Assessing the phylogenetic relationship among varieties of Toona ciliata (Meliaceae) in sympatry with chloroplast genomes

Abstract

Toona ciliata is an endangered species due to over‐cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well‐mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL‐trnF) and showed that genetic differentiation was generally insignificant among varieties (Фst = 0%–5%). Purifying selection occurred in all protein‐coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein‐coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome‐based phylogeny did not support the morphology‐based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

Population Structure and Genetic Diversity of the Toona ciliata (Meliaceae) Complex Assayed with Chloroplast DNA Markers

“…Information on well-mixed genetic relationships among all samples derived from phylogenetic relationships (Figures 5 and 6) is partially consistent with the results of four varieties assayed with chloroplast sequences [21]. This supports the previous recommendation of conserving the genetic variation of this species in terms of the T. ciliata complex rather than individual varieties.…”

“…The distribution of haplotypes in the western region was consistent with previous results. Xiao et al [ 21 ] showed well-mixed phylogenetic relationships among individuals of four varieties of T. ciliata in Yunnan Province ( T. ciliata var. ciliata , T. ciliata var.…”

“…They showed that there were significant population differentiation and isolation-by-distance (IBD) effects in the natural distribution of the T. ciliata complex in China. Xiao et al [ 21 ] showed that four varieties of T. ciliata (without T. ciliata var. sublaxiflora among the five varieties) in sympatry were genetically well mixed in terms of chloroplast genomes.…”

“…Also, it is expected that genetic differentiation derived from cpDNA markers is greater than that from nuclear markers due to smaller genetic drift effects and both seed and pollen flow for the nuclear markers [ 31 ]. To compare with previous studies [ 18 , 21 ], we investigated range-wide populations of the T. ciliata complex. By synthesizing information on genetic variation from nuclear and organelle genome markers, we assessed the genetic diversity and population structure of the T. ciliata complex from the whole genome perspective.…”

A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation

“…Its genetic conservation is of increasing concern due to overcutting and a low natural regeneration rate in China. A conservation strategy based on the T. ciliata complex rather than a single variety was recommended from the analysis of the population genetic structure [3] and phylogenetic relationships among varieties [45]. A similar case was also reported in an endangered Araucaria angustifolia, whose varieties were rarely considered in conservation strategies [46,47].…”