DOI: 10.5061/dryad.3bk3j9khj
title: Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

description: The role of whole-genome duplication in facilitating shifts into novel
 biomes remains unknown. Focusing on two diverse woody plant groups in New
 Zealand, Coprosma (Rubiaceae) and Veronica (Plantaginaceae), we
 investigate how biome occupancy varies with ploidy level, and test the
 hypothesis that whole-genome duplication increases the rate of biome
 shifting. Ploidy levels and biome occupancy (forest, open, and alpine)
 were determined for indigenous species in both clades. The distribution of
 low ploidy (Coprosma: 2x, Veronica: 6x) vs high ploidy (Coprosma: 4–10x,
 Veronica: 12–18x) species across biomes was tested statistically.
 Estimation of the phylogenetic history of biome occupancy and whole-genome
 duplication was performed using time-calibrated phylogenies and the R
 package BioGeoBEARS. Trait-dependent dispersal models were implemented to
 determine support for an increased rate of biome shifting among high
 ploidy lineages. We find support for a greater than random portion of high
 ploidy species occupying multiple biomes. We also find strong support for
 high ploidy taxa showing a three to eight-fold increase in the rate of
 biome shifts. These results suggest that whole-genome duplication promotes
 ecological expansion into new biomes.
description: Each species was either present or absent in three key New
 Zealand biomes: forest, open, and alpine. The study groups included all
 native species of <em>Coprosma </em>and
 <em>Veronica</em> sect. <em>Hebe</em>. Three
 species which lacked any chromosome count data were not included in this
 study (<i>Coprosma antipoda</i>, <i>C.
 polymorpha</i> and <i>Veronica spectabilis</i>). Three
 other species (<i>C. talbrockiei</i>, <i>V.
 calycina</i>,<i> </i>and <i>V. plebeia</i>)
 were removed as they<i> </i>fall outside the otherwise
 monophyletic <i>Coprosma </i>and <i>Veronica</i>
 sect. <i>Hebe </i>clades. Biome occupancy
 for the study species was determined through floras, ecological
 literature, and expert opinion. Ploidy levels for species were compiled
 using the Chromosome Count Database. Species with a ploidy level higher
 than the lowest in New Zealand were treated as “high ploidy”, those at the
 lowest level were treated as “low ploidy”. Eight species with multiple
 recorded cytotypes were treated as multiploids for the subsequent
 analyses, with ploidy scored as "?". The two
 phylogenies used are taken Meudt et al. (2015) and Cantley et al. (2016).
 The latter phylogeny was carefully digitised from a published figure using
 TreeRogue, with non-NZ species pruned out. The <i>Veronica</i>
 phylogeny was extracted from a larger phylogeny of the global
 genus. Also included is the code used for both the
 chi-squared tests of independence and the biogeographc
 modelling. Additional details on the methods used in
 this study can be found in the Supplementary Materials (Supp 2.)
description: "independence_test_data.csv",
 "independence_test_script.R", "single biome independence
 test data.csv" and "single biome independence test data.R"
 contain the data and R code for the chi-square tests of independence
 between biome occupy and ploidy. In the "single biome"
 files, species occupying multile biomes have been removed. The data and
 code for this is fairly straightforward. All other
 files are for the biome occupancy modelling in BioGeoBEARs. This includes
 the code for running the 12 different biogeography models on both
 <em>Veronica </em>and
 <em>C</em><em>oprosma </em>("CoprosmaBAYAREA.R", "CoprosmaDEC.R", "CoprosmaDIVA.R" and the comparable files <em>Veronica</em>) . Also included is an excel spreadsheet used for model selection and estimation of model-weighted parameter estimates ("coprosma model comparison.xlxs" and "veronica model comparison.xlsx"), the code to generate figures 1 & 2 ("CoprosmaFig1.R", "CoprosmaFig2.R" and the same for <em>Veronica</em>), and the code for the biogeographic stochastic mapping (CoprosmaBSM1.R", "CoprosmaBSM2.R", and the same for <em>Veronica</em>). Note that when doing the biogeographic stochastic mapping, only models without trait-dependent dispersal can be run. Because of this, the best supported trait-independent model is used instead. The various .txt files contain information on ploidy, biome occupancy and time consrtraints for biome availability. The .newick files contain the phylogenetic trees used.