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Data from: Modeling phylogenetic biome shifts on a planet with a past

Citation

Landis, Michael; Edwards, Erika; Donoghue, Michael (2020), Data from: Modeling phylogenetic biome shifts on a planet with a past, Dryad, Dataset, https://doi.org/10.5061/dryad.pvmcvdnhj

Abstract

The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time, we developed a phylogenetic biome shift model in which each lineage shifts between biomes and disperses between regions at rates that depend on the lineage’s biome affinity and location relative to the spatiotemporal distribution of biomes at any given time. To study the behavior of the biome shift model in an empirical setting, we developed a literature-based representation of paleobiome structure for three mesic forest biomes, six regions, and eight time strata, ranging from the Late Cretaceous (100 Ma) through the present. We then fitted the model to a time-calibrated phylogeny of 119 Viburnum species to compare how the results responded to various realistic or unrealistic assumptions about paleobiome structure. Ancestral biome estimates that account for paleobiome dynamics reconstructed a warm temperate (or tropical) origin of Viburnum, which is consistent with previous fossil-based estimates of ancestral biomes. Imposing unrealistic paleobiome distributions led to ancestral biome estimates that eliminated support for tropical origins, and instead inflated support for cold temperate ancestry throughout the warmer Paleocene and Eocene. The biome shift model we describe is applicable to the study of evolutionary systems beyond Viburnum, and the core mechanisms of our model are extensible to the design of richer phylogenetic models of historical biogeography and/or lineage diversification. We conclude that biome shift models that account for dynamic geographical opportunities are important for inferring ancestral biomes that are compatible with our understanding of Earth history.

Methods

This Dryad dataset includes the input data analyzed in the main text and the Supplemental Information described in the main text. The main text describes how the data were collected in detail. These data were derived from the Dryad dataset: https://doi.org/10.5061/dryad.hx3ffbgb1. The zip file containing the data also contains a README.md file that overviews its contents.

Usage Notes

RevBayes code for the phylogenetic analysis and plotting scripts for the figures are hosted on GitHub: https://github.com/mlandis/biome_shift

Funding

National Science Foundation, Award: DBI-1612153

National Science Foundation, Award: DEB-1557059

National Science Foundation, Award: DEB-1753504