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Data from: Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict-containing dioecious forest tree

Citation

Zhu, Shanshan et al. (2021), Data from: Patterns of genotype variation and demographic history in Lindera glauca (Lauraceae), an apomict-containing dioecious forest tree, Dryad, Dataset, https://doi.org/10.5061/dryad.70rxwdbtw

Abstract

Aim: The historical circumstances promoting the transition from sexual to apomictic reproduction in dioecious plant species remains poorly understood. Here, we investigated the divergence and demographic history of Lindera glauca, a dioecious tree considered to be facultatively apomictic in China while comprising only females (obligate apomicts) in Japan.

Location: East Asia (China and Japan)

Methods: Samples from 42 populations were genotyped using chloroplast DNA and nuclear microsatellite (nSSR) loci to assess genetic diversity and structure. The nSSR genotypes were also used to detect the mode of reproduction in Chinese and Japanese populations, respectively. Approximate Bayesian Computation on nSSRs and palaeoclimatic niche models provided further insights into the evolutionary and population demographic history.

Results: Chinese L. glauca was found to harbour both sexual and asexual genotypes. Chinese and Japanese L. glauca underwent roughly contemporaneous bottlenecks during a mid-Pleistocene glacial period, possibly marking the split-time of the island lineage from its mainland ancestor. In contrast to Chinese L. glauca, the Japanese lineage experienced a massive range contraction during the Last Glacial Maximum and postglacial expansions.

Main conclusions: While reproductive assurance plays an important role in the selection of apomixis in Chinese L. glauca, the lack of male plants in Japan likely reflects population demographic history driven by (Late) Quaternary climate change. Hence, the present study demonstrates a possible link between palaeoclimate change and the transition to exclusively apomictic reproduction in a dioecious tree.

Methods

All 617 samples were genotyped at 19 nSSR loci using primers and amplification protocols developed specifically for Lindera glauca (Echt, Deemer, Kubisiak, & Nelson, 2006; Edwards & Niesenbaum, 2007; Xiong et al., 2016; Zhu, Ding, Yap, & Qiu, 2016; see Table S2). Alleles were manually scored and determined using genemarker (version 2.2.0; SoftGenetics, State College, PA, USA).

We performed demographic history analysis based on these data using ABC and also provided the R scripts.

We also provided a file of the Maxent process and the results.

Usage Notes

The original population code has a separate form file.

The microsatellite genotype for all 617 Lindera glauca samples is included in the abc_scripts190326.zip.

The ReadMe file for R scripts is also included.

Funding

State Key Basic Research and Development Plan of China*, Award: 2017YFA0605104

National Natural Science Foundation of China, Award: 31872652

National Natural Science Foundation of China, Award: 31570214

National Natural Science Foundation of China, Award: 31561143015

State Key Basic Research and Development Plan of China, Award: 2017YFA0605104