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<p>The palm family (Arecaceae) is one of the most diverse groups of Angiosperms, characterized by significant economic, medicinal, and ornamental value, as well as wide morphological diversity and complex natural history. Phylogenetic studies in Arecaceae have struggled to achieve definitive resolution. Integrating morphological characters with plastid and nuclear genetic information is a promising approach to understanding the family's natural history. However, developing effective plant DNA barcodes remains challenging due to limitations in the proposed loci for species identification. This study focuses on DNA barcoding for two palm species from the Colombian Andes, assessing the <i>rbc</i>La locus as a potential barcode marker. We analyzed 488 unique species sequences from all five subfamilies and added new DNA sequences to databases. The <i>rbc</i>L locus showed limitations in species discrimination across most subfamilies but could preliminarily distinguish Calamoideae species from other palms. Low genetic differentiation, narrow nucleotide diversity, and negative Tajima’s D test values indicate purifying selection at the cpDNA locus, which limits allelic variation among species. Additionally, synonymous mutations were common across all subfamilies, indicating a conserved nature of the RUBISCO gene in palms. While the <i>rbc</i>La locus may be suitable for supra-generic level discrimination, alternative loci should be evaluated for accurate species-level identification.</p>

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Evaluation of evolutionary patterns limiting the utility of the rbcLa DNA barcoding locus in palms

  • 期刊论文

  • 发表日期：

    2026年1月5日

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  • Marily Rafaela Mendoza Rojas,
  • Marly Grajales Amorocho,
  • Alejandra Varón Pardo,
  • Nhora Helena Ospina Calderón,
  • Nicola S. Flanagan,
  • Jorge Mario Londoño Caicedo

摘要

The palm family (Arecaceae) is one of the most diverse groups of Angiosperms, characterized by significant economic, medicinal, and ornamental value, as well as wide morphological diversity and complex natural history. Phylogenetic studies in Arecaceae have struggled to achieve definitive resolution. Integrating morphological characters with plastid and nuclear genetic information is a promising approach to understanding the family's natural history. However, developing effective plant DNA barcodes remains challenging due to limitations in the proposed loci for species identification. This study focuses on DNA barcoding for two palm species from the Colombian Andes, assessing the rbcLa locus as a potential barcode marker. We analyzed 488 unique species sequences from all five subfamilies and added new DNA sequences to databases. The rbcL locus showed limitations in species discrimination across most subfamilies but could preliminarily distinguish Calamoideae species from other palms. Low genetic differentiation, narrow nucleotide diversity, and negative Tajima’s D test values indicate purifying selection at the cpDNA locus, which limits allelic variation among species. Additionally, synonymous mutations were common across all subfamilies, indicating a conserved nature of the RUBISCO gene in palms. While the rbcLa locus may be suitable for supra-generic level discrimination, alternative loci should be evaluated for accurate species-level identification.