Comparative Phylogeography of Medicinal Plants Across Biogeographic Regions

Thesis Abstract

The study addresses the persistent gap in understanding how historical biogeography and contemporary ecological processes shape genetic diversity and population structure of medicinal plants with widespread pharmacological relevance. Despite extensive ethnobotanical use and high value for drug discovery, comparative phylogeographic patterns across biogeographic regions remain underexplored, limiting inferences about lineage diversification, local adaptation, and conservation prioritization. The aim is to elucidate how demographic history, climatic oscillations, and habitat connectivity have driven spatial genetic structure in selected medicinal taxa across distinct biogeographic realms. Specific objectives are to (i) assess intraspecific genetic diversity and population differentiation using plastid and nuclear markers, (ii) reconstruct species-level phylogeographic histories with coalescent-based inference, (iii) compare environmental and geographic correlates of genetic structure across regions using landscape genetics, (iv) evaluate congruence between phylogeographic patterns and known ethnobotanical distributions, and (v) generate region-wide conservation recommendations based on identified evolutionary lineages and refugia. The methodology adopts a comparative, cross-regional design focusing on five medicinal plant species representing diverse taxonomic groups and biogeographic histories. Population sampling comprises at least 40 populations per species, with 15–20 individuals per population, totaling approximately 600–800 samples per taxon. Field collection is complemented by herbarium vouchers and geo-referenced occurrence data from national botanical databases to ensure representative geographic coverage. Data collection employs both organellar (trnH-psbA, rbcL) and nuclear (ITS, low-copy nuclear loci) markers, complemented by genome-wide single-nucleotide polymorphism (SNP) data generated via Restriction-site Associated DNA Sequencing (RAD-seq) to capture fine-scale structure. Environmental variables (precipitation, temperature, land cover, elevation) are extracted from high-resolution climatic layers and remote sensing products to support landscape genetic analyses. Analytical procedures integrate multiple approaches. Sequence data are aligned and edited before estimating genetic diversity indices (haplotype/allelic richness, nucleotide diversity) and population differentiation (FST, G’ST) using Arlequin and GenAlEx. Population structure is inferred with STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Phylogeographic inferences employ coalescent-based methods (BEAST for time-calibrated phylogenies, IMa2 for historical gene flow) to reconstruct divergence times and ancestral demography. Genome-wide SNP data are analyzed with PCA, admixture analysis, and outlier detection (Bayescan) to identify selection and to correlate genomic differentiation with environmental gradients. Landscape genetics frameworks are applied using resistance surfaces and circuit theory (Circuitscape) to evaluate isolation-by-distance and isolation-by-environment patterns, while Mantel tests and multiple regression on distance matrices (MRDM) quantify associations between genetic structure and geographic/climatic variables. The study also tests phylogeographic congruence across taxa with comparative methods and uses approximate Bayesian computation (ABC) to evaluate alternative historical scenarios. Expected findings include detection of region-specific refugia and lineage diversification corresponding to Pleistocene climate oscillations, with differential retention of ancestral haplotypes among regions. It is anticipated that nuclear markers will reveal higher gene flow relative to plastid markers in most species, while RAD-seq data will uncover cryptic structure reflecting microrefugia and adaptive divergence along elevational and climatic gradients. The study expects varying degrees of concordance between ethnobotanical usage patterns and genetic lineages, suggesting localized adaptation or cultural dissemination shaping current distributions. The contribution to knowledge lies in providing an integrative, cross-regional phylogeographic framework for medicinal plants, combining organellar and nuclear genomic data with landscape and environmental analyses to reveal processes shaping diversity and distribution. The findings will inform conservation strategies by identifying evolutionarily significant units, refugia, and migration corridors critical for maintaining genetic diversity and biocultural value. The research concludes that regional histories and contemporary landscapes jointly sculpt phylogeographic patterns, recommending region-specific ex-situ and in-situ conservation actions, sustainable harvesting guidelines, and integration of phylogeographic insights into bioprospecting policies.