DOI: 10.5061/dryad.65th6
title: Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

description: All species of the genus Populus (poplar, aspen) are dioecious, suggesting
 an ancient origin of this trait. Despite some empirical counter examples,
 theory suggests that nonrecombining sex-linked regions should quickly
 spread, eventually becoming heteromorphic chromosomes. In contrast, we
 show using whole-genome scans that the sex-associated region in Populus
 trichocarpa is small and much younger than the age of the genus. This
 indicates that sex determination is highly labile in poplar, consistent
 with recent evidence of ‘turnover’ of sex-determination regions in
 animals. We performed whole-genome resequencing of 52 P. trichocarpa
 (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals
 of known sex. Genomewide association studies in these unstructured
 populations identified 650 SNPs significantly associated with sex. We
 estimate the size of the sex-linked region to be ~100 kbp. All SNPs
 significantly associated with sex were in strong linkage disequilibrium
 despite the fact that they were mapped to six different chromosomes (plus
 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that
 this is likely due to genome misassembly. The segregation pattern of
 sex-associated SNPs revealed this to be an XY sex-determining system.
 Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are
 much more recent than the divergence of P. trichocarpa (poplar) and
 Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we
 found no XY haplotype divergence within the P. trichocarpa sex-determining
 region. These two species therefore have a different genomic architecture
 of sex, suggestive of at least one turnover event in the recent past.
description: PairwiseLDThis file contains estimates of pairwirse linkage disequilibrium (r^2) for all 623 SNPs significantly associated with gender in mapping population T52.chr19_tree_MLNewick tree file for Figure 3 panel b (concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107)chr19Fasta aligment of concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.chr19_treeFasta aligment of concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for generating phylogenetic tree on Figure 3b.sanger_7690067_oneclone_MLNewick tree file for Figure 3 panel a (Amplicon1:Chr09:7690067)sanger_7690067_annoFasta aligment of Amplicon1:Chr09:7690067, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.sanger_7690067_onecloneFasta aligment of Amplicon1:Chr09:7690067, used for generating phylogenetic tree on Figure 3a.sanger_7690067_MLNewick tree file for Figure S2 panel a (Amplicon1:Chr9:7690067, all P. tremuloides clones included)sanger_7690067Fasta aligment of Amplicon1:Chr9:7690067 with all P. tremuloides clones included used for generating phylogenetic tree on Figure S2 panel a40024_sanger_nousat_fortree_MLNewick tree file for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)40024_sanger_nousat_fortreeFasta alignment for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)41515_sanger_all_tree_MLNewick tree file for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)41515_sanger_all_treeFasta alignment for Figure S2 panel d (Chr19 Amplicon2:Chr19:41515, all P. tremuloides clones included)44107_sanger_tree_MLNewick tree file for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)44107_sanger_treeFasta alignment for Figure S2 panel e (Chr19 Amplicon3:Chr19:44107 , all P. tremuloides clones included)Association_SNPfiles_PlinkPlink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for GWAS in T52 (T52v2maf01gr09), B34 (B34v2maf01gr09) and BT68 (BT68v2maf01gr09new)Admixture_inputfilesPlink input SNP files (from mapping to the P. trichocarpa reference genome v2.2) used for Admixture analysis in T52 (T52v2maf01gr1_LDprunned_thin01), B34 (B34v2maf01gr1_LDprunned) and BT68 (BT68v2POPSTnew)