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Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci

Citation

Zhang, Zhi-Yong et al. (2020), Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci, Dryad, Dataset, https://doi.org/10.5061/dryad.wpzgmsbk8

Abstract

Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18,555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus and Engleriana) and most sections was well supported, except for sect. Lucida, which was paraphyletic with respect to sect. Longipetiolata. We also found a major phylogenetic conflict among North American, East Asian and West Eurasian lineages of subgen. Fagus. Three segregates that have isolated distribution (F. mexicana, F. multinervis, and F. orientalis) were independent evolutionary units. Biogeographic analysis with fossils suggested that Fagus could have originated in North Pacific region in late Early Eocene. Major diversifications coincided with a climate aberration at the Eocene/Oligocene boundary and the global cooling since Mid-Miocene. The Late Miocene accelerated global cooling and the Pleistocene glaciations would have driven beeches into East Asia, North America and West Eurasia. Meanwhile, range reduction and extinction in high latitudes, in central Asia and in western North America converged to form beech modern distribution pattern. This study provides a first attempt to disentangle the biogeographic history of beeches in the context of a nearly resolved and time-calibrated phylogeny, which may shed new insights into the formation of the temperate biome in the Northern Hemisphere.

Methods

Total genomic DNA was isolated from silica-gel dried leaves, using a modified CTAB protocol. Twenty-eight nuclear loci were successfully amplified using the primers designed in this paper. All PCR reactions were performed in a volume of 25 μL, including 1 μl 40–100 ng of template DNA, 22 μl 1.1×T3 Super PCR Mix (Tsingke, Beijing), 1 μl 10 μM of each primer. The PCR programs for all 28 loci were as follows: 98 ℃ for 3 min; 30 cycles at 98 ℃ for 10 s, 50–60 ℃ for 10 s, 72 ℃ for 15 s; followed by a single cycle at 72 ℃ for 2 min; finally stopped at 10 ℃. The PCR products were sequenced on an ABI 3730XL sequencer (Applied Biosystems, Foster City, CA, USA) using the PCR primers. The fragments with heterozygous sites were sequenced bidirectionally. New sequences generated in this study were deposited in GenBank (under accession numbers MT727083–MT729360). The orthologous sequences in seven published genomes,C. mollissima, Quercus suber L., Q. robur L., Q. lobata Née and F. sylvatica, were extracted using Blastn algorithm. All sequences of a locus were aligned using the online service MAFFT.

Funding

National Natural Science Foundation of China, Award: 31770236, 30760016, and 31560064

Strategic Priority Research Program, Chinese Academy of Sciences, Award: XDB31000000

Strategic Priority Research Program, Chinese Academy of Sciences, Award: XDB31000000