Abstract

The Indian subcontinent, encompassing India and Sri Lanka, is a region of exceptional plant diversity shaped by deep geological and evolutionary history. Its forest communities, dominated by woody plants, harbour a large proportion of this biodiversity. Understanding the evolutionary relationships among these taxa is crucial for exploring the processes of speciation, extinction, dispersal, and assembly of ecological communities.
This study reconstructs a phylogenetic framework for 2,208 woody plant species spanning 47 orders and 143 families using five commonly used genetic markers: chloroplast genes or genomic regions (rbcL, matK, psbA-trnH) and nuclear ribosomal genomic regions (ITS1, ITS2). A supermatrix alignment of nucleotide sequences from 1,356 taxa was generated and used for multilocus-based reconstruction of the phylogeny. The inclusion of nuclear markers notably enhanced tree resolution, reducing overall polytomies from 13.48% to 6.63%. For example, polytomies in Ficus decreased from 67.57% to 20%, and Cinnamomum nodes were fully resolved where ITS data were present.
Comparisons between chloroplast- and nuclear DNA sequence data-based trees revealed lineage-specific variation in phylogenetic informativeness. Nuclear ITS data improved resolution in Laurales, Malpighiales, Rosales, and Myrtales, while chloroplast markers performed better in Lamiales, Ericales, and Brassicales.
These results provide a robust phylogenetic framework for understanding community assembly and diversification processes in the forests of India and Sri Lanka, offering valuable insights for ecological research and biodiversity conservation.