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Rosid Radiation and the Rapid Rise of Angiosperm-Dominated Forests

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Rosid radiation and the rapid rise of angiosperm-dominated forests Hengchang Wanga,b, Michael J. Moorec, Pamela S. Soltisd, Charles D. Belle, Samuel F. Brockingtonb, Roolse Alexandreb, Charles C. Davisf, Maribeth Latvisb,f, Steven R. Manchesterd, and Douglas E. Soltisb,1 aWuhan Botanical Garden, The Chinese Academy of Science, Wuhan, Hubei 430074 China; bDepartment of Botany and dFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; cBiology Department, Oberlin College, Oberlin, OH 44074-1097; eDepartment of Biological Sciences, University of New Orleans, New Orleans, LA 70148; and fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 Communicated by Peter Crane, University of Chicago, Chicago, IL, January 4, 2009 (received for review April 1, 2008) The rosid clade (70,000 species) contains more than one-fourth of all nitrogen-fixing bacteria (nitrogen-fixing clade) and defense mech- angiosperm species and includes most lineages of extant temperate anisms such as glucosinolate production (Brassicales) and cyano- and tropical forest trees. Despite progress in elucidating relationships genic glycosides (2). Many important crops, including legumes within the angiosperms, rosids remain the largest poorly resolved (Fabaceae) and fruit crops (Rosaceae), are rosids. Furthermore, 4 major clade; deep relationships within the rosids are particularly of the 5 published complete angiosperm nuclear genome sequences enigmatic. Based on parsimony and maximum likelihood (ML) anal- are rosids (with 2 other rosids, Manihot and Ricinus, well under- yses of separate and combined 12-gene (10 plastid genes, 2 nuclear; way): Arabidopsis (Brassicaceae), Carica (Caricaceae), Populus >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening (Salicaceae), and Vitis (Vitaceae, sister to other rosids). The spacers; >25,000 bp) datasets for >100 rosid species, we provide a variation in morphological, chemical, and ecological features and greatly improved understanding of rosid phylogeny. Vitaceae are the importance of rosids as genetic and genomic models require a sister to all other rosids, which in turn form 2 large clades, each with phylogenetic perspective for interpreting large-scale evolutionary a ML bootstrap value of 100%: (i) eurosids I (Fabidae) include the patterns across the clade. Finally, most lineages of extant temperate nitrogen-fixing clade, Celastrales, Huaceae, Zygophyllales, Malpighia- and tropical forest trees are rosids (e.g., Betulaceae, Celtidaceae, les, and Oxalidales; and (ii) eurosids II (Malvidae) include Tapisciaceae, Fabaceae, Fagaceae, Malvaceae, Sapindaceae, and Ulmaceae). In EVOLUTION Brassicales, Malvales, Sapindales, Geraniales, Myrtales, Crossosoma- temperate North America Ϸ71% of the forest tree species are tales, and Picramniaceae. The rosid clade diversified rapidly into these rosids (15). Similarly, rosids often constitute Ͼ50% of tropical tree major lineages, possibly over a period of <15 million years, and species diversity. For example, they comprise 59% of the tree perhaps in as little as 4 to 5 million years. The timing of the inferred species on Barro Colorado Island, Panama (16), 60% of the tree rapid radiation of rosids [108 to 91 million years ago (Mya) and 107–83 flora of Paraguay (17), 60% on Puerto Rico and the Virgin Islands Mya for Fabidae and Malvidae, respectively] corresponds with the (18), and 63% of the tree species of Brazil (19). Analysis of tropical rapid rise of angiosperm-dominated forests and the concomitant forest plots from around the world again suggests a major role of diversification of other clades that inhabit these forests, including rosid trees (20). Half the species richness of the Neotropical plots amphibians, ants, placental mammals, and ferns. is made up of just 11 families, 4 of which are rosids, with Fabaceae the most important (Moraceae, Meliaceae, and Euphorbiaceae are community assembly ͉ divergence time estimates ͉ phylogeny ͉ other major rosids in the Neotropics); Fabaceae are also the most rapid radiation important family of trees in Africa, but are replaced as number one by another rosid family, Dipterocarpaceae, in Southeast Asia (20). reat progress has been made in elucidating deep-level angio- The important ecological role of many rosid families further argues Gsperm relationships during the past decade. The eudicot clade, Ϸ for greater resolution of rosid phylogeny. with 75% of all angiosperm species, comprises several major Although studies agree on the composition of the rosid clade, subclades: rosids, asterids, Saxifragales, Santalales, and Caryophyl- deep-level relationships within the rosids remain enigmatic. Vita- lales (1–3). Investigations have converged on the branching pattern ceae usually appear as sister to all other rosids, although support for of the basalmost angiosperms, revealing that Amborellaceae, Nym- this placement is generally low (reviewed in refs. 2 and 10). Most phaeales [in the sense of APG II (3) and including Hydatellaceae remaining rosids appear in 2 large subclades (1–3): eurosids I (4)], and Austrobaileyales are successive sisters to all other extant [Fabidae (21)] and eurosids II [Malvidae (21)], with jackknife angiosperms (reviewed in ref. 2). Analyses of complete plastid support of 77% and 95%, respectively. Fabidae include (i) the genome sequences have resolved other problematic deep-level relationships, suggesting that Chloranthaceae and magnoliids are nitrogen-fixing clade (Rosales, Fabales, Cucurbitales, and Fagales); sister to a clade of monocots and eudicots plus Ceratophyllaceae (5, (ii) Zygophyllales; and (iii) a weakly supported clade of Celastrales, 6). Likewise, progress has been made in clarifying relationships Oxalidales, and Malpighiales [COM group (22)]. Malvidae include within the large monocot (7) and asterid (8) clades. Brassicales, Malvales, Sapindales, and Tapisciaceae. Despite these successes, the rosids stand out as the largest and Some rosid clades (Crossosomatales, Geraniales, and Myrtales), least-resolved major clade of angiosperms; basal nodes within the however, do not fall into either Fabidae or Malvidae, and their clade have consistently received low internal support (1, 2, 9, 10). The rosid clade comprises Ϸ70,000 species and 140 families (2, 11). Ϸ Author contributions: P.S.S., S.R.M., and D.E.S. designed research; H.W., M.J.M., C.D.B., Containing more than a quarter of total angiosperm and 39% of S.F.B., R.A., C.C.D., and M.L. performed research; M.J.M., C.D.B., and D.E.S. analyzed data; eudicot species diversity, the rosid clade is broader in circumscrip- and M.J.M., P.S.S., C.D.B., S.R.M., and D.E.S. wrote the paper. tion than the traditional Rosidae or Rosanae (e.g., 12; reviewed in The authors declare no conflict of interest. ref. 2). The oldest fossil flowers conforming to the rosids are from Freely available online through the PNAS open access option. Ϸ the late Santonian to Turonian ( 84–89.5 Mya) (9, 11, 13, 14). Data deposition: The sequences reported in this paper have been deposited in the GenBank Rosids exhibit enormous heterogeneity in habit, habitat, and life database (accession nos. EU002149 to EU002556). form, comprising herbs, shrubs, trees, vines, aquatics, succulents, 1To whom correspondence should be addressed. E-mail: [email protected]fl.edu. and parasites. The rosid clade also contains novel biochemical This article contains supporting information online at www.pnas.org/cgi/content/full/ pathways, such as the machinery necessary for symbiosis with 0813376106/DCSupplemental. www.pnas.org͞cgi͞doi͞10.1073͞pnas.0813376106 PNAS Early Edition ͉ 1of6 Downloaded by guest on September 30, 2021 relationships remain unclear. Myrtales are often resolved as sister to all other rosids, which in turn form 2 large clades, Fabidae and to Fabidae, whereas Crossosomatales and Geraniales appear with an expanded Malvidae, each with a bootstrap value of 100%. Malvidae, but without strong support (1, 2, 10). Furthermore, the The approximately unbiased (AU) topology test indicated that placements of several problematic families—Aphloiaceae, Apo- the sister relationship of Zygophyllales to Malvidae observed in MP danthaceae, Geissolomataceae, Huaceae, Ixerbaceae, Picramni- can be rejected (P Ͻ 0.001) in favor of the ML placement of aceae, and Strasburgeriaceae—also need to be ascertained. Zygophyllales as sister to an expanded Fabidae using both the total Rosid diversification, like angiosperm phylogeny as a whole, is evidence dataset and the 12 targeted genes dataset. characterized by repeating patterns of radiation from deep to shallow levels (2). Lack of resolution at the base of the rosid Divergence Time Estimates. Cross-validation determined a smooth- phylogeny in previous studies suggests an early radiation of crown- ing value of 1,000 for each of the penalized likelihood (PL) analyses. group rosids into major clades. Similar polytomies are evident In general, when the root of the tree was fixed to an age of 125 Mya, within both Fabidae and Malvidae and within clades further nested age estimates were an average of 5–10 million years older than when within Fabidae (i.e., Malpighiales). However, it is unclear whether the root was constrained to a maximum age of 125 Mya (Table 1). the apparent radiations within the rosids are real or merely artifacts Likewise, based on the bootstrap estimates of variation, the 2 due to poorly resolved relationships. Improved analysis of phylog- different methods usually did not fall within
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