• DOI:10.1038/s41477-021-00964-4
• Corpus ID: 232282918

Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms

@article{Stull2021GeneDA,
  title={Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms},
  author={Gregory W. Stull and Xiao-Jian Qu and C. Tomomi Parins-Fukuchi and Ying-Ying Yang and Jun-bo Yang and Zhiyun Yang and Yi Hu and Hong Ma and Pamela S. Soltis and Douglas E. Soltis and De‐Zhu Li and Stephen A. Smith and Tingshuang Yi},
  journal={Nature Plants},
  year={2021},
  volume={7},
  pages={1015 - 1025}
}

• Gregory W. Stull, Xiao-Jian Qu, +10 authors T. Yi
• Published 17 May 2021
• Biology
• Nature Plants

Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution—including gene and genome duplication, genome size, and chromosome number—with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants. By examining the relationship of various facets of genomic changes with phenotypic evolution, this study found that pulses of phenotypic innovation in gymnosperms are strongly associated with gene duplications and genomic conflict.