Horticultural breeding mediates the selection of traits of interest, providing an opportunity for tracking phylogenetic potential of the trait shift. Here, we used Acer L. Sect. Palmata Pax and A. palmatum Thunb. cultivars as models to test phylogenetic signals of taxonomically relevant traits. Common chloroplast DNA barcoding markers facilitated the evaluation of genetic distance and phylogenetic relationships between these maple species. The determined short genetic distances resulted in unresolved relationships between A. palmatum cultivars and other Acer Sect. Palmata species after non-metric multidimensional scaling analysis, but was improved by discriminate analysis of principal components. However, genetic relationships among cultivars were clustered and admixed, indicating the same maternal source species for horticultural breeding. Phylogenetic reconstruction revealed an early Miocene origin for Acer Sect. Palmata. Cultivars and varieties of A. palmatum coalesced earlier than expected, indicating that the chloroplast markers cannot reflect the horticultural and breeding history of maples. Similar macroevolutionary rates of the infraspecies of A. palmatum with the species of Acer Sect. Palmata imply that the domestication and breeding process did not alter the speciation rate of this group. Nonsignificant phylogenetic signals for all the examined traits of Acer Sect. Palmata suggested that such species diversification could be explained by adaptive plasticity to paleoclimatic change. However, strong phylogenetic signals for leaf traits of infraspecies of A. palmatum suggested a phylogenetic-related trait shift during initial species divergence. Because the breeding process simulates divergent selection, we infer that genetic-based trait conservatism ensured a stable genetic basis for trait shift during initial species divergence.
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