DOI: 10.5061/dryad.q2bvq83fv
title: Combined genotype and phenotype analyses reveal patterns of genomic adaptation to local environments in the subtropical oak Quercus acutissima

description: Understanding the effects of the demographic dynamics and environmental
 heterogeneity on the genomic variation of forest species is important not
 only for uncovering the evolutionary history of the species but also for
 predicting their ability to adapt to climate change. In this study, we
 combined a common garden experiment with range-wide population genomics
 analyses to infer the demographic history and characterize patterns of
 local adaptation in a subtropical oak species, Quercus acutissima. We
 scanned about 8% of the oak genome using a balanced representation of both
 genic and non-genic regions and identified a total of 55,361 SNPs in 167
 trees. Genomic diversity analyses revealed an east-west split in the
 species distribution range. Coalescent-based model simulations inferred a
 late Pleistocene divergence in Q. acutissima between the east and west
 groups as well as subsequent pre-glaciation population expansion events.
 Consistent with observed genetic differentiation, morphological traits
 also showed east-west differentiation and the biomass allocation in
 seedlings was significantly associated with precipitation. Environment was
 found to have a significant and stronger impact on the non-neutral than
 the neutral SNPs, and also significantly associated with the phenotypic
 differentiation, suggesting that apart from the geography, environment had
 played a role in determining non-neutral and phenotypic variation. Our
 approach, which combined a common garden experiment with landscape
 genomics data, validated the hypothesis of local adaptation of this
 long-lived oak tree of subtropical China. Our study joins the small number
 of studies that have combined genotypic and phenotypic data to detect
 patterns of local adaptation.
description: The RAD-seq library was prepared using 200ng DNA from each
 individual tree; after extraction, DNA samples were digested with the
 restriction enzyme EcoRI. Illumina sequencing adaptor and a unique barcode
 were ligated to EcoRI-digested fragments. All the individual libraries
 were pooled and randomly sheared, and amplified by PCR using Illumina
 sequencing primers. DNA fragments with insert fragment sizes from 200–400
 bp were isolated from a 2.0% agarose gel using QiaQuick gel extraction
 kits (Qiagen, Inc., Hilden, Germany). These fragments were then double–end
 sequenced on an Illumina HiSeq2500 (Illumina Inc., San Diego,
 USA). We scored the phenotypic traits of three
 1-year-old seedlings that were randomly selected from each population
 grown in the common garden<b>.</b>The traits that we measured
 included total mass, leaf area, leaf mass fraction (LMF, g leaf mass
 g<sup>-1</sup> total mass), stem mass fraction (SMF, g stem
 mass g<sup>-1</sup> total mass), root mass fraction (RMF, g
 root mass g<sup>-1</sup> total mass), and specific taproot
 length (STRL, mm root length g<sup>-1</sup> root mass), which
 measures the root extension achieved per unit root mass. LMF, SMF, and RMF
 represent biomass partitioning among the major organs, and STRL represents
 the efficiency of soil depth penetration to access deeper water.