This SPECIES_ESTABLISHMENTreadme.txt file was generated on 2022-09-15 by BODIL HÄGGSTRÖM GENERAL INFORMATION 1. Title of Dataset: Effect of arginine-phosphate addition on early survival and growth of Scots pine, Norway spruce and silver birch 2. Author Information A. Principal Investigator Contact Information Name: Bodil Häggström Institution: Swedish University of Agricultural Sciences Address: Umeå Plant Science Centre Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences 90183 Umeå Sweden Email: bodil.haggstrom@slu.se B. Associate or Co-investigator Contact Information Name: Annika Nordin Institution: Swedish University of Agricultural Sciences Address: Umeå Plant Science Centre Department of Forest Genetics and Plant Physiology Swedish University of Agricultural Sciences 90183 Umeå Sweden Email: annika.nordin@slu.se 3. Date of data collection: 2020-10-16 to 2021-12-09 4. Geographic location of data collection: Site S: 57.193157 N 14.821763 E Site NE: 64.162174 N 19.661918 E Site NW: 64.102337 N 18.149540 E 5. Information about funding sources that supported the collection of the data: Funding of the field study data collection was provided by the Trees and Crops for Future program at the Swedish University of Agricultural Sciences SLU and the Knut and Alice Wallenberg Foundation. SHARING/ACCESS INFORMATION 1. Links to publications that cite or use the data: Not yet published 2. Was data derived from another source? No A. If yes, list source(s): 6. Recommended citation for this dataset: Bodil Häggström. Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology (2021). Data for the scientific article " Effect of arginine-phosphate addition on early survival and growth of Scots pine, Norway spruce and silver birch ". Svensk nationell datatjänst. Version 1. DATA & FILE OVERVIEW 1. File List: a. effects_APtreatment_data_S_second_season.csv Content: Survival and damage registration, height and stem base diameter measurements of Scots pine, Norway spruce and silver birch planted at the south (S) site. For each seedling, plot number, row within each plot, species, status, damage cause, AP-treatment (Yes= one dose of arginine-phosphate added at planting) and species composition within the plot. b. effects_APtreatment_data_NE_second_season.csv Content: Survival and damage registration, height and stem base diameter measurements of Scots pine, Norway spruce and silver birch planted at the northeast (NE) site. For each seedling, plot number, species, status, damage cause, AP-treatment (Yes= one dose of arginine-phosphate added at planting) and species composition within the plot. c. effects_APtreatment_data_NW_second_season.csv Content: Survival and damage registration, height and stem base diameter measurements of Scots pine, Norway spruce and silver birch planted at the northwest (NW) site. For each seedling, plot number, row within each plot, species, status, damage cause, AP-treatment (Yes= one dose of arginine-phosphate added at planting) and species composition within the plot. 2. Relationship between files, if important: No. 3. Additional related data collected that was not included in the current data package: The pine seedlings included in all three files was measured for leader shoot as well. These data were not used in analyses since growth of species was compared and leader shoot was not measured on the spruce and birch seedlings. There are inventories from first year in field that the survival data was compared against to detect seedlings that were missing other than seedlings already registered as missing during inventories. For the NE site these missing seedlings are added last per plot in the data set, for the NW site last per row. At the NW site one entire row in plot 6, 2 entire rows in plot 10 and one row in block 12 was missed during inventory due to unclear rows. Instead of adding these as missing, these rows were instead excluded from the data set to not create a bias towards lower survival. There is also an inventory from the third year in field at the NW site that was not used in the paper since the other two sites only had second season data in order to keep the discussion coherent, I.e., only dealing with second season development of seedlings of the three species. 4. Are there multiple versions of the dataset? No. METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Field inventory was performed in the end of the second growing season in October 2020 (NW), September 2021 (NE) and December 2021 (S). All seedlings that were alive were classified as living and dead and missing seedlings were classified as dead at analyses. Seedlings that were undamaged at the NE and NW site and seedlings with damage level 0 (undamaged) and 1 (minor damage) at the S site were classified as vital. Where possible, damage type or cause was registered. Every seedling classified as vital at the S and NE site and every second vital at the NW site of each species was measured for growth variables. 2. Methods for processing the data: Second season inventory was matched against first year inventory to detect additional missing seedlings. The data set was prepared in excel and then uploaded in R where survival and damage were sorted in binary lists. Prior to analysis of damage, a subset of alive only was made so that the results concern damaged out of living. Prior to analysis of growth variables (height and stem base diameter) a subset of only vital seedlings was made, to avoid effects of damage to interfere with the targeted effect of AP-treatment. Each site was analysed separately. 3. Instrument- or software-specific information needed to interpret the data: R-studio software were used in all statistical analyses (R Core Team, 2021). Following R-packages were used for analyses and visual interpretation of the data: dplyr, lmerTest, pbkrtest, lme4, car, emmeans, ggplot2, ggthemes, Rmisc, ggpubr, ggpmisc, multcomp, multcompView, sjPlot, grid, gridExtra. Analysis of variance (ANOVA) (using the R car-package) was performed for generalised mixed effect models on survival and damage (using the glmer function in the lme4 package) and linear mixed models on growth (using the lmer function in lmerTest package). 4. Environmental/experimental conditions: The data was retrieved from seedlings that had been planted at three field sites which represent different environmental conditions. Environment variables that might affect seedling development such as elevation, length of growing season, mean annual temperature and precipitation, soil type, moist class, landscape- and vegetation type are specified for each site in table below. The inventory of survival and growth was performed following the second growing season in field which means that the seedlings have been exposed to varying environment conditions through two growing seasons and one winter. Site South (S) Northeast (NE) Northwest (NW) Elevation (m.a.s.l) 225-230 160-165 295-300 Establishment date June 17th 2020 June 22nd 2020 June 17th 2019 Growing season 190-200 days 150-160 days 140-150 days Mean an. Temp °C 6-7 2-3 1-2 Mean an. Prec. 600-800 mm 600-800 mm 400-600 mm Soil Silty-sandy till Clay-sitly till Silty sandy till Soil depth Shallow Deep Deep Stoniness high low moderate-high Moist class mesic to dry mesic dry- mesic Harvested stand spruce spruce pine Landscape hummocky flat to W slope ridges, flat-gentle slope Vegetation type grass+raspberry bilberry bilberry+lingonberry 5. Describe any quality-assurance procedures performed on the data: The data was crosschecked with inventory data from the year of planting to account for missing seedlings, to avoid bias towards higher survival. 6. People involved with sample collection, processing, analysis and/or submission: Bodil Häggström, Annika Nordin, Reimo Lutter, Fredrik Sjödin, Tomas Lundmark. DATA-SPECIFIC INFORMATION FOR: [effects_APtreatment_data_S_second_season.csv] 1. Number of variables: 11 2. Number of cases/rows: 1133 3. Variable List: Site: Sites S = south (all entries are from this site in this data set) Plot_no: Identifies from which of plot 1-14 the seedling is Row_no: Identifies from which row within each plot the seedling is Species: Identifies which species the planted seedling is, where 1 = Scots pine, 2 = Norway spruce and 3 = silver birch Status: The status of seedlings used in analyses, where vital = undamaged (damage level 0) and seedlings with minor damage (damage level 1), damaged = seedlings of damage level 2-4, dead = seedlings of damage level 5 and 6. Damage_level: The original classification at inventory where 0 = undamaged, 1 = minor damage, 2 = moderate damage, 3 = severe damage, 4 = life-threatening damage, 5 = dead, 6 = missing/dead since former years’ inventory. Damage_cause: Identifies the cause of damage when known, Pineweevil = the seedling is damaged by Hylobius abietis L., Browsed = top shoot bitten off*, Otherinsect = the seedling has damage caused by insect other than Hylobius abietis L., Oxygendeficit = the spot where the seedling was planted was waterlogged and the seedling died from oxygen deficit, None = the seedling is not damage, Unknown = cause of damage not identified. *ungulates are the most common agents of damage regarding browsing, however small sized seedlings could technically have been bitten of by other animals, such as rodents or birds, this is why the word “browsed” is used instead of defining damage cause as “ungulates”. Height_cm: The seedling height in cm measured from ground level to top of terminal bud. Diameter_mm: The seedling stem diameter in mm just above ground level (as low as measurable). AP_treatment: Yes = one dose* of granular arginine-phosphate (arGrow® Granulat, Arevo AB, Umeå, Sweden) was added in the bottom of the planting hole together with each plant at the time of planting, No = no nutrients added. *One dose arGrow® Granulat contains 40 mg N and 22 mg P, the active substance is L-arginine phosphate (C6H17N4O6P). Composition: Species composition in the plot, P = only pine, S= only spruce, B = only birch, PS = pine + spruce mix, i.e., every second seedling is pine and every second seedling is spruce, PB = pine + birch mix, i.e., every second seedling is pine and every second seedling is birch, SB = spruce + birch mix, i.e., every second seedling is spruce and every second seedling is birch, and PSB = pine + spruce + birch mix, i.e., every third seedling is pine, every third seedling is spruce and every third seedling is birch. 4. Missing data codes: None. DATA-SPECIFIC INFORMATION FOR: [effects_APtreatment_data_NE_second_season.csv] 1. Number of variables: 9 2. Number of cases/rows: 1094 3. Variable List: Site: Sites NE = northeast (all entries are from this site in this data set) Plot_no: Identifies from which of plot 1-14 the seedling is Species: Identifies which species the planted seedling is, where 1 = Scots pine, 2 = Norway spruce and 3 = silver birch Status: The status of seedlings used in analyses, where vital = undamaged seedlings, damaged = seedlings that are damaged, dead = seedlings that are dead, missing = seedlings that were registered the previous season and were not found this season, identified by crosschecking the second season data in this data set with the inventory from previous year and added last in each plot. Notes on flawed entries: Entry no 496 is marked as dead but is measured, this is most likely a tree that was wrongly assigned dead but is analysed as such, and the measurement data is not included in analyses. Entry 920 is classified as vital and is therefore included in growth analyses even though it is classified as browsed. The choice was made to keep them according to the identified status class rather than removing them. Damage_cause: Identifies the cause of a seedling being classified as damaged, where Browsed = top shoot bitten off*, Forked = the seedling had two or more leader shoots (applicable mainly on the conifers), Leaning** = seedling was heavily leaning so that the height growth was or will be affected, Lying** = the seedling had tipped over completely, Drying = the seedling is alive but close to dying of drought, Drytop = the top of the tree remains but is entirely dried, Topbreak = top is broken or missing without visible signs of browsing, could be due to snowload, None = the seedling is not damage, Unknown = cause of damage not identified. Waterlogged = these seedlings were classified as vital, but the growth might have been affected. Since there were very few occasions of this classification, this would not be useful as indicating growth loss depending on water logging, why these seedlings were included in growth analysis. *Ungulates are the most common agents of damage regarding browsing, however small sized seedlings could technically have been bitten of by other animals, such as rodents or birds, this is why the word “browsed” is used instead of defining damage cause as “ungulates”. ** The major reason for seedlings classified as Leaning or Lying is most likely frost-heaving, though they could have been trampled or pushed down by snow as well. Height_cm: The seedling height in cm measured from ground level to top of terminal bud. Diameter_mm: The seedling stem diameter in mm just above ground level (as low as measurable). AP_treatment: Yes = one dose* of granular arginine-phosphate (arGrow® Granulat, Arevo AB, Umeå, Sweden) was added in the bottom of the planting hole together with each plant at the time of planting, No = no nutrients added. *One dose arGrow® Granulat contains 40 mg N and 22 mg P, the active substance is L-arginine phosphate (C6H17N4O6P). Composition: Species composition in the plot, P = only pine, S= only spruce, B = only birch, PS = pine + spruce mix, i.e., every second seedling is pine and every second seedling is spruce, PB = pine + birch mix, i.e., every second seedling is pine and every second seedling is birch, SB = spruce + birch mix, i.e., every second seedling is spruce and every second seedling is birch, and PSB = pine + spruce + birch mix, i.e., every third seedling is pine, every third seedling is spruce and every third seedling is birch. 4. Missing data codes: None. DATA-SPECIFIC INFORMATION FOR: [effects_APtreatment_data_NW_second_season.csv] 1. Number of variables: 10 2. Number of cases/rows: 1988 3. Variable List: Site: Sites NW = northwest (all entries are from this site in this data set) Plot_no: Identifies from which of plot 1-14 the seedling is Row_no: Identifies from which row within each plot the seedling is Species: Identifies which species the planted seedling is, where 1 = Scots pine, 2 = Norway spruce and 3 = silver birch Status: The status of seedlings used in analyses, where vital = undamaged seedlings, damaged = seedlings that are damaged, dead = seedlings that are dead, missing = seedlings that were registered the previous season and were not found this season, identified by crosschecking the second season data in this data set with the inventory from previous year and added last in each plot. Notes: One entire row in plot 6, 2 entire rows in plot 10 and one row in block 12 was missed during inventory due to unclear rows. Instead of adding these as missing, these rows were excluded from the data set to not create a bias towards lower survival. Damage_cause: Identifies the cause of a seedling being classified as damaged, where Browsed = top shoot bitten off*, None = the seedling is not damage, Unknown = cause of damage not identified. *Ungulates are the most common agents of damage regarding browsing, however small sized seedlings could technically have been bitten of by other animals, such as rodents or birds, this is why the word “browsed” is used instead of defining damage cause as “ungulates”. Height_cm: The seedling height in cm measured from ground level to top of terminal bud. Diameter_mm: The seedling stem diameter in mm just above ground level (as low as measurable). AP_treatment: Yes = one dose* of granular arginine-phosphate (arGrow® Granulat, Arevo AB, Umeå, Sweden) was added in the bottom of the planting hole together with each plant at the time of planting, No = no nutrients added. *One dose arGrow® Granulat contains 40 mg N and 22 mg P, the active substance is L-arginine phosphate (C6H17N4O6P). Composition: Species composition in the plot, P = only pine, S= only spruce, B = only birch, PS = pine + spruce mix, i.e., every second seedling is pine and every second seedling is spruce, PB = pine + birch mix, i.e., every second seedling is pine and every second seedling is birch, SB = spruce + birch mix, i.e., every second seedling is spruce and every second seedling is birch, and PSB = pine + spruce + birch mix, i.e., every third seedling is pine, every third seedling is spruce and every third seedling is birch. 4. Missing data codes: None. 5. Session information for Code_manuscript_SND.R For complete log of R session, se Code_manuscript_SND.log.txt, which was generated by: Rscript Code_manuscript_SND.R > Code_manuscript_SND.log.txt Equivalent output should be expected in RStudio when running: source('Code_manuscript_SND.R', echo=TRUE) or running "Source with echo" from the Source menu with Code_manuscript_SND.R loaded. R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Arch Linux Matrix products: default BLAS: /usr/lib/libopenblasp-r0.3.21.so LAPACK: /usr/lib/liblapack.so.3.10.1 locale: [1] LC_CTYPE=sv_SE.UTF-8 LC_NUMERIC=C [3] LC_TIME=sv_SE.UTF-8 LC_COLLATE=sv_SE.UTF-8 [5] LC_MONETARY=sv_SE.UTF-8 LC_MESSAGES=sv_SE.UTF-8 [7] LC_PAPER=sv_SE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=sv_SE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] glmmTMB_1.1.4 gridExtra_2.3 sjPlot_2.8.11 multcompView_0.1-8 [5] multcomp_1.4-20 TH.data_1.1-1 MASS_7.3-57 survival_3.3-1 [9] mvtnorm_1.1-3 ggpmisc_0.5.0 ggpp_0.4.5 ggpubr_0.4.0 [13] Rmisc_1.5.1 plyr_1.8.7 lattice_0.20-45 ggthemes_4.2.4 [17] ggplot2_3.3.6 emmeans_1.8.1-1 car_3.1-0 carData_3.0-5 [21] pbkrtest_0.5.1 lmerTest_3.1-3 lme4_1.1-30 Matrix_1.5-0 [25] dplyr_1.0.10