Pioneering polyploids: the impact of whole-genome duplication on biome shifting in New Zealand Coprosma (Rubiaceae) and Veronica (Plantaginaceae)
- 1. University of Auckland
- 2. University of Otago
- 3. Museum of New Zealand Te Papa Tongarewa
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.
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 provided by: Marsden Fund
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100009193
Award Number: LCR 1702
Funding provided by: Marsden Fund
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100009193
Award Number: 16-UOA-277
Funding provided by: Marsden Fund
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100009193
Award Number: 18-UOA-034
Funding provided by: University of Auckland
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001537
Award Number: FRDF Project #3722433
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