AUTHOR=Yan Mengxiao , Xiong Yanshi , Liu Ruibin , Deng Min , Song Jiaojiao 

TITLE=The Application and Limitation of Universal Chloroplast Markers in Discriminating East Asian Evergreen Oaks

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00569

DOI=10.3389/fpls.2018.00569

ISSN=1664-462X

ABSTRACT=<p>The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers <italic>atp</italic>I-<italic>at</italic>pH, <italic>mat</italic>K, <italic>psb</italic>A-<italic>trn</italic>H, and <italic>ycf</italic>1, can discriminate the two evergreen oak sections in Asia – <italic>Cyclobalanopsis</italic> and <italic>Ilex.</italic> Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the <italic>Quercus</italic> sections was also compared. Overall, we found that universal chloroplast DNA (<italic>cp</italic>DNA) barcoding markers could resolve two clades in <italic>Quercus</italic>, i.e., subgenus <italic>Cerris</italic> (Old World Clade) and subgenus <italic>Quercus</italic> (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each <italic>cp</italic>DNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the <italic>cp</italic>DNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of <italic>cp</italic>DNA markers to discriminate different species. When comparing diversification pattern across <italic>Quercus</italic> sections (<italic>Cyclobalanopsis, Ilex, Cerris, Quercus</italic>, and <italic>Protobalanus</italic>), we found that section <italic>Ilex</italic> was the most genetically diverse, and section <italic>Cyclobalanopsis</italic> was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.</p>