Comparative phylogeography of floodplain specialist birds based on sequences of ultra conserved elements: inferring Amazoniam biogeografic patterns

Author(s)

Gregory Thom

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB)
• Defense date: 2018-05-09

Examining board members

Cristina Yumi Miyaki; Maria Cristina Arias; Scott Vernon Edwards; Evandro Marsola de Moraes; Marcio Roberto Pie

• Advisor: Cristina Yumi Miyaki

Abstract

This Ph.D. Dissertation inferred the historical processes that seem to have built the avian community assemblage restricted to the Amazonian floodplains based on their patterns of diversification and geological and climatic data. We analyzed three species complexes widely distributed over the Amazon Basin and specialists of river edge forests, Myrmoborus lugubris, Thamnophilus nigrocinereus/T. cryptoleucus, and Myrmotherula assimilis. In order to access their genetic diversity and perform phylogenetic and demographic analyses, we captured and sequenced ~2,300 Ultra Conserved Elements. This Dissertation was subdivided into three chapters that discuss distinct diversification aspects of these taxa. In Chapter 1, we explored the effects of microevolutionary processes in M. lugubris, especially gene flow and incomplete lineage sorting in phylogenetic reconstructions of its populations. We demonstrated the potential bias of estimating species tree without accommodating gene flow in recent scenarios of divergence. Additionally, we explored the evolutionary history of this lineage, supporting the presence of gene flow between nonsister populations and a hybrid zone with potential heterosis. In Chapter 2 we performed a comparative phylogeographic study including all three species complexes. The results indicated that climatic oscillations during the Quaternary that altered the pattern of sedimentation and formation of river edge forests seem to have promoted cyclical periods of allopatry and secondary contact. In the third chapter we explored how the genetic diversity of populations restricted to the Solimões river is currently distributed in space and if historical demographic alterations could be related to geographic range expansions. A signal of range expansion was detected only for T. cryptoleucus but not for M. lugubris and M. assimilis, suggesting that at the intra-populational scale species-specific ecological variables may promote distinct patterns of genetic diversity. However, despite the absence of a shared pattern of range expansion the genetic diversity of each of the three taxa is heterogeneously distributed in the landscape. The data presented in this Dissertation allowed an unprecedented test of diversification hypotheses for the bird community that occurs throughout the Amazonian floodplains, suggesting that organisms from environments poorly explored by phylogeographic studies may reveal new facets about the diversification of the Amazonian diversity (AU)

• FAPESP's process: 14/00113-2 - Comparative phylogeography of four Amazonian lineages of birds: accessing biogeographic patterns based on ultra-conserved elements
• Grantee: Gregory Thom e Silva
• Support Opportunities: Scholarships in Brazil - Doctorate