Population and conservation genetics using RAD sequencing in four endemic conifers from South America

The emblematic conifer flora of Chile has experienced widescale habitat loss and fragmentation. Coupled with the complex topography of the region, this leads to a prediction of high levels of genetic drift and isolation leading to strong population differentiation, and the potential for negative genetic consequences. To address the degree to which these predictions are realised, we conducted a comparative population genetic survey in four endemic conifers from South America each with a restricted area of distribution and of conservation concern. Between seven and ten populations (per species) were included in this investigation, covering their entire natural distribution in Chile. We used restriction site-associated DNA markers (RAD-seq), including optimisation (de novo assembly) to accommodate the large and complex genomes of conifers. The main finding of population genetic analyses was a similar level of nucleotide diversity (pi= 0.11-0.27 %) and low levels of genetic structure in all four species (FST = 0.017-0.062). These results are likely due to the extreme longevity of individuals of these species restricting divergence due to genetic drift. Thus, despite their currently highly fragmented ranges, we did not detect evidence for high levels of population differentiation and genetic isolation. This suggests some resilience to negative genetic impacts of habitat fragmentation, and the longevity of the individual trees may provide considerable buffering capacity. We recommend following studies focusing on genotyping the seedling generation, on a basis to assess whether there is any evidence for an early warning of genetic isolation and/or elevated inbreeding in the currently establishing cohorts.