Population Genetic Differentiation and Taxonomy of Three Closely Related Species of Saxifraga (Saxifragaceae) from Southern Tibet and the Hengduan Mountains

Abstract

The effects of rapid, recent uplift of the Hengduan Mountains on evolution and diversification of young floristic lineages still remain unclear. Here, we investigate diversification of three closely related Saxifraga species with a distribution restricted to the Hengduan Mountains (HM) and southern Tibet, and comment on their taxonomy based on molecular evidence. Three chloroplast DNA fragments (rbcL, trnL-F, trnS-G) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to study genetic structure across 104 individuals from 12 populations of Saxifraga umbellulata, S. pasumensis, and S. banmaensis. Chloroplast DNA (cpDNA) phylogenies revealed two well supported clades, corresponding to S. umbellulata and S. pasumensis plus S. banmaensis. Topology of the ITS phylogeny was largely congruent with that generated from cpDNA haplotypes, but with minor conflicts which might be caused by incomplete lineage sorting. Analyses of molecular variance of both cpDNA and ITS datasets revealed that most variation was held between S. pasumensis s.l. (with S. banmaensis) and S. umbellulata (92.31% for cpDNA; 69.78% for ITS), suggesting a high degree of genetic divergence between them. Molecular clock analysis based on ITS dataset suggested that the divergence between S. pasumensis s.l. and S. umbellulata can be dated to 8.50 Ma, probably a result of vicariant allopatric diversification associated with the uplift events of the HM. Vicariance associated with HM uplifts may also have been responsible for infraspecific differentiation in S. pasumensis. In contrast, infraspecific differentiation in S. umbellulata was most likely triggered by Quaternary glaciations. The much lower levels of gene diversity within populations of S. pasumensis compared with S. umbellulata could have resulted from both range contractions and human collection on account of its putative medicinal properties. Combining evidence from morphology, geographical distributions and molecular phylogenetic data, we recommend that S. banmaensis should be treated as a synonym of S. pasumensis which in turn, and based on the same sources of evidence, should be treated as a separate species rather than as a variety of S. umbellulata.

Peer Review #2 of "Comparative analysis of chloroplast genomes for five Dicliptera species (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution (v0.1)"

“…Khakhlova et al (2006) suggested that gene divergence with less variability in the IR and coding regions may be a result of copy corrections during gene conversion, which can correct or delete the mutation. Codons were shown to have a strong tendency toward A or U at the third codon position, which is similar to the expression of an A/U ending in other plants (Gao et al, 2017;Clegg et al, 1994;Mader et al, 2018;Meng et al, 2018). This phenomenon may explain why the Adenine-Thymine (AT) content is slightly higher than the GC content in the cp genome of Dicliptera.…”

Comparative analysis of chloroplast genomes for fiveDiclipteraspecies (Acanthaceae): molecular structure, phylogenetic relationships, and adaptive evolution

“…Khakhlova & Bock (2006) suggested that gene divergence with less variability in the IR and coding regions may be a result of copy corrections during gene conversion, which can correct or delete the mutation. Codons were shown to have a strong tendency toward A or U at the third codon position, which is similar to the expression of an A/U ending in other plants (Gao et al, 2017;Clegg et al, 1994;Mader et al, 2018;Meng et al, 2018). This phenomenon may explain why the Adenine-Thymine (AT) content is slightly higher than the GC content in the cp genome of Dicliptera.…”

The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

“…Saxifraga L. is the largest genus of Saxifragaceae, consisting of 450-500 species in at least 13 sections (Tkach et al 2015;Ebersbach et al 2017a;Gao et al 2017;Li et al 2018). The most species-rich section of Saxifraga is 1 3…”