DOI: 10.21950/vf8mwv
title: Data to reproduce the analyses described in the manuscript: Acorn removal and seedling age determine oak (Quercus ilex L. and Q. suber L.) restoration outcome in ungulate-dominated Mediterranean environments

description: &lt;p&gt; Description of the project&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;p&gt;Context: In the face of anthropogenic global change, Mediterranean oak-dominated ecosystems confront increased biotic (ungulate herbivory) and abiotic (drought) stressors, compromising forest regeneration. Restoration measures are imperative to address this scenario.&lt;/p&gt;
&lt;p&gt;Aims: This study assesses the impact of different mitigation measures on the survival and biochemical traits of two widespread Mediterranean oak species.&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;p&gt;4. Description of the dataset&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;p&gt;The dataset encompasses information from the planting of 300 Quercus seedlings in Cabañeros (Quercus ilex; N=200) and Doñana (Quercus suber; N=100), subjected to various treatments: cotyledon/acorn removal, seedling age (1 vs. 2-year-old), and herbivore protection (fenced vs. non-fenced).&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;p&gt;Monthly measurements of the seedlings were conducted from February to September 2021. Each visit consisted of recording: the seedling survival status (alive vs. dead), the damage caused by biotic and abiotic stress agents and the identification of the main stress agent, namely wild boar, deer, rabbit, fungi, insect or drought. &lt;/p&gt;
&lt;p&gt;We considered the main stress agent the one leading to the plant death, or, in the case of surviving seedlings, the one identified with the highest intensity score. &lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;p&gt;To compare seedling physiological leaf biochemical responses to different treatments and plant ages, several non-destructive measures of chlorophyll, anthocyanin and flavonoid concentrations and the nitrogen balance index (NBI) were taken using the leaf clamp fluorescence sensor Dualex ® TMScientific+, Force One. The Dualex measures were taken on 5 leaves previously marked, from top to bottom, only in alive seedlings.&lt;/p&gt;
description: Methodology
For detailed information, please refer to the "Materials and Methods / Experimental Design" section in:

Peláez M, Carranza G, Gambra-Caravantes D, Rodríguez-Calcerrada J, Gordaliza G, Fedriani JM, Gil L, & Perea R. Acorn removal and seedling age determine oak restoration outcome in ungulate-dominated Mediterranean environments. Annals of Forest Science.

Files 

Database name: Plnttn.xlsx
Description: This database contains the information of the oak seedlings planted as part of the experiment described in the manuscript “Acorn removal and seedling age determine oak restoration outcome in ungulate-dominated Mediterranean environments”
Variables description:
 SITE: Text indicating the name of the National Park where measurements were taken. Possible values are "Cabañeros" or "Doñana."
 PLANT_NUMBER: Alphanumeric code assigned to each plant in the field, ranging from 1 to 25. If the code includes "SB," it signifies that the acorn was removed before planting; otherwise, the plant had the acorn attached.
 Plantation_Date: Date the oaks were planted. 
 Treatment: Code summarizing the location and treatment applied to each oak seedling. Options include: 
 •IN_OPEN: Planted inside the fence, in the open, with the acorn attached.
 •OUT_OPEN: Planted outside the fence, in the open, with the acorn attached.
 •IN_OPEN_SB: Planted inside the fence, in the open, with the acorn removed before planting. 
 •OUT_OPEN: Planted outside the fence, in the open, with the acorn removed before planting.
 Fenced: Indicates whether the oak seedlings were planted inside or outside a fenced area. Values are "Yes" (inside a fenced area) or "No" (not protected by a fence). 
 Acorn: Indicates whether the plant had the acorn attached or not. “Acorn” when the plant had the acorn attached and “No Acorn” when the acorn was removed before planting. 
 Age: Numeric either 1yr (1 year) or 2yr (2 years) describing the age of the oak planted.
 Status: Binary variable indicating whether the plant was alive (0) or dead (1).
 Month_death: Binary variable indicating the moment when the plant died (1) and the rest of the time (0). 
 time: Numerical value representing the visit number, starting from 0 (date of planting) and increasing with each subsequent visit, typically conducted monthly. 
 group: Numeric identifier recorded by the Dualex each time the leaves of a plant were measured. Each plant had five leaves measured, and this number connects with the column in the database named "Dualex " along with the field date.
 date: Date when the data was collected, linking with the column in the database named "Dualex ".
 Browsing_wildboar: Numeric score (0-5) describing the level of damage inflicted by wild boars on the plant, as per Perea et al. (2015).
 Browsing_deer: Numeric score (0-5) describing the level of damage inflicted by deer on the plant. 
 Browsing_rabbit: Numeric score (0-5) describing the level of damage inflicted by rabbits on the plant. 
 Insect_damage: Numeric score (0-5) describing the level of damage inflicted by insects on the plant.
 Drought: Numeric score (0-5) describing the level of chlorosis to water stress observed on the leaves of the plant, possibly linked to water stress. .
 Fungi: Numeric score (0-5) describing the level of damage inflicted by fungi on the leaves of the plant.
 max_stress: Numeric value (0-5) representing the maximum observed damage across all stressors (wild boar browsing, deer browsing, rabbit browsing, insect damage, drought, and fungi).
 Mortality_agent2: Text indicating the cause of mortality when the plant status is 1 and max stress is 5. Options include "Wild Boar," "Deer," "Rabbit," "Insect," "Drought," "Fungi," or "NA" if unknown.
 main_stress: Text indicating the primary stressor among wild boar browsing, deer browsing, rabbit browsing, insect damage, drought, and fungi. In cases of multiple stressors, it highlights the one with the highest numeric score. 'NA' is assigned when no discernible stressor is present.
 
Database name: Dualex.xlsx
This data base contains the data obtained from the Dualex ® TMScientific+ measurements. 
Variables description:
 group: Numeric identifier recorded by the Dualex each time the leaves of a plant were measured. Each plant had five leaves measured, and this number connects with the column named group in the database named "Plnttn.xls" along with the field date.
 date: Date when the data was collected, linking with the date column in the "Plnttn.xls" database.
 Chl: Average chlorophyll value obtained from five leaves of the same plant, measured using the Dualex.
 NBI: Average nitrogen balance index obtained from five leaves of the same plant, measured using the Dualex.
 Flav: Average flavonoid concentrations obtained from five leaves of the same plant, measured using the Dualex.
 Anth: Average anthocyanin value obtained from five leaves of the same plant, measured using the Dualex.
description: All analyses were performed using the R 4.1.2 software (www.r-project.org).