Abstract
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 atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia – Cyclobalanopsis and Ilex. 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 Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA 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 cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis 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.
Highlights
Understanding the biodiversity of ecosystems is critical for revealing the biome assembly and its function in different ecosystems (Hebert et al, 2003; Lahaye et al, 2008; Pitman et al, 2008)
One hundred and forty-seven individuals belonging to 29 species of Quercus section Cyclobalanopsis from East Asia and 125 individuals of the 28 species of section Ilex from East Asia were included in our studies
One individual of Lithocarpus henryi was used as outgroup to root the tree of genus Quercus
Summary
Understanding the biodiversity of ecosystems is critical for revealing the biome assembly and its function in different ecosystems (Hebert et al, 2003; Lahaye et al, 2008; Pitman et al, 2008). The key diagnostic traits may be under selection or subjected to parallel evolution providing false information on the identity of the taxa. Complementing techniques such as DNA sequences under neutral evolution have become an efficient way to identify species (Hollingsworth, 2007; CBOL Plant Working Group, 2009; Valentini et al, 2009; Hollingsworth et al, 2016). There is a challenge for DNA barcoding to discriminate closely related species, especially for those with shallow phylogeny and complex evolutionary history (Newmaster et al, 2008; Chen et al, 2015; Yan et al, 2015), such as species-rich genera, Quercus
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