ORIGINAL PAPER Genetic diversity and inbreeding in natural and managed populations of Scots pine M. Rosario García Gil & Valentina Floran & Lars Östlund & T. J. BTim^ Mullin & Bengt Andersson Gull Received: 5 November 2014 /Revised: 4 February 2015 /Accepted: 23 February 2015 /Published online: 11 March 2015 # Springer-Verlag Berlin Heidelberg 2015 Abstract We carried out a study on Scots pine (Pinus sylvestris L.) in Sweden, where our objective was to quantify the genetic diversity and inbreeding associated with two wide- ly used managed-regeneration practices, planting with im- proved material from seed orchards and seed-tree regenera- tion, and compare these with that found in unmanaged natural forests. A total of 196 evenly spaced trees were sampled from a naturally regenerated and two managed-regeneration stands (plantation and seed-tree), in each of three different regions in Sweden (Arjeplog, Vihelmina, and Hammerdal). Population parameters were estimated for microsatellite loci from the nu- clear and chloroplast genomes (5 and 11 loci, respectively) and a single mitochondrial locus (nad7). Analysis of variance (ANOVA) shows no significant effects of stand management on the level of nuclear and mitochondrial genetic diversity or inbreeding (p <0.05). Duncan post-hoc analysis suggested sig- nificantly lower values for the chloroplast number of effective alleles (N ea_CP ) and total gene diversity (H t_CP ) for natural and plantation practices, as compared with seed-tree regeneration. The ANOVA supported a rather weak effect of the manage- ment factor (M) on N ea_CP and H t_CP , with p values of 0.08 and 0.07, respectively. Inbreeding coefficient (F 5 ) indicated a de- viation from random mating in all stands caused by an excess of homozygotes. All the stands are composed of a mixture of half- and full-sibs, but no pattern of spatial relatedness was detected in any of them. Our data suggest that genetic diver- sity is similar in both natural stands and those with managed regeneration, probably because regeneration practices did not decrease the population size to a point where random drift effects might be important. The estimates for the nuclear and mitochondrial (mt) genomes should be regarded with caution, as only five nuclear microsatellite (nSSR) loci less affected by null alleles (<25 %) were analyzed. Our investigation indi- cates that the reduction to five nSSR loci does not change the main finding of an absence of differences in genetic diver- sity among stands, except for the number of rare alleles (RA), which is lower when estimated from data for eight nSSR loci. Keywords Nuclear SSR . Chloroplast SSR . nad7 . Natural regeneration . Managed regeneration . Genetic diversity . Inbreeding . Pinus sylvestris Introduction Commercial forestry activity is primarily focused on forest tree species that are in an early stage of domestication, even if the application of breeding and silvicultural treatments are intensive. It is important to evaluate the genetic consequences of these operations, as they can have a direct bearing on the capacity of forests to adapt to new climatic conditions and possible pest outbreaks. While most boreal forest tree species have large populations and substantial genetic diversity, there is a question of how forest management activities might ad- versely affect population size and genetic structure. Communicated by J. Beaulieu Electronic supplementary material The online version of this article (doi:10.1007/s11295-015-0850-5) contains supplementary material, which is available to authorized users. M. R. García Gil (*) : V. Floran : B. Andersson Gull Department of Forest Genetics and Plant Physiology, SLU, 901 83 Umeå, Sweden e-mail: M.Rosario.Garcia@slu.se L. Östlund Department of Forest Ecology and Management, SLU, 901 83 Umeå, Sweden T. J. &. Mullin : B. Andersson Gull Skogforsk (The Forestry Research Institute of Sweden), PO Box 3, 918 21 Sävar, Sweden Tree Genetics & Genomes (2015) 11: 28 DOI 10.1007/s11295-015-0850-5