RESEARCH ARTICLE Genetic structure and diversity identify incipient domestication of Piquia ´[Caryocar villosum (Aubl.) pers.] along the lower Tapajo ´s River, Brazilian Amazonia Ana Fla ´via Francisconi . Rubana Palhares Alves . Charles R. Clement . Gabriel Dequigiovanni . Igor A. S. de Carvalho . Elizabeth A. Veasey Received: 30 May 2020 / Accepted: 2 December 2020 / Published online: 4 January 2021 Ó The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature 2021 Abstract In Amazonia there are at least 85 arboreal species with domesticated populations, among which piquia ´[Caryocar villosum (Aubl.) Pers.] is widely distributed. In some regions, there is ethnobotanical evidence of domestication for its fruit. To understand more about piquia ´ domestication, we evaluated genetic diversity and structure of two regions, sam- pling 130 trees in forests and homegardens (92 trees in the Tapajo ´s National Forest and 38 in the Rio Ouro Preto Extractive Reserve), using seven microsatellite markers. In Tapajo ´s, piquia ´ trees form large aggrega- tions near archaeological sites, while in Ouro Preto the aggregations are smaller. The Tapajo ´s presented higher effective number of alleles, allelic richness and expected heterozygosity, with lower observed heterozygosity and, consequently, a higher fixation index and lower apparent outcrossing rate. Genetic structure exists between regions, forming four prob- able groups: one that corresponds mainly to Ouro Preto and the others in the Tapajo ´ s. When the Tapajo ´s was analyzed separately, we found four genetic groups that do not correspond to homegarden and forest systems. In the homegardens we found lower number of effective alleles, allelic richness and observed heterozygosity. These subtle differences in genetic diversity between homegarden and forest trees iden- tify piquia ´’s incipient domestication, agreeing with ethnobotanical evidence. The piquia ´ stands near archaeological sites and the existence of four genetic groups suggest that piquia ´ was introduced into the Tapajo ´s during pre-Columbian times from at least three different sources. Trail registration numbers: Supporting information The online version of this article (https://doi.org/10.1007/s10722-020-01078-0) contains sup- plementary material, which is available to authorized users. A. F. Francisconi (&) Á I. A. S. de Carvalho Á E. A. Veasey Departamento de Gene ´tica, Escola Superior de Agricultura ‘‘Luiz de Queiroz’’, Universidade de Sa ˜o Paulo, Av. Pa ´dua Dias, 11, Bairro Sa ˜o Dimas, Piracicaba, Sa ˜o Paulo 13418-900, Brazil e-mail: anaf_f@hotmail.com R. P. Alves (&) Programa de Po ´s-Graduac ¸a ˜o Em Ecologia, Instituto Nacional de Pesquisas da Amazo ˆnia, Av. Andre ´ Arau ´jo, 2936, Bairro Petro ´polis, Manaus, Amazonas 69067-375, Brazil e-mail: rubanapalhares@gmail.com C. R. Clement Coordenac ¸a ˜o de Tecnologia E Inovac ¸a ˜o, Instituto Nacional de Pesquisas da Amazo ˆnia, Av. Andre ´ Arau ´jo, 2936, Bairro Petro ´polis, Manaus, Amazonas 69067-375, Brazil G. Dequigiovanni Centro Universita ´rio Univel, Tito Mufatto Avenue, 2317, Bairro Santa Cruz, Cascavel,, Parana ´ 85806-080, Brazil 123 Genet Resour Crop Evol (2021) 68:1487–1501 https://doi.org/10.1007/s10722-020-01078-0