The Plant Press

From The Plant Press, Vol. 28, No. 1, January 2025.

A new grass family phylogeny is published

A collaborative effort from the Grass Phylogeny Working Group III has resulted in the publication of a new grass phylogeny inferred from 331 nuclear genes for more than 1,100 grass species entitled, “A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence” (New Phytologist, https://doi.org/10.1111/nph.20263). The international team of 74 scientists, including the Smithsonian Institution’s Paul Peterson and Rob Soreng, provide a corrected framework for revising the grass tree of life, which will support further research into grass evolution. 

The grass family has nearly 11,800 species in 791 genera, 109 subtribes, 54 tribes, 7 supertribes, and 12 subfamilies (Soreng et al., 2022; https://doi.org/10.1111/jse.12847; classification posted on TROPICOS). Poaceae is among the largest plant families of the world and is widely used by humans for food (rice, corn, wheat), building materials (reed, bamboo), and biofuels (sugarcane, switchgrass). Knowing the evolutionary history of this important plant family and how the taxa are related will help advance comparative biological research, the impact of hybridization, studies in crop breeding, understanding biodiversity and ecosystem conservation, and improve our classification among the subfamilies, tribes, subtribes, and genera. 

The newly published nuclear DNA tree covers 79% of grass genera. Herbarium specimens were used to sequence 21 rare genera and one hybrid for the first time (Pharoideae: Scrotochoa. Bambusoideae: Ekmanochloa, Fimbribambusa, Miniochloa, Parabambusa, Pinga, Ruhooglandia, Widjagachloa. Pooideae: Agropyropsis. Panicoideae: Asthenochloa, Bhidia, Dilophotriche, Hydrothauma, Oryzidium, Pogonachne, Pseudodichanthium, Thedachloa, Thyridachne, Trilobachne. Chloridoideae: Kampochloa, Pommeruella, × Cynochloris), confirming or fine-tuning their classifications.

The gene set was leveraged from five diverse sets of genomic data: (1) 450 Illumina target capture read accessions enriched with the Angiosperm353 probe set; (2) 295 Illumina shotgun whole-genome sequencing accessions; (3) 17 Illumina target capture read accessions enriched with 122 nuclear loci; (4) 343 assembled transcriptomes assembled from two recent studies; and (5) 48 whole genome sequences from PHYTOZOME v.13. The nuclear gene tree topology was compared to plastome regions by a 910-tip tree using the sequences of 70 coding plastome regions and the trnL‒trnF intergenic region. Evidence for reticulations (hybridization, introgression, and lateral transfers) was investigated using gene tree‒species tree reconciliation methods. Supported conflicts at the tribal level were detected for five genera; plastome data was not included for three other genera that resolved in different tribes than previously classified in Soreng et al. (2022). These conflicts need further study. 

The timeline of grass evolution continues to be a hot topic among agrostologists, and this new phylogeny supports earlier biogeography studies (Gallaher et al., 2022; https://doi.org/10.1111/jse.12857) suggesting the Poaceae began to diversify in the early–late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Africa clearly served as the center of origin for much of the early diversification of the lineages within the family.