DOI: 10.5281/zenodo.7520510
title: Natural History, Biogeography and Evolution of the Iberian white oak syngameon (Quercus L. Sect. Quercus) - Digital Annex

description: Digital Annex for the following thesis: Vila-Viçosa, C. (2023). <em>Natural History, Biogeography and Evolution of the Iberian white oak syngameon </em>(Quercus <em>L. Sect.</em> Quercus). Ph.D. Thesis, Faculdade de Ciências da Universidade do Porto, Portugal Abstract: The genus <em>Quercus</em> L. is one of the most diverse and important group of woody plants, particularly when considering that they are the trees that rule the Northern Hemisphere forests. Oaks have an intricate Biogeography that criss-crosses diverse climatic and edaphic gradients, encompassing a huge ambiguity in terms of species delimitation. Frequently, the taxonomic proposals brought by traditional Linnaean Botany are either insufficient or rather inflate the number of species and nomenclatural assignments, which are further diluted into inconsistent taxonomic ranks, varying from species to subspecies and varieties. The supremacy given to morphological characters that are inherently fragile and plastic, spread across the distribution areas of distinct lineages, may carry ambiguity on the identification and proper species delimitation. From the oaks that are distributed across the Western Palearctic region, the ones that are deciduous or brevi-deciduous present higher levels of ambiguity in terms of species number and their delimitation. This ambiguity is particularly strong in the circummediterranean region and in the transitional areas between the two major biogeographic Regions of the western Palearctic region, the Euro-Siberian and Mediterranean. This degree of uncertainty, which increases towards the Southern European Peninsulas, is amplified by the ease that the different species of oaks tend to hybridize among them. The present work provides a holistic framework that covers multiple areas, from the taxonomic and evolutive study of this genus, to biogeography and molecular characterization. Its major objective was to resolve the species delimitation of the Iberian deciduous and marcescent oaks and putative introgression among them, enhancing the available knowledge about species diversity, which can foster suitable species and forest conservation. A specific objective was to cross-reference the natural history revision and the different taxonomic treatments brought by distinct authors, with personal observations. These data were then incorporated into ecological modelling and molecular characterization, which in the end fed a newly updated taxonomic proposal. In Section A we obtained results from extensive field, herbaria, and literature review, updating the nomenclature of the Portuguese and western Mediterranean oaks. Section B was supported by Section A’s in-depth review and enabled finer species distribution models, nurturing both hindcast (since <em>ca.</em> 20 Kyr) and forecast (2070-2100) exercises of the range dynamics of Mediterranean oaks species. The study of past and future range shifts solved important pending biogeographic questions, especially related to past range-shifts. Such past-range shifts improved our knowledge on species responses to climate dynamics and allowed a better anticipation of future responses of range shifts driven by climate change. Section C encompassed the molecular characterization of Iberian white oak species and their hybrids, whose delimitation is often faltering when one intends to infer about species rank, or hypothesize about the participation of parent taxon in natural hybrid swarms. This work allowed us to solve the phylogenetic backbone of western Palearctic white oaks, suggesting a significant segregation of the Iberian pedunculate oaks and unveiling two subsections inside Section <em>Quercus</em>. These subsections are biogeographically well-segregated and present diverse levels of introgression among species. Results demonstrated the efficiency of RADSeq for rebuilding the reticulate phylogeny of the Eurasian white oaks, showcasing the significance of the Iberian Peninsula as a major hotspot for oak diversity. We implemented a circular approach to these methods, which retro-fed themselves in terms of insight generation, enabling a powerful strategy to solve the evolutionary history of this difficult groups of plants. We estimate that the reticulate historical biogeography of the western Palearctic white oaks deserves further scrutiny by adding vicariant oak populations from northern Africa, the Near East and southern European Peninsulas. Methods should again follow this similar additive and sequential process of adjoining deep Natural History examination, with extensive fieldwork in type populations and genome-wide molecular surveys, in order to solve this group of plants. With the present work, we were able to significantly improve on the depiction of the basic unit of Biodiversity (the Species), in the complex <em>Quercus</em> genus. We provided tools to enable further efforts for the conservation of the Mediterranean oak forests, which overwhelm one of the most important (and one of the most threatened) Biomes for plant conservation at the global scale.