This study focuses on the frequency of reproductive modes and the role of reproductive mode variation in diversification of the genus Sorbus s.l. and evolutionary success of individual taxa. Our sampling covers all four ploidies known in Sorbus and includes stabilized taxa and recently formed biotypes. We infer reproductive modes of 3660 seeds using the flow cytometric seed screen method; we also calculated ploidy of contributing pollen. Sorbus shows high variability in reproduction pathways (sexuality, apomixis, formation of BIII hybrids, haploid parthenogenesis). Diploids are sexual, whereas polyploids show predominantly pseudogamous apomixis. In half of the polyploids studied, several reproductive modes were present and even intra-individual variation was detected. Diploids, tetraploids and pentaploids are pollinated by conspecific pollen, whereas triploids are largely, but not fully, dependent on the pollen of other species. In pseudogamous seeds, fertilization of the central cell by both sperms is a dominant pathway of endosperm origin. Flow cytometry of pollen did not detect unreduced pollen at any ploidy. The principal mechanisms of diversification in Sorbus are residual sexuality in apomicts, production of triploid taxa from diploid–tetraploid crosses and production of BIII hybrids. Evolutionary success of Sorbus taxa is largely dependent on the breeding system and is determined by self-(in)compatibility and the interplay between stabilizing apomixis and variation-generating sexuality.

Parallel adaptation results from the independent evolution of similar traits between closely related lineages and allows us to test to what extent evolution is repeatable. Similar gene expression changes are often detected but the identity of genes shaped by parallel selection and the causes of expression parallelism remain largely unknown. By comparing genomes and transcriptomes of four distinct foothill-alpine population pairs across four treatments, we addressed the genetic underpinnings, plasticity and functional consequences of gene expression parallelism in alpine adaptation. Seeds of eight populations of Arabidopsis arenosa were raised under four treatments that differed in temperature and irradiance, factors varying strongly with elevation. Parallelism in differential gene expression between the foothill and alpine ecotypes was quantified by RNA-seq in leaves of young plants. By manipulating temperature and irradiance, we also tested for parallelism in plasticity (i.e., gene-environment interaction, GEI). In spite of global non-parallel patterns transcriptome wide, we found significant parallelism in gene expression at the level of individual loci with an over-representation of genes involved in biotic stress response. In addition, we demonstrated significant parallelism in GEI, indicating a shared differential response of the originally foothill versus alpine populations to environmental variation across mountain regions. A fraction of genes showing expression parallelism also encompassed parallel outliers for genomic differentiation, with greater enrichment of such variants in cis-regulatory elements in some mountain regions. In summary, our results suggest frequent evolutionary repeatability in gene expression changes associated with the colonization of a challenging environment that combines constitutive expression differences and plastic interaction with the surrounding environment.

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27Parallel adaptation results from independent evolution of similar traits between closely related 28 lineages and allows testing to which extent evolution is repeatable. Parallel adaptation often 29 involves similar gene expression changes but the identity of genes shaped by parallel selection 30 and the causes of expression parallelism remains largely unknown. By comparing genomes 31 and transcriptomes of four independent foothill-alpine population pairs across four 32 treatments, we addressed genetic basis, plasticity and functional consequences of gene 33 expression parallelism in alpine adaptation. Seeds of four population pairs of Arabidopsis 34 arenosa from distinct mountain regions were raised under four treatments that differed in 35 temperature and irradiance, factors varying strongly with elevation. Parallelism in gene 36 expression was quantified by RNA-seq in leaves of young plants. By manipulating 37temperature and irradiance, we also tested for parallelism in plasticity (gene-by-environment 38 interaction [GEI]). We found significant parallelism in differential gene expression across 39 four independently recruited alpine ecotypes with an overrepresentation of genes involved in 40 biotic stress response. In addition, we demonstrated significant parallelism in GEI indicating 41 shared response to environmental variation in our foothill and alpine populations. Fraction of 42 genes showing expression parallelism also encompassed genomic variants showing outlying 43 differentiation, with greater enrichment of such variants in cis-regulatory elements. In 44 summary, our results suggest frequent evolutionary repeatability in shaping expression 45 difference associated with colonization of an alpine environment and support the hypothesis 46 of an important role of genetic variation in cis-regulatory elements in gene expression 47 parallelism.48 49

Hybridization associated with polyploidization and apomixis is a frequent mechanism of speciation. Sorbus is a genus with ongoing hybridization resulting in a polyploid complex with different parental lineage. Triparens is the smallest hybridogenous subgenus of Sorbus so far known to comprise only two taxa, S. intermedia and S. × liljeforsii that combine the genomes of three taxa (S. aria agg., S. aucuparia and S. torminalis). To elucidate the origins of S. dacica, S. paxiana and S. tauricola, three new trigenomic candidates formerly believed to be of biparental origin with either S. aria agg. × S. aucuparia or S. aria agg. × S. torminalis lineage we combined data from HPLC and chloroplast DNA analysing additional 33 related taxa as well. We concluded that the ‘torminalis-type’ flavonoid profile and the ‘aucuparia-type’ plastid indicate the participation of both S. torminalis and S. aucuparia resulting in the formation of S. dacica, S. paxiana and S. tauricola. Sorbus aria agg. as the third ancestor and as a necessary link to meet genes of S. torminalis and S. aucuparia in one genome is obvious from morphological features (densely tomentose undersides of leaves). The tetraploid cytotypes and obligate pseudogamy of S. dacica and S. paxiana were determined by flow cytometry and are published here for the first time. The most probable evolutionary scenario for Triparens species is: 1. a diploid sexual S. aucuparia as pollen acceptor hybridized with a tetraploid apomictic taxon from the S. aria agg. producing a triploid apomictic taxon with ‘aucuparia-type’ plastid inherited maternally; 2. during a second crossing event this subgenus Soraria hybrid as maternal progenitor hybridized with the sexual diploid S. torminalis (providing gene(s) of apigenin O-glucuronide synthesis) forming a tetraploid Triparens hybrid with ‘aucuparia-type’ plastid and ‘torminalis-type’ flavonoids.