Genetic Diversity and Phylogeographic Patterns of L. franchetii: Responses to Quaternary Climate Changes and Geological Events

This study investigated the genetic diversity and phylogeographic structure of L. franchetii , an endemic halophyte along China's Yellow Sea and Bohai Sea coasts. We analyzed 201 individuals from 14 populations using cpDNA fragments (trnL-trnF, matK, ndhF-rpl32) to assess genetic structure, glacial refugia, and population dynamics influenced by Quaternary climatic and geological events. L. franchetii exhibited high genetic diversity ( Ht = 0.930) and substantial differentiation ( Fst = 0.6958). AMOVA indicated 69.59% of variation occurred within populations. A Mantel test confirmed significant geographic isolation. PERMUT analysis revealed a pronounced phylogeographic structure, identifying 26 haplotypes across populations. Divergence time ranged from 3.01 to 0.25 Ma. Haplotype network and phylogenetic analyses divided haplotypes into northern and southern lineages, with H1 and H4 as ancestral haplotypes. Populations ZFD, ZJC, and HLH were inferred as glacial refugia. Mismatch analysis and neutrality tests showed no significant population expansion or contraction. Expansion of haplotypes H6 and H7 was associated with post-glacial warming and Bohai Sea geological activities. The genetic structure of L. franchetii was shaped by geographic isolation, marine transgression and regression, and ocean currents in the Yellow Sea and Bohai Sea. Severe fragmentation in some populations suggests the need for protected areas and ecological corridors to conserve genetic diversity.