Colli-Silva Matheus, Richardson James Edward, Pirani José Rubens, Figueira Antonio
Departamento de Botânica, Centro de Biociências Universidade Federal de Pernambuco Recife Brazil.
Royal Botanic Gardens, Kew Richmond UK.
Ecol Evol. 2025 Jul 22;15(7):e71746. doi: 10.1002/ece3.71746. eCollection 2025 Jul.
Cacao (), the primary source for chocolate manufacturing, is native to the Upper Amazon basin. It was introduced into Mesoamerica by pre-Columbian societies and later spread globally following European colonization, becoming a commercially significant crop. Today, cacao populations exist along a continuum from wild to naturalized and cultivated forms across the Tropical Americas, complicating efforts to distinguish genuinely wild populations from those influenced by human activity. Here, we investigate genomic diversity, population structure, and domestication signals in three groups using RAD-sequencing: Upper Amazonian populations (including Contamana, Marañón, Iquitos and Nanay), the Guiana population, and the Amelonado variety introduced into Eastern Brazil in the 18th century. The Upper Amazonian populations exhibited the highest genetic diversity and limited evidence of recent selection, reaffirming their role as the primary genetic source of cacao. The Amelonado group displayed signatures of artificial selection, including reduced genetic diversity and evidence of balancing selection, consistent with its introduction to Bahia before its later expansion to West Africa. The Guiana population showed intermediate genetic diversity and tight clustering but minimal differentiation from Upper Amazonian populations, suggesting they could represent an isolated wild lineage rather than an introduced group. These findings highlight the complexity of cacao's domestication history, shaped by multiple independent selection events and long-term human influence. Understanding this continuum is important for unraveling the species' evolutionary history for supporting conservation and breeding strategies for cacao, a crop of major economic and cultural importance.
可可树（）是巧克力生产的主要原料来源，原产于亚马逊河上游流域。它在哥伦布发现新大陆之前就被中美洲社会引入，后来随着欧洲殖民扩张在全球传播，成为一种具有重要商业价值的作物。如今，在整个热带美洲，可可树种群呈现出从野生到归化及栽培形式的连续变化，这使得区分真正的野生种群和受人类活动影响的种群变得复杂。在这里，我们利用RAD测序技术研究了三组可可树的基因组多样性、种群结构和驯化信号：亚马逊河上游种群（包括孔塔马纳、马拉尼翁、伊基托斯和纳奈）、圭亚那种群以及18世纪引入巴西东部的阿梅洛纳多品种。亚马逊河上游种群表现出最高的遗传多样性，近期选择的证据有限，再次证实了它们作为可可树主要遗传来源的作用。阿梅洛纳多组显示出人工选择的特征，包括遗传多样性降低和平衡选择的证据，这与其在后来扩展到西非之前被引入巴伊亚的情况一致。圭亚那种群表现出中等遗传多样性和紧密聚类，但与亚马逊河上游种群的分化最小，这表明它们可能代表一个孤立的野生谱系，而不是一个引入的群体。这些发现凸显了可可树驯化历史的复杂性，其受到多个独立选择事件和长期人类影响的塑造。了解这种连续变化对于揭示该物种的进化历史、支持可可树的保护和育种策略非常重要，可可是一种具有重大经济和文化意义的作物。
