Populations intermediate between the diploid and sexual Sorbus aucuparia and the tetraploid and facultative apomictic Sorbus hybrida are scattered in coastal regions of southern Scandinavia. Our aims were to investigate whether these populations were of local and independent origins, whether they were morphologically and molecularly distinct from each other and whether they could give rise to constant offspring by apomixis. Six intermediate populations from the Baltic Sea basin were studied for variation at nuclear and plastid microsatellite loci, for morphological differentiation patterns, and for ploidy level by flow cytometry. Seeds were sown to check for constancy with the mother plants. Three populations from Gotland and possibly the small population from Uppland were in each case fixed for a unique combination of genetic markers, had restricted variation in leaf shape and were morphologically divergent from each other. Flow cytometry analysis showed that the four genetically monomorphic populations were consistently triploid. Cultivation showed that offspring from trees within two of the monomorphic populations had leaf shapes closely similar to the mother individuals. In contrast, a population from Gotland and a population from Åland were variable at molecular marker loci and were variable in leaf shape. The three monomorphic Gotland populations and possibly also the Uppland population propagate asexually by apomixis, and they have independent origins. The two variable populations are apparently composed of hybrids that have been formed repeatedly and independently between individuals of the two parental species growing at the same sites. One of the Gotland apomicts has already been described as Sorbus teodori. Sorbus faohraei Hedrén & J.Levin and Sorbus atrata Hedrén & J.Levin are described as new apomictic species from Gotland.

New sequencing technologies allow development of genome-wide markers for any genus of ecological interest, including plant genera such as Betula (birch) that have previously proved difficult to study due to widespread polyploidy and hybridisation. We present a de novo reference genome sequence assembly, from 67X short read coverage, of Betula nana (dwarf birch) – a diploid that is the keystone woody species of sub-arctic scrub communities but of conservation concern in Britain. We also present 100bp PstI RAD markers for B. nana and closely related Betula tree species. Assembly of RAD markers in 15 individuals by alignment to the reference B. nana genome yielded 44k-86k RAD loci per individual, whereas de novo RAD assembly yielded 64k-121k loci per individual. Of the loci assembled by the de novo method, 3k homologous loci were found in all 15 individuals studied, and 35k in 10 or more individuals. Matching of RAD loci to RAD locus catalogs from the B. nana individual used for the reference genome, showed similar numbers of matches from both methods of RAD locus assembly but indicated that the de novo RAD assembly method may over-assemble some paralogous loci. In 12 individuals hetero-specific to B. nana 37k-47k RAD loci matched a catalog of RAD loci from the B. nana individual used for the reference genome, whereas 44k-60k RAD loci aligned to the B. nana reference genome itself. We present a preliminary study of allele sharing among species, demonstrating the utility of the data for introgression studies and for the identification of species-specific alleles.