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Resolving Deep Relationships of PACMAD Grasses: a Phylogenomic Approach Joseph L

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Cotton et al. BMC Plant Biology (2015) 15:178 DOI 10.1186/s12870-015-0563-9 RESEARCHARTICLE Open Access Resolving deep relationships of PACMAD grasses: a phylogenomic approach Joseph L. Cotton1*†, William P. Wysocki1†, Lynn G. Clark2, Scot A. Kelchner5, J Chris Pires3, Patrick P. Edger4, Dustin Mayfield-Jones6 and Melvin R. Duvall1† Abstract Background: Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats. Results: New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya. Conclusions: Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate. Keywords: Complete plastome, Divergence estimates, PACMAD Clade, Panicoideae, Phylogenomics, Rapid radiation Background particular interest in this study because despite its Poaceae have been the subject of numerous phylogenetic paramount economic and ecological importance, phylo- studies due to their economic and ecological importance, genetic relationships among its major lineages remain as well as their dominance in major terrestrial biomes uncertain. [1–5]. The current phylogenetic classification of Poa- The sister group to the BEP clade has been variously de- ceae includes a deep grade of three lineages: Anomo- fined as the PACC, PACCAD, PACCMAD, or PACMAD chlooideae, Pharoideae, and Puelioideae, as well as the clade with different constituent subfamilies. A previous crown grasses represented by the BEP (Bambusoideae, study [1] utilized the plastid gene sequence ndhF, which Ehrhartoideae, Pooideae) [2] and PACMAD (Panicoideae, supported a monophyletic PACC (Panicoideae, Arundi- Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, noideae, Chloridoideae, Centothecoideae) clade, as well as Danthonioideae) [3] clades. The PACMAD clade is of indicating the polyphyletic nature of Arundinoideae. Subsequent work by the Grass Phylogeny Working Group * Correspondence: [email protected] (GPWG) [2] addressed weak support within and among †Equal contributors the grass subfamilies by making use of informative charac- 1Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois 60115-2861, U.S.A ters in seven molecular datasets along with a morphological Full list of author information is available at the end of the article © 2015 Cotton et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Cotton et al. BMC Plant Biology (2015) 15:178 Page 2 of 11 dataset. For comparative purposes we will refer to well-supported topology at the subfamilial level, espe- their results for three plastid sequences (ndhF, rbcL, cially for deep relationships within the PACMAD clade, trnK/matK), and not their eight-dataset analysis, as which requires sufficient molecular sequences. Previous these did not differ in subfamilial arrangement, or divergence estimates of the PACMAD clade are highly provide further resolution. variable and have been examined in the stem Aristidoi- The GPWG also increased taxon sampling over those of deae (28.8 to 61.1 mya), crown PACMAD (38 to 61.1 previous phylogenetic studies to include representatives of mya), and stem Panicoideae (26 to 42.1 mya) [8, 10–12]. 62 genera, 30 of which fell within a group described under These four studies used a relatively small number of the newly established PACCAD (Panicoideae, Arundi- molecular markers in their phylogenetic analyses and noideae, Chloridoideae, Centothecoideae, Aristidoideae, the lack of informative characters likely caused the top- Danthonioideae) clade [2]. Three taxa that nested within ologies to vary. the PACCAD clade (Eriachne, Gynerium, and Micraira) Phylogenomic studies using complete plastomes from were classified as incertae sedis (of uncertain placement). Poaceae have provided strong support for the relation- Arundinoideae were also found to lack unifying morpho- ships within and among other subfamilies [13–15]. This logical or molecular synapomorphies to establish it as study addresses the weak support in previous research for monophyletic. The genera classified as incertae sedis were deep nodes in the PACMAD clade by utilizing complete analyzed further in a separate study with other representa- plastomes. A plastome from one arundinoid species tives from Eriachne and Micraira through the use of (Hakonechloa macra) was sequenced using Sanger tech- 69 structural characters as well as ndhF and rpl16 plastid nology to provide a reference for annotation, and 12 sequences [6]. Their reinstatement of Micrairoideae as a additional complete plastomes were determined by next distinct subfamily changed the PACCAD acronym to generation sequencing (NGS) methods for PACMAD PACCMAD. With increased taxon sampling across taxa. Complete plastomes were analyzed phylogenomically Panicoideae and Centothecoideae in a subsequent study and divergence dates estimated to seek potential selective [7], it was concluded that Centothecoideae were para- causes for the PACMAD radiation. The analyses presented phyletic with Panicoideae “…and the name should not here utilize more phylogenetically informative characters have phylogenetic implications” (p. 1738). This study and well supported phylogenomic relationships to provide defined the constituent subfamilies of the PACMAD a greater accuracy of divergence estimates through the use clade and established a backbone phylogenetic hypoth- of complete plastomes. esis against which deeper phylogenetic relationships Mitochondrial and plastome sequences may produce could be explored. incongruent gene trees due to incomplete lineage sort- The second GPWG constructed the most detailed grass ing, recombination events, or potential elevated rates of phylogeny to date [4]. One of their major goals was to de- substitution in grasses [16, 17]. Mitochondrial sequences termine the number of C4 photosynthesis origins across were here explored with the goal of increasing maternally the PACMAD clade. They analyzed 452 PACMAD spe- inherited character sampling among representative taxa. cies, encompassing two thirds of the genera within the Mitochondrial sequence data were extracted and analyzed, clade using the same plastid markers from the previous as a source of potentially conserved characters, which GPWG study (rbcL, ndhF, trnK/matK). Multiple phylo- have proven useful in determining subfamilial relation- genetic analyses and an increase in taxonomic sampling ships in combination with plastome sequences [18–20]. provided support for Aristidoideae as the sister subfamily to the rest of the clade. However, the relationship between Results Panicoideae and the CMAD (Chloridoideae, Micrairoideae, Outgroup selection, plastome Arundinoideae, Danthonioideae) clade was only weakly The PACMAD topology based on plastome data supported (bootstrap (bs) value: 61 %, posterior probability remained largely consistent across likelihood analyses (pp): 0.99), as well as the relationship between the MA conducted with different outgroups. In analyses of all (Micrairoideae, Arundinoideae) and DC (Danthonioideae, but one outgroup taxon, Panicoideae were sister to the Chloridoideae) clades (bs value: 51 %, pp: 0.98). Further- remaining PACMAD taxa. When the single taxon Oryza more, the arundinoids were only weakly supported as sativa was selected as the outgroup, Aristidoideae were monophyletic. sister to the remaining PACMAD taxa with a bs value of Deep divergence time estimates of PACMAD grasses 56 %. Note that the use of O. rufipogon as an outgroup have been relatively few. This is partly because of the did not alter the topology in this way. paucity of confidently dated grass fossils for use as cali- Outgroup selection greatly influenced support values for bration
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  • Chapter 5 Phylogeny of Poaceae Based on Matk Gene Sequences

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    Chapter 5 Phylogeny of Poaceae Based on matK Gene Sequences 5.1 Introduction Phylogenetic reconstruction in the Poaceae began early in this century with proposed evolutionary hypotheses based on assessment of existing knowledge of grasses (e.g., Bew, 1929; Hubbard 1948; Prat, 1960; Stebbins, 1956, 1982; Clayton, 1981; Tsvelev, 1983). Imperical approaches to phylogenetic reconstruction of the Poaceae followed those initial hypotheses, starting with cladistic analyses of morphological and anatomical characters (Kellogg and Campbell, 1987; Baum, 1987; Kellogg and Watson, 1993). More recently, molecular information has provided the basis for phylogenetic hypotheses in grasses at the subfamily and tribe levels (Table 5.1). These molecular studies were based on information from chloroplast DNA (cpDNA) restriction sites and DNA sequencing of the rbcL, ndhF, rps4, 18S and 26S ribosomal DNA (rDNA), phytochrome genes, and the ITS region (Hamby and Zimmer, 1988; Doebley et al., 1990; Davis and Soreng, 1993; Cummings, King, and Kellogg, 1994; Hsiao et al., 1994; Nadot, Bajon, and Lejeune, 1994; Barker, Linder, and Harley, 1995; Clark, Zhang, and Wendel, 1995; Duvall and Morton, 1996; Liang and Hilu, 1996; Mathews and Sharrock, 1996). Although these studies have refined our concept of grass evolution at the subfamily level and, to a certain degree, at the tribal level, major disagreements and questions remain to be addressed. Outstanding discrepancies at the subfamily level include: 1) Are the pooids, bambusoids senso lato, or herbaceous bamboos the