Title : Preliminary phylogenomic study of sida sect malacroideae across neotropical and paleotropical regions
Abstract:
The genus Sida L. (Malvaceae) comprises more than 200 species distributed mainly in tropical and subtropical regions and is known for its taxonomic complexity. Infrageneric relationships remain poorly understood, as most previous classifications have been based exclusively on morphology and few molecular data are available. Recent advances in target capture sequencing offer new perspectives for resolving long-standing uncertainties in Malvaceae systematics. In this study, preliminary phylogenomic results are presented for Sida sect. Malacroideae, representing the first dataset generated within the broader framework of a doctoral research project. The studied section comprises 30 species, occurring mainly in South America (24 species) and a smaller number in Africa, Sri Lanka, and India (6 species). Members of this section exhibit notable morphological variation, particularly in stipule shape, mericarp characters, and the presence of apical stipules in the inflorescences. Despite this diversity, the section has been traditionally recognized based on a combination of these morphological traits, which guided species delimitation prior to molecular studies. DNA was extracted from herbarium specimens, including challenging samples with high levels of polysaccharides. Libraries were enriched through target capture A353-bait set and sequenced using high-throughput platforms. Raw data were processed with the CAPTUS pipeline for quality control, assembly, extraction and alignments. Phylogenetic inference was conducted under both concatenation and coalescent approaches. Maximum likelihood analyses were performed in IQ-TREE and species tree estimation was carried out with ASTRAL. Preliminary results consistently recover the focal section as monophyletic, with strong support across analytical frameworks. Furthermore, the analyses recovered African and Neotropical species in well-supported clades; however, relationships among species within each clade were not consistent, with taxa appearing intermixed rather than forming cohesive groups, which may indicate ongoing evolutionary diversification within the section. Although analyses of other sections are ongoing, these preliminary findings highlight the potential of genomic data to provide robust support for taxonomic decisions in Sida. By integrating molecular and morphological evidence, this work aims to clarify generic limits within Malvaceae, contributing not only to a more stable classification of Sida but also to a better understanding of evolutionary diversification in Neotropical lineages and its relationship within the Paleotropical species. This study represents the first phylogenomic attempt to address infrageneric relationships in Sida, and its results will serve as a foundation for a comprehensive taxonomic revision of the group.
