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

The emblematic conifer flora of Chile has experienced wide-scale 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 resulting in 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 of conservation concern and with a restricted distribution area. Between seven and ten populations per species were sampled, covering their entire natural distribution in Chile. We used restriction site-associated DNA markers (RAD-seq), with de novo assembly and optimisation, to accommodate the large and complex genome of conifers. The main finding was low levels of genetic structure in all four conifer species (F-ST = 0.017-0.062). This pattern was strikingly consistent across all four species. These results are likely due to the extreme longevity of individuals restricting divergence due to genetic drift. Thus, despite the currently highly fragmented ranges of these conifer species, 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 follow-up studies focusing on genotyping the seedling generation, to assess whether there is any evidence for the early warning of genetic isolation and/or elevated inbreeding in the currently established cohorts.