DOI: 10.5061/dryad.78j501j
title: Data from: A multiscale approach to detect selection in non-model tree species: widespread adaptation despite population decline in Taxus baccata L.

description: Detecting the molecular basis of local adaptation and identifying
 selective drivers is still challenging in non-model species. The use of
 purely population genetic approaches is limited by some characteristics of
 genetic systems, such as pleiotropy and polygenic control, and parallel
 evidence from phenotypic-based experimental comparisons is required. In
 long-lived organisms, the detection of selective pressures might also be
 precluded by evolutionary lag times in response to the environment. Here,
 we used the English yew to showcase an example of a multiscale integrative
 approach in a non-model species with limited plant and genomic resources.
 We combined information from two independent sources, phenotypes in a
 common environment and genomic data in natural populations, to investigate
 the signature of selection. Growth differences among populations in a
 common environment, and phenological patterns of both shoot elongation and
 male strobili maturation, were associated with climate clines, providing
 evidence for local adaptation and guiding us in the selection of
 populations for genomic analyses. We used information on over 25,000 SNPs
 from c. 1,200 genes to infer the demographic history and to test for
 molecular signatures of selection at different levels: SNP, gene and
 biological pathway. Our results confirmed an overall demographic history
 of population decline, but we also found evidence for putative local
 adaptation at the molecular level. We identified or confirmed several
 candidate genes for positive and negative selection in forest trees,
 including the Pseudo-response regulator 7 (PRR7), an essential component
 of the circadian clock in plants. In addition, we successfully tested an
 approach to detect polygenic adaptation in biological pathways, allowing
 us to identify the Flavonoid biosynthesis pathway as a candidate
 stress-response pathway that deserves further attention in other plants.
 Finally, our study contributes to the emerging view that explaining
 contemporary standing genetic variation requires considering adaptation to
 past climates, especially for long-lived trees.
description: Taxus baccata SNP
 fileThis VCF file includes
 the filtered SNP dataset for 120 Taxus baccata samples (25,726
 SNPs).taxus_filtered_HWE3.vcfCorrespondence between plate codes and sample codes.This file includes the correspondece between plate codes and sample codes for the 120 Taxus baccata samples.Correspondence_plates_samples.xlsxTaxus Shoot Growth DataThis file contains data for Taxus baccata shoot growth measured in the Valsaín clonal bank during four consecutive years (2009-2012). The file also contains individual information about provenance (population), genet and sex.Taxus Shoot ElongationThis file contains data for Taxus baccata phenology of shoot elongation from 2010 to 2012. The file also contains individual information about provenance (population), genet and sex.Taxus Male StrobiliThis file contains data for Taxus baccata phenology of male strobili maturation from 2010 to 2012. The file also contains individual information about provenance (population) and genet.