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 widely used managed-regeneration practices, planting with improved material from seed orchards and seed-tree regeneration, 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 nuclear 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 significantly 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 management 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 deviation 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 diversity 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 indicates that the reduction to five nSSR loci does not change the main finding of an absence of differences in genetic diversity among stands, except for the number of rare alleles (RA), which is lower when estimated from data for eight nSSR loci.
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References
Abrahamsson S, Ahlinder J, Waldmann P, Garca-Gil MR (2013) Maternal heterozygosity and progeny fitness association in an inbred Scots pine population. Genetica 141(1–3):41–50
Adams WT, Zuo J, Shimizu JY, Tappeiner JC (1998) Impact of alternative regeneration methods on genetic diversity in coastal Douglas-fir. For Sci 44:390–396
Allendorf FW (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biol 5:181–190
Amos W (2005) IR macroN3. IR Manual. http://www.zoo.cam.ac.uk/zoostaff/amos/#ComputerPrograms. Accessed 10 Apr 2009
Androsiuk P, Shimono A, Westin J, Lindgren D, Fries A, Wang XR (2013) Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden. Silvae Genet 62(3):127–136
Bergmann F, Ruetz W (1991) Isozyme genetic variation and heterozygosity in random tree samples and selected orchard clones from the same Norway spruce populations. For Ecol Manag 46:39–47
Buchert GP, Rajora OP, Hood JV, Dancik BP (1997) Effects of harvesting on genetic diversity in old-growth eastern white pine (Pinus strobus L.) in Ontario, Canada. Conserv Biol 11:747–758
Chaisurisri K, El-Kassaby YA (1994) Genetic diversity in a seed production population vs. natural populations of Sitka spruce. Biodivers Conserv 3:512–523
Charlesworth B (1998) Measures of divergence between populations and the effect of forces that reduce variability. Mol Biol Evol 15(5):538–543
Cheliak WM, Murray G, Pitel JA (1988) Genetic effects of phenotypic selection of white spruce. For Ecol Manag 24:139–149
Chybicki IA, Dzialuk M, Trojankiewicz M, Slawski M, Burczyk J (2007) Spatial genetic structure within two contrasting stands of Scots pine (Pinus sylvestris L.). Silvae Genet 57:4–5
Coulon A (2010) GENHET: an easy-to-use R function to estimate individual heterozygosity. Mol Ecol Resour 10:167–169
Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Stat Soc 39:1–38
Don RH, Cox PT, Wainwright BJ, Baker K, Mattick JS (1991) Touchdown PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19(14):4008
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Dvornyk V, Sirvio A, Mikkonen M, Savolainen O (2002) Low nucleotide diversity at the pal1 locus in the widely distributed Pinus sylvestris. Mol Biol Evol 19:179–188
El-Kassaby YA, Ritland K (1996) Impact of selection and breeding on the genetic diversity in Douglas-fir. Biodivers Conserv 6:795–813
El-Kassaby YA, Dunsworth BG, Krakowski J (2003) Genetic evaluation of alternative silvicultural systems in coastal montane forests: western hemlock and amabilis fir. Theor Appl Genet 107:598–610
Fageria MS, Rajora OP (2013) Effects of harvesting of increasing intensities on genetic diversity and population structure of white spruce. Evol Appl 6:778–794
Fageria MS, Rajora OP (2014) Effects of silvicultural practices on genetic diversity and population structure of white spruce in Saskatchewan. Tree Genet Genomes 10:287–296
Faris MA, Milton JB (1984) Population density, outcrossing rate, and heterozygote superiority in ponderosa pine. Evolution 38:1151–1154
Ganea LS, Ranade SS, Hall D, Abrahamsson S, García-Gil MR (2015) Development and transferability of two multiplex nSSR in Scots pine (Pinus sylvestris L.). J For Res. doi:10.1007/s11676-015-0042-z
García-Gil MR, Francois O, Kamruzzahan S, Waldmann P (2009) Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine. Heredity 103:90–96
Gauli A, Gailing O, Stefenon VM, Finkeldey R (2009) Genetic similarity of natural populations and plantations of Pinus roxburghii Sarg. in Nepal. Ann For Sci 66:703
Goudet J (2001) FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices Version 2.9.3: www.unil.ch/izea/softwares/fstat.html
Griffin AR, Lindgren D (1985) Effect of inbreeding on production of filled seed in Pinus radiata—experimental results and a model of gene action. Theor Appl Genet 71:334–343
Gullberg U, Yazdani R, Rudin D, Ryman N (1985) Allozyme variation in Scots pine (Pinus sylvetris L.) in Sweden. Silvae Genet 34:193–201
Hurlbert SH (1971) The non concept of species diversity: a critique and alternative parameters. Ecology 52:577–586
Icgen Y, Kaya Z, Cengel B, Velioglu E, Ozturk H, Onde S (2006) Potential impact of forest management and tree improvement on genetic diversity of Turkish red pine (Pinus brutia Ten.) plantations in Turkey. For Ecol Manag 225:328–337
Jaramillo-Correa JP, Beaulieu J, Bousquet J (2004) Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer. Mol Ecol 13:2735–2747
Josefsson T, Olsson J, Östlund L (2010) Linking forest history and conservation efforts: Long-term impact of low-intensity timber harvest on forest structure and wood inhabiting fungi in northern Sweden. Biol Conserv 143:1803–1811
Karhu A, Hurme P, Karjalainen M, Karvonen P, Karkkainen K, Neale D, Savolainen O (1996) Do molecular markers reflect patterns of differentiation in adaptive traits of conifers? Theor Appl Genet 93:215–221
Kärkkäinen K, Savolainen O (1993) The degree of early inbreeding depression determines the selfing rate at the seed stage: model and results from Pinus sylvestris (Scots pine). Heredity 71:160–166
Kärkkäinen K, Kuittinen H, van Treuren R, Vogl C, Oikarinen S, Savolainen O (1999) Genetic basis of inbreeding depression in Arabis petraea. Evolution 53:1354–1365
Koski V (1971) Embryonic lethals of Picea abies and Pinus sylvestris. Commun Inst For Fenn 75:1–30
Krouchi F, Derridj A, Lefevre F (2003) Year and tree effect on reproductive organization of Cedrus atlantica in a natural forest. For Ecol Manag 197:181–189
Kuchma O, Vornam B, Finkeldey R (2011) Mutation rates in Scots pine (Pinus sylvestris L.) from the Chernobyl exclusion zone evaluated with amplified fragment-length polymorphisms (AFLPs) and microsatellite markers. Mutat Res 725:29–35
Lande R (1998) Risk of population extinction from fixation of deleterious and reverse mutations. Genetica 102–103(1–6):21–27
Lande R, Schemske DW, Schultz ST (1994) High inbreeding depression, selective interference among loci and the threshold selfing rate for purging recessive lethal mutation. Evolution 48:965–978
Lewandowski A, Boratynski A, Mejnartowicz L (2000) Allozyme investigations on the differentiation between closely related pines—Pinus sylvestris, P. mugo, P. uncinata and P. uliginosa (Pinaceae). Plant Syst Evol 221:1–24
Loehle C, Namkoong G (1987) Constraints on tree breeding: growth tradeoffs, growth strategies, and defensive investments. For Sci 33:1089–1097
Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766
Lynch M, Conery J, Burger R (1995) Mutation accumulation and the extinction of small populations. Am Nat 146(4):489–518
Macdonald SE, Thomas BR, Cherniawsky DM, Purdy BG (2001) Managing genetic resources of lodgepole pine in west-central Alberta: patterns of isozyme variation in natural populations and effects of forest management. For Ecol Manag 152:45–58
Maghuly F, Pinsker W, Praznik W, Fluch S (2006) Genetic diversity in managed subpopulations of Norway spruce [Picea abies (L) Karst]. For Ecol Manag 222:266–271
Marquardt PE, Echt CS, Epperson BK, Pubanz DM (2007) Genetic structure, diversity, and inbreeding of eastern white pine under different management contitions. Can J For Res 37:2652–2662
Muona O, Harju A (1989) Effective population sizes, genetic variability and mating system in natural stands and seed orchards of Pinus sylvestris. Silvae Genet 38(5–6):221–228
Namroud MC, Bousquet J, Doerksen T, Beaulieu J (2012) Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce. Evol Appl 5(6):641–656
Naydenov K, Senneville S, Beaulieu J, Tremblay F, Bousquet J (2007) Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor. BMC Evol Biol 7:233
Neale DB, Adams WT (1985) The mating system in natural and shelterwod stands of Douglas-fir. Theor Appl Genet 71:201–207
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10
Nowakowska JA, Zachara T, Konecka A (2014) Genetic variability of Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies L. Karst.) natural regeneration compared with their maternal stands. Leśne Prace Badawcze 75:47–54
Östlund L, Zackrisson O, Axelsson AL (1997) The history and transformation of a Scandinavian boreal forest landscape since the 19th century. Can J For Res 27:1198–1206
Peakall R, Smouse P (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539
Provan J, Soranzo N, Wilson N et al (1998) Gene-pool variation in Caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple-sequence repeats. Proc R Soc B Biol Sci 265:1697–1705
Pyhäjärvi T, Salmela MJ, Savolainen O (2008) Colonization routes of Pinus sylvestris inferred from distribution of mitochondrial DNA variation. Tree Genet Genomes 4:247–254
R Development Core Team (2013) R: a language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. URL http://www.R-project.org
Raja RG, Tauer CG, Wittwer RF, Huang Y (1998) Regeneration methods affect genetic variation and structure in shortleaf pine (Pinus echinata Mill.). For Genet 5:171–178
Rajora OP (1999) Genetic biodiversity impacts of silvicultural practices and phenotypic selection in white spruce. Theor Appl Genet 99:954–961
Rajora OP, Pluhar SA (2003) Genetic diversity impacts of forest fires, forest harvesting and alternative reforestation practices in black spruce (Picea mariana). Theor Appl Genet 106:1203–1212
Rajora OP, Rahman MH, Buchert GP, Dancik BP (2000) Microsatellite DNA analysis of genetic efforts of harvesting in old-growth eastern white pine (Pinus strobus) in Ontario, Canada. Mol Ecol Resour 9:339–348
Ratman W, Rajora OP, Finkeldy R, Aravanopoulos F, Bouvet JM, Vaillancourt RE, Kanashiro M, Fady B, Tomita M, Vinson C (2014) Genetic effects of forest management practices: global synthesis and perspectives. For Ecol Manag 333:52–65
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43:223–225
Robledo-Arnuncio JJ (2011) Wind pollination over mesoscale distances: an investigation with Scots pine. New Phytol 190:222–233
Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106
Rudin D, Eriksson G, Ekberg I, Rasmuson M (1974) Studies of allele frequencies and inbreeding in Scots pine populations by the aidof the isozyme technique. Silvae Genet 23:10–13
Scalfi M, Piotti A, Rossi M, Piovani P (2009) Genetic variability in Italian southern Scots pine (Pinus sylvestris L.) populations: the rear edge of the range. Eur J For Res 128:377–386
Shea KL (1987) Effects of population structure and cone production on outcrossing rates in Engelman spruce and subalphine fir. Evolution 41:124–136
Skogsstyrelsen (2012) Skogsstatistisk årsbok. Swedish statistical yearbook of forestry. Jönköping, Sweden
Soranzo N, Provan J, Powell W (1998) Characterization of microsatellite loci in Pinus sylvestris L. Mol Ecol 7:1260–1261
Stoehr MU, El-Kassaby YA (1997) Levels of genetic diversity at different stages of the domestication cycle in interior spruce in British Columbia. Theor Appl Genet 94:83–90
Szmidt AE, Muona O (1985) Genetic effects of Scots pine (Pinus sylvestris L.) domestication. Lect Notes Biomath 60:241–252
Thomas BR, Macdonald SE, Hicks M, Adams DL, Hodgetts RB (1999) Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplied polymorphic DNA markers. Theor Appl Genet 98:793–801
Vendramin G, Lelli L, Rossi P, Morgante M (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Mol Ecol 5:595–598
Wachowiak W, Salmela MJ (2011) High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland. Heredity 106(5):775–787
Wahlund S (1928) The combination of populations and the appearance of correlation examined from the standpoint of the study of heredity. Hereditas 11:65–106
Wang J (2004) Sibship reconstruction from genetic data with typing errors. Genetics 166:1963–1979
Wang JL (2011) COANCESTRY: a program for simulating, estimating and analysing relatedness and inbreeding coefficients. Mol Ecol Resour 11(1):141–145
Wang J, Santure AW (2009) Parentage and sibship inference from multilocus genotype data under polygamy. Genetics 181(4):1579–1594
Yazdani R, Muona O, Rudin D, Szmidt AE (1985) Genetic structure of a Pinus sylvestris L. seed-tree stand and naturally regenerated understorey. For Sci 31:430–436
Yazdani R, Lindgren D, Stewart S (1989) Gene dispersion within a population of Pinus sylvestris. Scand J For Res 4(3):295–306
Acknowledgments
We gratefully acknowledge Sonali Ranade, Stefana Ganea, Anna-Maria Rautio, Axel Bergsten, Sara Svanlund, Lydia McCarthy, Anna Hallmén, and especially Mikael Westerlund for conducting the fieldwork. We also would like to thank Per Linder, Fastighetsverket, and Lars Andersson for help with finding and permission to use suitable forest stands. This work was supported by grants from Föreningen Skogsträdförädling and Crops for Future-SLU (TC4F). We also acknowledge the Swedish research Council (VR) and the Swedish Governmental Agency for Innovation Systems (VINNOVA).
Data archiving statement
Nuclear SSR, chloroplast SSR and nad7 genotypic data sets were submitted to TreeGenes (https://dendrome.ucdavis.edu/tgdr/) (accession numbers TGDR039, TGDR040, and TGDR041, respectively).
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The authors declare that they do not have competing interests and they have conducted the study following the rules of ethical and good science practice.
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García Gil, M.R., Floran, V., Östlund, L. et al. Genetic diversity and inbreeding in natural and managed populations of Scots pine. Tree Genetics & Genomes 11, 28 (2015). https://doi.org/10.1007/s11295-015-0850-5
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DOI: https://doi.org/10.1007/s11295-015-0850-5