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<p><i>Oenocarpus minor Mart.</i> (bacabinha) is a native Amazonian palm occurring across central and western Brazilian Amazonia, typically in low-density, scattered populations. Despite its ecological and socioeconomic relevance, including fruit use and oil extraction, its genetic diversity and population dynamics remain poorly characterized, limiting informed conservation planning. Here, we present the first genome-wide population genomic assessment of <i>O. minor</i>, based on 15,491 high-quality single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) from 167 individuals sampled across 19 localities spanning most of the species’ known distribution. Stringent filtering produced a robust dataset with high depth and low missing data. Genetic diversity varied markedly among populations, with elevated heterozygosity and negative fixation indices in some regions, and high numbers of private alleles in river-isolated populations, suggesting localized demographic independence. Both Wright’s F-statistics and discriminant analysis of principal components (DAPC) revealed moderate to strong genetic differentiation, identifying 11 genetic clusters distributed across major river basins. The neighbor-joining tree with 1000 bootstrap replicates further supported deep splits among populations separated by the Madeira, Negro, and other major Amazonian rivers, indicating that these hydrographic barriers play a central role in restricting gene flow. The concentration of rare alleles and singletons in river-isolated populations also suggests long-term drift and limited historical connectivity. Although <i>O. minor</i> maintains substantial genetic variation, the strong regional structuring and signals of inbreeding in some populations underscore a mosaic of resilience and vulnerability. These findings demonstrate that river-mediated isolation is a key driver of divergence in <i>O. minor</i> and highlight genetically distinct populations, especially those with high private allele richness or located in isolated basins, as priority units for conservation. This study provides the first genomic baseline for the species, reinforcing the importance of incorporating widespread yet structured palms into Amazonian conservation strategies.</p>

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Genomic diversity and population structure of Oenocarpus minor in the Brazilian Amazon: implications for conservation

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Kauanne Karolline Moreno Martins,
  • Ana Flávia Francisconi,
  • Matheus Sartori Moro,
  • Caroline Bertocco Garcia,
  • Matheus Scaketti,
  • João Victor da Silva Rabelo-Araújo,
  • Thiago Deomar Ludwig,
  • Santiago Linorio Ferreyra Ramos,
  • Maria Teresa Gomes Lopes,
  • Ricardo Lopes,
  • Jeferson Luis Vasconcelos de Macêdo,
  • Maria Imaculada Zucchi

摘要

Oenocarpus minor Mart. (bacabinha) is a native Amazonian palm occurring across central and western Brazilian Amazonia, typically in low-density, scattered populations. Despite its ecological and socioeconomic relevance, including fruit use and oil extraction, its genetic diversity and population dynamics remain poorly characterized, limiting informed conservation planning. Here, we present the first genome-wide population genomic assessment of O. minor, based on 15,491 high-quality single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) from 167 individuals sampled across 19 localities spanning most of the species’ known distribution. Stringent filtering produced a robust dataset with high depth and low missing data. Genetic diversity varied markedly among populations, with elevated heterozygosity and negative fixation indices in some regions, and high numbers of private alleles in river-isolated populations, suggesting localized demographic independence. Both Wright’s F-statistics and discriminant analysis of principal components (DAPC) revealed moderate to strong genetic differentiation, identifying 11 genetic clusters distributed across major river basins. The neighbor-joining tree with 1000 bootstrap replicates further supported deep splits among populations separated by the Madeira, Negro, and other major Amazonian rivers, indicating that these hydrographic barriers play a central role in restricting gene flow. The concentration of rare alleles and singletons in river-isolated populations also suggests long-term drift and limited historical connectivity. Although O. minor maintains substantial genetic variation, the strong regional structuring and signals of inbreeding in some populations underscore a mosaic of resilience and vulnerability. These findings demonstrate that river-mediated isolation is a key driver of divergence in O. minor and highlight genetically distinct populations, especially those with high private allele richness or located in isolated basins, as priority units for conservation. This study provides the first genomic baseline for the species, reinforcing the importance of incorporating widespread yet structured palms into Amazonian conservation strategies.