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The Effects of Pleistocene Climatic Cycles on Avian Historic Demography Across Amazonia

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The Effects of Pleistocene Climatic Cycles on Avian Historic Demography Across Amazonia The effects of Pleistocene climatic cycles on avian historic demography across Amazonia Laís Araújo Coelho Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2020 © 2020 Laís Araújo Coelho All Rights Reserved Abstract The effects of Pleistocene climatic cycles on avian historic demography across Amazonia Laís Araújo Coelho Understanding the history of Amazonian diversity and how it relates to past environmental changes in the region is fundamental for elucidating processes behind the origin of global diversity distribution patterns and understanding future threats to its preservation. The diversification of Amazonian biota has been a topic of debate for centuries. Recent studies have found that biodiversity in Amazonia is highly underestimated and that many taxa are younger than previously thought. The distribution and dynamics of rivers, vegetation, soil types and moisture gradients created a complex scenario of diversification in the region. These emerging patterns have brought forth new and previously unanswered puzzles regarding the effects of landscape history in Amazonian biodiversity. Climate cycles of the Pleistocene were important in shaping biodiversity patterns worldwide, and they have been hypothesized to be drivers of diversification in Amazonia. However, little is known about the effects of historic climate cycles on Amazonian organisms. I addressed this knowledge gap by leveraging recently gathered abiotic evidence of past changes in precipitation across Amazonia as well as population genetics methods to make an explicit investigation of the effects of climate cycles in the historic demography of upland forest birds. Specifically, I compared the demographic histories of bird populations occurring in regions with contrasting climatic histories: Northwestern Amazonia (NW, relatively stable paleoclimate and humid during the Last Glacial Maximum) and Southeastern Amazonia (SE, marked paleoclimatic cycles and dry in the LGM). Demographic history was assessed in two time- scales: late Pleistocene (mtDNA of 33 taxa) and mid-late Pleistocene (whole genomes of four taxa). I hypothesized that: 1) populations co-occurring in the SE would show signals of recent, synchronous co-expansion due to rainfall increase since the LGM; 2) NW populations would have idiosyncratic demographic histories in response to drivers other than climatic cycles, given the milder regional precipitation oscillation; 3) populations occurring in SE would show cycles of population size change spanning multiple glacial cycles, that would be more pronounced and off-phase with NW counterparts. I found synchronous changes in population size using both mtDNA and genomic reconstructions. Most populations in both regions (23 in each) underwent expansions, based on ABC model testing with mtDNA. Contrary to my expectations, both the SE and NW populations had co-expansion (87-97% of populations co-expanding in SE and 94-99% in NW), and both these expansion events preceded the LGM (106-121 Kya for SE and 120-138 Kya for NW). These results were corroborated by whole genome based demographic reconstructions: the focus populations showed signs of increase (Rhegmatorhina gymnops, Psophia dextralis and Psophia napensis) and decrease (R. melanosticta) during the transition from the penultimate glacial maximum and the last interglacial period (~120Kya). These synchronous demographic changes across Amazonia suggest joint response to changes in the environment spanning the whole region, which points to climatic cycles of the Pleistocene. Amazonian forest birds respond to habitat change in concurrence, and they were sensitive to even relatively subtle changes in precipitation during the mid to late Quaternary. Table of Contents List of Figures ................................................................................................................................ iv List of Tables .................................................................................................................................. v Appendices ..................................................................................................................................... vi Introduction ..................................................................................................................................... 1 Overview ......................................................................................................................................... 5 CHAPTER 1-Convergent demographic history of lowland birds across Amazonia ...................... 8 1.Introduction .................................................................................................................................. 8 2.Methods...................................................................................................................................... 13 2.1 Data collection ........................................................................................................................ 13 2.2 Population delimitation ........................................................................................................... 13 2.3 Demographic history inference ............................................................................................... 18 2.4 Effects of climate on genetic diversity and magnitude of population size change ................. 21 2.5 Coexpansion modelling .......................................................................................................... 22 2.6 Simulations for method validation .......................................................................................... 24 3.Results ........................................................................................................................................ 27 3.2 Pairwise comparisons of summary statistics between regions ............................................... 32 3.3 Co-expansion modelling ......................................................................................................... 33 3.4 Synchronicity estimation assessment ...................................................................................... 37 4.Discussion .................................................................................................................................. 40 4.1 Genetic diversity and magnitude of population size change across Amazonia ...................... 40 4.2 Synchronicity and timing of expansion across Amazonia ...................................................... 43 i 4.3 Considerations about mechanisms driving demography ........................................................ 46 5. Conclusions ............................................................................................................................... 47 CHAPTER 2-A Multireference-Based Whole Genome Assembly for the Obligate Ant-Following Antbird, Rhegmatorhina melanosticta (Thamnophilidae) ............................................................ 48 1. Introduction ............................................................................................................................... 48 2. Methods..................................................................................................................................... 51 2.1 Genome Sequencing and De Novo Assembly ........................................................................ 51 2.2 Single reference assisted chromosome level assembly………………………………………53 2.3 Multiple reference assisted chromosome level assembly……………………………………55 2.4 Evaluation of genome completeness…………………………………………………………58 2.5 Genotyping-by-sequencing (GBS) reference mapping………………………………………60 3. Results…………………………………………………………………………………………61 3.1 De-novo assembly…………………………………………………………………………....61 3.2 Reference-Based Assembly .................................................................................................... 61 3.3 Genome Completeness............................................................................................................ 63 3.4 Synteny ................................................................................................................................... 65 3.5 GBS Reference Mapping ........................................................................................................ 68 4. Discussion ................................................................................................................................. 68 4.1 General Genome Structure, Contiguity and Content .............................................................. 68 5. Conclusions ............................................................................................................................... 72 CHAPTER 3- Demographic history of amazonian bird populations over multiple glacial cycles ....................................................................................................................................................... 74 1.Introduction ................................................................................................................................ 74 ii 2.Methods...................................................................................................................................... 78 2.1 Reference genomes ................................................................................................................. 80 2.2 Genome resequencing
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