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Modeling phylogenetic biome shifts on a planet with a past

View ORCID ProfileMichael J. Landis, Erika J. Edwards, Michael J. Donoghue
doi: https://doi.org/10.1101/832527
Michael J. Landis
1Department of Biology, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, USA
2Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520, USA
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  • For correspondence: michael.landis@wustl.edu
Erika J. Edwards
2Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520, USA
3Division of Botany, Yale Peabody Museum of Natural History, P.O. Box 208118, New Haven, Connecticut 06520, USA
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Michael J. Donoghue
2Department of Ecology & Evolutionary Biology, Yale University, PO Box 208106, New Haven, Connecticut 06520, USA
3Division of Botany, Yale Peabody Museum of Natural History, P.O. Box 208118, New Haven, Connecticut 06520, USA
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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.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 01, 2020.
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Modeling phylogenetic biome shifts on a planet with a past
Michael J. Landis, Erika J. Edwards, Michael J. Donoghue
bioRxiv 832527; doi: https://doi.org/10.1101/832527
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Modeling phylogenetic biome shifts on a planet with a past
Michael J. Landis, Erika J. Edwards, Michael J. Donoghue
bioRxiv 832527; doi: https://doi.org/10.1101/832527

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