DOI: 10.5061/dryad.5mkkwh76b
title: Abundance of Anolis bicaorum, and niche measurements of plots on the island Utila, Honduras

description: The question of what controls animal abundance has always been fundamental
 to ecology, but given rapid environmental change, understanding the
 drivers and mechanisms governing abundance is more important than ever.
 Here, we determine how multidimensional environments and niches interact
 to determine population abundance along a tropical habitat gradient.
 Focusing on the endemic lizard Anolis bicaorum on the island of Utila
 (Honduras), we evaluate direct and indirect effects of three interacting
 niche axes on abundance: thermal habitat quality, structural habitat
 quality, and prey availability. We measured A. bicaorum abundance across a
 series of thirteen plots and used N-mixture models and path analysis to
 disentangle direct and indirect effects of these factors. Results showed
 that thermal habitat quality and prey biomass both had positive direct
 effects on anole abundance. However, thermal habitat quality also
 influenced prey biomass, leading to a strong indirect effect on abundance.
 Thermal habitat quality was primarily a function of canopy density,
 measured as leaf area index (LAI). Despite having little direct effect on
 abundance, LAI  had a strong overall effect mediated by thermal
 quality and prey biomass. Our results demonstrate the role of
 multidimensional environments and niche interactions in determining animal
 abundance and highlight the need to consider interactions between thermal
 niches and trophic interactions to understand variation in abundance,
 rather than focusing solely on changes in the physical environment.
description: Combination of Data sources
 collected on the island of Utila, Honduras - Datasets outlined
 below.  1. Anole
 Count Data - collected using mark recapture methods over 4 survey visits
 (9am, 1pm, 5pm and 9am the following day)-
 (Count_Abicaorum.xlsx).  2. bicaCovs.csv - dataset used as
 covariates within the unmarked package (Unmarked_Code_Abicaorum.R) All
 columns described below.  Time and date columns
 - used for estimates as a basic unmarked matrix. 
 LAI Transects
 - mean leaf area index of two cross sectional transects captured using an
 Accupar Lp-80 ceptometer.  Shannon.Div.Sweep -
 Shannons diversity for plot invertebrate sweep net
 samples.  Simpson.div.sweep -
 simpsons diversity for plot invertebrate sweep net
 samples sweep.net.biomass -
 biomass (g) of sweep net invertebrate samples 
 combined prey
 shannon - combined sweep net and leaf litter invertebrate samples -
 shannon diversity  combined prey simpson
 -  combined sweep net and leaf litter invertebrate samples - simpson
 diversity  Combined biomass
 -  biomass (g) - combined sweep net and leaf litter invertebrate
 samples Tpref.Dev - Total
 deviation (total oC) of all 3d models within plot away from Tpref range
 during thermal survey period - collected with ibutton and 3d anolis
 models.  Tpref.3 - percent of
 time (out of 39 survey hours) that the 3d models were within the tpref
 range in each plot.  Air.Temp - mean air
 temperature during anole surveys - collected using consistent hour logging
 of air temp by shaded ibutton within plot over 10
 weeks.  No.perches - number
 of perches within each plot - measured manually in
 plot.  Basal.area - basal
 area (m2) of each plot c\alculated suing standard basal area calculation
 of diameter at breast height for each tree/perch in
 plot.  Sagrei.abundance -
 abundance calculated from unmarked models of - Anolis sagrei abundance
 within plots - note this not used in paper. 
 Dev.Above
 - Total deviation (total oC) of all 3d models within plot being above
 the Tpref range during thermal survey period - collected with ibutton and
 3d anolis models. Dev.Below - Total
 deviation (total oC) of all 3d models within plot below the Tpref range
 during thermal survey period - collected with ibutton and 3d anolis
 models.  3. AirTemp_6amto6pm_wholeseason.xls – hourly air temperature measures from 06:00 to 18:00 for the whole of the survey season – approx. 10 weeks – for each plot. , measured using ibutton. 4. AirTemp_duringsurveys – air temperature recorded with same ibutton as dataset above – for the time/day that surveys were conducted at each plot (abundance surveys). 5. bicao.csv – Matrix of anole individual encounters – gathered from mark recapture methods – (dataset 1) – to be inputted into unmarked model code  - (Unmarked_Code_Abicaorum.R). 6. A.bicaorum abundance.csv – abundance estimates for each plot calculated using Unmarked_Code_Abicaorum.R allowing abundance only to vary by plot. 7. Invertebrate Samples – Analysis and Dataset – All invertebrate #(prey availability) data collected for each plot,. Including genus and weight – used to calculate metrics within bicaCovs.csv. 8. Path_variables – input for ‘path anlysis .R’ – including all data for plots used in the path analysis -  outlined in ‘bicaCovs.csv’ above. 9. Tpref_bica_allind_filter15. Csv – Measurements of body temperature of lizards (Abicaorum)  on the Tpref gradient –(oC – measured with thermocouple inserted into cloaca and measured every 10 seconds) – with a 15 minute adjustment period removed. 10. Tpref_diffinds.R – R code to calculated the Tpref of individuals from daset above. 11. Uncal bicao.csv and Uncal_bicaCovs.csv – same covariates as outlined above – but using uncalibrated 3d anolis model data. 12. Variables.csv and Variablesuncal.csv – variables – same as outlined above – for use to plot graphics.
description: No additional notes - data and code as used.