Genomic insights into rapid speciation within the world’s largest tree genus Syzygium
Yee Wen Low, Sitaram Rajaraman, Crystal Tomlin, Joffre Ali Ahmad, Wisnu Handoyo Ardi, Kate Armstrong, Parusuraman Athen, Ahmad Berhaman, Ruth E. Bone, Martin Cheek, Nicholas R W Cho, Le Min Choo, Ian D Cowie, Darren M. Crayn, Steven J. Fleck, Andrew Ford, Paul I. Forster, Deden Girmansyah, D. J. Goyder, Bruce H. Gray, Charlie D. Heatubun, Ali Abdulhafidh Ibrahim, Bazilah Ibrahim, Himesh Jayasinghe, Muhammad Ariffin Kalat, Hashendra Kathriarachchi, Endang Kintamani, Sin Lan Koh, Joseph Tuck Kwong Lai, Serena M. L. Lee, P.K.F. Leong, Wei Hao Lim, Shawn K. Y. Lum, Ridha Mahyuni, William J. McDonald, Faizah Metali, Wendy A. Mustaqim, Akiyo Naiki, Kang Min Ngo, Matti A. Niissalo, Subhani Ranasinghe, Rimi Repin, Himmah Rustiami, Victor Immanuel Simbiak, Rahayu Sukmaria Sukri, Siti Sunarti, Liam Trethowan, Anna Trias‐Blasi, Thaís Vasconcelos, Jimmy F. Wanma, Pudji Widodo, Siril Wijesundara, Stuart Worboys, Jing Wei Yap, Kien‐Thai Yong, Gillian Khew, Jarkko Salojärvi, Todd P. Michael, David J. Middleton, David F. R. P. Burslem, Charlotte Lindqvist, Eve Lucas, Victor A. Albert
Abstract
Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.