DOI: 10.5061/dryad.n5tb2rc40
title: Data from: Avian phylogenetic and functional diversity are better conserved by land-sparing than land-sharing farming in lowland tropical forests

description: The transformation of natural habitats for farming is a major driver of
 tropical biodiversity loss. To mitigate impacts, two alternatives are
 promoted: intensifying agriculture to offset protected areas (land
 sparing) or integrating wildlife-friendly habitats within farmland (land
 sharing). In the montane and dry tropics, phylogenetic and functional
 diversity, which underpin evolutionary values and the provision of
 ecosystem functioning and services, are best protected by land sparing. A
 key question is how these components of biodiversity are best conserved in
 the more stable environments of lowland moist tropical forests. Focusing
 on cattle farming within the Colombian Amazon, we sampled how the
 occupancy of 280 bird species varies between forest and pasture spanning
 gradients of wildlife-friendly features. We then simulated scenarios of
 land-sparing and land-sharing farming to predict impacts on phylogenetic
 and functional diversity metrics. Predicted metrics differed marginally
 between forest and pasture. However, community assembly varied
 significantly. Wildlife-friendly pastures were inadequate for most
 forest-dependent species, while phylogenetic and functional diversity
 indices showed minimal variation across gradients of wildlife-friendly
 features. Land sparing consistently retained higher levels of Faith’s
 phylogenetic diversity (~30%), functional richness (~20%), and
 evolutionarily distinct lineages (~40%) than land sharing, and did so
 across a range of landscape sizes. Securing forest protection through
 land-sparing practices remains superior for conserving overall community
 phylogenetic and functional diversity than land sharing. Synthesis and
 applications: To minimise the loss of avian phylogenetic diversity and
 functional traits from farming in the Amazon, it is imperative to protect
 large blocks of undisturbed and regenerating forests. The intensification
 required within existing farmlands to make space for spared lands whilst
 meeting agricultural demand needs to be sustainable, avoiding long-term
 negative impacts on soil quality and other ecosystem services. Policies
 need to secure the delivery of both actions simultaneously.
description: # Data from: Avian phylogenetic and functional diversity are better
 conserved by land-sparing than land-sharing farming in lowland tropical
 forests
 [https://doi.org/10.5061/dryad.n5tb2rc40](https://doi.org/10.5061/dryad.n5tb2rc40) Files provided include raw (field) and pre-processed datasets (CSV and RDS files), and R software scripts (4 files) to conduct all analyses described in the Journal article. ## Description of the data and file structure We provide the minimum amount of data necessary to reproduce all the code. Scripts are numbered and should be run sequentially as each script relies on outputs generated in the previous ones. ### Attached files. ED_values_amazonbirds.csv * species: Scientific name following taxonomy from Jetz et al., (2012) * ED_mean: Evolutionary distinctness computed using the fair proportions method (Kembel et al., 2010) and averaged across 10000 phylogenetic trees. * EDR_mean: ED divided by species range area from Tobias et al., (2022) Functional_traits_amazonbirds.csv * species: Scientific name following taxonomy from Jetz et al., (2012) * Beak_Length_Culmen: Length from the tip of the beak to the base of the skull (mm) * Beak_Length_Nares: Length from the anterior edge of the nostrils to the tip of the beak (mm) * Beak_Width: Width of the beak at the anterior edge of the nostrils (mm) * Beak_Depth: Depth of the beak at the anterior edge of the nostrils (mm) * Tarsus_Length: Length of the tarsus from the posterior notch to the acrotarsium (mm) * Wing_Length: Length from the carpal joint to the tip of the longest primary (mm) * Kipps_Distance: Length from the tip of the first secondary feather to the tip of the longest primary (mm) * Secondary1: Length from the carpal joint to the tip of the first secondary (mm) * Hand_Wing_Index: 100*Kipp’s distance / Wing length * Tail_Length: Distance between the longest rectrix tip and central rectrices protrusion (mm) * logMass: Body mass given as species average (g, log scaled) * LogClutch_Size: Average number of eggs per clutch (log scaled) * Gen_Length: Average age of parents (log scaled) * Trophic_Level: Categorical variable. Herbivore: species obtaining at least 70% of food resources from plants; Carnivore: species obtaining at least 70% of food resources by consuming live invertebrate or vertebrate animals; Scavenger: species obtaining at least 70% of food resources from carrion or refuse; Omnivore: species obtaining resources from multiple trophic level in roughly equal proportion. * Trophic_Niche: Categorical variable. Frugivore: species obtaining at least 60% of food resources from fruit; Granivore: species obtaining at least 60% of food resources from seeds or nuts; Nectarivore: species obtaining at least 60% of food resources from nectar; Herbivore: species obtaining at least 60% of food resources from other plant materials in non-aquatic systems; Herbivore aquatic: species obtaining at least 60% of food resources from plant materials in aquatic systems; Invertivore: species obtaining at least 60% of food resources from invertebrates in terrestrial systems; Vertivore: species obtaining at least 60% of food resources from vertebrate animals in terrestrial systems; Aquatic Predator: species obtaining at least 60% of food resources from vertebrate and invertebrate animals in aquatic systems; Scavenger: species obtaining at least 60% of food resources from carrion, offal or refuse; Omnivore: Species using multiple niches, within or across trophic levels, in relatively equal proportions * Primary_Lifestyle: Categorical variable. Aerial: species spends much of the time in flight, and hunts or forages predominantly on the wing; Terrestrial: species spends majority of its time on the ground, where it obtains food while either walking or hopping; Insessorial: species spends much of the time perching above the ground, either in branches of trees and other vegetation (i.e. arboreal), or on other raised substrates including rocks, buildings, posts, and wires; Aquatic = species spends much of the time sitting on water, and obtains food while afloat or when diving under the water's surface; Generalist = species has no primary lifestyle because it spends time in different lifestyle classes. * Nest_Placement: Categorical variable. Extent to which a species depends of forest structures for nest placement. Ground open nesting; elevated open nesting; cavity nesting. names_lookup_amazonbirds.csv * model: Currently valid scientific name * species: Scientific name following taxonomy from Jetz et al., (2012) dataset_raw_amazonbirds.csv * point: Sampling point identifier. * species: Currently valid scientific name. * v1: Detections (1), non-detections (0) in visit 1. * v2: Detections (1), non-detections (0) in visit 2. * v3: Detections (1), non-detections (0) in visit 3. * v4: Detections (1), non-detections (0) in visit 4. * Q: Presence (1), Absence (0) of species across visits. * lat: Geographic coordinates (WGS84) latitude. * lon: Geographic coordinates (WGS84) longitude. * site: Study site identifiers; PS: Amazonas, PL: Putumayo, SG: Guaviare. * cluster: sampling cluster identifier. * habitat: Categorical, sampling point habitat; forest or pasture. * habitat2: habitat in numerical form; -1: pasture, 1: forest * elev_ALOS: Sampling point elevation in meters above sea level. * forest_dependency: Species dependency to forest habitat according to birdlife.org; High, medium, low * obs1: Identifier of researcher conducting sampling during visit 1. * obs2: Identifier of researcher conducting sampling during visit 2. * obs3: Identifier of researcher conducting sampling during visit 3. * obs4: Identifier of researcher conducting sampling during visit 4. * prop: Proportion of wildlife-friendly features in sampling point * prop_sc: Proportion of wildlife-friendly features in sampling point, standardised and centred. * hps1_sc: Time of day in scientific notation, standardised and centred during visit 1. * hps2_sc: Time of day in scientific notation, standardised and centred during visit 2. * hps3_sc: Time of day in scientific notation, standardised and centred during visit 3. * hps4_sc: Time of day in scientific notation, standardised and centred during visit 4. * site_sp: Species and study site interaction effect identifier. phylogeny_amazonbirds.rds * Trimmed phylogenetic tress (10000) to observed species, stored as an RDS object to be open in R software. 0_Modelling_and_simulation.R * R programming language script to 1) model occupancy of amazon birds in forest and pasture habitats and 2) Predict avian communities in habitats and simulated agricultural landscapes. 1_PD_FD_habitats.R * R programming language script to compute Phylogenetic and Functional Diversity metrics across forest and pastures habitats across a gradient of wildlife-friendly features. 2_PD_FD_sharing_sparing.R * R programming language script to compute Phylogenetic and Functional Diversity metrics across land-sharing and land-sparing simulated agriultural landscapes.  3_PD_FD_figures.R   * R programming language script to replicate plots, figures and results from analyses in the journal article. ## Sharing/Access information Links to other publicly accessible locations of the data: * [https://github.com/gapz01/PhD_year_one](https://github.com/gapz01/PhD_year_one) Data was derived from the following sources: * vertlife.org: [https://birdtree.org/downloads/](https://birdtree.org/downloads/) * [https://figshare.com/s/b990722d72a26b5bfead](https://figshare.com/s/b990722d72a26b5bfead) ## Code/Software The following packages must be installed in R for scripts to run (R version used 4.0.2) flocker, brms, tidyverse, DataCombine, ape, PhyloMeasures, mFD, fundiversity, picante, viridis, patchwork, ggpubr, tidybayes, bayestestR.