TreeBASE Search-Trees for study 22054

@ARTICLE{TreeBASE2Ref27989, author = {Yezi Xiang and Chien-Hsun Huang and Yi Hu and Jun Wen and Shisheng Li and Tingshuang Yi and Hongyi Chen and Jun Xiang and Hong Ma}, title = {Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication}, year = {2017}, keywords = {coalescence, fruit evolution, molecular clock, nuclear phylogeny, Rosaceae, genome duplication}, doi = {10.1093/molbev/msw242}, url = {http://}, pmid = {}, journal = {Molecular Biology and Evolution}, volume = {34}, number = {2}, pages = {262--281}, abstract = {Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dis- persing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with 3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of 101.6Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.} }