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Natural hybrid zones in forest trees provide systems to study the transfer of adaptive genetic variation by introgression. Previous landscape genomic studies in Populus trichocarpa, a keystone tree species, indicated genomic footprints of admixture with its sister species Populus balsamifera and identified candidate genes for local adaptation. Here, we explored the patterns of introgression and signals of local adaptation in P. trichocarpa and P. balsamifera, employing genome resequencing data from three chromosomes in pure species and admixed individuals from wild populations. Local ancestry analysis in admixed P. trichocarpa revealed a telomeric region in chromosome 15 with P. balsamifera ancestry, containing several candidate genes for local adaptation. Genomic analyses revealed signals of selection in certain genes in this region (e.g. PRR5, COMT1), and functional analyses based on gene expression variation and correlations with adaptive phenotypes suggest distinct functions of the introgressed alleles. In contrast, a block of genes in chromosome 12 paralogous to the introgressed region showed no signs of introgression or signatures of selection. We hypothesize that the introgressed region in chromosome 15 has introduced modular or cassette-like variation into P. trichocarpa. These linked adaptive mutations are associated with a block of genes in chromosome 15 that appear to have undergone neo- or subfunctionalization relative to paralogs in a duplicated region on chromosome 12 that show no signatures of adaptive variation. The association between P. balsamifera introgressed alleles with the expression of adaptive traits in P. trichocarpa supports the hypothesis that this is a case of adaptive introgression in an ecologically important foundation species.

Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole-genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, aspens, cottonwoods), Populus alba and P. tremula, using >8.6 million single nucleotide polymorphisms (SNPs) from WGS of population pools. We used the genomic data to (i) scan these species' genomes for regions of elevated and reduced divergence, (ii) assess key aspects of their joint demographic history based on genomewide site frequency spectra (SFS) and (iii) infer the potential roles of adaptive and deleterious coding mutations in shaping the genomic landscape of divergence. We identified numerous small, unevenly distributed genome regions without fixed polymorphisms despite high overall genomic differentiation. The joint SFS was best explained by ancient and repeated gene flow and allowed pinpointing candidate interspecific migrant tracts. The direction of selection (DoS) differed between genes in putative migrant tracts and the remainder of the genome, thus indicating the potential roles of adaptive divergence and segregating deleterious mutations on the evolution and breakdown of RI. Genes affected by positive selection during divergence were enriched for several functionally interesting groups, including well-known candidate 'speciation genes' involved in plant innate immunity. Our results suggest that adaptive divergence affects RI in these hybridizing species mainly through intrinsic and demographic processes. Integrating genomic with molecular data holds great promise for revealing the effects of particular genetic pathways on speciation.

Aim To elucidate the phylogeographical patterns in three Cenozoic relict species: Zelkova sicula, Z. abelicea and Z. carpinifolia (Ulmaceae).Location Sicily, Crete and Transcaucasia.Methods Two chloroplast loci (trnH-psbA and trnL) and the nuclear ribosomal markers ITS1 and ITS2 were sequenced for 154 samples collected from 14 populations of Z. abelicea, 16 populations of Z. carpinifolia, and the two known populations of Z. sicula. We obtained georeferenced data, calculated median joining networks and carried out diversity analyses. A few ex situ samples collected from botanical gardens, of the East Asian species Zelkova serrata, Z. schneideriana and Z. sinica, were also analysed for comparative purposes.Results High levels of variability were found in the chloroplast markers within Z. carpinifolia (15 haplotypes) and Z. abelicea (33 haplotypes), in association with strong phylogeographical structure. Conversely, Z. sicula was characterized by low diversity, with each population exhibiting a single haplotype. Lower variability was found for ITS1 and ITS2 within Z. carpinifolia and Z. abelicea (13 and 7 ribotypes per species, respectively), with Z. carpinifolia showing a high proportion of populations with no intragenomic polymorphism. In the triploid and clonal Z. sicula, all individuals displayed intragenomic polymorphism and seven ribotypes were identified.Main conclusions The chloroplast diversity of Z. abelicea and Z. carpinifolia suggests a very ancient history of diversification and structuring, with footprints of past expansions and more recent bottlenecks. Zelkova sicula has had a history of severe isolation and is likely to be of hybrid origin.

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