, Nomura F (2006) Characterization and taxonomic key for tadpoles (Amphibia: Anura) from the northwestern region of São Paulo State, Brazil. Biota Neotropica, 5. doi: 10.1590/S1676-06032006000100014
37. McDiarmid RW, Altig R (1999) Tadpoles: The biology of Anuran Larvae. University of Chicago Press.
38. Natale GS, Alcalde L, Herrera R, et al. (2011) Underwater acoustic communication in the macrophagic carnivorous larvae of Ceratophrys ornata (Anura: Ceratophryidae). Acta Zoologica, 92, 46–53.
39. Laia RC, Rocha CFD(2012). Adults and tadpoles of species of Hylodidae (Anura): History and taxonomy perspectives. Zoologia, 29, 89–94.
40. Berger L, Speare R, Daszak P, Green DE, Cunningham AA, Goggin CL, Slocombe R, Ragan MA, Hyatt AD, McDonald KR, Hines HB, Lips KR, Marantelli G, Parkes H. (1998) Chytridiomycosis causes amphibian mortality associated with population declines in the rainforests of Australia and Central America. Proceedings of the National Academy of Sciences of the United States of America, 95, 9031–9036. doi: 10.1073/pnas.95.15.9031 9671799
41. Daszak P, Cunningham AA, Hyatt AD (2003) Infectious disease and amphibian population declines. Diversity and Distributions, 9, 141–150.
42. Vences M, Thomas M, Bonett RM, Vieites DR (2005b) Deciphering amphibian diversity through DNA barcoding: Chances and challenges. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1859–1868.
43. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society B Biological Sciences, 270, 313–321.
44. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology, 54, 852–859. doi: 10.1080/10635150500354886 16243770
45. Golding RDH, Hebert PDN (2009) Preface. Molecular Ecology Resources, 9(Suppl.1), iv–vi.
46. Smith MA, Poyarkov NA Jr, Hebert PD (2007) DNA barcoding amphibians: take the chance, meet the challenge. Molecular Ecology Notes, 8, 235–46.
47. Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM (2004) Identification of birds through DNA barcodes. PLoS Biology, 2, 1657–1663.
48. Kerr KCR, Lijtmaer DA, Barreira AS, Hebert PDN, Tubaro PL (2009) Probing evolutionary patterns in Neotropical birds through DNA barcodes. PloSONE 4, e4379.
49. Jämergren J, Schander C, Sneli JA, Ronningen V, Young CM (2007) Four genes, morphology and ecology: distinguishing a new species of Acesta (Mollusca; Bivalvia) from the Gulf of Mexico. Marine Biology, 152, 43–55.
50. Janzen DH, Hajibabaei M, Burns JM (2005) Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 270, 96–99.
51. Silva-Brandão KL, Lyra ML, Freitas AVL (2009) Barcoding lepidoptera: current situation and perspectives on the usefulness of a contentious technique. Neotropical Entomology, 38, 441–451. 19768260
52. Barret RDH, Hebert PDN (2005) Identifying spiders through DNA barcodes. Canadian Journal of Zoology, 83, 481–491.
53. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN (2005) DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1847–1857.
54. Amaral CR, Brito PM, Silva DA, Carvalho EF (2013) A new cryptic species of South American freshwater pufferfish of the genus Colomesus (Tetraodontidae), based on both morphology and DNA data. PloS One, 8, e74397. doi: 10.1371/journal.pone.0074397 24040239
55. Borisenko AB, Lim BK, Ivanova NV, Hanner RH, Hebert PDN (2008) DNA barcoding in surveys of small mammal communities: a field study in Suriname. Molecular Ecology Resources, 8, 471–479. doi: 10.1111/j.1471-8286.2007.01998.x 21585824
56. Vieites DR, Wollenbergb KC, Andreone F, Kohler J, Glaw F, Vences M (2009) Vast underestimation of Madagascar’s biodiversity evidenced by an integrative amphibian inventory. Proceedings of the National Academy of Sciences of the Unites States of America, 106, 8267–8272.
57. Vences M, Gehara M, Köhler J, Glaw F (2012) Description of a new Malagasy treefrog (Boophis) occurring syntopically with its sister species, and a plea for studies on non-allopatric speciation in tropical amphibians. Amphibia-Reptilia, 33, 503–520.
58. Verdade VK, Valdujo PH, Carnaval AC, Schiesari L, Toledo LF, et al. (2012) A leap further: the Brazilian amphibian conservation action plan. Alytes, 29, 8–43.
59. Almeida-Gomes M, Siqueira CC, Borges-Junior VNT, Vrcibradic D, Fusinatto LA, Rocha CFD (2014) Herpetofauna of the Reserva Ecológica de Guapiaçu (REGUA) and its surrounding areas, in the state of Rio de Janeiro, Brazil. Biota Neotropica, 14(3), e20130078. doi: 10.1590/1676-0603007813
60. Palumbi SR (1996) Nucleic acids II: the polymerase chain reaction. Molecular Systematics, 205–247.
61. Lyra ML, Hadadd CFB, Azeredo-Espin AML (2017) Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers. Molecular Ecology, 17, 966–980. doi: 10.1111/1755-0998.12648 28029226
62. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA: Molecular evolutionary genetics analysis using Maximum Likelihood, evolutionary distance, and Maximum Parsimony methods. Molecular Biology and Evolution, 10, 1093.
63. van Sluys M, Cruz CAG, Vrcibradic D, Silva HR, Almeida-Gomes M, Rocha CFD (2009) Anfíbios nos remanescentes florestais de Mata Atlântica no Estado do Rio de Janeiro. In: Bergallo HG, Fidalgo ECC, Rocha CFD, Uzêda MC, Bebianno MC, Alves MAS, van Sluys M, Santos MA, Correa e Castro TC, Cozzolino ACR (eds.) Estratégias e ações para a conservação da biodiversidade no Estado do Rio de Janeiro. Rio de Janeiro, Instituto Biomas, 175–182.
64. Arntzen JW (1989) The identification of eggs of some species of palaearctic newts (genus Triturus) by starch gel electrophoresis. Isozyme Bulletin. 22, 69.
65. Veith M, Kosuch J, Feldmann R, Martens H, Seitz A (2000) A test for correct species declaration of frog legs imports from Indonesia into the European Union. Biodiversity Conservation, 9, 333–341. doi: 10.1023/A:1008906918236
66. Wilson AC, Maxson LR, Sarich VM (1974) Two types of molecular evolution. Evidence from studies of interspecific hybridization. Proceedings of the National Academy of Sciences of the Unites States of America, 71, 2843–2847.
67. Heyer WR, McDiarmid RW, Weigmann DL (1975) Tadpoles, predation, and pond habitats in the tropics. Biotropica, 7, 100–111.
68. Fatorelli PC & Rocha CFD (2008) O que molda a distribuição das guildas de girinos tropicais? Quarenta anos de busca por padrões. Oecologia brasiliensis, 12, 733–742.
69. Wiens JJ, & Graham CH (2005) Niche conservatism: integrating evolution, ecology, and conservation biology. Annual Review of Ecology, Evolution, and Systematics, 36, 519–539.
70. Thomas M, Raharivololoniaina L, Glaw F, Vences M, Vieites D.R (2005) Montane tadpoles in Madagascar: molecular identification and description of the larval stages of Mantidactylus elegans, Mantidactylus madecassus, and Boophis laurenti from the Andringitra Massif. Copeia, 1, 74–183.
Článok vyšiel v časopise
PLOS One
2019 Číslo 10
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Nejasný stín na plicích – kazuistika
- Masturbační chování žen v ČR − dotazníková studie
- Úspěšná resuscitativní thorakotomie v přednemocniční neodkladné péči
- Fixní kombinace paracetamol/kodein nabízí synergické analgetické účinky
Najčítanejšie v tomto čísle
- Correction: Low dose naltrexone: Effects on medication in rheumatoid and seropositive arthritis. A nationwide register-based controlled quasi-experimental before-after study
- Combining CDK4/6 inhibitors ribociclib and palbociclib with cytotoxic agents does not enhance cytotoxicity
- Experimentally validated simulation of coronary stents considering different dogboning ratios and asymmetric stent positioning
- Prevalence of pectus excavatum (PE), pectus carinatum (PC), tracheal hypoplasia, thoracic spine deformities and lateral heart displacement in thoracic radiographs of screw-tailed brachycephalic dogs