Phylogenomics and Plastome Evolution of Tropical Forest Grasses (Leptaspis, Streptochaeta: Poaceae)

Abstract

Studies of complete plastomes have proven informative for our understanding of the molecular evolution and phylogenomics of grasses. In this study, a plastome phylogenomic analysis sampled species from lineages of deeply diverging grasses including Streptochaeta spicata (Anomochlooideae), Leptaspis banksii, and L. zeylanica (both Pharoideae). Plastomes from next generation sequences for three species were assembled by de novo methods. The unambiguously aligned coding and non-coding sequences of the entire plastomes were aligned with those from 43 other grasses and the outgroup Joinvillea ascendens. Outgroup sampling of grasses has previously posed a challenge for plastome phylogenomic studies because of major rearrangements of the plastome. Here, over 81,000 bases of homologous sequence were aligned for phylogenomic and divergence estimation analyses. Rare genomic changes, including persistently long ψycf1 and ψycf2 loci, the loss of the rpoC1 intron, and a 21 base tandem repeat insert in the coding sequence for rps19 defined branch points in the grass phylogeny. Marked differences were seen in the topologies inferred from the complete plastome and two gene matrices, and mean maximum likelihood support values for the former were 10% higher. In the full plastome phylogenomic analyses, the two species of Anomochlooideae were monophyletic. Leptaspis and Pharus were found to be reciprocally monophyletic, with the estimated divergence of two Leptaspis species preceding those of Pharus by over 14 Ma, consistent with historical biogeography. Our estimates for deep divergences among grasses were older than previous such estimates, likely influenced by more complete taxonomic and molecular sampling and the use of recently available or previously unused fossil calibration points.

The grass subfamily Pooideae: Cretaceous–Palaeocene origin and climate‐driven Cenozoic diversification

“…Compared with many earlier estimates, our age estimates (Figure a; Table ) indicate a relatively older age of the Pooideae and Poaceae, with crown node ages at 61–77 and 101–112 Ma, respectively. Our findings are, however, in line with recent analyses that have taken into account updated information from the fossil record (Bouchenak‐Khelladi et al, ; Burke et al, ; Christin et al, ; Marcussen et al, ; Prasad et al, ; Vanneste, Maere, & Peer, ; Wang et al, ). Studies that found considerably younger ages (i.e., 59–70 Ma for Poaceae) typically did not include these fossils (Bouchenak‐Khelladi, Muasya, & Linder, ; Christin et al, ; Kellogg, ; Marcussen et al, ; Vicentini, Barber, Aliscioni, Giussani, & Kellogg, ) or inferred ages by molecular substitution rates rather than fossil calibration (Goff et al, ; Paterson, Bowers, & Chapman, ; Schlueter et al, ; Wang et al, 2015; The International Brachypodium Initiative, ).…”

“…The age of Pooideae has been difficult to establish, but ages ranging from 45 to 64 Ma have been suggested (Bouchenak‐Khelladi, Verboom, Savolainen, & Hodkinson, ; Burke, Lin, Wysocki, Clark, & Duvall, ; Christin et al, ; Prasad et al, ; The International Brachypodium Initiative, ; Vanneste, Maere, & Van de Peer, ; Wang et al, ). During the time range of suggested origin for Pooideae, the global climate was warm, with little difference in temperatures at high and low latitudes (Mudelsee, Bickert, Lear, & Lohmann, ; Zachos et al, ); there were few or no incidents of frost, and seasonality in temperature was relatively low (Archibald, Bossert, Greenwood, & Farrell, ).…”

Leaf shape and size track habitat transitions across forest–grassland boundaries in the grass family (Poaceae)

“…S1 and S2). Subfamilial and tribal relationships agree with other recent plastome-based studies (Cotton et al 2015;Wysocki et al 2015;Burke et al 2016a;Teisher et al 2017;Saarela et al 2018). Support <0.99 PP and <99% bootstrap was found for 20 and 60 nodes, respectively, including relatively low support for the node supporting Panicoideae as the sister group to the remaining subfamilies of the PACMAD clade.…”

Grass diversification in Madagascar: In situ radiation of two large C3 shade clades and support for a Miocene to Pliocene origin of C4 grassy biomes

“…Arundinelleae and the Asian Jansenella griffithiana at least to the Early Miocene. A recent phylogenomic study (Burke, Wysocki, et al, 2016) placed it at the base of the core Panicoideae, suggesting it may be even older. Lecomtella is very likely the oldest endemic grass lineage in Madagascar.…”