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Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)

Citation

Liddell, Luke et al. (2020), Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae), Dryad, Dataset, https://doi.org/10.5061/dryad.3bk3j9khj

Abstract

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.

Methods

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 Coprosma and Veronica sect. Hebe. Three species which lacked any chromosome count data were not included in this study (Coprosma antipoda, C. polymorpha and Veronica spectabilis). Three other species (C. talbrockiei, V. calycina, and V. plebeia) were removed as they fall outside the otherwise monophyletic Coprosma and Veronica sect. Hebe 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 Veronica 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.)

Usage Notes

"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 Veronica and Coprosma ("CoprosmaBAYAREA.R", "CoprosmaDEC.R", "CoprosmaDIVA.R" and the comparable files Veronica) . 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 Veronica), and the code for the biogeographic stochastic mapping (CoprosmaBSM1.R", "CoprosmaBSM2.R", and the same for Veronica). 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.

Funding

Marsden Fund, Award: LCR 1702

Marsden Fund, Award: 16-UOA-277

Marsden Fund, Award: 18-UOA-034

University of Auckland, Award: FRDF Project #3722433