James Timothy Y, Stajich Jason E, Hittinger Chris Todd, Rokas Antonis
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; email:
Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, California 92521, USA; email:
Annu Rev Microbiol. 2020 Sep 8;74:291-313. doi: 10.1146/annurev-micro-022020-051835. Epub 2020 Jul 13.
In this review, we discuss the current status and future challenges for fully elucidating the fungal tree of life. In the last 15 years, advances in genomic technologies have revolutionized fungal systematics, ushering the field into the phylogenomic era. This has made the unthinkable possible, namely access to the entire genetic record of all known extant taxa. We first review the current status of the fungal tree and highlight areas where additional effort will be required. We then review the analytical challenges imposed by the volume of data and discuss methods to recover the most accurate species tree given the sea of gene trees. Highly resolved and deeply sampled trees are being leveraged in novel ways to study fungal radiations, species delimitation, and metabolic evolution. Finally, we discuss the critical issue of incorporating the unnamed and uncultured dark matter taxa that represent the vast majority of fungal diversity.
在本综述中，我们讨论了全面阐明真菌生命树的现状和未来挑战。在过去15年中，基因组技术的进步彻底改变了真菌分类学，引领该领域进入系统发育基因组学时代。这使得原本不可想象的事情成为可能，即能够获取所有已知现存分类单元的完整遗传记录。我们首先回顾真菌树的现状，并强调需要进一步努力的领域。然后，我们审视由数据量带来的分析挑战，并讨论在众多基因树的情况下恢复最准确物种树的方法。高分辨率和深度采样的树正以新颖的方式被用于研究真菌辐射、物种界定和代谢进化。最后，我们讨论纳入代表绝大多数真菌多样性的未命名和未培养的暗物质分类单元这一关键问题。
