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Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia

Citation

Jiang, Kai et al. (2021), Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia, Dryad, Dataset, https://doi.org/10.5061/dryad.9zw3r22f5

Abstract

This dataset contains one README file and two raw data files on the distribution and genetic data described in the paper: Jiang et al. (2021) Shifting roles of the East China Sea in the phylogeography of Machilus thunbergii (Lauraceae) in East Asia. Journal of Biogeography.

Ecological niche modeling was employed to predict the potential distribution of M. thunbergii during the Last Glacial Maximum (LGM) and the last interglacial period. Nuclear microsatellite and chloroplast markers were used to reveal the phylogeographic pattern and infer the population history of 33 M. thunbergii populations.

The ecological niche models suggested that the ECS provided potentially suitable habitats for M. thunbergii during the LGM. A sharp change in cpDNA haplotypes was found along the eastern China coasts, while microsatellites revealed a clinal pattern for genetic composition from eastern China to central Japan. The divergent lineages formed an admixture on the Zhoushan Archipelago of China and Kyushu Island of Japan. The estimated divergent and admixture times were c. 68 kyr and c. 15 kyr, corresponding to the periods where there were rising sea levels after the MIS4 glaciation and falling sea levels during the LGM, respectively. 

Machilus thunbergii probably underwent alternating population isolation during interglacial periods and connection during glacial maxima across the ECS, but such periodicity of isolation and connection seems not to have promoted diversification as suggested by the species pump hypothesis. Incipient divergence has been periodically wiped out due to frequent coalescence, rendering the ECS more like a “species vacuum”, particularly for species with relatively long generation lengths.

Methods

All 640 samples were genotyped at 9 nSSR loci using primers and amplification protocols developed specifically for Machilus thunbergii (Kaneko et al. 2012, see Table S2), and 361 samples were sequenced using primers redesigned according to a M. thunbergii complete chloroplast sequence (GenBank accession number: NC_038204.1) (see Table S3). Detailed amplification protocols and conditions are described in Fan et al. (2016) and Wu et al. (2006). The amplified products were bi-directionally sequenced with an ABI 3730xl sequencer.

Fan, D., Hu, W., Li, B., Morris, A. B., Zheng, M., Soltis, D. E., & Zhang, Z. (2016). Idiosyncratic responses of evergreen broad-leaved forest constituents in China to the late Quaternary climate changes. Scientific Reports, 6, 31044. https://doi.org/10.1038/srep31044

Wu, S. H., Hwang, C. Y., Lin, T. P., Chung, J. D., Cheng, Y. P., & Hwang, S. Y. (2006). Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in Taiwan. Journal of Biogeography, 33(5), 936–947. https://doi.org/10.1111/j.1365-2699.2006.01431.x

Usage Notes

The Coordinates_of_Machilus_thunbergii.csv file includes the locations of Machilus thunbergii which is used for ecological niche model analysis.

The Raw_microsatellite_genotypes.xslx file includes the original microsatellite genotypes.

The README file contains an explanation of the distribution and genetic data in detail.

Funding

National Natural Science Foundation of China, Award: 31630008

National Key Research and Development Program of China, Award: 2016YFC0503102

Shanghai Municipal Administration of Forestation and City Appearances, Award: F132415

Shanghai Municipal Administration of Forestation and City Appearances, Award: G182418

Shanghai Municipal Administration of Forestation and City Appearances, Award: F132415