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.

中文翻译：

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模拟具有过去的行星上的系统发育生物群落变化

生物群落的空间分布随着时间的推移发生了很大变化，因此进化谱系转移到新生物群落的地理机会可能取决于生物群落的可用性和连通性如何随时间变化。为了更好地理解谱系如何在空间和时间上在生物群落之间转移，我们开发了一个系统发育生物群落转移模型，其中每个谱系在生物群落之间转移并以取决于谱系的生物群落亲和力和相对于生物群落时空分布的位置的速率在区域之间分散任何给定时间。为了研究实证环境中生物群落转变模型的行为，我们针对从晚白垩世（100 Ma）到现在的三个中等森林生物群落、六个区域和八个时间层开发了一种基于文献的古生物群落结构表示. 然后，我们将该模型拟合到 119 种荚莲属物种的时间校准系统发育中，以比较结果如何响应关于古生物群落结构的各种现实或不现实的假设。考虑到古生物群落动力学的祖先生物群落估计重建了荚莲属的暖温带（或热带）起源，这与先前基于化石的祖先生物群落估计一致。强加不切实际的古生物群落分布导致祖先生物群落估计消除了对热带起源的支持，而是在整个较暖的古新世和始新世夸大了对冷温带祖先的支持。我们描述的生物群落转移模型适用于 Viburnum 以外的进化系统研究，我们模型的核心机制可以扩展到历史生物地理学和/或谱系多样化的更丰富的系统发育模型的设计。我们得出结论，考虑到动态地理机会的生物群落转变模型对于推断与我们对地球历史的理解相一致的祖先生物群落非常重要。