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ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages ofQuercusand relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages ofQuercusand relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors ofCastanea + Castanopsis,Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors ofChrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups. 

Abstract. Since the middle Miocene (15 Ma, million years ago), the Earth's climate has undergone a long-term cooling trend, characterised by a reduction in ocean temperatures of up to 7–8 ∘C. The causes of this cooling are primarily thought to be due to tectonic plate movements driving changes in large-scale ocean circulation patterns, and hence heat redistribution, in conjunction with a drop in atmospheric greenhouse gas forcing (and attendant ice-sheet growth and feedback). In this study, we assess the potential to constrain the evolving patterns of global ocean circulation and cooling over the last 15 Ma by assimilating a variety of marine sediment proxy data in an Earth system model. We do this by first compiling surface and benthic ocean temperature and benthic carbon-13 (δ13C) data in a series of seven time slices spaced at approximately 2.5 Myr intervals. We then pair this with a corresponding series of tectonic and climate boundary condition reconstructions in the cGENIE (“muffin” release) Earth system model, including alternative possibilities for an open vs. closed Central American Seaway (CAS) from 10 Ma onwards. In the cGENIE model, we explore uncertainty in greenhouse gas forcing and the magnitude of North Pacific to North Atlantic salinity flux adjustment required in the model to create an Atlantic Meridional Overturning Circulation (AMOC) of a specific strength, via a series of 12 (one for each tectonic reconstruction) 2D parameter ensembles. Each ensemble member is then tested against the observed global temperature and benthic δ13C patterns. We identify that a relatively high CO2 equivalent forcing of 1120 ppm is required at 15 Ma in cGENIE to reproduce proxy temperature estimates in the model, noting that this CO2 forcing is dependent on the cGENIE model's climate sensitivity and that it incorporates the effects of all greenhouse gases. We find that reproducing the observed long-term cooling trend requires a progressively declining greenhouse gas forcing in the model. In parallel to this, the strength of the AMOC increases with time despite a reduction in the salinity of the surface North Atlantic over the cooling period, attributable to falling intensity of the hydrological cycle and to lowering polar temperatures, both caused by CO2-driven global cooling. We also find that a closed CAS from 10 Ma to present shows better agreement between benthic δ13C patterns and our particular series of model configurations and data. A final outcome of our analysis is a pronounced ca. 1.5 ‰ decline occurring in atmospheric (and ca. 1 ‰ ocean surface) δ13C that could be used to inform future δ13C-based proxy reconstructions.