Title: The effects of Pleistocene climatic cycles on avian historic demography across Amazonia
Description: 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.