Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae

ARTICLE Received 9 Jun 2010 | Accepted 17 Aug 2011 | Published 20 Sep 2011 DOI: 10.1038/ncomms1482 Late Cretaceous origin of the rice tribe provides evidence for early diversification in Poaceae V. Prasad1, C.A.E. Strömberg2, A.D. Leaché2, B. Samant3, R. Patnaik4, L. Tang5, D.M. Mohabey6, S. Ge5 & A. Sahni7 Rice and its relatives are a focal point in agricultural and evolutionary science, but a paucity of fossils has obscured their deep-time history. Previously described cuticles with silica bodies (phytoliths) from the Late Cretaceous period (67–65 Ma) of India indicate that, by the latest Cretaceous, the grass family (Poaceae) consisted of members of the modern sub clades PACMAD (Panicoideae–Aristidoideae–Chloridoideae–Micrairoideae–Arundinoideae– Danthonioideae) and BEP (Bambusoideae–Ehrhartoideae–Pooideae), including a taxon with proposed affinities to Ehrhartoideae. Here we describe additional fossils and show that, based on phylogenetic analyses that combine molecular genetic data and epidermal and phytolith features across Poaceae, these can be assigned to the rice tribe, Oryzeae, of grass subfamily Ehrhartoideae. The new Oryzeae fossils suggest substantial diversification within Ehrhartoideae by the Late Cretaceous, pushing back the time of origin of Poaceae as a whole. These results, therefore, necessitate a re-evaluation of current models for grass evolution and palaeobiogeography. Birbal Sahni Institute of Palaeobotany, 53 University Road, Lucknow 226 007, India. 2 Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington 98195, USA. 3 Postgraduate Department of Geology, Rashtrasant Tukadoji Maharaj Nagpur University, Nagpur 440001, India. 4 Centre for Petroleum and Applied Geology, Panjab University, Chandigarh 160014, India. 5 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China. 6 Geological Survey of India, Nagpur 440006, India. 7 Centre of Advanced Study in Geology, Lucknow University, Lucknow 226007, India. Correspondence and requests for materials should be addressed to C.A.E.S. (email: ). 1 nature communications | 2:480 | DOI: 10.1038/ncomms1482 | www.nature.com/naturecommunications © 2011 Macmillan Publishers Limited. All rights reserved.  ARTICLE nature communications | DOI: 10.1038/ncomms1482 T he critical dependence of humans on rice (Oryza sativa) as a crop species has made it a major research focus in both basic and applied plant science1–3. Numerous studies have sought to elucidate its domestication history4–7 clarify the relationships of species within the genus Oryza and to other genera in the rice tribe2,8,9–11, and track the evolutionary history of the subfamily that rice belongs to, Ehrhartoideae, within the grass family as a whole12–14. In these studies, the Ehrhartoideae is reconstructed as consisting of the tribes Oryzeae, Ehrharteae and Phyllorachidae15. The subfamily is commonly found to be nested within a monophyletic group consisting of the Bambusoideae, Ehrhartoideae and the Pooideae (the BEP clade)13,16,17; alternatively, the Bambusoideae, Ehrhartoideae and the Pooideae clades form a paraphyletic grade with reference to the PACMAD (Panicoideae–Aristidoideae–Chloridoideae–Micrairoideae–Arundinoideae–Danthonioideae) clade, with Pooideae as the sister taxon to the PACMADs18,19. Recent molecular clock estimates calibrated by selected grass fossils indicate that the Ehrhartoideae arose after the K–Pg (Cretaceous–Paleogene) boundary, by the Early Eocene (~53 Ma)17, that the Oryzeae diverged from the Ehrharteae by the Late Eocene–Early Oligocene (34.5 ± 6.8 Ma)16 and that Oryza emerged very recently, by the Middle Miocene period (15–14)10. However, beyond these analytical age-estimates, very little is known about the evolutionary history of ehrhartoid grasses, and the rice tribe in particular. The macrofossil record of these groups is virtually absent, with the oldest known macrofossil of the Oryzeae extending back only to the Late Miocene20,21. Prasad et al.22 described microscopic silica bodies (phytoliths) of grasses in dinosaur coprolites from the Late Cretaceous period (67–65 Ma) of India, some of which showed affinity to the Ehrhartoideae (Matleylites indicum) but could not be clearly assigned to this subfamily based on available data. The coprolites studied by Prasad et al. were recovered from the Maastrichtian (67–65 Ma) Lameta Formation, which consists of alluvial to limnic sediments associated with the Deccan Volcanics (infraand inter-trappean) of Central India. These deposits are known for their wealth of fossils, including dinosaur bones, coprolites, egg–shell fragments, remains of turtles, frogs, fishes and mammals, as well as macro- and micro-floral remains23–25. Continued sampling22,26,27 both from Lameta Formation sediments and associated titanosaurid sauropod coprolites from Pisdura (east and south sections) and sediments of the Lameta Formation at Dhamni, Piraya and Polgaon has yielded grass pollen and additional leaf cuticle with embedded grass silica short cell (GSSC) phytoliths similar to those found in oryzoid grasses (often referred to as ‘oryzoid’ silica bodies28). Here we report on these newly recovered fossil cuticles and associated phytoliths (referred to as morphotypes Changii indicum and Tateokai deccana) and use them to suggest a different scenario and timing for the emergence and diversification of the rice tribe than what is widely assumed among evolutionary biologists. We first infer a phylogenetic tree for the Poaceae based on molecular and morphological data, which allows us to deduce the placement of the new fossils in the context of 56 extant grass species. Divergence times for Poaceae lineages are then estimated using seven previously published fossils and our new fossils, and this framework is employed to investigate the evolutionary history of seven leaf epidermis and phytolith morphology characters. These characters were also scored for 14 taxa formerly used in phylogenetic analysis of the Ehrhartoideae10. Our analysis reveals that Changii indicum and Tateokai deccana most likely were members of the Oryzeae, and that diversification of the rice tribe began before the end of the Cretaceous. Results Systematic palaeontology. Fossil phytolith morphotype. Changii indicum (Fig. 1a). ICPN name. Vertical bilobate/cross with pointed lobes epidermal short cell + rectangular sinuate multi-papillate epidermal long cells + papillate subsidiary cells.   tymology. Genus named in honour of Te-Tzu Chang, who E has done pioneering work on the biosystematics, evolution and biogeography of rice, including theories regarding a Gondwana origin of rice: species referring to the country India. Holotype. One piece of cuticle, BSIP 13160 (Q-14-3). Locality and horizon. Coprolites from Red clays, Lameta Formation; Pisdura East and Pisdura South (Fig. 2). Other ref (...truncated)