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Looking to the past and the future: were the Madeira River rapids a geographical barrier to the boto (Cetacea: Iniidae)?


In the present study we tested if a series of 18 rapids on the upper Madeira River form an effective barrier to gene flow, and in particular if they delimit the distribution of the boto Inia boliviensis—which it is believed to occurs only in the Bolivian sub-basin, above the rapids—and I. geoffrensis, which occurs throughout the Amazon basin and below the upper Madeira River rapids. We analyzed 125 individuals from the Madeira River basin sampled from upstream and downstream of the rapids. As the two species are morphologically similar, we used diagnostic molecular characters from known reference specimens to assign individuals to species. We observed that all individuals of Inia from the Bolivian sub-basin up to almost the mouth of the Madeira River belong to the species I. boliviensis. Therefore we concluded that the rapids do not delimit the distribution of I. boliviensis upstream and I. geoffrensis downstream of the rapids as previously hypothesized. Since we registered I. boliviensis along almost the entire length of the Madeira River, we estimated gene flow, time of divergence and effective population sizes of the upstream (Bolivian) and downstream (Madeira River) groups of I. boliviensis using IMa2. We concluded that gene flow is uni-directional from the upstream to the downstream group. Divergence time between the two groups was estimated to have occurred ~122 thousand years ago. The coalescent effective population size for the upstream group was estimated at ~131 thousand individuals, while for the downstream group it was estimated at ~102 thousand individuals. Recently two dams have been constructed in the region of the rapids; neither has a mechanism that will maintain connectivity between the upstream and downstream regions, and together with anthropogenic alterations to the hydrodynamic regime and ecology of the river will likely pose serious long-term and short-term consequences for I. boliviensis and other aquatic taxa.

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    After this paper was accepted, a third species Inia araguaiaensis was described from the Araguaia-Tocantins River basin (Hrbek et al. 2014).


  1. Akaike H (1974) A new look at the statistical model identification. IEEE Trans Automat Contr 19:716–723. doi:10.1109/TAC.1974.1100705

    Article  Google Scholar 

  2. Alter SE, Rynes E, Palumbi SR (2007) DNA evidence for historic population size and past ecosystem impacts of gray whales. Proc Natl Acad Sci USA 104:15162–15167. doi:10.1073/pnas.0706056104

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  3. Banguera-Hinestroza E, Cárdenas H, Ruiz-García M et al (2002) Molecular identification of evolutionarily significant units in the Amazon River dolphin Inia sp. (Cetacea: Iniidae). J Hered 93:312–322. doi:10.1093/jhered/93.5.312

    CAS  PubMed  Article  Google Scholar 

  4. Best RC, da Silva VMF (1989a) Amazon river dolphin, boto Inia geoffrensis (de Blainville, 1817). In: Perrin WF, Brownell Jr RL, Kaiya Z, Jionkang L (eds) Handb. Mar. Mamm. River Dolphins Larg. Toothed Whales. Academic Press, London, pp 23–34

  5. Best RC, da Silva VMF (1989b) Biology, status and conservation of Inia geoffrensis in the Amazon and Orinoco River basins. In: Perrin WF, Brownell Jr RL, Kaiya Z, Jionkang L (eds) Biol. Conserv. River Dolphins. IUCN, Gland, Switzerland, pp 23–34

  6. Best RC, da Silva VMF (1993) Inia geoffrensis. Mamm Species 426:1–8

    Google Scholar 

  7. Casinos A, Ocaña J (1979) A craniometrical study of the genus Inia D’Orbigny, 1834, Cetacea, Platanistoidea. Saugetierkd Mitteilung 27:194–206

    Google Scholar 

  8. Cella-Ribeiro A, Torrente-Vilara G, Hungria DB, Oliveira M de (2013) As corredeiras do Rio Madeira. Peixes do Rio Madeira. pp 47–53

  9. FURNAS, Construtora Norberto Odebrecht S.A., LEME Engenharia (2005) Estudo de impacto ambiental de aproveitamentos hidrelétricos Santo Antônio e Jirau, Rio Madeira - RO. 8 Vols

  10. D’Orbigny MA (1834) Notice sur un nouveau genre de cetacé des rivieres du centre de l’Amerique meridionale. Nouv Ann du Mus d’Historie Nat Paris 3:28–36

    Google Scholar 

  11. Da Silva VMF (1994) Aspects of the biology of the Amazonian dolphins genus Inia and Sotalia fluviatilis. Ph.D. Thesis, The Cambridge University, Cambridge, UK, pp 327

  12. Da Silva VMF (2009) Amazon River Dolphin (Inia geoffrensis). In: Perrin WF, Wursig B, Thewissen JGM (eds) Encycl. Mar. Mamm. Academic Press, London, UK, pp 18–20

  13. Da Silva VMF, Martin AR (2000) A study of the boto, or Amazon River dolphin (Inia geoffrensis), in the Mamiraua Reserve, Brazil: Operation and techniques. Biol. Conserv. Freshw. Cetaceans Asia. Occas. Pap. IUCN, Species Surviv. Comm. No. 23 23:

  14. Drummond AJ, Ashton B, Buxton S, et al. (2012) Geneious v5.6.3.

  15. Energia Sustentável do Brasil (2010) Energia Sustentável do Brasil web page

  16. Energia Sustentável do Brasil (2012) Relatório técnico do Programa de Conservação da Fauna Silvestre na área de influência da AHE Jirau. 16

  17. Espurt N, Baby P, Brusset S et al (2007) How does the Nazca Ridge subduction influence the modern Amazonian foreland basin? Geology 35:515–518. doi:10.1130/G23237A.1

    Article  Google Scholar 

  18. Espurt N, Baby P, Brusset S, et al. (2010) The Nazca Ridge and uplift of the Fitzcarrald Arch: implications for regional geology in northern South America. In: Hoorn C, Wesselingh FP (eds) Amaz. Landsc. Species Evol. A Look into Past. Wiley-Blackwell, pp 89–100

  19. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. doi:10.1111/j.1755-0998.2010.02847.x

    PubMed  Article  Google Scholar 

  20. Farias IP, Torrico JP, García-Dávila C et al (2010) Are rapids a barrier for floodplain fishes of the Amazon basin? A demographic study of the keystone floodplain species Colossoma macropomum (Teleostei: characiformes). Mol Phylogenet Evol 56:1129–1135. doi:10.1016/j.ympev.2010.03.028

    PubMed  Article  Google Scholar 

  21. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package) version 3.5.

  22. Finer M, Jenkins CN (2012) Proliferation of hydroelectric dams in the Andean Amazon and implications for Andes-Amazon connectivity. PLoS One 7:e35126. doi:10.1371/journal.pone.0035126

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  23. Frankham R, Ballou JD, Briscoe DA (2004) A primer of conservation genetics. Cambridge University Press, Cambridge, UK, pp 220

  24. Gomez-Salazar C, Trujillo F, Portocarrero-Aya M, Whitehead H (2012) Population, density estimates, and conservation of river dolphins (Inia and Sotalia) in the Amazon and Orinoco river basins. Mar Mammal Sci 28:124–153. doi:10.1111/j.1748-7692.2011.00468.x

    Article  Google Scholar 

  25. Goulding M (1979) Ecologia de pesca do Rio Madeira. Editora INPA, Manaus, Brazil, pp 172

  26. Hamilton H, Caballero S, Collins AG, Brownell RL Jr (2001) Evolution of river dolphins. Proc R Soc Lond Ser B 268:549–556. doi:10.1098/rspb 2000.1385

    CAS  Article  Google Scholar 

  27. Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Lond Ser B 270:313–321. doi:10.1098/rspb 2002.2218

    CAS  Article  Google Scholar 

  28. Hey J, Nielsen R (2007) Integration with the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA 104:2785–2790. doi:10.1073/pnas.0611164104

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  29. Ho SYW, Phillips MJ, Cooper A, Drummond AJ (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol 22:1561–1568. doi:10.1093/molbev/msi145

    CAS  PubMed  Article  Google Scholar 

  30. Ho SYW, Shapiro B, Phillips MJ et al (2007) Evidence for time dependency of molecular rate estimates. Syst Biol 56:515–522. doi:10.1080/10635150701435401

    PubMed  Article  Google Scholar 

  31. Hollatz C, Vilaça ST, Redondo RAF et al (2011) The Amazon River system as an ecological barrier driving genetic differentiation of the pink dolphin (Inia geoffrensis). Biol J Linn Soc 102:812–827. doi:10.1111/j.1095-8312.2011.01616.x

    Article  Google Scholar 

  32. Hrbek T, Vasconcelos WR, Rebêlo GH, Farias IP (2008) Phylogenetic relationships of South American alligatorids and the Caiman of Madeira River. J Exp Zool Part A 309A:588–599. doi:10.1002/jez.430

    CAS  Article  Google Scholar 

  33. Hrbek T, da Silva VMF, Dutra N, Gravena W, Martin, AR, Farias IP (2014) A new species of river dolphin from Brazil or: how little do we know our biodiversity. PloS One 9(1):e0083623. doi:10.1371/journal.pone.0083623

  34. Jabot F, Etienne RS, Chave J (2008) Reconciling neutral community models and environmental filtering: theory and an empirical test. Oikos 117:1308–1320. doi:10.1111/j.2008.0030-1299.16724.x

    Article  Google Scholar 

  35. Jackson JA, Baker CS, Vant M et al (2009) Big and slow: phylogenetic estimates of molecular evolution in baleen whales (suborder Mysticeti). Mol Biol Evol 26:2427–2440. doi:10.1093/molbev/msp169

    CAS  PubMed  Article  Google Scholar 

  36. Junk WJ, Bayley PB, Sparks R (1989) The flood pulse concept in river-floodplain systems. Can Spec Publ Fish Aquat Sci 106:110–127

    Google Scholar 

  37. Khan KM, Naizi MS (1989) Distribution and population status of the Indus Dolphin, Platanista minor. In: Perrin WF, Brownell Jr RL, Kaiya Z, Jionkang L (eds) Biol. Conserv. River Dolphins. IUCN, Gland, Switzerland, pp 77–80

  38. Leatherwood S (1996) Distributional ecology and conservation status of river dolphins (Inia geoffrensis and Sotalia fluviatilis) in portions of the Peruvian Amazon. Texas A&M University Press, College Station, TX, pp 466

  39. Martin AR, da Silva VMF (2006) Sexual dimorphism and body scarring in the boto (Amazon River Dolphin) Inia geoffrensis. Mar Mammal Sci 22:25–33. doi:10.1111/j.1748-7692.2006.00003.x

    Article  Google Scholar 

  40. Muniz F (2012) Phylogeography and population genetics of the broad-snouted caiman (Paleosuchus palpebrosus) along the Madeira River and the Paraguay River basin (Pantanal). Masters Thesis, INPA, Manaus, Brazil, pp 98

  41. Pearse DE, Arndt AD, Valenzuela N et al (2006) Estimating population structure under nonequilibrium conditions in a conservation context: continent-wide population genetics of the giant Amazon River turtle, Podocnemis expansa (Chelonia: Podocnemididae). Mol Ecol 15:985–1006. doi:10.1111/j.1365-294X.2006.02869.x

    CAS  PubMed  Article  Google Scholar 

  42. Peixun C, Yuanyu H (1989) Distribution, population size and protection of Lipotes vexillifer. In: Perrin WF, Brownell Jr RL, Kaiya Z, Jionkang L (eds) Biol. Conserv. River Dolphins. IUCN, Gland, Switzerland, pp 81–85

  43. Pesole G, Gissi C, De Chirico A, Saccone C (1999) Nucleotide substitution rate of mammalian mitochondrial genomes. J Mol Evol 48:427–434. doi:10.1007/PL00006487

    CAS  PubMed  Article  Google Scholar 

  44. Pilleri G, Gihr M (1977) Observations on the Bolivian, Inia boliviensis, (D’Orbigny, 1834) and the Amazonian bufeo, Inia geoffrensis (Blainville, 1817), with a description of a new subspecies (Inia geoffrensis humboldtiana). In: Pilleri G (ed) Investig. Cetacea. Bogotá, Colombia, pp 11–76

  45. Pilleri G, Gihr M (1981) Additional considerations on the taxonomy of the genus Inia. Investig Cetacea 12:15–27

    Google Scholar 

  46. Portocarrero-Aya M, Ferrer A, Lasso CA, et al. (2010) Status, distribution and conservation of the river dolphins Inia geoffrensis and Sotalia spp. in Venezuela. In: Trujillo F, Crespo E, van Damme PA, Usma JS (eds) Action Plan South Am. River Dolphins 2010-2020. WWF, Fundación Omacha, WDS, WDCS, Solamac, Bogotá, D.C., Colombia, pp 17–28

  47. Posada D (2008) jModelTest: phylogenetic Model Averaging. Mol Biol Evol 25:1253–1256. doi:10.1093/molbev/msn083

    CAS  PubMed  Article  Google Scholar 

  48. Queiroz LJ de, Torrente-Vilara G, Ohara WM, et al. (2013) Peixes do rio Madeira. Editora Dialeto, São Paulo, Brazil, pp 1169

  49. Reeves RR, Leatherwood S (2004) Dams and river dolphins: can they co-exist? Ambio 23:172–175

    Google Scholar 

  50. Richmond GM, Fullerton DS (1986) Summation of quaternary glaciations in the United States of America. Quat Sci Rev 5:183–196. doi:10.1016/0277-3791(86)90184-8

    Article  Google Scholar 

  51. Roy M, Clark PU, Barendregt RW et al (2004) Glacial stratigraphy and paleomagnetism of late Cenozoic deposits of the north-central United States. Geol Soc Am Bull 116:30. doi:10.1130/B25325.1

    CAS  Article  Google Scholar 

  52. Salzburger W, Ewing GB, Von Haeseler A (2011) The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Mol Ecol 20:1952–1963. doi:10.1111/j.1365-294X.2011.05066.x

    PubMed  Article  Google Scholar 

  53. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Springs Harbor Laboratory Press, Cold Springs Harbor

    Google Scholar 

  54. Santo Antônio Energia (2011) Santo Antônio Energia web page

  55. Shrestha TK (1989) Biology, status and conservation oof the Ganges River Dolphin, Platanista gangetica, in Nepal. In: Perrin WF, Brownell Jr RL, Kaiya Z, Jionkang L (eds) Biol. Conserv. River Dolphins. IUCN, Gland, Switzerland, pp 70–76

  56. Smith BD, Braulik GT (2012) Platanista gangetica. In: IUCN Red List Threat. Species

  57. Smith BD, Reeves RR (2012) River cetaceans and habitat change: generalist resilience or specialist vulnerability? J Mar Biol 2012:1–11. doi:10.1155/2012/718935

    Article  Google Scholar 

  58. Tavera G, Aliaga-Rossel ER, van Damme PA, Crespo A (2010) Distribution and conservation status of the Bolivian river dolphin Inia boliviensis (d’Orbigny 1832). In: Trujillo F, Crespo E, van Damme PA, Usma JS (eds) Action Plan South Am. River Dolphins 2010-2020. WWF, Fundación Omacha, WDS, WDCS, Solamac, Bogotá, D.C., Colombia, pp 99–122

  59. Taylor BL, Chivers SJ, Larese J, Perrin WF (2007) Generation length and percent mature estimates for IUCN assessments of cetaceans, Administrative Report LJ-07-01, National Marine Fisheries Service, Southwest Fisheries Science Center. 24

  60. Templeton AR (2006) Population Genetics and Microevolutionary Theory. Wiley & Sons, New York, NY, pp 720

  61. Torrente-Vilara G, Zuanon J, Leprieur F, et al. (2011) Effects of natural rapids and waterfalls on fish assemblage structure in the Madeira River (Amazon Basin). Ecol Freshw Fish 20:588–597. doi: 10.1111/j.1600-0633.2011.00508.x

  62. Trujillo F, Aya MP, Gomez-Salazar C, et al. (2010) Status, conservation of the river dolphins Inia geoffrensis and Sotalia fluviatilis in the Orinoco and Amazonas basins in Colombia. In: Trujillo F, Crespo E, van Damme PA, Usma JS (eds) Action Plan South Am. River Dolphins 2010-2020. WWF, Fundación Omacha, WDS, WDCS, Solamac, Bogotá, D.C., Colombia, pp 29–58

  63. Tuomisto H, Ruokolainen K, Yli-Halla M (2003) Dispersal, environment, and floristic variation of western Amazonian forests. Science 299:241–244. doi: 10.1126/science.1078037

    Google Scholar 

  64. Turvey ST (2008) Witness to Extinction: How We Failed to Save the Yangtze River Dolphin. Oxford University Press, Oxford, UK, pp 256

  65. Turvey ST, Pitman RL, Taylor BL et al (2007) First human-caused extinction of a cetacean species? Biol Lett 3:537–540. doi:10.1098/rsbl 2007.0292

    PubMed Central  PubMed  Article  Google Scholar 

  66. Werle E, Schneider C, Renner M et al (1994) Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res 22:4354–4355

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  67. Willis SC, Macrander J, Farias IP, Ortí G (2012) Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data. BMC Evol Biol 12:96. doi:10.1186/1471-2148-12-96

    PubMed Central  PubMed  Article  Google Scholar 

  68. Xiong Y, Brandley MC, Xu S et al (2009) Seven new dolphin mitochondrial 30 genomes and a time-calibrated phylogeny of whales. BMC Evol Biol 9:20. doi:10.1186/1471-2148-9-20

    PubMed Central  PubMed  Article  Google Scholar 

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This research was supported by grants from National Counsel of Technological and Scientific Development (CNPq) PPG7 557090/2005-0, CT-Amazônia 575603/2008-9 and Universal 483408/2009-3 and 482253/2012-6 to IPF, CNPq/Universal-482662/2013-1 to TH and the Scott Neotropical Fund and the Society for Marine Mammalogy to WG. Collecting permits were provided to IPF by IBAMA/ICMBIO (No. 11325-1 and No. 13462-1). The protocol for handling and removing tissue samples from live animals was approved by the Committee on the Ethics of Animal Use (Comissão de Ética do Uso de Animais—CEUA) of the National Research Institute of the Amazon (INPA).TH and IPF were supported by a Bolsa de Pesquisa scholarship from CNPq during the study and WG by a CNPq fellowship. We are grateful to the team of the Hydrogeochemistry laboratory of the Federal University of Rondônia (UNIR). We thank all the fishermen involved in the capture of the animals, Valéria Machado and Mario Nunes for their help in the field and the laboratory, and Luiz Cleyton Holanda Lobato for sharing his detailed knowledge of the Madeira-Mamoré-Guaporé River system.

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Correspondence to Tomas Hrbek.

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Gravena, W., Farias, I.P., da Silva, M.N.F. et al. Looking to the past and the future: were the Madeira River rapids a geographical barrier to the boto (Cetacea: Iniidae)?. Conserv Genet 15, 619–629 (2014).

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  • Inia
  • Amazon River dolphin
  • Gene flow
  • Species limits
  • Species distribution