DOI: 10.5061/dryad.tqjq2bvx4
title: Data from: Light availability predicts mortality probability of conifer saplings in Swiss mountain forests better than radial growth and tree size

description: Radial and height growth rates are suitable indicators of impending tree
 mortality risk of adult trees, but their applicability to saplings remains
 unknown. We compared radial growth of living and dead saplings of
 different heights and quantified the effects of light availability, growth
 and tree size on mortality. We sampled an equal number of living and dead
 saplings of four coniferous tree species (Pinus cembra, Larix decidua,
 Picea abies, Abies alba) in nine forests along an elevational gradient of
 the Swiss Alps. Based on tree-ring widths reconstructed from stem disks at
 multiple tree heights, we calculated radial growth rates. We observed a
 divergent pattern in radial growth of living and dead saplings, with
 reduced growth of dead saplings starting several years prior to death. By
 matching living and dead saplings of similar ages, we tested whether
 mortality probabilities of saplings were influenced by light availability,
 recent growth rates and diameter. Mortality of coniferous saplings in
 mountain forests was mainly influenced by light availability, with
 changing effects along the elevational gradient. Recent radial growth rate
 and tree size were only weakly associated with sapling mortality. Our
 study establishes the importance of long-term predisposing factors for the
 mortality probability of conifer saplings in mountain forests, thus
 extending well-established findings from the adult stage to saplings,
 which represent a critical stage of forest dynamics.
description: Site selection and species sampled We studied four tree species with
 different light requirements and shade tolerances, respectively: European
 larch - <i>Larix decidua </i>(low shade tolerance), Swiss
 stone pine - <i>Pinus cembra </i>(intermediate shade
 tolerance), Norway spruce - <i>Picea abies</i> (intermediate
 to high shade tolerance) and silver fir - <i>Abies alba
 </i>(very high shade tolerance). Saplings were sampled in nine
 mountain forests along an elevational gradient in three climatic regions
 of Switzerland (Southern, Central and Northern Swiss Alps; cf. Appendix
 1), each site covering an area of approximately 400 m x 500 m (20 ha).
 Tree species distribution maps based on data from the first Swiss National
 Forest Inventory  were used for site selection. The main criteria were:
 (1) co-occurrence of at least two of the four conifer species; (2)
 presence of a sufficient number of both living and dead saplings of
 different heights; (3) natural (as opposed to planted) regeneration of the
 saplings; and (4) no recent thinning or silvicultural intervention. Two
 co-occurring tree species were sampled at each site, with the species
 combination varying along elevation (Table 1). The species <i>P.
 cembra</i> and <i>L. decidua</i> were sampled at the
 three highest sites in La Punt and Chamues-ch (2085 and 2052 m a.s.l.,
 both Central Swiss Alps) and Samprou (1900 m a.s.l., Southern Swiss Alps);
 <i>L. decidua </i>and <i>P. abies</i> at the three
 intermediate sites in Bergün and Filisur (1585 and 1440 m a.s.l., both
 Central Swiss Alps) and Predasca (1435 m a.s.l., Southern Swiss Alps); and
 <i>P. abies</i> and <i>A. alba</i> at the three
 lowest sites in Campra (1424 m a.s.l., Southern Swiss Alps), Grabs and
 Entlebuch (1219 and 908 m a.s.l., both Northern Swiss Alps).
 Field sampling and data preparation At each site, an equal number of
 naturally established saplings were sampled in 2016 across four height
 classes (10-40 cm, 40-70 cm, 70-100 cm, and 100-130 cm), four species (two
 co-occurring at each site) and status (dead vs. living), resulting in a
 perfectly balanced dataset. Only saplings without evidence of browsing or
 other mechanical damages as major mortality cause were sampled. Dead
 saplings were sampled only (i) if they had died recently (i.e., in 2016 or
 2015), i.e. sampled saplings did not have any green needles left, but
 still carried brown needles, or (ii) if the stems were very flexible and
 twigs were moist inside in the case of <i>L. decidua</i>, the
 only deciduous conifer native to Central Europe. We selected for each dead
 sapling the nearest living sapling of the same species and similar height
 (i.e., within the same height subclass of 10 cm height). By sampling
 saplings in the neighborhood within the same forest stands, our sample
 consisted of dead and living saplings that were exposed to nearly
 identical meteorological conditions, which allowed us to exclude death due
 to climatic influences. For example, 2015 was a particularly warm year in
 Switzerland (Appendix 1) that could have influenced tree mortality in some
 regions or specific forest stands. A total of 1’440 saplings were sampled:
 at each of the nine sites, 160 living and dead saplings were sampled,
 corresponding to 40 dead and 40 living saplings of each species (i.e., 10
 dead and 10 living saplings for each of the four height classes, cf.
 above). From each sapling, a stem disk was taken as close as possible to
 the root-shoot boundary. Depending on sapling height, additional stem
 disks were taken at 40 cm, 70 cm and 100 cm height. A distinct advantage
 of stem disks compared to increment cores is that disks always contain the
 pith and thus allow for inferring tree age and cambial age, respectively,
 in addition to radial growth rate. For each sapling, the following
 information was recorded: species, status (dead/alive), height, diameter
 above the root collar (DRC), and light availability. Light availability
 was derived from hemispherical photographs using a Canon EOS 70D camera
 with a Sigma 4.5 mm F2.8 Model EX DC HSM circular fisheye lens. The
 photographs were taken after sampling the saplings 40 cm above ground at
 the exact point where each sapling was growing. The photographs were
 analyzed with the software Hemisfer, version 2.2 to calculate the total
 (diffuse and direct) effective radiation (W/m<sup>2</sup>)
 available for each sapling. In the tree-ring lab, the stem disks were
 sanded and the ring widths measured with an accuracy of 0.01 mm on a
 LINTAB measurement table using the TSAP-Win software according to standard
 dendrochronological procedures. We measured tree ring widths on only one
 radius, opposite to the widest radius. Due to the low number of tree
 rings, we could neither visually nor quantitatively cross-date the tree
 rings of the stem disks. However, we do not assume that partial or missing
 tree rings occurred frequently because (1) we worked with stem disks that
 allows more easily to detect partial tree rings unlike increment cores;
 and (2) the four investigated species rarely show missing rings at the
 adult stage in these temperate climates, which is probably related to the
 lack of severe drought. Based on the measured tree rings,
 the mean age of the sampled saplings was 21.5 (range: 5 – 63) years for
 <i>P. cembra</i>, 18.2 (3 – 86) years for <i>L.
 decidua</i>, 25.4 (5 – 68) years for <i>P. abies</i> and
 25.1 (5 – 64) years for <i>A. alba</i>. The mean height was
 71.2 (range: 10 – 130) cm for <i>P. cembra</i>, 72.7 (10 –
 130)  cm for <i>L. decidua</i>, 71.0 (11 – 130) cm for
 <i>P. abies</i>, and 72.2 (10 – 130) cm for <i>A.
 alba</i>. The mean diameter above the root collar (DRC) was 1.9
 (range: 0.3 – 6) cm for <i>P. cembra</i>, 1.4 (0.2 – 4.6) cm
 for <i>L. decidua</i>, 1.9 (0.2 – 5.2) cm for <i>P.
 abies</i>, and 1.7 (0.1 – 5.0) cm for <i>A.
 alba</i>. Statistical analyses Based on tree-ring data, we
 analyzed the radial growth rate of the selected radius for stem disks at
 different heights and calculated height growth rate, respectively, to
 compare growth patterns of living and dead saplings of different tree
 species across sites. Each dead sapling was paired retrospectively to a
 living sapling of the same species and site with tree age as matching
 variable using the function “pairmatch” of the “optmatch” package, version
 0.9-10, in the software R. Tree age is more suitable as a matching
 variable than diameter or height, because paired saplings with the same or
 similar age have grown during the same period and under the same climatic
 conditions. In contrast, paired saplings of the same or similar diameter
 or height may have substantially different life histories and thus be less
 comparable. This would for example be the case if a slowly growing living
 sapling was exposed to different weather conditions than a rapidly growing
 dead sapling of the same diameter or height. The difference in light
 availability, recent radial growth and diameter above the root collar
 within the matched pairs was statistically tested using a paired t-test,
 separately for each species but with all height classes pooled together.
 Because severable observations were available per site, we fitted linear
 mixed effect models with the function “lme” of the “nlme” package, version
 3.1: <i>∆w</i><sub><i>ij</i></sub><i>=β+</i><i>u</i><sub><i>i</i></sub><i>+</i><i>ε</i><sub><i>ij</i></sub>                                                                                                                                                                             (1) <i>u</i><sub><i>i</i></sub><i>~N</i><i>0,</i><i>σ</i><sub><i>u</i></sub><sup><i>2</i></sup><i>, ε</i><sub><i>ij</i></sub><i>~N(0, </i><i>σ</i><sup><i>2</i></sup>) i.i.d. where the response variable Dw<sub>ij</sub> is the difference in light availability, recent radial growth and diameter above the root collar, respectively, of sapling pair j (i.e., difference between a living and a dead paired sapling of the same species) at site i (i.e, one of the nine forests). The fixed effect b is the expected difference between living and dead saplings, u<sub>i</sub> is the random effect with site as grouping variable, and e<sub>ij</sub> are the errors. To calculate the recent radial growth rate, we considered tree-ring widths at DRC of saplings over the last 5 years only because (1) stem disks from different heights showed similar growth patterns, particularly in <i>L. decid</i>ua and <i>P. abies</i>, and (2) on average over all saplings, the growth of living and dead saplings began to diverge approximately 5 years before dying and sampling, respectively. The radial growth rate of the last 5 years (RGR<sub>5</sub>) was therefore used as explanatory variable in the conditional logistic models (see below) as in other tree mortality studies. We used the same linear mixed effect model (Equation 1) to test for differences within the matched pairs for RGR<sub>5</sub> separately for each species and height class. The matched pairs were then used to fit 18 species- and site-specific conditional logistic regression models with the function “clogit” of the “survival” package, version 2.41‐3. Conditional logistic regression is an extension of logistic regression that offers the advantage of adjusting for non-independent case-control data. The conditional likelihood takes into account the information relative to the matched pairs. The conditional logistic regression model is defined as the log-odds of mortality probability p: <i>log</i><i>p</i><i>1-p</i><i>=</i><i>α</i><sub><i>1</i></sub><i>+</i><i>α</i><sub><i>2</i></sub><i>g</i><sub><i>2</i></sub><i>+…+</i><i>α</i><sub><i>k</i></sub><i>g</i><sub><i>k</i></sub><i>+</i><i>β</i><sub><i>1</i></sub><i>x</i><sub><i>1</i></sub><i>+…+</i><i>β</i><sub><i>n</i></sub><i>x</i><sub><i>n</i></sub>                                                                                                                                                                             (2) where α are the coefficients of the matched pairs variable g, the coefficients β those of the covariates x. The binary variable g encodes living saplings as g = 0 (control) and dead saplings as g = 1 (case). As covariates x, we used (1) effective total radiation, representing light availability; (2) diameter above the root collar (DRC); and (3) mean radial growth rate at DRC of the last five years prior to death or sampling (i.e., radial growth rate, RGR<sub>5</sub>). A positive coefficient b means that the mortality probability increases with increasing values of the covariate, a negative coefficient means that the mortality probability decreases with increasing values of the covariate.
description: This file contains 16 columns (variables) x 54046 rows (excluding
 the first row, which contains the header with the variable names). The
 data was used to create the Figures and to fit the survival models.
 Weather data used for Table 1 and Appendix 1 are property of MeteoSwiss
 and are not included. The variables are:
 Year The variable
 "year" (integer) indicates the year of formation of each tree
 ring. 
 IDstemdisk The variable
 "IDstemdisk" is a unique identifier of each stemdisk, where the
 first letter indicates the “alps”, the second letter the “site”, the third
 letter the “status”, the fourth letter the “species, and the first two
 numbers indicate a unique number within each site, status, species, and
 the last number indicate the “stemdisk.position”. E.g. “SCTP20_2”
 identifies the second stem disk (at position of 40 cm height) of the
 twentieth sapling of <i>Picea abies</i> dead sampled in Campra
 in the Southern Swiss Alps. 
 Tree.ring.width The variable
 “tree.ring.width” (unit: 0.01 mm) indicates the width of the tree rings
 measured on a LINTAB measurement table using the TSAP-Wind software (both
 of Rinntech, Heidelberg, Germany. 
 IDsapling The variable
 "IDsapling" is a unique identifier of the tree sapling, where
 the first letter indicates the “alps”, the second letter the “site”, the
 third letter the “status”, the fourth letter the “species, and the two
 numbers indicate a unique number within each site, status, species. E.g.
 “NELA01” identifies the first sapling of <i>Abies alba</i>
 living sampled in Entlebuch in the Northern Swiss Alps. Stemdisk.position 
 The variable “stemdisk.position” indicates 4 categories of
 sapling heights where stem disks were taken: “1” for stem disks taken at
 the root-shoot boundary (above root collar), “2” for stem disks taken at
 40 cm height, “3” for stem disks taken at 70 cm height, and “4” for stem
 disks taken at 100 cm height. 
 Height.class The variable
 “height.class” indicates 4 categories of sapling height: “10-40 cm”,
 “40-70 cm”, “70-100 cm”, and “100-130 cm”. Height 
 The variable "height" (unit: cm) corresponds to the
 sapling height at sampling, which was measured perpendicularly from the
 soil surface to the apical meristem. Diameter 
 The variable "diameter" (unit: cm) corresponds to the
 sapling diameter above the root collar at sampling, which was measured
 with a calliper. 
 Alps The variable
 "alps" indicates 3 categories of Swiss Alps: “Southern”,
 “Central” and “Northern”. 
 Site The variable
 "site" indicates 9 categories of study sites: “La Punt” at
 46.57724°/9.90593°, “Chamues-ch” 46.54883°/9.97125°, “Samprou”
 46.54446°/8.82848°, “Bergün” 46.63347°/9.7259°, “Filisur”
 46.66112°/9.6733°, “Predasca” 46.55417°/8.91808°, “Campra”
 46.51982°/8.88549°, “Grabs” 47.19159°/9.36694°, “Entlebuch”
 47.02119°/8.09121° (latitude/longitude, WG84 coordinates) in
 Switzerland. 
 Status The variable
 "status" indicates 2 categories of a sapling state at sampling:
 "living" and "dead". Species 
 The variable "species" indicates 4 categories of tree
 species sampled: “<i>Pinus cembra</i>”, “<i>Larix
 decidua</i>”, “<i>Picea abies</i>”, “<i>Abies
 alba</i>”. 
 TOTheff The variable
 "TOTheff" (unit: W/m^2) indicates the total (sum of direct and
 diffuse) radiation at the exact position where each sapling was sampled,
 measured with hemisferical photographs and analysed with the software
 Hemisfer. 
 Age.IDstemdisk The variable
 “age.IDstemdisk” (unit: yr) indicates the number of tree rings formed in
 each stemdisk. 
 Matches The variable “matches”
 identifies pairs of dead and living saplings of the same species within
 the same site paired retrospectively with tree age as matching variable
 using the function “pairmatch” of the “optmatch” package, version 0.9-10
 (Hansen & Klopfer 2006). 
 RGR5.IDstemdisk The variable
 "RGR5.IDstemdisk" (unit: 0.01 mm/yr) indicates the
 stemdisk-specific radial growth rate of the last five years prior to
 sampling of living saplings and prior to death of the dead saplings,
 respectively.