DOI: 10.5061/dryad.9zw3r22f5
title: Shifting roles of the East China Sea in the phylogeography of red nanmu in East Asia

description: 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.
description: All 640 samples were genotyped at 9 nSSR loci using primers and
 amplification protocols developed specifically for <em>Machilus
 thunbergii</em> (Kaneko et al. 2012, see Table S2), and 361 samples
 were sequenced using primers redesigned according to a <em>M.
 thunbergii</em> 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. <i>Scientific Reports</i>, <i>6</i>, 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, <i>Machilus thunbergii</i> and <i>Machilus kusanoi</i> (Lauraceae), in Taiwan. <i>Journal of Biogeography</i>,<b> </b><i>33</i>(5), 936–947. https://doi.org/10.1111/j.1365-2699.2006.01431.x
description: The Coordinates_of_Machilus_thunbergii.csv file includes the
 locations of <em>Machilus thunbergii</em> 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.