DOI: 10.6086/d1267d
title: Data from: Integrating ontogeny and ontogenetic dependency into community assembly

description: To gain more insights into the process influencing forest dynamics in
 Southern California, we have established the 4ha San Jacinto Forest
 Dynamics Plot (SJFDP) on the west slope of Mt. San Jacinto in Southern
 California. This area is adjacent to the University of California James
 Reserve and is in the U.S. Forest Service (USFS) Hall Canyon research
 natural area. This dataset include three files. Census data is data on
 every free-standing woody stem (live or dead) greater than 1cm in diameter
 which has identified to species, mapped, measured, and tagged for
 long-term monitoring. Seedling data includes data from 256 1m2 plots where
 every seedling woody stem less than 1m tall has been identified to
 species, mapped, measured, and tagged for long-term monitoring.
 Envrionmental data includes soil and topographic variables that were
 collected within each of 100 20x20m quadrats withint he SJFDP.
description: To quantify woody species adult composition across the SJFDP, we
 subdivided the SJFDP into 100 20x20 all free-standing stems of woody
 species greater than 1cm diameter at breast height (DBH) that have been
 tagged, identified, measured, and mapped following CTFS-ForestGEO
 protocols (Condit, 1998). To quantify woody species seedling composition
 across the SJFDP, we surveyed the central 64 20x20m quadrats (out of 100
 total quadrats) in 2021, leaving a 20-meter buffer between seedling plots
 and the edge of the SJFDP. The purpose of the buffer was to ensure that
 adult composition is quantified for all of the 8 quadrats surrounding
 every quadrat in which seedling composition was quantified so that we can
 more accurately assess the influence of adult composition on seedling
 composition. To estimate seedling composition within each of the central
 64 quadrats, we established four 1m<sup>2</sup> subplots
 (n=256 subplots). Each subplot was positioned 7m from the corner of each
 quadrat and aligned on a 45-degree angle relative to the x-y axes of the
 SJFDP grid (65º, 155º, 245º, 335º). Subplot locations were moved to the
 nearest suitable location if the initial subplot location was completely
 occupied by a log or rock. In each subplot, we identified all seedlings
 (defined as individuals under 1m tall following the CTFS-ForestGEO
 protocol (Condit, 1998)) to species, mapped their locations in a 100-cell
 grid, measured their height, and added an identification tag unique to
 each individual. To quantify environmental variation
 among quadrats we measured 8 soil variables and 6 topographic variables.
 In the center of each 20x20m quadrat, we collected a sample of ~500g of
 soil (0- to 10-cm depth) excluding the top organic horizon and analyzed
 organic matter (OM, by loss on ignition), phosphorus (P; Weak Bray and
 Sodium Bicarbonate), potassium (K), magnesium (Mg), calcium (Ca), sodium
 (Na), and cation exchange capacity (CEC, cations and CEC by ammonium
 acetate method) and pH (analysis was done by A & L Western
 Laboratories, Modesto, CA., USA). For each 20x20 m quadrat, we
 additionally calculated 6 topographic variables: mean elevation, slope,
 convexity, aspect, topographic position index, topographic ruggedness
 index, and flow direction. Mean elevation above sea level was quantified
 as the mean elevation of the four corners of each quadrat. Slope was
 quantified using the slope tool in ArcGIS 10.1. To quantify the remaining
 terrain characteristics,  we used a 1-m digital elevation model (DEM) from
 the USGS 3D Elevation Program (3DEP) and the raster package in R (Hijmans
 et al., 2013). Because aspect is a circular variable, we used
 cosine(aspect) in our analyses (Legendre et al., 2009). South aspect was
 measured as cos(aspect)*sin(slope), where higher values correspond to
 south-facing slopes that are associated with warmer and/or drier site
 conditions (Ackerly et al., 2020). Finally, we calculated the topographic
 position index (TPI) as the difference between the elevation of a quadrat
 and the mean elevation of the eight surrounding quadrats; topographic
 ruggedness index (TRI) as the mean absolute difference between the
 elevation of a quadrat and the elevation of the eight surrounding
 quadrats; and flow direction (flowdir) as the direction of the greatest
 drop in elevation for a given quadrat.