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Microsatellite data of 21 EST-SSR loci from all 503 Emmenopterys henryi samples

Citation

Xu, Wuqin (2021), Microsatellite data of 21 EST-SSR loci from all 503 Emmenopterys henryi samples, Dryad, Dataset, https://doi.org/10.5061/dryad.3tx95x6fj

Abstract

Aim: Several hypotheses are available to predict change in genetic diversity at expanding peripheral ranges. However, empirical evidence to test predictions of the centre-periphery hypothesis (CPH) at contracting range limits is scarce. To address this issue, we assessed spatial patterns of genetic variation, effective population size, and contemporary and historical gene flow in a widespread, Tertiary relict tree species from subtropical China.

Location: Warm-temperate deciduous forests of subtropical China.

Taxon:Emmenopterys henryi (Rubiaceae)

Methods: We applied kernel density estimation to determine the centre of the species’ geographical range. Using microsatellite markers, we assessed genetic structure and diversity in 36 populations (503 individuals) sampled in the centre and periphery across the species’ range. We further examined both historical and contemporary gene flow. Finally, we applied coalescent methods to simulate population demography.

Results: In support of CPH predictions, the highest density of E. henryi coincided with the geographical centre of the species’ distribution range, and genetic diversity significantly declined with distance from this range centre. Historical migration from the core to the edge was significantly higher than in the opposite direction, whereas contemporary migration followed an opposite pattern. Central and peripheral populations had similar levels of genetic differentiation.

Main conclusions: Core-to-edge patterns of genetic diversity, but not genetic differentiation, were consistent with the CPH in E. henryi. Also in line with the CPH, historical (but not contemporary) migration from the core to the edge was significantly higher than in the opposite direction. Results suggest that the complex topography in subtropical China and population demographic processes may strongly influence whether CPH predictions are met in different population genetic parameters.

Methods

Total genomic DNA was extracted from the dried leaf tissue using DNA Plantzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s protocol. Following protocols of Zhu et al. (2016), we developed a total of 21 polymorphic EST-SSR (expressed sequence tags-simple sequence repeat) markers from the transcriptome of E. henryi (GenBank accession number: SRR9878962). The EST-SSR loci were polymerase chain reaction (PCR) amplified following Zhu et al. (2016) and loaded on a 3730xl DNA Analyzer (Applied Biosystems, Foster City, CA, USA). Alleles were manually scored and determined using GeneMarker 2.4.0 (SoftGenetics, State College, PA, USA).