DOI: 10.5061/dryad.3ffbg79q7
title: Deer dietary responses to wildfire: optimal foraging, individual specialization, or opportunism?

description: Increasing impacts of wildfire on arid regions of the world fueled by
 climate change highlight the need to better understand how natural
 communities respond to fire.  While plant communities have
 received much attention, less is known about responses of keystone
 herbivores, such as ungulates.  Large herbivores may temporarily
 vacate burned areas as vegetation decreases, returning as vegetation
 recovers, and concentrating in burn areas as early successional herbaceous
 species begin to flourish.  However, few data exist to assess
 herbivore trophic niches in burned and unburned habitats.  We
 took advantage of a large (1,660-km2) wildfire that erupted in northern
 California during an in-progress study of black-tailed deer (Odocoileus
 hemionus columbianus) to investigate deer use of and diets within burned
 and unburned habitats before and after the fire.  Depending on
 whether deer diet selection conformed better to optimal foraging models
 (including the niche variation hypothesis), or to that of a generalist
 forager, we expected that dietary breadth would either increase or
 decrease, respectively, in direct response to the reduction in forage
 associated with the fire and then decrease or increase again as the plant
 community recovered.  We used fecal pellet counts and
 metabarcoding to document changes in habitat use and diet relative to the
 fire. Pellet counts supported predictions that deer increased use of
 unburned sites and reduced use of burn sites after the fire and began to
 return to burned sites in subsequent sampling years.  Diet
 diversity did not differ significantly between control and burn sites
 before the fire, but was lower in burn than control sites post-fire (P
 &lt; 0.001), when and where diet was dominated by oak (Quercus
 spp).  In contrast, during subsequent years, diet diversity was
 higher (including more herbaceous plants) in burn than control sites (P
 &lt; 0.05). In contrast to predictions of optimal foraging and niche
 variation hypotheses, individual deer foraged as generalists for which
 diversity of the plant community as determined by fire was the primary
 determinant of their dietary niche breadth.
description: All data can be accessed with any text editor or spreadsheet
 software. Analysis scripts are for use in open source software, including
 DAD2 and R. 
description: # Deer dietary responses to wildfire: optimal foraging, individual
 specialization, or opportunism? --- This accession includes all of the raw
 sequencing reads for samples and controls used in the study, along with an
 ASV table(ASV_counts.txt) and ASV sequences (ASV.fa), output from DADA2.
 The sample names referenced in the ASV table correspond to the names of
 the fastq files, each of which corresponds to a single sample or control.
 ## Description of the data and file structure ### **Fastq files (n =
 865)**: Each fastq file contains all of the raw forward sequencing reads
 for a single pellet group sample or control sample. The first portion of
 the filename contains the sample name, which can be cross-referenced with
 the ASV table and other data files listed below. Conventions for names are
 Samples: Sxx_xxxx, where x = a numeral, e.g., S20_1660 Replicated samples
 extracted for surface of pellet: SSxx_xxxx Replicated samples extracted
 for interior of pellet: SIxx_xxxx No-template controls: NTC Positive
 control 1 (Salicornia): SAL Positive control 2 (Atriplex): ATR
 **Cutadapt_DADA2_script.docx** : Filtering and bioinformatic sorting into
 ASVs ASV sequences and tabular summary of numbers of ASVs corresponding to
 each fecal DNA and control sample from DADA2: **ASV_counts.txt** : This
 contains the raw read count corresponding to each ASV in each control and
 sample output from DADA2. **ASVs.FA** : This contains the sequences
 clustered into ASVs in DADA2 that were used to BLAST and assign plant
 taxa. Data analysis scripts and files included in 4 zipped folders: ###
 **Folder 1: DietDiff** : describes procedure for Dietary Differences -
 PERMANOVA analysis. **DietDiff.R** : Includes multi-way permanovas
 starting will all variables and working down to the final PERMANOVAs used
 in the paper, betadisper analysis with ANOVA and TukeyHSD -- Includes one
 line explanation of how to repeat with FOO data (for supplementary table)
 **Data Files** * 1 test, 4 variables (site, visit, sex, habitat):
 **R_genus4.csv**\ **R_sample_lookup.csv** * 2 tests, 2 variables (site,
 visit): **shrub_domRRA.csv**\ **shrub_dom_samplelookup.csv**\
 **tree_domRRA.csv**\ **tree_dom_samplelookup.csv** * 4 tests, 1 variable
 (visit): **shrub_burn_RRA.csv**\ **shrub_burn_lookup.csv**\
 **shrub_control_RRA.csv**\ **shrub_control_lookup.csv**\
 **tree_burn_RRA.csv**\ **tree_burn_lookup.csv**\ **tree_control_RRA.csv**\
 **tree_control_lookup.csv** **Variables** * sample: Unique sample ID for
 each sample collected * lat: Latitude where the sample was collected in
 decimal degrees, WGS84 * lon: Longitude where the sample was collected in
 decimal degrees, WGS84 * day: Day of the month the sample was collected on
 * month: Month the sample was collected in, ranging 4-7 for April-July *
 year: Year the sample was collected in, ranging from 2017 - 2021 * plate:
 Unique ID for each plate DNA samples were processed on * success: Success
 of determining the genotype of the individual deer, 2 variables. Yes:
 genotyping was successful, fail: genotyping was unsuccessful and
 individual ID or sex were not identified * individual: Individual ID of
 the deer determined by genotyping * sex: Sex of the deer determiened by
 genotyping, 3 variables. M: male, F: female, NA: unknown * plot: Unique ID
 for each sampled transect * pre_treecover: Percent of tree cover estimated
 in the field before the Ranch Fire burned, 7 variables. 1: &lt;1%, 2:
 1-5%, 3: 6-15%, 4: 16-25%, 5: 26-50%, 6: 51-75%, 7: &gt;75% *
 pre_shrubcover: Percent of shrub cover estimated in the field before the
 Ranch Fire burned, 7 variables. 1: &lt;1%, 2: 1-5%, 3: 6-15%, 4: 16-25%,
 5: 26-50%, 6: 51-75%, 7: &gt;75% * dom_TvS: Dominant habitat type,
 determied by percent cover codes in pre_treecover and pre_shrubcover, 2
 variables. tree_dom: tree dominated, percent cover of trees was higher
 than percent cover of shrubs prefire. shrub_dom: shrub dominated, percent
 cover of shrubs was higher than that of trees prefire * dom_TSO: Dominant
 habitat type, determied by percent cover codes in pre_treecover and
 pre_shrubcover and tree composition, 3 variables. tree_dom: tree
 dominated, percent cover of trees was higher than percent cover of shrubs
 prefire. shrub_dom: shrub dominated, percent cover of shrubs was higher
 than that of trees prefire. open_tree: tree dominated habitat primarily
 open oak woodland * site: Sampling site, 2 variables. control: sampling
 sites that never burned, burn: sampling sites that burned in the Ranch
 Fire * visit3: Sampling period, 3 variables. prefire: 2017-2018, before
 the Ranch fire burned. postfire: 2019, first year after the Ranch fire
 burned. recovery: 2020-2021, 2-3 years after the Ranch fire burned *
 visit: Sampling period, 4 variables. A: 2017-2018, pre-Ranch fire. B:
 2019, 1 year postfire. C: 2020, 2 years post-Ranch fire. D: 2021, 3 years
 post-Ranch fire. * visit_burned_r: Site burned in the Ranch Fire relative
 to sampling date, three variables. unburned: site never burned, prefire:
 site burned at a later date after sample collection, postfire: site burned
 before sample collection * twoclass_severity_r: Ranch Fire soil burn
 severity, 0: unburned, 1: Very Low-Low, 2: Moderate-Severe *
 twoclass_severity_a: August Complex Fire soil burn severity, 0: unburned,
 1: Very Low-Low, 2: Moderate-Severe * severity_r: Ranch Fire soil burn
 severity, 0: unburned, 1: Very Low, 2: Low, 3: Moderate, 4: Severe *
 severity_a: August Complex Fire soil burn severity, 0: unburned, 1: Very
 Low, 2: Low, 3: Moderate, 4: Severe * ranch: Site burned in the Ranch
 Fire, TRUE or FALSE * august: Site burned in the August Complex Fire, TRUE
 or FALSE * abies...vitis: plant genus detected in the sample and
 corresponding Relative Read Abundance ### **Folder 2: DietDiversity**
 Dietary Diversity and ANOVA analysis. **DietDiv.R** Includes fully
 factorial ANOVA model with all 3 variables, 3 one-way ANOVAs to test
 effect of treatment on visit Includes one line explanation of how to
 repeat with FOO data (for supplementary table) **Files** All samples
 pooled, RRA: **R_genus4.csv R_sample_lookup.csv** (included in DietDiff
 folder) Three one ways, effect of site on visit: **prefireRRA.csv,
 prefireLookup.csv postfireRRA.csv, postfireLookup.csv recoveryRRA.csv,
 recoveryLookup.csv** **Variables** same as above, see "Folder 1:
 DietDiff" ### **Folder 3: NicheVar** Niche Variation RinSp analysis.
 **NicheVar.R** : Includes examination of TNW, WID, AID in each period for
 burn and control sites **Files** * **BurnCounts.csv** *
 **ControlCounts.csv** **Variables** o sample: Unique sample ID for each
 sample collected o lat: Latitude where the sample was collected in decimal
 degrees, WGS84 o lon: Longitude where the sample was collected in decimal
 degrees, WGS84 o day: Day of the month the sample was collected on o
 month: Month the sample was collected in, ranging 4-7 for April-July o
 year: Year the sample was collected in, ranging from 2017 - 2021 o plate:
 Unique ID for each plate DNA samples were processed on o success: Success
 of determining the genotype of the individual deer, 2 variables. Yes:
 genotyping was successful, fail: genotyping was unsuccessful and
 individual ID or sex were not identified o individual: Individual ID of
 the deer determined by genotyping o sex: Sex of the deer determiened by
 genotyping, 3 variables. M: male, F: female, NA: unknown o plot: Unique ID
 for each sampled transect o site: Sampling site, 2 variables. control:
 sampling sites that never burned, burn: sampling sites that burned in the
 Ranch Fire o visit: Sampling period, 4 variables. A: 2017-2018, pre-Ranch
 fire. B: 2019, 1 year postfire. C: 2020, 2 years post-Ranch fire. D: 2021,
 3 years post-Ranch fire. o visit3: Sampling period, 3 variables. prefire:
 2017-2018, before the Ranch fire burned. postfire: 2019, first year after
 the Ranch fire burned. recovery: 2020-2021, 2-3 years after the Ranch fire
 burned o dom_TvS: Dominant habitat type, determied by percent cover codes
 in pre_treecover and pre_shrubcover, 2 variables. tree_dom: tree
 dominated, percent cover of trees was higher than percent cover of shrubs
 prefire. shrub_dom: shrub dominated, percent cover of shrubs was higher
 than that of trees prefire o twoclass_severity_r: Ranch Fire soil burn
 severity, 0: unburned, 1: Very Low-Low, 2: Moderate-Severe o
 twoclass_severity_a: August Complex Fire soil burn severity, 0: unburned,
 1: Very Low-Low, 2: Moderate-Severe o severity_r: Ranch Fire soil burn
 severity, 0: unburned, 1: Very Low, 2: Low, 3: Moderate, 4: Severe o
 severity_a: August Complex Fire soil burn severity, 0: unburned, 1: Very
 Low, 2: Low, 3: Moderate, 4: Severe o ranch: Site burned in the Ranch
 Fire, TRUE or FALSE o august: Site burned in the August Complex Fire, TRUE
 or FALSE o abies...vitis: plant genus detected in the sample and
 corresponding Frequency of Occurance, the count of reads detected in each
 sample ### **Folder 4: DietComp** Diet Composition K-W test.
 **DietComp.R**: Includes tests of significance for differences in
 proportions of plant form in the diet between treatments in each period,
 and for differences in mean RRA of taxon between treatments in each period
 **Files** Change in proportion of plant forms in diet
 **FormVisitA_both.csv** **FormVisitA_Lookup.csv** **FormVisitB_both.csv**
 (no longer need lookup) **FormVisitC_both.csv** **Ashrub.csv**
 **Atree.csv** **Bshrub.csv** **Btree.csv** **Cshrub.csv** **Ctree.csv**
 **Variables** o sample: Unique sample ID for each sample collected o site:
 Sampling site, 2 variables. control: sampling sites that never burned,
 burn: sampling sites that burned in the Ranch Fire o visit3: Sampling
 period, 3 variables. prefire: 2017-2018, before the Ranch fire burned.
 postfire: 2019, first year after the Ranch fire burned. recovery:
 2020-2021, 2-3 years after the Ranch fire burned o tree: Relative read
 abundance of all tree genera in each sample o shrub: Relative read
 abundance of all shrub genera in each sample o grass: Relative read
 abundance of all grass genera in each sample o herb: Relative read
 abundance of all herbacious genera in each sample o undetermined: Relative
 read abundance of all unknown genera in each sample o abies...vitis: plant
 genus detected in the sample and corresponding Relative Read Abundance ##
 Sharing/Access information Data was derived from the following sources:
 DNA extracted from fecal pellets from black-tailed deer. ## Code/Software
 Code is all listed above. Software included R and DADA2, both open source.