DOI: 10.5061/dryad.tmpg4f4z4
title: Ecological interactions shape the evolution of flower colour in communities across a temperate biodiversity hotspot

description: Processes driving the divergence of floral traits may be integral to the
 extraordinary richness of flowering plants and the assembly of diverse
 plant communities. Several models of pollinator-mediated floral evolution
 have been proposed; floral divergence may (i) be directly involved in
 driving speciation or may occur after speciation driven by (ii) drift or
 local adaptation in allopatry or (iii) negative interactions between
 species in sympatry. Here, we generate predictions for patterns of trait
 divergence and community assembly expected under these three models, and
 test these predictions in Hakea (Proteaceae), a diverse genus in the
 Southwest Australian biodiversity hotspot. We quantified functional
 richness for two key floral traits (pistil length and flower colour), as
 well as the phylogenetic distance between species and across communities,
 and compared these patterns to null models of community assembly. We
 estimated the statistical relationship between rates of trait evolution
 and lineage diversification across the phylogeny. Patterns of community
 assembly suggest that flower colour, but not floral phenology or
 morphology, or phylogenetic relatedness, is more divergent in communities
 than expected. Rates of lineage diversification and flower colour
 evolution were negatively correlated across the phylogeny. These results
 support a role for diversity-dependent species interactions driving floral
 divergence during the Hakea radiation, contributing to the development of
 the extraordinary species richness of southwest Australia.
description: "Hakea_trait_data.csv" &
 "Hakea_flowering_times_overlap_matrix.csv" = Morphological and
 Phenological data from the Flora of Australia vol. 17B and Skeels, A., and
 M. Cardillo. 2019a. Equilibrium and non-equilibrium phases in the
 radiation of Hakea and the drivers of diversity in Mediterranean-Type
 Ecosystems. Evolution 73:1392–1410.
 "Hakea_phylogeny.newick" = Phylogenetic data from
 Cardillo, M., P. H. Weston, Z. K. M. Reynolds, P. M. Olde, A. R. Mast, E.
 M. Lemmon, A. R. Lemmon, and L. Bromham. 2017. The phylogeny and
 biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a
 continental plant radiation. Evolution 71:1928–1943.
 "Hakea_presence_absence_matrix" &
 "site_coordinates.csv" = Community survey data from Gibson, N.,
 G. Keighery, M. Lyons, and A. Webb. 2004. Terrestrial flora and vegetation
 of the Western Australian wheatbelt. Rec. West. Aust. Museum Suppl.
 67:139–189.
 "RGB_histogram_for_colordistance.rds" &
 "Hakea_RGB_measurements" = Flower colour data from this study
 and methods explained in the main text and Appendix S1.
 "Hakea_macroevolutionary_rates_by_branch.csv" = ClaDS
 and RRPhylo analyses, methods in main text.
 "FD_and_mpd_on_null_models" folder = simulated
 communities under two different null models (independant swap and
 dispersal null models) methods in main text.
description: Dataset contains all data required to replicate the analyses. The
 data comes from a variety of sources outlined below and the flower colour
 data was collected for this study. Data are either .csv, .newick
 (phylogeny), or .rds and can be read in R following the included script
 provided with read.csv(), read.tree(), or readRDS(). Please contact
 Alexander Skeels (alexander.skeels@gmail.com) for any questions about the
 data or R code. Data sources and methods:
 "Hakea_trait_data.csv" &
 "Hakea_flowering_times_overlap_matrix.csv" = Morphological and
 Phenological data from the Flora of Australia vol. 17B and Skeels, A., and
 M. Cardillo. 2019a. Equilibrium and non-equilibrium phases in the
 radiation of Hakea and the drivers of diversity in Mediterranean-Type
 Ecosystems. Evolution 73:1392–1410.
 "Hakea_phylogeny.newick" = Phylogenetic data from
 Cardillo, M., P. H. Weston, Z. K. M. Reynolds, P. M. Olde, A. R. Mast, E.
 M. Lemmon, A. R. Lemmon, and L. Bromham. 2017. The phylogeny and
 biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a
 continental plant radiation. Evolution 71:1928–1943. Pruned to contain the
 species found in the Southwest survey, with three species without
 molecular data added based on taxonomy as polytomies at the node of the
 most recent common ancestor based on intra-generic
 classifications.
 "Hakea_presence_absence_matrix" &
 "site_coordinates.csv" = Community survey data from Gibson, N.,
 G. Keighery, M. Lyons, and A. Webb. 2004. Terrestrial flora and vegetation
 of the Western Australian wheatbelt. Rec. West. Aust. Museum Suppl.
 67:139–189. Presence/Absence data of 52 Hakea species + site coordinates
 necessary for determining distances between sites.
 "RGB_histogram_for_colordistance.rds" &
 "Hakea_RGB_measurements.csv" = Flower colour data from this
 study collected in May-September 2019, and methods explained in the main
 text and Appendix S1. Histogram object is used to create Earth
 Mover's colour distance matrices and is based on the raw data -
 "Hakea_RGB_measurements"
 "Hakea_macroevolutionary_rates_by_branch.csv" = ClaDS
 and RRPhylo analyses, methods in main text. This data was used to fit
 APGLMM models in the phyr package.
 "FD_and_mpd_on_null_models" folder = simulated
 communities under two different null models (independant swap and
 dispersal null models) methods in main text. MPD/FRic were calculated on
 these matrices to get a distribution to compare the empirical observations
 with.