Comparative phylogeography of four Amazonian lineages of birds: accessing biogeographic patterns based on ultra-conserved elements

• Grant number: 14/00113-2
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: July 01, 2014
• End date: January 31, 2018
• Field of knowledge: Biological Sciences - Genetics - Animal Genetics
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Cristina Yumi Miyaki
• Grantee: Gregory Thom e Silva
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 12/50260-6 - Structure and evolution of the Amazonian biota and its environment: an integrative approach, AP.BTA.TEM
• Associated scholarship(s): 15/12551-7 - Comparative phylogeography of three "varzea" forest bird lineages: surveying new biogeographic patterns for Amazonia, BE.EP.DR

Abstract

The application of molecular biology has been contributing substantially to the knowledge of how historical processes shaped the high and complex Amazonian biodiversity. The development of this discipline has allowed the inclusion of more evolutionary features to analytical procedures, considerably changing the methods of interpretation of genetic data. Despite some biogeographical hypotheses suggest different scenarios for the formation of the Amazonian biodiversity, it is a consensus that simultaneous events of isolation and dispersion followed by divergence, allowed the existence of syntopic distinct lineages. In this context, comparative phylogeographic studies can contribute to a better understanding on how paleoenvironmental and paleoclimatic processes led the formation of the current biodiversity. Thus, we selected three lineages (species complexes; Thamnophilus nigrocinereus/cryptoleucus, Myrmoborus lugubris, Myrmotherula assimilis) of the family Thamnophilidae as models for a comparative phylogeographic study. The selected species are restricted of flooded forests (várzea) of the Amazon River and large tributaries, an environment poorly studied in phylogeographic approaches. Phylogenetic and population genetic analyses based on empirical and Approximate Bayesian Computation estimates will be applied to generate a spatial and temporal scenario of diversification of each lineage based on data generated by target enrichment of Ultra Conserved Elements (UCE) and by Sanger sequencing of mitochondrial genes. We intend to answer the following questions: 1) How in a temporal and spatial context the diversification patterns of the three species complexes were formed? 2) Are there spatial and temporal overlaps in the diversification processes of the studied lineages? 3) Which paleoenvironmental and paleoclimatic scenarios can explain the diversification of the studied lineages? (AU)

Scientific publications

(6)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

THOM, GREGORY; DO AMARAL, FABIO RAPOSO; HICKERSON, MICHAEL J.; ALEIXO, ALEXANDRE; ARAUJO-SILVA, LUCAS E.; RIBAS, CAMILA C.; CHOUERI, ERIK; MIYAKI, CRISTINA Y.. Phenotypic and Genetic Structure Support Gene Flow Generating Gene Tree Discordances in an Amazonian Floodplain Endemic Species. Systematic Biology, v. 67, n. 4, p. 700-718, JUL 2018. (11/50143-7, 15/12551-7, 13/50297-0, 14/00113-2, 11/23155-4, 12/50260-6)

THOM, GREGORY; RIBAS, CAMILA C.; SHULTZ, EDUARDO; ALEIXO, ALEXANDRE; MIYAKI, CRISTINA Y.. Population dynamics of Amazonian floodplain forest species support spatial variation on genetic diversity but not range expansions through time. Journal of Biogeography, v. 49, n. 10, p. 11-pg., 2022-09-08. (14/00113-2, 13/50297-0, 15/12551-7, 17/25720-7, 12/50260-6, 18/17869-3)

SILVA, SOFIA MARQUES; TOWNSEND PETERSON, A.; CARNEIRO, LINCOLN; TORTOLA BURLAMAQUI, TIBERIO CESAR; RIBAS, CAMILA C.; SOUSA-NEVES, TIAGO; MIRANDA, LEONARDO S.; FERNANDES, ALEXANDRE M.; D'HORTA, FERNANDO M.; ARAUJO-SILVA, LUCAS EDUARDO; et al. A dynamic continental moisture gradient drove Amazonian bird diversification. SCIENCE ADVANCES, v. 5, n. 7, JUL 2019. (14/00113-2, 12/50260-6)

THOM, GREGORY; XUE, ALEXANDER T.; SAWAKUCHI, ANDRE O.; RIBAS, CAMILA C.; HICKERSON, MICHAEL J.; ALEIXO, ALEXANDRE; MIYAKI, CRISTINA. Quaternary climate changes as speciation drivers in the Amazon floodplains. SCIENCE ADVANCES, v. 6, n. 11, MAR 2020. (13/50297-0, 17/25720-7, 14/00113-2, 18/17869-3, 12/50260-6, 15/12551-7)

DO AMARAL, FABIO RAPOSO; MALDONADO-COELHO, MARCOS; ALEIXO, ALEXANDRE; LUNA, LEILTON W.; DO REGO, PERICLES SENA; ARARIPE, JULIANA; SOUZA, THAINARA O.; SILVA, WEBER A. G.; THOM, GREGORY. Recent chapters of Neotropical history overlooked in phylogeography: Shallow divergence explains phenotype and genotype uncoupling in Antilophia manakins. Molecular Ecology, v. 27, n. 20, p. 4108-4120, OCT 2018. (13/50297-0, 17/25720-7, 14/00113-2, 15/18287-0, 15/12551-7, 16/11439-1, 11/23155-4, 11/50143-7)

CHOUERI, ERIK L.; GUBILI, CHRYSOULA; BORGES, SERGIO H.; THOM, GREGORY; SAWAKUCHI, ANDRE O.; SOARES, EMILIO A. A.; RIBAS, CAMILA C.. Phylogeography and population dynamics of Antbirds (Thamnophilidae) from Amazonian fluvial islands. Journal of Biogeography, v. 44, n. 10, p. 2284-2294, OCT 2017. (15/12551-7, 14/00113-2, 11/06609-1, 12/50260-6)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

SILVA, Gregory Thom e. Comparative phylogeography of floodplain specialist birds based on sequences of ultra conserved elements: inferring Amazoniam biogeografic patterns. 2018. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB) São Paulo.