Unraveling cacaos: systematics and evolution of Theobroma L and Herrania Goudot (Malvaceae, Byttnerioideae)

Author(s)

Matheus Colli Silva

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB)
• Defense date: 2023-06-06

Examining board members

Jose Rubens Pirani; Alison Gonçalves Nazareno; Jefferson Prado; Daniela Cristina Zappi

• Advisor: Jose Rubens Pirani; James Edward Richardson

Abstract

Amazonia is the largest and most biodiverse rainforest of the world, source of a large amount of plant species, and the main repository of ecosystem services relevant globally. The forest is the cradle of many plants from Tropical Americas, and a significant amount of these have played a major role in human history since early Holocene. Studying the origin and history of such groups is, therefore, the basis to build an integrative understanding of Amazonia, and the cacao group, with species traditionally allocated to two generaTheobroma and Herrania is one such example. In this PhD project, I revisited the nomenclatural and taxonomic status of the wild cacao species, associated to an assessment of morphological, evolutionary and populational genomics of selected taxa. Specifically, I aimed at (1) revisit the morphology and distribution of current taxa, reevaluating taxonomic delimitations at species levels; (2) look for morphological synapomorphies and discuss how the evolution of such characters might have occurred; (3) evaluate how genetic variation of populations of cacao (T. cacao) behave regarding its divergence levels of genes under selection; and (4) depict the origin and geographic history of cupuaçu (T. grandiflorum), a tree crop economically relevant in Brazil, known for its humongous fruit and appreciated for its pulp. This dissertation is organized in nine chapters and four parts: taxonomic treatment, phylogenetics and evolution, populational genomics and data mobilization and by-product studies, each one tackling one or more goals associated to this project. First, results for the taxonomic revision consist of complete and updated descriptions of a total of 35 species of Theobroma/Herrania divided into six sections, including three new species here described. Second, a new phylogeny revealed the paraphyly of Theobroma, all of which subsidized a reestablishment of Theobroma including Herrania as a section of the first. Third, using a high-throughput sequencing approach, I could track differential effects of selection on different populations of cacao. Additionally, for the first time I demonstrated that cupuaçu is actually not a natural species, but a domesticated form selected from a wild close relative, cupuí (T. subincanum), so that I could not only track where and when this happened, but also pinpointed a single domestication event that happened in the Middle-Upper Amazon Basin in the mid-Holocene, mediated by indigenous people that had the forest as its source of livelihood long before European colonization. Finally, I compiled a biodiversity dataset of preserved specimen collections of Theobroma, and I present a by-product study that discussed the native area of T. cacao under a remote sensing approach. Results not only deeply impact our understanding on the evolution of wild cacao species, the flora and the people from Amazonia, but shed light on the study of the origin and history of wild crop relatives as a whole. (AU)

• FAPESP's process: 20/01375-1 - Unraveling cacao: systematics and evolution of Theobroma L. and Herrania Goudot (Malvaceae, Byttnerioideae)
• Grantee: Matheus Colli Silva
• Support Opportunities: Scholarships in Brazil - Doctorate