Ancient relicts in the limelight :an evolutionary study of diversity and demographic history in species of the broad-leaved temperate forest tree genus Tilia

Abstract

Tilia L. is a temperate-forest tree genus with a wide northern hemisphere distribution. Several species within the genus are affected by forest fragmentation. Three species were the focus of this study, T. cordata Mill. (small-leaved lime) and T. platyphyllos Scop. (large-leaved lime) from the UK, Austria, Poland, and western Siberia and T. sibirica Bayer (Siberian lime) from southern Siberia. Tilia specific microsatellite markers were used to assess various population genetics indices. Genetic diversity and structure of UK T. cordata and T. platyphyllos populations were estimated. To determine the genetic and demographic history of T. sibirica and T. cordata, Approximate Bayesian Computation (ABC) analyses were used. An investigation into the clonal architecture of the three species was carried out to assess the level of clonality and the impact of clonal reproduction on genetic diversity. In addition, Next Generation Sequencing of the Tilia leaf transcriptome was carried out using direct RNA sequencing Results confirm that the three species are diploid and outcrossing. Although hybridisation occurs among T. cordata and T. platyphyllos, the two are distinct biological units with high genetic diversity and intra-specific population structure. Significant genetic differentiation was observed between T. sibirica and T. cordata and low genetic diversity in the Siberian lime was revealed. ABC analysis suggests a relatively recent (Early Holocene) divergence between the Siberian lime and the small-leaved lime. The Holocene split coincided with a westerly migration of Tilia genotypes that may have contributed to the recolonization of T. cordata in Europe. Fewer clones were observed in T. platyphyllos than the other two species and range-edge populations experience greater clonality than central European populations. Clonal occurrence does not appear to have had a negative effect on genetic diversity. A method for the de novo assembly and annotation of the leaf transcriptome from T. cordata and T. platyphyllos is provided. Potentially thousands of simple sequence repeats (SSRs) from each species have been identified.