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Evolutionary Ecology

, Volume 33, Issue 1, pp 111–148 | Cite as

Integrating phylogeography and ecological niche modelling to test diversification hypotheses using a Neotropical rodent

  • Arielli Fabrício MachadoEmail author
  • Mário Silva Nunes
  • Cláudia Regina Silva
  • Marcelo Augusto dos SantosJr.
  • Izeni Pires Farias
  • Maria Nazareth Ferreira da Silva
  • Marina Anciães
Original Paper

Abstract

Several hypotheses have been used to explain diversification in the Neotropics. Integrating evolution with ecology extends the scope of testing the frameworks of these hypotheses. We test diversification hypotheses by integrating phylogeography and ecological niche models (ENMs) using the rodent Hylaeamys megacephalus (Azara’s broad-headed oryzomys or large headed rice rat) of the Amazon and dry forests, as a model. We estimated divergence times, ancestral areas, diversification events, historical demography, haplotype sharing, and genetic distances based on the mitochondrial cytochrome b gene. We generated ENMs and tested for niche divergence between lineages; integrated genetic data to predict gene flow corridors; and projected paleodistributions for comparison with historical demography. We found high structuring in northern Amazonia on the left bank of the Amazon River, and less structure but secondary contact in southern Amazonia and dry forests. The Northern Amazonian lineage diverged from the other lineages through dispersal followed by vicariance due to the Amazon River about 1.35 Mya, while the Southern Amazonian and Cerrado lineages diverged through dispersal about 0.78 Mya. Paleodistribution models revealed expansions of dry forest lineages consistent with the Refugia Hypothesis, but not retraction for the humid forest lineage, which were not congruent with historical demography data. Niche divergence was not supported for the Northern Amazonian lineage, whereas habitat corridors linking current lineages suggest environmental continuity to their distributions that is concordant with a riverine barrier. In contrast, niche divergence was supported between the Southern Amazonian and Cerrado lineages, indicating that isolation followed by ecological divergence likely acted on this diversification. The recent Amazon River barrier and ecological differentiation observed here will surely provide insight for future studies and hypotheses of biodiversity diversification in the Neotropics. Studies that integrate evolution and ecology promise to disentangle alternative hypotheses and shed light on the biogeography of this megadiverse region.

Keywords

Biogeography Amazon River Neotropical rodent Riverine barrier Refugia Ecological speciation Niche conservatism 

Notes

Acknowledgements

We thank A. Townsend Peterson, Fernanda P. Werneck, Rafael N. Leite and Igor L. Kaeffer for help in delineating the project; Rafael N. Leite and Rogério Rossi for providing tissue samples; Cleuton L. Miranda for reviewing the manuscript and William T. Peçanha for help with phylogenetic analyses. We also thank the team from LEGAL for helping with molecular sampling and analyses, and Camila D. Ritter, Cristiane F. Marks and Tomas Hrbek for help with phylogenetic analyses and for reviewing this manuscript. Thanks got to Glenn H. Shepard and Erik Wild for helping with the English language. This research was supported by CNPq/FAPEAM/SISBIOTA (Rede BioPHAM) 563348/2010 to IPF and MNFS. This study is part of AFM’s Master’s thesis in the ecology graduate program of INPA, and was supported by a fellowship from CNPq. The authors declare no conflicts of interest.

Supplementary material

10682_2019_9968_MOESM1_ESM.docx (14 kb)
S1. Laboratory techniques used for amplification of mitochondrial cytochrome b gene sequence fragments. (DOCX 15 kb)
10682_2019_9968_MOESM2_ESM.xlsx (16 kb)
Table S2. Occurrence records for Hylaeamys megacephalus used for producing the ecological niche model (ENM) for the entire species. ID = identification number. The records with identification number 66, 68, 69, 90, 92 102, 104, 113 and 114 were added for the ENM of the Southern Amazonian lineage (black dots in Fig. 1). (XLSX 16 kb)

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Arielli Fabrício Machado
    • 1
    • 6
    Email author
  • Mário Silva Nunes
    • 2
  • Cláudia Regina Silva
    • 4
    • 5
  • Marcelo Augusto dos SantosJr.
    • 1
  • Izeni Pires Farias
    • 2
  • Maria Nazareth Ferreira da Silva
    • 3
  • Marina Anciães
    • 3
  1. 1.Programa de Pós-Graduação em EcologiaInstituto Nacional de Pesquisas da Amazônia – INPAManausBrazil
  2. 2.Laboratório de Evolução e Genética Animal - LEGALUniversidade Federal do Amazonas – UFAMManausBrazil
  3. 3.Coordenação de Pesquisas em Biodiversidade/COBIO e Coleções ZoológicasInstituto Nacional de Pesquisas da Amazônia – INPAManausBrazil
  4. 4.Programa de Pós-Graduação em Genética, Conservação e Biologia EvolutivaInstituto Nacional de Pesquisas da Amazônia – INPAManausBrazil
  5. 5.Laboratório de MamíferosInstituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá - IEPAMacapáBrazil
  6. 6.Phylogenetic and Functional Ecology Lab (LEFF)Porto AlegreBrazil

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