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The endemic ‘sugar canes’ of (, Saccharinae: Lasiorhachis) are close relatives of sorghum Maria Vorontsova, Guillaume Besnard, Jacqueline Razanatsoa, Jan Hackel

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Maria Vorontsova, Guillaume Besnard, Jacqueline Razanatsoa, Jan Hackel. The endemic ‘sugar canes’ of Madagascar (Poaceae, Saccharinae: Lasiorhachis) are close relatives of sorghum. Botanical Jour- nal of the Linnean Society, Linnean Society of London, 2020, 192 (1), pp.148-164. ￿10.1093/botlin- nean/boz067￿. ￿hal-02988767￿

HAL Id: hal-02988767 https://hal.archives-ouvertes.fr/hal-02988767 Submitted on 23 Apr 2021

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Botanical Journal of the Linnean Society

The endemic “sugar canes” of Madagascar (Poaceae, Saccharinae: Lasiorhachis) are close relatives of sorghum

Journal: Botanical Journal of the Linnean Society

Manuscript ID BOTJLS-Mar-2019-3303-ART.R2

Manuscript Type: Original Article

Date Submitted by the 19-Aug-2019 Author:

Complete List of Authors: Vorontsova, Maria; Royal Botanic Gardens, Kew, HLAA Besnard, Guillaume; CNRS, Université Paul Sabatier, EDB, Laboratoire EvolutionPDF & Diversité Proof Biologique Razanatsoa, Jacqueline; Tsimbazaza Botanical and Zoological Park and Research Centre, Département Flore Hackel, Jan; Royal Botanic Gardens, Kew, HLAA; CNRS, Université Paul Sabatier, EDB, Laboratoire Evolution & Diversité Biologique

Madagascar < Geography, phylogenetic relationships < Systematics, Keywords: phylogenetics < Systematics, nuclear markers < Genetics, chloroplast DNA < Genetics, Poaceae < Taxa, Taxonomy, Evolution

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 The endemic “sugar canes” of Madagascar (Poaceae, Saccharinae: Lasiorhachis) are close relatives 11 12 of sorghum 13 14 Running title: Malagasy Lasiorhachis 15 16 17 18 19 MARIA S. VORONTSOVA1,*, GUILLAUME BESNARD2, JACQUELINE RAZANATSOA3 and JAN HACKEL1,2 20 21 1Comparative and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK 22 23 2CNRS, Université de Toulouse, IRD, UMR5174, EDB (Laboratoire Évolution & Diversité Biologique), 24 25 118 route de Narbonne, 31062 Toulouse, France PDF Proof 26 27 3Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, BP 4096, 28 29 101, Madagascar 30 31 *Corresponding author. E-mail: [email protected]. 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 1 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 11 12 Crop wild relatives are important but often poorly known. This is the case for subtribe Saccharinae 13 14 (Poaceae: ) which includes sugarcane () and sorghum (Sorghum). We 15 present a phylogenetic and taxonomic account of the Malagasy endemic Lasiorhachis, 16 17 previously included in Saccharum. New plastome and nuclear sequences were assembled from 18 19 genome skimming data. Phylogenetic analyses of whole plastomes place Lasiorhachis as sister to 20 Sorghum and only distantly related to the interbreeding Saccharum complex. This is also supported 21 22 by analyses of nuclear ITS and partial assemblies for eight low-copy regions. Some nuclear regions 23 24 suggest that Lasiorhachis is closer to Sorghum section Sorghum than other Sorghum spp. sometimes 25 PDF Proof segregated as Vacoparis. We present a full taxonomic treatment of Lasiorhachis with an 26 27 identification key, synonymy, typification, descriptions, drawings, and a distribution map of the 28 29 three , all endemic to the central highlands of Madagascar. Lasiorhachis species occupy 30 contrasting ecological niches and at least one of them, L. viguieri, has significance for ecosystem 31 32 function. As crop wild relatives of sorghum, Lasiorhachis species should be included in germplasm 33 34 collections. 35 36 KEYWORDS 37 38 Andropogoneae – crop wild relative – grass – lectotype – phylogenetics – Malagasy – nuclear genes 39 40 – plastome – Saccharum – shotgun sequencing – – typification 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 2 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 11 12 INTRODUCTION 13 14 15 The value of wild relatives of crop species is increasingly acknowledged. Besides their interest for 16 comparative studies of domestication and traits related to productivity or stress resistance, they 17 18 provide an important genetic reservoir that may be harnessed through traditional breeding or 19 20 genetic engineering for sustainable agriculture (Brozynska, Furtado & Henry, 2016; Castañeda- 21 22 Álvarez et al., 2016; Dempewolf et al., 2017; Zhang et al., 2017). In many cases however, these wild 23 relatives are insufficiently known, rare, narrow in distribution or threatened, and they are often not 24 25 represented in germplasm collections; poorly resolvedPDF taxonomy ofProof many groups impedes targeted 26 27 collection, curation and conservation of crop wild relatives (Castañeda-Álvarez et al., 2016). 28 29 Poaceae subtribe Saccharinae [: Andropogoneae; including Sorghinae as defined by 30 31 Kellogg (2015) and Soreng et al. (2017)] comprise important food and biofuel crops, valued for their 32 rapid growth in tropical and subtropical climates, partly due to their C photosynthetic pathway 33 4 34 (Kellogg, 2015). Outstanding among them is sugarcane, i.e. the three cultivated species of 35 36 Saccharum L. and their commercial hybrid cultivars. In 2017, the world produced 1.8 billion tonnes 37 of sugarcane, far outstripping any other single crop (FAOSTAT, 2019). Sorghum, Sorghum bicolor (L.) 38 39 Moench, is an important grain and fodder crop with > 57 million tonnes annual production 40 41 (FAOSTAT, 2019). Species of Andersson, which also grow in cooler regions, have 42 43 attracted increasing interest due to their potential use as second-generation biofuel (Heaton, 44 Dohleman & Long, 2008; Brosse et al., 2012; Sacks et al., 2013; Zhuang et al., 2013). Underlining this 45 46 importance as crops, the genome sequence of S. bicolor was made available in 2009 (Paterson et al., 47 48 2009) and was followed more recently by M. sinensis Andersson (Energy Biosciences Institute and 49 Joint Genome Institute, 2017) and the highly polyploid genome of sugarcane (Garsmeur et al., 2018), 50 51 “probably the most complex of all plant crops” (Aitken, Berkman & Rae, 2016). 52 53 54 55 56 57 3 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Andropogoneae, including Saccharinae, have been recognized as among the most morphologically 11 12 complex groups of grasses (Clayton & Renvoize, 1986). The evolutionary history of Saccharinae is just 13 14 beginning to be untangled, and the taxonomic delimitation is being reconsidered as our 15 understanding of the evolutionary history of the group develops. Phylogenetic evidence for their 16 17 monophyly is contradictory (Hodkinson et al., 2002; Kellogg, 2013; Hawkins et al., 2015; Saarela et 18 19 al., 2018), and there are no obvious morphological synapomorphies (Kellogg, 2015). The 20 classification by Kellogg (2015) included 16 genera, with 177 species, whereas Soreng et al. (2017) 21 22 accepted 26 genera. 23 24 Several genera of Saccharinae, including some potentially allied to Saccharum, e.g. Kunth, are 25 PDF Proof 26 highly polyphyletic (Kellogg, 2015). Saccharum s.s. includes only six species, and several others 27 28 traditionally included are either closer to Miscanthus or entirely unrelated (Hodkinson et al., 2002; 29 Kellogg, 2013, 2015; Evans et al. 2019). The Saccharum complex, as originally defined for plant 30 31 breeders by Mukherjee (1954) and expanded by Daniels & Daniels (1975), included Saccharum, 32 33 Erianthus Michx. section Ripidium Henrard, Miscanthus and Sclerostachya (Andersson ex Hackel) 34 A.Camus and Narenga Bor (both now part of Miscanthus). Erianthus section Ripidium is now treated 35 36 as a separate genus, Tripidium H.Scholz, not directly related to either Saccharum or Erianthus Michx. 37 38 (Welker et al., 2015; Evans at al., 2019; Welker et al., 2019). Evans et al. (2019) updated the 39 40 definition of the Saccharum complex to include all groups interbreeding in the wild: Miscanthus, 41 Miscanthidium Stapf, Saccharum and New World Erianthus. Outside this complex, Sorghum is 42 43 polyphyletic, and Sarga Ewart now includes around half of the former Sorghum spp. (Spangler, 2003; 44 45 Hawkins et al., 2015; Kellogg, 2015). Reticulate evolution with frequent allopolyploidization, as in 46 many other Andropogoneae (Estep et al., 2014), probably characterizes Saccharinae and leads to 47 48 genes with diverging histories (Kellogg, 2013; Welker et al., 2015). Identifying and preserving wild 49 50 relatives of sugarcane, sorghum and Miscanthus is therefore non-trivial. For example, the World 51 Collection of Sugarcane and Related Grasses (WCSRG at the USDA-ARS Subtropical Horticulture 52 53 54 55 56 57 4 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Research Station in Miami, Florida) includes a wide array of species of Saccharinae for which 11 12 relationships are not yet fully understood (Todd et al., 2017). 13 14 Species of Saccharinae endemic to Madagascar remain poorly known and have so far not been 15 16 included in germplasm collections due to the sparseness of scientific links and difficulties in 17 18 accessing material. The first awnless endemic species was described by Hackel (1885) as 19 hildebrandtii Hack. and placed in the new Andropogon section Lasiorhachis Hack., named after the 20 21 soft woolly texture of its synflorescence. Andropogon section Lasiorhachis was raised to the rank of 22 23 subgenus (Hackel, 1889) and then to genus (Stapf, 1927). Stapf (1927) noted that “the structure of 24 the panicle and of the spikelets has more in common with Sorghum than with any other genus”. The 25 PDF Proof 26 other two species have awns and were originally described in Erianthus (Camus, 1924), moved to 27 28 Miscanthidium (Camus, 1959) and brought together with the awnless L. hildebrandtii (Hack.) Stapf in 29 Lasiorhachis (Hack.) Stapf by Bosser (1968). The genus was then incorporated into Saccharum by 30 31 Clayton (1981), even though “its true position lies between Saccharum and Hemisorghum” (Clayton, 32 33 1981). The first DNA sequence data for Lasiorhachis were not published until Hackel et al. (2018): 34 the plastid markers ndhF, rbcL and trnk-matK placed the three species, with Eulalia villosa (Spreng.) 35 36 Nees, close to Sorghum, but with weak support. A plastome sequence of the type species L. 37 38 hildebrandtii was published by Piot et al. (2018) and strongly supported the species as sister to 39 40 Sorghum bicolor. 41 42 We present an account of Lasiorhachis, comprising three species endemic to Madagascar that were 43 44 previously classified in Saccharum, but are now accepted as a separate genus again (Kellogg, 2015; 45 Soreng et al., 2017; Vorontsova et al., 2018). A full taxonomic treatment is given alongside new 46 47 plastome and nuclear genetic data to reassess their phylogenetic position. We confirm that 48 49 Lasiorhachis is the sister genus of Sorghum, which helps further clarify the taxonomy of Saccharinae 50 and brings new relevance to this genus of crop wild relatives. 51 52 53 MATERIAL AND METHODS 54 55 56 57 5 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 ACCESSIONS AND TAXONOMY 11 12 Collection trips were conducted across Madagascar during the period 2011 – 2018. Ten occurrences 13 14 of Lasiorhachis were seen in the wild and collections were made (Fig. 1). Cultivation of Lasiorhachis 15 16 perrieri (A.Camus) Bosser was attempted at the Parc Botanique et Zoologique de Tsimbazaza, but 17 18 without success. A full taxonomic analysis of the 76 collections held at the K, P and TAN herbaria was 19 carried out. Descriptive morphological terms such as “” are used for recognition and 20 21 communication purposes only, and further research will be required to align these to 22 23 developmentally correct terminology such as “synflorescence”, as reviewed by Kellogg (2015). This 24 study focuses on macromorphological characters and does not attempt to examine 25 PDF Proof 26 micromorphology or anatomy. 27 28 SEQUENCING AND MARKER ASSEMBLY 29 30 31 Genomic DNA from two Lasiorhachis specimens (L. hildebrandtii LRK2008 and L. perrieri NOP140) 32 was extracted and shotgun-sequenced on a HiSeq machine as described in Besnard et al. (2013), 33 34 producing 125-bp paired-end reads. The full L. hildebrandtii plastid genome (plastome) has been 35 36 published by Piot et al. (2018), and we assembled the plastome of L. perrieri as described therein. 37 We also assembled partial nuclear ribosomal DNA (nrDNA) containing the internal transcribed spacer 38 39 regions (ITS) for both accessions. For this, reads were mapped to S. bicolor 5.8S nrDNA sequence 40 41 (MH762138.1) in Geneious v. 8.0.5 (Biomatters Ltd.), using the built-in mapping algorithm with 42 43 default parameters, and mapping again to a 75% majority consensus sequence for ten iterations. 44 Coverage for nrDNA was >1000x in both accessions. Partial coding sequences (CDS) were further 45 46 assembled for eight low-copy nuclear regions for which sufficient homologues from Andropogoneae 47 48 were available in GenBank: the aberrant panicle organization 1 gene (apo1); the DELLA-encoding 49 protein gene dwarf8 (dwarf8); floricaula/leafy-like (floricaula); the granule-bound starch synthase 1 50 51 gene (GBSSI or waxy); erect panicle 2 exons 7 and 8 (ep2-7 and ep2-8); the phytochrome B gene 52 53 (phyB); and retarded palea 1 (rep1). For assembly, reads were mapped to the exon sequences from 54 55 56 57 6 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 the S. bicolor genome (GCF_000003195.3) in Geneious. A 75% majority consensus sequence was 11 12 then called and sites with total base phred quality <30 or not covered were coded as N. Assembled 13 14 exons were finally merged, not using exons with >50% ambiguous bases. Mean coverage per exon 15 ranged from 0.9 to 4.7×. The sequencing reads have been submitted to the Sequence Read Archive 16 17 (BioProject No. [to be added]), assembled plastome and nrDNA sequences to GenBank (accession Commented [MF1]: Numbers in this paragraph to be added by 18 authors at proof stage. 19 numbers MF563371.1 and [to be added], and [to be added] and [to be added], respectively), and the 20 incomplete low-copy gene assemblies are available as supplementary file XX. 21 22 23 PHYLOGENETIC ANALYSIS 24 25 The plastome sequences were combined with 54 otherPDF full plastomes, Proof including representatives of 26 27 Andropogoneae selected from recent studies (Burke et al., 2016; Arthan et al., 2017) and all 28 plastomes of Eulalia, Miscanthus, Miscanthidium, Saccharum, Sarga and Sorghum that are available 29 30 on GenBank. After excluding the second inverted repeat region, they were aligned using the default 31 32 MAFFT v. 7.407 (Katoh & Standley, 2013) algorithm. CDS and non-coding regions were extracted 33 from the alignment and phylogenetic trees inferred separately using Bayesian estimation in MrBayes 34 35 v. 3.2.6 (Ronquist & Huelsenbeck, 2003; Altekar et al., 2004) with a GTR+γ substitution model, 36 37 running two analyses with four chains until the standard deviation of splits was <0.01. We also re- 38 estimated a phylogeny based on ndhF-rbcL-trnk/matK for Saccharinae and selected outgroup taxa. 39 40 For this, we combined the data used by Hackel et al. (2018) with the respective regions extracted 41 42 from the full plastomes, aligned each marker set using the MAFFT G-INS-i algorithm, trimmed 43 44 alignment ends with >90% missing data and concatenated the three alignments. A phylogenetic tree 45 was produced from the concatenated alignment using MrBayes as described above, partitioning by 46 47 gene. We also compared topologies with the monophyly of Lasiorhachis constrained or not via a 48 49 likelihood ratio test in RAxML v. 8.2.12 for the ndhF-rbcL-trnk/matK alignment. Finally, for ITS and 50 the low-copy nuclear genes, we retrieved homologous sequences for Andropogoneae via blastn 51 52 searches (Camacho et al., 2009) against GenBank, retaining only the longest matching sequence per 53 54 55 56 57 7 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 NCBI taxon for ITS and the longest among identical sequences for the low-copy genes. Each set of 11 12 sequences was then aligned with the Lasiorhachis assemblies using MAFFT-G-INS-i, alignment ends 13 14 trimmed and trees inferred using MrBayes as described above. We used P.Beauv. for 15 rooting the plastome tree given its early-diverging position in Andropogoneae s.s. based on the 16 17 plastome analyses of Arthan et al. (2017). Sequences of Arthraxon were not available for all nuclear 18 19 markers and we chose Arundinella Raddi, which was consistently available, as a less closely related 20 lineage outside Andropogoneae s.s. for rooting. 21 22 23 RESULTS 24 25 TAXONOMYPDF Proof 26 27 A visual examination of specimens, spikelet dissections and living suggested the presence of 28 29 three clearly distinct species with different morphologies and ecological niches in Madagascar. None 30 31 of these has been recorded outside the island. None of the previously published treatments of these 32 species by Bosser (1968, 1969) and Clayton (1981) included parallel descriptions and identification 33 34 keys. The first full taxonomic treatment of Lasiorhachis is presented below. 35 36 PHYLOGENETIC ANALYSIS 37 38 39 Plastome sequences strongly supported L. perrieri NOP140 and L. hildebrandtii LRK2008 as sister to 40 each other and placed both as sister to Sorghum (represented by S. bicolor and S. mekongense 41 42 A.Camus), with Sarga timorensis (Kunth) Spangler being the next closest relative (Figs 2, S1). 43 44 Lasiorhachis thus fell in Andropogoneae subtribe Saccharinae (fide Kellogg, 2015, Soreng et al., 45 2017) but was clearly distinct from the Saccharum complex. Support was generally higher for the 46 47 tree inferred from non-coding parts of the plastome alignment, but CDS supported the same 48 49 position for Lasiorhachis and recovered most of the other clades. The plastid ndhF-rbcL-trnk/matK 50 51 tree did not resolve relationships among Sarga, Sorghum and Lasiorhachis, despite more species 52 being sampled (Fig. 3). It also placed two accessions of Eulalia villosa in Lasiorachis with weak 53 54 55 56 57 8 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 support; a likelihood ratio test, however, did not reject the monophyly of Lasiorhachis compared to 11 12 an unconstrained topology (p=0.23, logL difference -0.005). 13 14 The trees for ITS and the eight low-copy regions, containing between 47 and 320 tips, received only 15 16 weak support for the backbone of Andropogoneae (Figs 3, S1 A-I). However, all trees grouped 17 18 Lasiorhachis with Sorghum spp., distinct from the species of the Saccharum complex and a Sarga 19 clade (= Sorghum sections Stiposorghum and Parasorghum). In four trees (apo1, dwarf8, ep2-7, ep2- 20 21 8) in which S.orghum laxiflorum F.M.Bailey and S. macrospermum E.D.Garber (Sorghum sections 22 23 Chaetosorghum and Heterosorghum, respectively) are represented, their sequences are placed sister 24 to or paraphyletic with respect to Lasiorhachis (Fig. 4 A, B, D, E), which is thus closer to a clade 25 PDF Proof 26 corresponding to Sorghum section Sorghum [Sorghum arundinaceum (Desv.) Stapf, S. bicolor, S. 27 28 halepense (L.) Pers. and/or S. propinquum (Kunth) Hitchc.; also including sequences identified as 29 indica (Houtt.) Veldkamp in rep1; Fig. S2 I]. Cleistachne sorghoides Benth. was placed with 30 31 either Sarga or Sorghum. The seven nuclear trees that included Eulalia villosa (ITS, dwarf8, ep2-7, 32 33 ep2-8, GBSSI, phyB ando rep1) placed it clearly distant from Lasiorhachis, Sarga and Sorghum. 34 35 DISCUSSION 36 37 The phylogenetic analysis presented here confirms Lasiorhachis spp. as close relatives of Sorghum, 38 39 as recognized by Stapf (1927). Lasiorhachis is closer to Sorghum s.s. than the species segregated 40 41 from it as Sarga (Spangler, 2003), and it is clearly distinct from sugarcane and its relatives in the 42 43 Saccharum complex. This confirms the result of Piot et al. (2018), who included only L. hildebrandtii 44 in their plastome analysis. A coalescent analysis of nuclear genome-wide markers also supports L. 45 46 hildebrandtii as sister to S. bicolor and suggests a dominant nuclear signal for this position (Bianconi 47 48 et al., unpublished data). Limited available nuclear sequence data for S. laxiflorum and S. 49 macrospermum included in our analysis suggest that these species (segregated as Vacoparis 50 51 Spangler; Spangler, 2003) may be more distant from Sorghum s.s. (i.e. Sorghum section Sorghum) 52 53 than Lasiorhachis. Paraphyly of sequences of these two species with regard to Lasiorhachis may 54 55 56 57 9 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 indicate an allopolyploidy event before the origin of Lasiorhachis and Sorghum. The single known 11 12 chromosome count in Lasiorhachis is 2n = 20 (recorded on the herbarium specimen Tateoka 3514, 13 14 P02643315 of L. hildebrandtii), suggesting that it is diploid based on the Andropogoneae base count 15 of x = 10 (Kellogg, 2015); due to the shallow sequencing and our assembly method, potential 16 17 paralogous genes resulting from any allopolyploidy could not be distinguished. 18 19 Taken together, the results strongly support Lasiorhachis as sister to Sorghum s.s. (= Sorghum 20 21 section Sorghum) and may warrant the recognition of Vacoparis as separate genus. It is also possible 22 23 that following more comprehensive analyses Lasiorhachis may become part of the broader Sorghum. 24 Additional data from all species of Sorghum and Lasiorhachis, especially from more variable plastid 25 PDF Proof 26 markers (or entire plastomes), are needed. Clearly, plastid ndhF + rbcL + trnK/matK are insufficient 27 28 to resolve relationships (see Fig. 3), and we expect the placement of Eulalia villosa in Lasiorhachis in 29 the three-gene tree to change with more data, especially since all nuclear trees including this species 30 31 place it in a distant position. 32 33 Macromorphological characters traditionally used in keys and taxonomic treatments do not provide 34 35 enough data for a clear differentiation of clades or genera in Lasiorhachis and its relatives, as 36 37 evidenced by the multiple alternative taxon delimitations discussed above. The variability in male 38 and female expression and development, of both sessile and pedicellate spikelets, were cited as a 39 40 distinguishing characteristic of Lasiorhachis by Stapf (1927) and Bosser (1968), but it does also occur 41 42 across Andropogoneae as pointed by Clayton (1981) and Kellogg (2015). Hackel (1885, 1889) 43 44 described L. hildebrandtii as having glabrous lodicules and an apically pilose ovary, and Stapf (1927) 45 corrected these to apically pilose lodicules and a glabrous ovary; we have also recorded pilose 46 47 lodicules and a glabrous ovary, although anatomical data needs confirmation through a more 48 49 detailed study. This study did not confirm the presence of the ovary appendage in L. hildebrandtii 50 recorded by Watson, Macfarlane & Dallwitz (1992 onwards) and Kellogg (2015): this could be due to 51 52 53 54 55 56 57 10 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 our focus on macromorphology and a lack of detailed micromorphological examination. Critical 11 12 micromorphological and anatomical study of fresh material is still necessary for all three species. 13

14 Functional traits of dominant C4 Poaceae determine ecosystem function in the subtropical grasslands 15 16 and savannas of Madagascar (Solofondranohatra et al., 2018), which cover at least 65% of the land 17 18 area (Moat & Smith, 2007). Lasiorhachis makes a non-trivial contribution to ecosystem function: the 19 most abundant species, L. viguieri (A.Camus) Bosser, dominates flammable rocky grasslands 20 21 alongside Panicum andringitrense A.Camus at c. 2200 m elevation on the granite plateau of 22 23 Andringitra National Park (site 6; Vorontsova et al., 2016). Its woody and thick culm bases 24 persist during fires and form the ground cover in several highland ecosystems (Vorontsova M.S., 25 PDF Proof

26 pers. obs.). Lasiorhachis hildebrandtii occupies a contrasting shady niche and is one of the few C4 27 28 plants to be found under forest canopy, at somewhat lower elevations. The niche of Lasiorhachis 29 perrieri is different again: the larger size of its tussocks restricts its habitats to those with a ready 30 31 source of running water. Occurrence of Sorghum in Madagascar is still poorly recorded, but there 32 33 are both native and introduced, wild, food and fodder species; these tend to occupy habitats at 34 lower elevations than Lasiorhachis, often found close to human dwellings and in disturbed areas. 35 36 37 Divergence in morphology and ecological niche in Lasiorhachis suggests a long evolutionary history. 38 The median stem age estimate of Hackel et al. (2018) for the two Lasiorhachis clades of between 39 40 2.5-4.0 Mya was modelled on a more poorly resolved tree topology. Bianconi et al. (unpublished 41 42 data), using genome-level data, dated the median split between S. bicolor and L. hildebrandtii at 4 43 44 Mya under a “younger” calibration scenario. This suggests that the diversification of Lasiorhachis in 45 Madagascar occurred during the Pleistocene or, potentially, the Late Miocene. Although the 46 47 majority of the grass flora of Madagascar probably dispersed from , Lasiorhachis was 48 49 estimated by Hackel et al. (2018) to have an Asian–Australasian origin, albeit based on a weakly 50 supported topology. If the relationship of the Australasian “Vacoparis” as sister to Malagasy 51 52 Lasiorhachis and Asian-African Sorghum s.s. proves to be correct, this would support an Australo- 53 54 55 56 57 11 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Asian origin of the group followed by dispersal to Africa and Madagascar. Any conclusion on the 11 12 origin and timing of Lasiorhachis and its diversification will require studies at the population level as 13 14 well as a better understanding of the whole of the enigmatic Saccharinae. 15 16 No accessions of Lasiorhachis have been successfully cultivated to date, despite of their horticultural 17 18 potential due to their beautiful inflorescence colours: snow-white in L. hildebrandtii, golden brown 19 in L. perrieri and a vivid pink-purple in L. viguieri. No seed collections have been made. No tests for 20 21 potentially useful alleles have been carried out. As well as providing a missing piece of the evolution 22 23 puzzle of Saccharinae, Lasiorhachis remains a mysterious knowledge gap in its own right. 24 25 TAXONOMIC PDFTREATMENT Proof 26 27 Lasiorhachis (Hack.) Stapf in Hooker's Icon. Pl. 32: t. 3124. 1927 as 'Lasiorrhachis' ≡ Andropogon 28 29 section Lasiorhachis Hack. in Flora 68: 142. 1885 ≡ Andropogon subgenus Lasiorhachis (Hack.) Hack. 30 31 in Monogr. Phan. [A.DC. & C.DC.] 6: 471. 1889. 32 33 Type: Lasiorhachis hildebrandtii (Hack.) Stapf (Andropogon hildebrandtii Hack.). 34 35 Coarse long-lived densely tufted perennials with short thick woody rhizomes and erect flowering 36 37 culms. All leaves basal. Ligule membranous to coriaceous. Auricles absent or deltoid. Leaf blades 38 39 thick, linear to narrow-lanceolate, with a pronounced white midrib. silky terminal 40 panicles with primary and secondary branching from the main culm. Spikelets paired. Internodes 41 42 apically cupulate. Internodes and pedicels villous. Callus truncate. Sessile spikelet lower floret sterile, 43 44 upper floret hermaphrodite. Glumes chartaceous to coriaceous, convex. Upper lemma bilobed, 45 ciliate at the apex, with or without an awn. Lodicules with apical hairs. Anthers three. Pedicelled 46 47 spikelets the same as sessile spikelets and hermaphrodite, or somewhat reduced in size and male. 48 49 Sometimes the pedicel and the pedicelled spikelet reduced or absent on some branches. 50 51 Notes: The three species of this genus are clearly distinct and easy to identify. Flowering culms are 52 53 generated, grow rapidly prior to flowering and dehisce shortly after flowering. Photosynthate seems 54 55 56 57 12 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 to be stored primarily in the woody rhizomes and the lowermost culm internodes. Lasiorhachis 11 12 viguieri frequently loses aboveground biomass to fires; leaves and culms regrow after fire from 13 14 lower parts of the plant. No signs of burning were noted on L. hildebrandtii or L. perrieri. 15 16 The presence, size, and reproductive functionality of the pedicelled spikelet varies between 17 18 different parts of the inflorescence and between plants. Complete absence of the pedicellate 19 spikelet is rare and has only been noted in some lowermost inflorescence branches of L. 20 21 hildebrandtii. The most common condition is a male pedicellate spikelet (L. perrieri) or a bisexual 22 23 pedicellate spikelet (L. hildebrandtii, L. viguieri). The dispersal unit is most commonly a single 24 spikelet which detaches as the spikelet callus is separated from the cupular apex of the internode. 25 PDF Proof 26 When the pedicellate spikelet is male, sterile or absent, the sessile hermaphrodite spikelet often falls 27 28 off together with its pedicel and the pedicellate spikelet. It also seems common for a section of an 29 inflorescence branch with c. 2-20 spikelets to detach as a whole. The relative roles of the 30 31 indumentum (thick in all species) and the awns (present in two of three species) in seed dispersal are 32 33 not clear. No seed dispersal agents are known. 34 35 KEY TO LASIORHACHIS: 36 37 1. Inflorescences snow-white in colour; inflorescence branches loose and pendent; awns absent. 38 39 …………………………………………………………………………………………………………………………….… 1. L. hildebrandtii 40 41 1. Inflorescences tinged brown or pink or purple; inflorescence branches erect; awns present.. 2 42 43 44 2. Flowering culms 1.5-2.0 m tall; inflorescences tinged brown; sessile spikelets 3.0-4.0(-4.5) mm 45 long ……………………………………………………………………………………………………………………………….. 2. L. perrieri 46 47 48 2. Flowering culms 0.50-1.15(-1.45) m tall; inflorescences tinged pink or purple; sessile spikelets (5- 49 )6-9 mm long ……………………………………………………………………………………………………………….… 3. L. viguieri 50 51 52 53 54 55 56 57 13 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 1. Lasiorhachis hildebrandtii (Hack.) Stapf in Hooker's Icon. Pl. 32: t. 3124. 1927 ≡ Andropogon 11 12 hildebrandtii Hack. Flora 68: 141. 1885 ≡ Saccharum hildebrandtii (Hack.) Clayton Kew Bull. 35(4): 13 14 818. 1981. Type: MADAGASCAR, Antananarivo, Andrangolaoka, Nov 1880, J.M.Hildebrandt 3755 15 (Lectotype designated here: W [W1916-0028387] (photograph!), isolectotypes: JE [JE00012628, 16 17 JE00012629] (photograph!), K [K000244592]!, P [P00450367, P00450368, P00450369]!, W [W1889- 18 19 0039830, W1916-0028386] (photograph!)). 20 21 Tufted perennial 0.6-1.5(-2.0) m. Flowering culm 2.5-5.0 mm diameter at base. Nodes dark, 22 23 glabrescent. Culms and leaves glabrescent. Basal leaf sheaths smooth, shiny. Ligule coriaceous, 24 truncate, 1 mm long. Auricles deltoid, acute to rounded, dark, 1-2 mm long, ciliate when young. Leaf 25 PDF Proof 26 blades pseudopetiolate, flat, 7-13 mm wide, the margins serrulate. Inflorescences 15-33 cm long, lax, 27 28 densely covered in white indumentum, the branches loose and pendent, with secondary branching, 29 the internodes and pedicels somewhat shorter or longer than the spikelets, the spikelets usually not 30 31 overlapping. Sessile spikelets 3.5-4.5(-6.0) mm long, ovate, hermaphrodite, villous. Callus hairs 1-2 32 33 mm long. Lower glume with two keels, five- to seven-nerved, with cross-veins visible on the inner 34 surface. Upper glume five- to seven-nerved. Anthers 2.5 mm long. Awns absent. Pedicellate spikelets 35 36 the same as sessile spikelets, hermaphrodite or smaller and male. Sometimes the pedicel and the 37 38 pedicellate spikelet reduced or absent on some branches. (Figs. 1B, 5). 39 40 Distribution: northern and central parts of the Malagasy highlands, with a single record from the 41 42 northern wet forests (Fig. 8). 43 44 Habitat: shaded understory of wet forest, gallery forest and sometimes seasonal forest or tapia, 45 46 often by the sides of streams; on laterite or granite; 700-1600m (the northernmost outlier record 47 48 Humbert & Capuron 21951 is recorded from 400-600m which could represent an error). 49 50 Notes: Easy to recognize by its silky snow-white inflorescences with pendent branches (Fig. 1B) and 51 52 no awns. It is the only species of the genus fully lacking awns, a feature that could be related to its 53 54 55 56 57 14 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 forest understory habitat. Of the two original annotated sheets from Hackel’s herbarium, the chosen 11 12 lectotype W1916-0028387 has the best flowering material. 2n = 20 (Tateoka 3514). 13 14 Specimens examined: Madagascar. Antananarivo: Ambatolaona, 4 September 1956, Descoings, B. 15 16 1773 (TAN); Ambatolaona, Morat, P. 552 (TAN); Ambatolaona, 11 November 1912, Viguier, R. & 17 18 Humbert, H. 1196 (P); Ambohitantely, Peltier, J. & Peltier, M. 4349b (TAN); Analabe, Betsitra, 19 October 1905, D'Alleizette, C. 1280 (P); Angavokely, May 1956, Bosser, J.M. 9579 (TAN); Angavokely, 20 21 April 1959, Bosser, J.M. 12727 (TAN); Angavokely, October 1960, Bosser, J.M. 14648 (P, TAN); 22 23 Angavokely, December 1960, Bosser, J.M. 14983 (P); Angavokely, 27 April 1947, Humbert, H. 20880 24 (P); Angavokely, 28 October 1970, Keraudren-Aymonin, M. & Aymonin, G.G. 25229 (P); Angavokely, 25 PDF Proof 26 28 October 1970, Keraudren-Aymonin, M. & Aymonin, G.G. 25201 (P); Angavokely, 14 January 1960, 27 28 Leandri, J. 2552 (P); Angavokely, October 1960, Leandri, J. 3219 (P); Angavokely, 10 January 1919, 29 Perrier de la Bâthie, H. 12926 (P,P,TAN); Angavokely, 25 June 1964, Tateoka, T. 3514 (P, TAN); 30 31 Antananarivo, 1960, Keraudren-Aymonin, M. 18 (P); Manankazo, September 1913, Perrier de la 32 33 Bâthie, H. 10726 (P). Antsiranana: Lokoho, 1948, Humbert, H. & Capuron, R. 21951(P). Fianarantsoa: 34 Andohantanimenaha, Itremo, 25 February 2013, Vorontsova, M.S. et al. 1004 (K,TAN); 35 36 Antsirakambiaty, Itremo, 12 March 2012, Vorontsova, M.S. et al. 739 (K,TAN); Itremo, 37 38 Andohatanimena, 19 February 2014, Nanjarisoa, O.P. et al. 146 (K,TAN). Toamasina: Andasibe, 9 39 40 January 1911, Perrier de la Bâthie, H. 10830 (P); Andrangovalo, October 1937, Humbert, H. & Cours, 41 G. 17946 (P); Ankaraoka, October 1937, Humbert, H. & Cours, G. 17534 (P); Lac Alaotra, Herbier de la 42 43 Station Agricole de l' Alaotra 34 (TAN); Lac Alaotra, Herbier du Jardin Botanique de Madagascar 3415 44 45 (P); Moramanga, Anosibe, September 1953, Bosser, J.M. 6600 (P); Moramanga, August 1953, Bosser, 46 J.M. 6618 (P); Nonokambo, 21 August 1937, Jardin Botanique de Tananarive 2851 (P); Sahamalaza, 47 48 Manakambahiny Est, Dequaire, J. 27854 (P); Sahatandra, 16 October 1912, Viguier, R. & Humbert, H. 49 50 764 (P); Sandrangato, December 1954, Descoings, B. 218 (P, TAN); Ambatovy, 24 November 2011, 51 Bernard, R. et al. 1836 (P). 52 53 54 55 56 57 15 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 2. Lasiorhachis perrieri (A.Camus) Bosser in Adansonia sér. 2, 8: 515. 1968 ≡Erianthus perrieri 11 12 A.Camus in Bull. Soc. Bot. France 71: 1182. 1925 ≡Miscanthidium perrieri (A.Camus) A.Camus in Bull. 13 14 Soc. Bot. France 106: 339. 1959 ≡Saccharum perrieri (A.Camus) Clayton in Kew Bull. 35(4): 818. 1981. 15 Type: MADAGASCAR, Antananarivo, , Oct 1913, H.Perrier de la Bâthie 10723 (Lectotype 16 17 designated here: P [P00450374]!, isolectotype: P [P03370850]!). 18 19 Tufted perennial 1.5-2.0 m. Flowering culm 5-10 mm diameter at base. Nodes dark, glabrescent. 20 21 Culms and leaves glabrescent. Basal leaf sheaths smooth, hardened. Ligule coriaceous, truncate, 22 23 reddish, 2-4 mm long. Auricles absent or rounded, dark, up to 1 mm long, glabrous. Leaf blades flat, 24 10-15 mm wide, the margins serrulate. Inflorescences 20-30 cm long, dense, with brownish 25 PDF Proof 26 indumentum, the branches close together and largely erect, with secondary branching, the 27 28 internodes and pedicels somewhat shorter than the spikelets, the spikelets overlapping. Sessile 29 spikelets 3.0-4.0(-4.5) mm long, ovate, hermaphrodite, loosely hirsute to glabrous. Callus hairs 1-2 30 31 mm long. Lower glume with two keels, seven- to nine-nerved, with cross-veins visible on the inner 32 33 surface. Upper glume three- to five-nerved. Anthers 2.8 mm long. Awns present, geniculate, twisted, 34 7-12 mm long, glabrous. Pedicellate spikelets similar to sessile spikelets but smaller, usually male 35 36 with no awns, sometimes hermaphrodite with awns. (Figs. 1C-E, 6). 37 38 Distribution: restricted area of the Central Highlands in the Antananarivo and Fianarantsoa 39 40 provinces. Known from five localities only. (Fig. 8). 41 42 43 Habitat: open rocky habitats near streams, on basalt or gneiss, 1300-1900 m (Fig. 1C). 44 45 Notes: The rarest member of the genus. Poor documentation of this species could be related to 46 47 infrequent flowering, and the difficulty of identification in the vegetative state. A population of L. 48 perrieri was recorded from Antsirakambiaty, Itremo, for the first time in 2014 (Fig. 1C-E) despite the 49 50 fact that this commonly visited area has been the subject of numerous previous botanical surveys, 51 52 including by the first author. Cultivation of this species has so far been unsuccessful. It is likely this 53 54 55 56 57 16 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 species requires a reliable water supply; the population in Antsirakambiaty is found on the edge of a 11 12 permanent stream. The lectotype sheet chosen here was previously marked as a holotype before 13 14 the second duplicate was found; it is more extensively annotated and contains superior quality 15 material. 16 17 18 Specimens examined: Madagascar. Antananarivo: Betafo, laves de l'Iantsifitra, 25 December 1928, 19 Humbert, H. 7138 (P); , May 1912, Perrier de la Bâthie, H. 10849 (P). Fianarantsoa: 20 21 Ambatofinandrahana, January 1953, Bosser, J.M. 5082 (TAN); Ambatofinandrahana, 25 January 22 23 1975, Croat, T.B. 29502 (TAN); Ambositra, January 1964, Bosser, J.M. 18996 (P, TAN, WAG); 24 Antsirakambiaty, Itremo, 18 February 2014, Nanjarisoa, O.P. et al. 140 (K,TAN); Antsirakambiaty, 25 PDF Proof 26 Itremo, 19 May 2014, Vorontsova, M.S. & Nanjarisoa, O.P. 1530 (TAN). 27 28 3. Lasiorhachis viguieri (A.Camus) Bosser in Adansonia sér. 2, 8: 515. 1968 ≡Erianthus viguieri 29 30 A.Camus in Bull. Soc. Bot. France 71: 1182. 1925 ≡Miscanthidium viguieri (A.Camus) A.Camus in Bull. 31 32 Soc. Bot. France 106: 339. 1959 ≡Saccharum viguieri (A.Camus) Clayton in Kew Bull. 35(4): 818. 1981. 33 Type: MADAGASCAR, Antananarivo, , pentes herbeuses sur le flanc ouest de 34 35 l'Ankaratra, entre Ambatofotsy et le Tsiafajavona, 27 Nov 1912, R.Viguier & H.M.Humbert 1721 36 37 (Holotype: P [P00450376]!, isotypes: P [P00450375, P00450377, P02356437]!). 38 39 = Miscanthidium antsirabense A.Camus in Bull. Soc. Bot. France 106: 338. 1959. Type: 40 41 MADAGASCAR, Antananarivo, environs d', Jan 1914, H.Perrier de la Bâthie10753 (Holotype: 42 43 P [P00450370]!, isotypes: P [P00450371, P00450372]). 44 45 Tufted perennial 0.50-1.15(-1.45) m. Flowering culm 1.5-4.0 mm diameter at base. Nodes villous. 46 47 Culms and leaves glabrescent. Basal leaf sheaths smooth, shiny, sometimes breaking down into 48 fibres. Ligule membranous, truncate, 1-4 mm long, surrounded by auricular hairs. Auricles absent. 49 50 Leaf blades usually rolled, 3-11 mm wide, the margins smooth. Inflorescences 8-16 cm long, lax, with 51 52 indumentum which is purple when fresh, the branches largely erect, usually branched only once, 53 54 55 56 57 17 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 with limited secondary branching, the internodes and pedicels 1/2-3/4 as long as the spikelets, the 11 12 spikelets overlapping. Sessile spikelets (5-)6-9 mm long, ovate, hermaphrodite, villous to almost 13 14 glabrous. Callus hairs 1-3 mm long. Lower glume with two keels, seven- to nine-nerved, with cross- 15 veins visible on the inner surface. Upper glume three- to five-nerved. Anthers 2.8-3.6 mm long. Awns 16 17 present, geniculate, twisted, 8-20 mm long, glabrous. Pedicelled spikelets the same as sessile 18 19 spikelets, hermaphrodite; sometimes reduced in size, male, with no awns. (Figs 1A, 7). 20 21 Distribution: central to southern highlands. (Fig. 8). 22 23 Habitat: open canopy montane grassy ecosystems, often associated with rocky outcrops and 24 25 streams, often with Erica L.; (1500-)1700-2500 m (Fig.PDF 1A). Proof 26 27 Notes: This is the most common and abundant Lasiorhachis sp., dominating a range of higher 28

29 elevation flammable C4 habitats, including the rocky plateau grassland at Andringitra National Park 30 31 (plot 6; Vorontsova et al., 2016). Found in drier and more open habitats than L. hildebrandtii and L. 32 perrieri, frequently those prone to fire. Charred leaf sheaths are frequently seen on herbarium 33 34 specimens. Adaptations to drier habitat could include its smaller height, and leaf blades that are 35 36 usually rolled; specimens with flat leaves could represent individuals growing in more humid 37 environments. The holotype sheet of Erianthus viguieri is the only one directly annotated by Aimée 38 39 Camus. The holotype sheet of Miscanthidium antsirabense shows signs of several annotates by 40 41 Aimée Camus, including pencil marks linking it to Miscanthidium viguieri. 42 43 Specimens examined: Madagascar. Antananarivo: Ambatolampy, Ankaratra, February 1957, Bosser, 44 45 J.M. 10748 (G, K, MO, P); Anjozorobe, December 1958, Bosser, J.M. 12401a (TAN); Ankaratra, 46 47 November 1955, Bosser, J.M. 8665 (P,TAN); Antananarivo, May 1962, Bosser, J.M. 16304 (P); 48 Antananarivo, Gillard s.n. (P); , Ambohimandroso, December 1955, Bosser, J.M. 8900 (P, 49 50 TAN); Antsampandrano, Ankaratra, December 1963, Bosser, J.M. 18490 (P, TAN); Antsirabe, May 51 52 1913, Perrier de la Bâthie, H. 15797 (P); , May 1962, Bosser, J.M. 15427 (P, TAN); Carion, 53 54 55 56 57 18 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 December 1958, Bosser, J.M. 12401b (P); Carion, October 1959, Bosser, J.M. 13256b (P); , 11 12 entre Ambatondradama et Ambatofotsy, 26 December 1912, Viguier, R. & Humbert, H. 1624 (P); 13 14 Iaranandriana, January 1954, Bosser, J.M. 7198 (P); Iaranandriana, January 1954, Bosser, J.M. 7202 15 (P,TAN); , 19 December 1950, Benoist, R. 475 (P); PK 28 route du sud, April 1962, 16 17 Bosser, J.M. 15572 (P); PK 39 route du sud, May 1962, Bosser, J.M. 15474 (P); Tsiafajavona, February 18 19 1957, Bosser, J.M. 10760 (P); , June 1967, Morat, P. 2864 (P, TAN). Fianarantsoa: Andringitra, 20 1924, Humbert, H. 3647 (P); Andringitra, 28 November 2013, Nanjarisoa, O.P. et al. 77 (K, P, TAN); 21 22 Andringitra, 13 December 2013, Vorontsova, M.S. et al. 1245 (TAN); Andringitra, 13 December 2013, 23 24 Vorontsova, M.S. et al. 1248 (TAN); Andringitra, 13 December 2013, Vorontsova, M.S. et al. 1259 25 PDF Proof (TAN); Andringtra, Andohariana, 13 January 1971, Guillaumet, J.L. 3745 (P); Andringtra, 28 26 27 November 2013, Nanjarisoa, O.P. et al. 76 (K,TAN); Fandriana, Miarinavaratra, January 1953, Bosser, 28 29 J.M. 5071 (P); Manandriana, Ivato, January 1964, Bosser, J.M. 18791 (P); Pic Boby, Andringitra, April 30 1964, Bosser, J.M. 19441 (P, TAN); Andringitra, 25 November 2009, Couch, C. et al. 589 (K, P); 31 32 33 ACKNOWLEDGEMENTS 34 35 We would like to thank the staff of the Kew Madagascar Conservation Centre, Stuart Cable (RBG 36 37 Kew), and Parc de Tsimbazaza for their long-term collaboration and support for Madagascar Poaceae 38 research. The Direction Générale des Forêts and Madagascar National Parks generously granted our 39 40 research permits. JH acknowledges an Idex UNITI mobility grant (RECAC15EX110; University of 41 42 Toulouse) for fieldwork in Madagascar. GB is a member of the Laboratoire Evolution & Diversité 43 44 Biologique (EDB) part of the LABEX “TULIP” managed by Agence Nationale de la Recherche (ANR-10- 45 LABX-0041) and LABEX “CEBA” (ANR-10-LABX-25-01). Curators of the Muséum National d'Histoire 46 47 Naturelle herbarium (P) and Parc de Tsimbazaza herbarium (TAN) made specimens available. Lucy 48 49 Smith made the beautiful drawings, and Sarah Ficinski created the distribution map. We are grateful 50 to Cassiano Welker (Universidade Federal de Uberlândia), Michael R. McKain (University of Alabama) 51 52 and Elizabeth Kellogg (Donald Danforth Plant Science Center) for discussion on Andropogoneae 53 54 55 56 57 19 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 evolution and the genus Eulalia. Thanks also to Emmet Judziewicz and an anonymous reviewer 11 12 whose comments improved this manuscript. 13 14 REFERENCES 15 16 Aitken K, Berkman P, Rae A. 2016. The first sugarcane genome assembly: how can we use it? 17 18 Proceedings of the Australian Society Sugar Cane Technology 38. 19 20 https://www.assct.com.au/media//pdfs/members/Ag%2005%20Aitken%20et%20al.pdf. 21 22 Accessed 19 December 2017. 23 24 Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F. 2004. Parallel Metropolis coupled Markov 25 PDF Proof 26 chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407–415. 27 28 Arthan W, McKain MR, Traiperm P, Welker CAD, Teisher JK, Kellogg EA. 2017. Phylogenomics of 29 30 Andropogoneae (Panicoideae: Poaceae) of mainland Southeast . Systematic Botany 42: 418– 31 431. 32 33 34 Besnard G, Christin P-A, Malé P-JG, Coissac E, Ralimanana H, Vorontsova MS. 2013. Phylogenomics 35 and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar. Annals 36 37 of Botany 112: 1057–1066. 38 39 Bosser J. 1968. Note sur les graminées de Madagascar–VII. Adansonia 8: 513–522. 40 41 42 Bosser J. 1969. Graminées des pâturages et des cultures à Madagascar. Paris, France: ORSTOM. 43 44 Brosse N, Dufour A, Meng X, Sun Q, Ragauskas A. 2012. Miscanthus: a fast-growing crop for biofuels 45 46 and chemicals production. Biofuels, Bioproducts and Biorefining 6: 580–598. 47 48 Brozynska M, Furtado A, Henry RJ. 2016. Genomics of crop wild relatives: expanding the gene pool 49 50 for crop improvement. Plant Biotechnology Journal 14: 1070–1085. 51 52 53 54 55 56 57 20 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Estep MC, McKain MR, Diaz DV, Zhong J, Hodge JG, Hodkinson TR, Layton DJ, Malcomber ST, 11 12 Pasquet R, Kellogg EA. 2014. Allopolyploidy, diversification, and the Miocene grassland 13 14 expansion. Proceedings of the National Academy of Sciences of the United States of America 111: 15 15149–15154. 16 17 18 Evans DL, Joshi SV, Wang J. 2019. Whole chloroplast genome and gene locus phylogenies reveal the 19 taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane. 20 21 BMC Evolutionary Biology 19: 33. 22 23 FAOSTAT. 2019. Food and agriculture data. Food and Agriculture Organization of the United 24 25 Nations, http://www.fao.org/faostat/en/, accessedPDF on 18 January Proof 2019. 26 27 Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, 28 29 Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan 30 31 A, Sluys MAV, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, Vossen E van der, 32 Henry R, Schmutz J, D’Hont A. 2018. A mosaic monoploid reference sequence for the highly 33 34 complex genome of sugarcane. Nature Communications 9: 2638. 35 36 Hackel E. 1885. Andropogoneae novae. Flora 68: 131–143. 37 38 39 Hackel E. 1889. Andropogon subgenus Lasiorhachis. Monographiae Phanerogamarum 6: 471–473. 40 41 Hackel J, Vorontsova MS, Nanjarisoa OP, Hall RC, Razanatsoa J, Malakasi P, Besnard G. 2018. Grass 42 43 diversification in Madagascar: In situ radiation of two large C3 shade clades and support for a 44 Miocene to Pliocene origin of C grassy biomes. Journal of Biogeography 45: 750–761. 45 4 46 47 Hawkins JS, Ramachandran D, Henderson A, Freeman J, Carlise M, Harris A, Willison-Headley Z. 48 2015. Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a 49 50 polyphyletic origin of the genus Sorghum. Annals of Botany 116: 291–299. 51 52 53 54 55 56 57 22 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Heaton EA, Dohleman FG, Long SP. 2008. Meeting US biofuel goals with less land: the potential of 11 12 Miscanthus. Global Change Biology 14: 2000–2014. 13 14 Hodkinson TR, Chase MW, Lledó DM, Salamin N, Renvoize SA. 2002. Phylogenetics of Miscanthus, 15 16 Saccharum and related genera (Saccharinae, Andropogoneae, Poaceae) based on DNA sequences 17 18 from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. Journal of 19 Plant Research 115: 381–392. 20 21 22 Katoh K, Standley DM. 2013. MAFFT Multiple Sequence Alignment Software Version 7: 23 improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. 24 25 PDF Proof 26 Kellogg EA. 2013. Phylogenetic Relationships of Saccharinae and Sorghinae. In: Paterson AH (ed.) 27 Genomics of the Saccharinae. Plant genetics and genomics: crops and models, vol. 11. New York: 28 29 Springer, 3–21. 30 31 Kellogg EA. 2015. Flowering plants. Monocots: Poaceae. In: Kubitzki K (ed.), The families and genera 32 33 of vascular plants, vol. 13. Heidelberg: Springer. 34 35 Moat J, Smith P. 2007. Atlas of the vegetation of Madagascar. Kew: Royal Botanic Gardens. 36 37 38 Mukherjee SK. 1954. Revision of the genus Saccharum Linn. Bulletin of the Botanical Society of 39 Bengal 8: 143–148. 40 41 42 Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, 43 Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, 44 45 Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, 46 47 Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller 48 B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, 49 50 Westhoff P, Mayer KFX, Messing J, Rokhsar DS. 2009. The Sorghum bicolor genome and the 51 52 diversification of grasses. Nature 457: 551–556. 53 54 55 56 57 23 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Piot A, Hackel J, Christin PA, Besnard G. 2018. One-third of the plastid genes evolved under positive 11 12 selection in PACMAD grasses. Planta 247: 255–266. 13 14 Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. 15 16 Bioinformatics 19: 1572–1574. 17 18 Sacks EJ, Juvik JA, Lin Q, Stewart JR, Yamada T. 2013. The gene pool of Miscanthus species and its 19 20 improvement. In: Paterson AH (ed.), Genomics of the Saccharinae. Plant genetics and genomics: 21 22 crops and models, vol. 11. New York: Springer New York, 73–101. 23 24 Spangler RE. 2003. Taxonomy of Sarga, Sorghum and Vacoparis (Poaceae: Andropogoneae). 25 PDF Proof 26 Australian Systematic Botany 16: 279–299. 27 28 Solofondranohatra CL, Vorontsova MS, Hackel J, Besnard G, Cable S, Williams J, Jeannoda V, 29 30 Lehmann CER. 2018. Grass functional traits differentiate forest and savanna in the Madagascar 31 central highlands. Frontiers in Ecology and Evolution 6: 184. 32 33 34 Soreng RJ, Peterson PM, Romaschenko K, Davidse G, Teisher JK, Clark LG, Barberá P, Gillespie LJ, 35 Zuloaga FO. 2017. A worldwide phylogenetic classification of the Poaceae (Gramineae) II: an 36 37 update and a comparison of two 2015 classifications. Journal of Systematics and Evolution 55: 38 39 259–290. 40 41 Stapf O. 1933 publ. 1927. Lasiorrhachis hildebrandtii. Hooker’s Icones Plantarum 32: t. 3124. 42 43 Todd J, Sandhu H, Hale A, Glaz B, Wang J. 2017. Phenotypic evaluation of a diversity panel selected 44 45 from the world collection of sugarcane (Saccharum spp.) and related grasses. Maydica 62: 19. 46 47 Vorontsova MS, Besnard G, Forest F, Malakasi P, Moat J, Clayton WD, Ficinski P, Savva GM, 48 49 Nanjarisoa OP, Razanatsoa J, Randriatsara FO, Kimeu JM, Luke WRQ, Kayombo C, Linder HP. 50 51 2016. Madagascar’s grasses and grasslands: anthropogenic or natural? Proceedings of the Royal 52 Society, Series B 283: 20152262. 53 54 55 56 57 24 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Vorontsova MS, Dransfield S, Renvoize S, Besnard G, McRobb A, Razanatsoa J, Nanjarisoa OP, 11 12 Andrianaivoravelona B, Rakotoarisoa SE, Ralimanana H. 2018. Identification guide to grasses 13 14 and bamboos in Madagascar. Kew: Royal Botanic Gardens. 15 16 Watson L, Macfarlane TD, Dallwitz MJ. 1992 onwards. The grass genera of the world: descriptions, 17 18 illustrations, identification, and information retrieval; including synonyms, morphology, anatomy, 19 physiology, phytochemistry, cytology, classification, pathogens, world and local distribution, and 20 21 references. Version: 15th February 2019. delta-intkey.com 22 23 Welker CAD, McKain MR, Vorontsova MS, Peichoto MC, Kellogg EA. 2019. Plastome phylogenomics 24 25 of sugarcane and relatives confirms the segregationPDF of the genus Proof Tripidium (Poaceae- 26 27 Andropogoneae), Taxon 68: 246-267. 28 29 Welker CAD, Souza-Chies TT, Longhi-Wagner HM, Peichoto MC, McKain MR, Kellogg EA. 2015. 30 31 Phylogenetic analysis of Saccharum s.l. (Poaceae; Andropogoneae), with emphasis on the 32 circumscription of the South American species. American Journal of Botany 102: 248–263. 33 34 35 Zhang H, Mittal N, Leamy LJ, Barazani O, Song BH. 2017. Back into the wild—apply untapped 36 genetic diversity of wild relatives for crop improvement. Evolutionary Applications 10: 5–24. 37 38 39 Zhuang Q, Qin Z, Chen M. 2013. Biofuel, land and water: , switchgrass or Miscanthus? 40 Environmental Research Letters 8: 015020. 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 25 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 11 12 FIGURE LEGENDS 13 14 Figure 1. Field photographs of Lasiorhachis. A, Lasiorhachis viguieri in Andringitra National Park, 15 Nanjarisoa et al. 77; B, Lasiorhachis hildebrandtii in Alaotra-Mangoro; C-E Lasiorhachis perrieri in 16 17 Itremo Protected Area, Vorontsova et al. 1530. Photographs by M.S. Vorontsova except B by Romer 18 19 Rabarijaona at www.inaturalist.org. 20 21 Figure 2. Bayesian phylogenetic tree estimated for non-coding regions of 56 Andropogoneae 22 23 plastomes, including two Lasiorhachis spp. (in bold). Subtribe Saccharinae and the Saccharum 24 complex are highlighted. Filled circles at nodes indicate a posterior clade support of 0.95 and higher 25 PDF Proof 26 with both non-coding plastome regions and coding regions; open circles indicate support only with 27 28 coding regions. See Figure S1 for precise node support values and plastome accession numbers. 29 30 Figure 3. Bayesian phylogenetic tree estimated for the plastid regions ndhF, rbcL and trnK/matK for 31 32 Saccharinae species, including four Lasiorhachis accessions (in bold), and outgroup taxa. The 33 Saccharum complex is highlighted. Circles at nodes indicate a posterior clade support of 0.7 and 34 35 higher (open circles) or 0.95 and higher (filled circles). 36 37 Figure 4. Schematic representation of Bayesian phylogenetic trees estimated for Andropogoneae 38 39 sequences of ITS (A) and eight low-copy nuclear regions (B-I). Lasiorhachis (arrow) and other clades 40 41 of interest of Saccharinae are highlighted. Triangle size is not proportional to the number of 42 43 collapsed tips. Sequences for two Lasiorhachis accessions were assembled from low-coverage 44 genome skims. All trees were rooted with Arundinella. The scale bar indicates 0.05 substitutions per 45 46 site, and circles at nodes indicate posterior support of 0.7 and higher (open) or 0.95 and higher 47 48 (filled). 49 50 Figure 5. Lasiorhachis hildebrandtii. A, habit; B, junction between the leaf sheath and the left blade, 51 52 lateral view; C, ligule; D, inflorescence branch; E, spikelet pair; F – M, sessile spikelet; F, lower glume, 53 54 55 56 57 26 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 ventral surface; G, lower glume, dorsal surface; H, upper glume, ventral surface; I, upper glume, 11 12 dorsal surface; J, lower lemma, ventral surface; K, lower lemma, dorsal surface; L, upper lemma, 13 14 ventral surface; M, upper lemma, dorsal surface. Scale bar: A = 4 cm, B, C = 4 mm, D = 5 mm, E = 2 15 mm, F – M = 1.6 mm. Drawn from Descoings 218 (K) by Lucy T. Smith. 16 17 18 Figure 6. Lasiorhachis perrieri: A, habit at base; B, flowering habit, culm continued from A; C, ligule; 19 D, inflorescence branch; E, spikelet pair; F – R, sessile spikelet; F, lower glume, ventral surface; G, 20 21 lower glume, dorsal surface; H, upper glume, ventral surface; I, upper glume, dorsal surface; J, 22 23 spikelet with the glumes removed, lateral view; K, lower lemma, ventral surface; L, lower lemma, 24 dorsal surface; M, lower palea, ventral surface; N, lower palea, dorsal surface; O, upper lemma, 25 PDF Proof 26 ventral surface; P, upper lemma, dorsal surface; Q, lodicules; R, immature caryopsis. Scale bar: A, B = 27 28 4 cm, C, D = 5 mm, E = 2.2 mm, F – R = 2 mm. Drawn from Bosser 1899b (K) by Lucy T. Smith. 29 30 Figure 7. Lasiorhachis viguieri. A, habit; B, ligule; C, inflorescence branch; D, spikelet pair; E – N, 31 32 sessile spikelet; E, lower glume, ventral surface; F, lower glume, dorsal surface; G, upper glume, 33 ventral surface; H, upper glume, dorsal surface; I, spikelet with the glumes removed, lateral view; J, 34 35 lower lemma, ventral surface; K, lower lemma, dorsal surface; L, upper lemma; M, lodicule; N, 36 37 ; O – T, pedicelled spikelet; O, lower glume, ventral surface; P, lower glume, dorsal 38 surface; Q, upper glume, ventral surface; R, upper glume, dorsal surface; S, lower lemma; T, upper 39 40 lemma. Scale bar: A = 4 cm, B = 1.6 mm, C = 7 mm, D – T = 2.2 mm. Drawn from Nanjarisoa 76 (K) by 41 42 Lucy T. Smith. 43 44 Figure 8. Distribution of Lasiorhachis including occurrence records from the specimens studied here 45 46 and field observations. Administrative province boundaries are marked in grey. 47 48 Appendix 1. Sequences assembled as part of this study. [to be added after review] 49 50 51

52 SUPPLEMENTARY MATERIAL 53 54 55 56 57 27 58 59 60

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1 2 3 4 5 6 Malagasy Lasiorhachis 7 8 9 10 Figure S1. Detailed versions of Bayesian phylogenetic trees estimated for coding (A) and non-coding 11 12 plastome regions, with Bayesian posterior support values at nodes and plastome accession numbers. 13 14 Figure S2. Detailed versions of Bayesian phylogenetic trees estimated for ITS (A) and eight low-copy 15 16 nuclear regions (B-I), with Bayesian posterior support values at nodes and accession numbers. 17 18 19 20 21 22 23 24 25 PDF Proof 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 28 58 59 60

Botanical Journal of the Linnean Society Page 29 of 47 Botanical Journal of the Linnean Society

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 287x203mm (300 x 300 DPI) 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 30 of 47

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 167x139mm (300 x 300 DPI) 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Page 31 of 47 Botanical Journal of the Linnean Society

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 Figure 3. 34 35 167x139mm (300 x 300 DPI) 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 32 of 47

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 167x224mm (300 x 300 DPI) 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Page 33 of 47 Botanical Journal of the Linnean Society

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 34 of 47

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Page 35 of 47 Botanical Journal of the Linnean Society

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 36 of 47

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 PDF Proof 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 84x126mm (600 x 600 DPI) 48 49 50 51 52 53 54 55 56 57 58 59 60 Botanical Journal of the Linnean Society Page 37 of 47 Botanical Journal of the Linnean Society A − Plastome CDS

1 1 Miscanthus sinensis NC_035752.1 2 1 Miscanthus floridulus NC_035750.1 3 1 Miscanthus sinensis NC_028721.1

4 1 Miscanthus × longiberbis NC_035753.1 5 Miscanthus sacchariflorus LN869219.1 6 1 Saccharum hybrid cultivar LN896359.1 7 1 1 Saccharum officinarum LN849913.1 8 0.001 subst./site Saccharum spontaneum LN896360.1 9 1 Miscanthidium junceum NC_035751.1 10 0.96

11 Pseudosorghum fasciculare KY596157.1 12 Eulalia siamensis KY596149.1 1 13 1 Sorghum mekongense NC_035022.1

14 1 Sorghum bicolor NC_008602.1 15 1 Lasiorhachis hildebrandtii LRK2008 1 1 16 Lasiorhachis perrieri NOP140 17 Sarga timorensis NC_023800.1 18 Germainia capitata NC_035046.1 19 1 1 paniceum NC_029881.1 20

21 cylindrica NC_030487.1

22 1 sericeum NC_035018.1 23 1 venustum NC_030622.1 24 1 alta NC_030621.1 25 PDF ProofIseilema macratherum NC_030611.1 26 1 quadrivalvis KY707773.1 27 1 1 KY707767.1 28 Themeda arundinacea NC_035014.1 29 1 contortus NC_035027.1 30 Hyparrhenia rufa NC_035011.1 31 1

32 1 Hyparrhenia subplumosa NC_030625.1 33 1 Diheteropogon amplectens var. catangensis KU291497.1

34 1 brevifolium NC_035013.1 35 1 Diectomis fastigiata NC_035010.1

36 1 flexuosus NC_035040.1 37 Heteropogon triticeus NC_035025.1 38 NC_030503.1 39 1 nutans NC_030498.1 40 1 binata NC_035049.1 41 1

42 Dimeria ornithopoda KY596130.1

43 1 Pseudopogonatherum contortum NC_035026.1 44 1 Andropogon burmanicus KY596164.1 45 1 Parahyparrhenia siamensis NC_035033.1 46 cf. cayennensis NC_029882.1 47 1 eriopoda NC_035023.1 48 1 1 Eremochloa ciliaris KY596146.1 49 helferi KY596162.1 50 orientalis NC_035047.1 51 0.9 1

52 KY596158.1 Kerriochloa siamensis KY596120.1 53 0.51 54 Tripidium arundinaceum NC_030777.1 55 1 Rottboellia cochinchinensis NC_030615.1 56 1 1 lacryma−jobi KY596160.1 57 afrum NC_030488.1 58 0.96 Zea mays NC_001666.2 59 digitata KY596178.1 60 1 Arthraxon prionodes NC_030613.1 Arthraxon microphyllus KY596183.1

Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 38 of 47 B − Plastome non−coding

1 1 Miscanthus sinensis NC_035752.1 2 1 Miscanthus floridulus NC_035750.1 3 1 Miscanthus sinensis NC_028721.1

4 1 Miscanthus × longiberbis NC_035753.1 5 Miscanthus sacchariflorus LN869219.1 6 1 1 Saccharum hybrid cultivar LN896359.1 7 1 Saccharum officinarum LN849913.1 8 0.001 subst./site 1 1 Saccharum spontaneum LN896360.1 9 Miscanthidium junceum NC_035751.1 10 1

11 Pseudosorghum fasciculare KY596157.1 12 Eulalia siamensis KY596149.1 1 13 1 Sorghum mekongense NC_035022.1

14 1 Sorghum bicolor NC_008602.1 15 Lasiorhachis hildebrandtii LRK2008 1 1 16 1 Lasiorhachis perrieri NOP140 17 Sarga timorensis NC_023800.1 18 Germainia capitata NC_035046.1 19 0.63 1 1 Pogonatherum paniceum NC_029881.1 20

21 Imperata cylindrica NC_030487.1

22 Sorghastrum nutans NC_030498.1 23 1 Dichanthium sericeum NC_035018.1 24 1 Capillipedium venustum NC_030622.1 25 PDF1 ProofBothriochloa alta NC_030621.1 1 26 Iseilema macratherum NC_030611.1 27 1 1 Themeda quadrivalvis KY707773.1 28 1 Themeda triandra KY707767.1 29 1 1 Themeda arundinacea NC_035014.1 30 NC_035027.1 31

32 1 Cymbopogon flexuosus NC_035040.1 NC_035025.1 33 0.98 1 Heteropogon triticeus

34 1 Hyparrhenia rufa NC_035011.1 35 Hyparrhenia subplumosa NC_030625.1 36 1 Diheteropogon amplectens var. catangensis KU291497.1 37 1 Schizachyrium brevifolium NC_035013.1 38 0.98 Diectomis fastigiata NC_035010.1 39 Eulalia aurea NC_030503.1 40 0.98 0.98 41 0.98 Kerriochloa siamensis KY596120.1

42 NC_035049.1 Dimeria ornithopoda KY596130.1 43 0.98 44 Tripidium arundinaceum NC_030777.1

45 1 Eremochloa eriopoda NC_035023.1

46 0.93 1 Eremochloa ciliaris KY596146.1 47 Rottboellia helferi KY596162.1 48 1 Rottboellia cochinchinensis NC_030615.1 49 1 Coix lacryma−jobi KY596160.1 50 Ischaemum afrum NC_030488.1 51 1

52 1 Pseudopogonatherum contortum NC_035026.1

53 1 Andropogon burmanicus KY596164.1 1 Parahyparrhenia siamensis NC_035033.1 54 1 55 1 Eriochrysis cf. cayennensis NC_029882.1

56 1 Chrysopogon orientalis NC_035047.1 1 57 Chrysopogon zizanioides KY596158.1 58 Polytoca digitata KY596178.1 59 Zea mays NC_001666.2 60 1 Arthraxon prionodes NC_030613.1 Arthraxon microphyllus KY596183.1

Botanical Journal of the Linnean Society Page 39 of 47 Botanical Journal of the Linnean Society A − ITS

0.34 Chrysopogon fulvus GQ856329.1 1 0.98 Chrysopogon verticillatus GQ856327.1 0.8 Chrysopogon perlaxus GQ856328.1 2 0.34 Chrysopogon aucheri GQ856331.1 0.63 Chrysopogon plumulosus GQ856330.1 3 0.5 Chrysopogon serrulatus GQ856320.1 4 0.01 subst./site 1 Chrysopogon fulvibarbis GQ856324.1 0.98 Chrysopogon orientalis GQ856325.1 5 Chrysopogon nodulibarbis GQ856333.1 0.4 0.36 Chrysopogon filipes GQ856360.1 6 0.47 Chrysopogon castaneus GQ856359.1 1 Chrysopogon oliganthus GQ856361.1 7 Chrysopogon tenuiculmis GQ856362.1

8 1 Chrysopogon elongatus GQ856341.1 0.55 1 Chrysopogon micrantherus GQ856340.1 9 0.63 Chrysopogon sylvaticus GQ856342.1 1 Chrysopogon subtilis GQ856344.1 10 0.56 Chrysopogon nemoralis GQ856343.1

11 0.34 Chrysopogon gryllus GQ856346.1 1 Chrysopogon gryllus subsp. gryllus GQ856345.1 0.92 Chrysopogon gryllus GQ856347.1 12 0.97 1 Chrysopogon festucoides GQ856338.1 13 1 Chrysopogon zizanioides GQ856337.1 14 Chrysopogon nigritanus GQ856335.1 1 Chrysopogon fallax GQ856351.1 15 0.14 0.65 Chrysopogon pallidus GQ856350.1 1 Chrysopogon setifolius GQ856349.1 16 1 Chrysopogon latifolius GQ856348.1 17 Chrysopogon aciculatus GQ856352.1 1 Coix lacryma−jobi KR005616.1 18 1 Coix lacryma−jobi var. ma−yuen AB571313.1 Coix gasteenii GQ870234.1 19 1 Glyphochloa bombaiensis KT387621.1 20 1 Glyphochloa talbotii KT387618.1 Glyphochloa henryi KT387614.1 0.98 21 1 Glyphochloa acuminata var. stocksii KT387610.1 1 Glyphochloa acuminata var. acuminata KT387609.1 22 0.76 Glyphochloa santapaui KT387617.1

23 0.99 Glyphochloa mysorensis KT387615.1 0.33 1 Glyphochloa divergens KT387611.1 Glyphochloa ratnagirica KT387616.1 24 0.03 Eulalia villosa AY116302.1 25 1 purpureus MK396909.1 26 0.06 1 Elionurus citreus MK396908.1 0.63 Elionurus tripsacoides DQ005046.1 27 0.16 exaltatus KT387622.1 granularis DQ172081.1

28 0.32 0.34 pratensis GQ870211.1 0.99 Hemarthria longiflora GQ870210.1 29 0.07 0.99 Hemarthria uncinata AF019821.1 30 0.49 Hemarthria sibirica KF163638.1 Heteropogon triticeus GQ870188.1 31 0.17 0.51 Rottboellia aurita DQ005063.1 1 Rottboellia rugosa DQ005033.1 32 0.28 KT387625.1 0.13 veldkampii 33 Mnesithea formosa GQ870212.1 0.05 Pogonatherum crinitum JN407510.1 34 Bothriochloa insculpta AF190756.1 35 zea GQ870213.1 0.01 0.34 Themeda quadrivalvis KY991096.1 36 1 Themeda triandra var. japonica FJ766187.1 0.99 Themeda triandra KF163704.1 37 0.56 Themeda novoguineensis KY991123.1 0.58 38 Themeda arguens KY991100.1 1 Themeda pseudotremula KY991118.1 39 0.3 Themeda tremula KY991114.1 0.35 Themeda mooneyi KY991120.1 0.83 40 1 Themeda saxicola KY991119.1 1 Themeda hookeri KY991091.1 41 Themeda anathera KY991076.1 42 Themeda cymbaria KY991124.1 0.34 Themeda trichiata KY991121.1 43 0.86 1 Themeda villosa KY991080.1 0.86 Themeda caudata KY991093.1 44 0.45 Themeda avenacea KY991116.1 45 0.85 Heteropogon contortus MH768196.1 Themeda arundinacea GQ870189.1 0.45 46 0.01 0.98 Iseilema prostratum DQ005059.1 0.7 Iseilema membranaceum DQ005058.1 47 Eulaliopsis binata GQ870224.1

48 1 Imperata cylindrica JN407505.1 1 Imperata cylindrica var. koenigii FJ766165.1 49 0.25 Imperata brevifolia MF963960.1 0.94 Tripidium arundinaceum JX156345.1 50 Tripidium ravennae AF019824.1

51 1 Hyparrhenia hirta DQ005056.1 0.46 Andropogon distachyos DQ005014.1 52 0.99 Hyparrhenia rufa GQ870187.1 0.95 Hyparrhenia anamesa AF190760.1 53 0.57 0.55 Hyperthelia dissoluta HM347015.1 54 Hyparrhenia diplandra GQ870186.1 0.31 Andropogon chinensis HM347004.1

55 1 DQ005072.1 Andropogon gerardii DQ005015.1

56 0.17 1 Andropogon eremicus MF963961.1 0.88 Schizachyrium gaumeri DQ005068.1 57 0.32 Andropogon bicornis DQ005013.1 58 0.41 0.41 DQ005075.1 0.19 elegans GQ870206.1 59 Schizachyrium cirratum DQ005067.1

0.05 Diectomis fastigiata DQ005044.1 60 0.15 1 Schizachyrium sanguineum DQ005070.1 1 Schizachyrium malacostachyum DQ005069.1 0.63 Schizachyrium condensatum KP878911.1 KF163597.1 0.510.31 Schizachyrium brevifolium Andropogon chinensis GQ870181.1 Schizachyrium semitectum DQ005073.1 0.32 Zea diploperennis U46591.1 0.48 Zea perennis U46588.1 0.21 1 Zea mays AJ309824.2 1 Zea luxurians U46594.1 1 laxum U46658.1

1 PDF Proof1 Tripsacum maizar U46657.1 Tripsacum australe U46653.1 0.61 U46649.1 Cymbopogon commutatus KJ004308.1 1 Cymbopogon winterianus KT309076.1 1 0.77 Cymbopogon nardus KT309074.1 1 Cymbopogon flexuosus KX828249.1 0.96 Cymbopogon goeringii KF163607.1

0.57 1 Cymbopogon pendulus KT309075.1 Cymbopogon citratus AF019823.1 Cymbopogon martinii DQ005037.1 0.04 0.98 Bothriochloa barbinodis MF963963.1 0.72 Bothriochloa laguroides DQ005026.1 1 Bothriochloa springfieldii DQ005029.1

0.98 Bothriochloa alta DQ005021.1 0.52 DQ005028.1

0.76 0.99 Bothriochloa compressa DQ005023.1 Bothriochloa macra DQ005027.1 0.86 Euclasta condylotricha DQ005050.1 Capillipedium spicigerum DQ005030.1 1 0.2 Bothriochloa ischaemum MH768166.1 0.2 Bothriochloa grahamii DQ005024.1 0.94 Dichanthium annulatum DQ005038.1 0.98 Capillipedium venustum DQ005031.1 1 Dichanthium sericeum DQ005042.1 0.44 Dichanthium caricosum GQ870217.1 0.99 Apocopis intermedius GQ870196.1 0.97 Apocopis courtallumensis GQ870195.1 0.99 Apocopis siamensis GQ870197.1 0.67 Apocopis collinus GQ870194.1 0.01 1 0.71 Germainia pilosa GQ870200.1 Germainia khasiana GQ870199.1 Germainia capitata GQ870198.1 0.33 Sorghum × drummondii KT933763.1 0.94 Sorghum arundinaceum KT933762.1 0.7 Sorghum bicolor XR_002448966.1 1 Sorghum halepense MH050285.1 0.99 Sorghum propinquum JX156341.1 0.73 Lasiorhachis perrieri NOP140 0.36 Lasiorhachis hildebrandtii LRK2008 1 Sorghum macrospermum U04798.1 0.91 Sorghum laxiflorum U04791.1 0.99 japonicum KF163847.1 1 Microstegium somae EU489072.1 Microstegium nudum EU489067.1 0.28 0.98 Sorghastrum secundum DQ005078.1 1 Sorghastrum incompletum DQ005076.1 0.99 Sorghastrum nutans DQ005080.1 DQ005085.1 0.04 0.37 1 spicatus Trachypogon spicatus DQ005084.1 Rottboellia cochinchinensis MF063652.1 1 cotulifer KF163700.1 0.98 HQ600493.1 Ischaemum afrum HM347038.1 0.21 Miscanthus floridulus MK138896.1 0.24 Miscanthus sinensis JN544317.1 0.06 1 Miscanthus sinensis LC113993.1 0.16 Miscanthus sinensis AY116271.1 0.99 Miscanthus tinctorius LC113999.1 0.35 Miscanthus oligostachyus LC113995.1 0.16 Miscanthus oligostachyus LC113997.1 1 Miscanthus × longiberbis HQ822028.1 0.18 Miscanthus lutarioriparius MK138898.1 0.76 Miscanthus sinensis JN544334.1 0.44 0.19 Miscanthus sacchariflorus JN544311.1 Miscanthus sacchariflorus var. gracilis HQ822019.1 0.77 Miscanthus paniculatus JN544345.1 Pseudopogonatherum quadrinerve GQ870221.1 AY116286.1 1 Saccharum spontaneum AB281142.1 0.27 0.71 Saccharum longesetosum AF345217.1 1 Saccharum narenga AF345234.1

0.22 Miscanthidium junceum AY116288.1 0.34 Saccharum giganteum DQ005048.1 0.250.98 Saccharum contortum AY116287.1 Saccharum baldwinii DQ005049.1 0.31 1 Miscanthus ecklonii AY116290.1 1 Saccharum robustum AB281156.1 0.98 Saccharum × sinense AB281152.1 1 0.3 Saccharum × sinense AB281148.1 Saccharum officinarum AF345231.1 1 Pseudosorghum zollingeri GQ856356.1 Pseudosorghum fasciculare GQ856355.1 0.2 1 Miscanthus nepalensis JN544347.1 Miscanthus nudipes JN544346.1 1 Eulalia siamensis GQ870222.1 0.32 Saccharum fallax AF345213.1 Eulalia aurea AF345218.1 0.47 Sorghum matarankense U04792.1 0.38 Sorghum brachypodum GQ121736.1 0.26 Sorghum exstans GQ121735.1 Sarga intrans GQ121733.1 0.77 0.75 0.26 Sarga timorensis U04788.1 0.78 0.47 Sorghum bulbosum GQ121732.1 0.96 1 Sarga stipoidea U04794.1

1 Sorghum amplum GQ121727.1 Sorghum interjectum GQ121738.1 0.79 DQ888629.1 0.49 Sarga leioclada 0.42 1 Capillipedium assimile HQ600505.1 Sorghum nitidum GQ856354.1 0.61 Sorghum purpureo−sericeum U04793.1 1 0.59 Cleistachne sorghoides U04790.1 Sarga versicolor KT933739.1 1 Polytrias indica GQ870228.1 Eulalia aurea DQ005052.1 1 Polytoca wallichiana GQ870233.1 Polytoca digitata GQ870232.1 0.23 1 Dimeria ornithopoda GQ870192.1 0.46 Dimeria chloridiformis GQ870191.1 0.74 Polytrias indica GQ870202.1

0.68 Ischaemum muticum GQ870203.1 0.88 Ischaemum filiforme KF163645.1 0.08 1 Ischaemum aristatum var. glaucum FJ766167.1

0.01 Ischaemum anthephoroides KF163644.1 mutica DQ005016.1 1 Microstegium vimineum KF163649.1 1 Microstegium fasciculatum GQ870225.1 0.74 Microstegium fasciculatum FJ170273.1 Microstegium glabratum EU489066.1 0.01 1 1 Microstegium fauriei EU489079.1 0.08 0.94 Microstegium geniculatum EU489071.1 Phacelurus latifolius FJ766173.1 Eremochloa ophiuroides HQ600489.1

0.04 1 Pseudopogonatherum contortum GQ870223.1 0.2 Pseudopogonatherum irritans AY116298.1 Kerriochloa siamensis GQ870204.1 0.94 Polytoca massiei GQ870231.1 0.86 Polytoca cyathopoda AF019819.1 0.38 nervosum GQ870205.1 Chrysopogon pauciflorus GQ856353.1 1 Arthraxon lanceolatus KP711098.1 DQ006027.1 1 Arundinella hirta KF163604.1 0.36 Arundinella bengalensis GQ870150.1 1 Arundinella berteroniana GQ870151.1 0.69 Arundinella hispida GQ870152.1

1 Arundinella hirta KP711102.1 0.59 Arundinella setosa var. setosa GQ870155.1 1 Arundinella setosa GQ870154.1 Arundinella nepalensis AF019816.1 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 40 of 47 B − apo1

0.92 Bothriochloa bladhii KM578477.1 1 1 Bothriochloa bladhii KM578475.1 0.99 Bothriochloa bladhii KM578476.1 2 1 Bothriochloa bladhii KM578451.1 0.9 Bothriochloa ischaemum KM578442.1 3 0.99 Bothriochloa laguroides KM578462.1 4 0.01 subst./site 1 Bothriochloa woodrovii KM578459.1 Bothriochloa macra KM578454.1 0.53 5 0.97 Bothriochloa insculpta KM578456.1 0.94 Bothriochloa insculpta KM578455.1 6 Bothriochloa insculpta KM578457.1 0.22 1 Bothriochloa insculpta KM578446.1 0.98 0.23 7 Bothriochloa decipiens KM578464.1 8 Bothriochloa bladhii KM578474.1 0.99 Bothriochloa exaristata KM578478.1 0.91 9 1 Bothriochloa barbinodis KM578453.1

10 Bothriochloa laguroides KM578463.1 1 Bothriochloa woodrovii KM578461.1 0.96 Bothriochloa woodrovii KM578460.1 11 0.84 Bothriochloa alta KM578452.1 12 1 Dichanthium foveolatum KM578543.1

13 1 Dichanthium foveolatum KM578542.1 0.73 Dichanthium foveolatum KM578544.1 0.81 14 Dichanthium foveolatum KM578541.1 1 Iseilema macratherum KM578441.1 15 Iseilema macratherum KM578440.1 1 1 Capillipedium spicigerum KM578470.1 16 1 Bothriochloa bladhii KM578450.1

17 0.55 Capillipedium spicigerum KM578370.1 0.54 Capillipedium spicigerum KM578369.1 18 1 Dichanthium caricosum KM578510.1 1 Dichanthium caricosum KM578509.1 19 Dichanthium aristatum KM578390.1 0.98 20 0.89 0.34 Dichanthium annulatum KM578431.1 0.98 Dichanthium annulatum JQ951749.1 21 1 Bothriochloa ischaemum KM578486.1 0.5 Dichanthium annulatum KM578430.1 22 Capillipedium assimile KM578504.1

23 1 Heteropogon triticeus KM578518.1 0.97 Heteropogon triticeus KM578516.1 0.96 Heteropogon triticeus KM578517.1 24 0.95 1 Themeda triandra KM578496.1 25 1 Themeda triandra KM578484.1 26 Themeda triandra KM578485.1 0.74 Apocopis intermedius KM578502.1 27 0.97 Apocopis intermedius KM578500.1 0.95 Apocopis intermedius KM578501.1 28 1 Germainia capitata KM578515.1 1 Apocopis siamensis KM578503.1 29 Apocopis courtallumensis KM578499.1 0.98 Cymbopogon obtectus KM578387.1 30 0.26 0.31 Cymbopogon obtectus KM578386.1 31 0.83 Cymbopogon refractus KM578389.1 Cymbopogon obtectus KM578471.1 32 1 0.36 Cymbopogon flexuosus KM578385.1

33 1 Cymbopogon flexuosus KM578384.1 1 Cymbopogon flexuosus KM578383.1 34 Cymbopogon flexuosus JQ951744.1 0.98 35 0.15 Cymbopogon distans KM578382.1 0.14 Cymbopogon distans KM578379.1 Cymbopogon distans KM578380.1 36 0.990.15 1 Cymbopogon distans KM578378.1 37 0.06 1 Cymbopogon distans KM578381.1 0.94 Cymbopogon jwarancusa subsp. olivieri KM578416.1 38 Cymbopogon commutatus KM578388.1 39 Cymbopogon martinii KM578415.1 1 Sehima nervosum KM578407.1 40 1 Sehima nervosum KM578406.1 1 Sehima nervosum KM578409.1 41 Sehima nervosum KM578408.1 0.67 42 1 Thelepogon elegans KM578539.1 1 Thelepogon elegans KM578538.1 43 Thelepogon elegans KM578537.1 0.67 0.21 Coix lacryma−jobi KM578429.1 44 0.21 Coix lacryma−jobi KM578427.1 45 0.97 Coix lacryma−jobi KM578425.1 1 Coix lacryma−jobi KM578426.1 46 0.86 Coix lacryma−jobi KM578428.1 Coix gasteenii KM578508.1 47 0.2 Sorghum interjectum KR494131.1 48 0.21 Sorghum exstans KR494100.1 1 Sarga intrans KR494103.1 49 0.09 Sarga intrans KR494102.1 0.02 Sorghum brachypodum KR494119.1 50 0.09 Sarga plumosa KR494130.1 0.09 51 Sarga angusta KR494120.1 0.09 Sarga plumosa KR494113.1 Sarga stipoidea KR494111.1 52 0.54 0.92 Sarga stipoidea KR494117.1 53 0.66 Sorghum ecarinatum KR494114.1 0.96 1 Sorghum ecarinatum KR494110.1 54 0.57 Sorghum interjectum KR494132.1 55 1 Sarga leioclada KR494122.1 Sorghum interjectum KR494133.1 56 Sarga purpureosericea KR494129.1 0.07 Saccharum asperum KP243046.1 57 0.12 0.01 Saccharum asperum KP243045.1

58 0.09 0.08 Saccharum giganteum KP243054.1 0.07 Saccharum asperum KP243044.1 59 0.07 Saccharum villosum KP243066.1 Saccharum asperum KP243048.1 60 0.011 0.1 Saccharum giganteum KP243052.1 Saccharum angustifolium KP243038.1 0.18 Saccharum villosum KP243057.1 1 Sorghum laxiflorum KR494126.1 0.98 Sorghum laxiflorum KR494123.1 Sorghum macrospermum KR494124.1 0.97 Sorghum halepense KR494108.1 0.98PDFSorghum Proof halepense KR494106.1 0.16 0.39 Sorghum halepense KR494109.1 1 Sorghum bicolor XM_002438766.2 0.65 Sorghum bicolor KM578411.1 1 Lasiorhachis perrieri NOP140 Lasiorhachis hildebrandtii LRK2008 0.7 0.99 Sorghum macrospermum KR494128.1 1 Sorghum macrospermum KR494105.1 0.89 Sorghum macrospermum KR494104.1 0.12 1 Sorghum laxiflorum KR494125.1 Sorghum laxiflorum KR494127.1 1 Zea mays XM_008661665.3 0.05 0.19 Tripsacum dactyloides KM578413.1 0.08 Zea mays XM_008650765.2 1 Spodiopogon sibiricus KM578535.1 1 Spodiopogon sibiricus KM578534.1 Spodiopogon sibiricus KM578536.1 0.12 1 Miscanthus sinensis KM578445.1 0.37 Miscanthus sinensis KM578444.1 Miscanthus sinensis KM578443.1 1 Saccharum narenga KM578529.1 1 Saccharum narenga KM578528.1 0.96 Miscanthus ecklonii KM578468.1 0.04 0.9 Miscanthus ecklonii KM578467.1 0.34 Tripidium ravennae KM578491.1 1 Tripidium ravennae KM578490.1 Tripidium ravennae KM578492.1 0.96 Saccharum asperum KP243051.1 0.1 Saccharum asperum KP243049.1

0.04 Saccharum villosum KP243067.1 0.98 Saccharum angustifolium KP243043.1 0.1 0.5 Saccharum angustifolium KP243039.1 Saccharum asperum KP243047.1

0.86 0.1 Saccharum giganteum KP243053.1 Saccharum angustifolium KP243041.1 0.88 Saccharum officinarum KP243056.1 Saccharum officinarum KP243055.1 0.96 Eriochrysis cayennensis KT449457.1 0.21 Eriochrysis cayennensis KT449455.1 Eriochrysis cayennensis KT449454.1 0.95 0.96 Eriochrysis villosa KT449449.1 0.16 0.330.21 Eriochrysis villosa KT449448.1 KT449433.1 0.99 Eriochrysis cayennensis Eriochrysis cayennensis KT449431.1 0.99 Eriochrysis cayennensis KT449434.1 0.32 Eriochrysis laxa KT449446.1 0.88 Eriochrysis laxa KT449444.1 0.95 Eriochrysis laxa KT449447.1 0.32 Eriochrysis holcoides KT449437.1 1 0.88 Eriochrysis holcoides KT449436.1 Eriochrysis holcoides KT449435.1 1 Eriochrysis warmingiana KT449458.1 0.99 Eriochrysis pallida KM578393.1 0.84 0.86 Eriochrysis pallida KM578392.1 Eriochrysis pallida KM578391.1 1 Pogonatherum paniceum KM578448.1 KM578447.1 0.83 Pogonatherum paniceum 0.95 Diheteropogon hagerupii KM578548.1 0.98 Diheteropogon hagerupii KM578546.1 0.67 1 Diheteropogon hagerupii KM578547.1 1 Diheteropogon hagerupii KM578545.1 Diheteropogon amplectens KM578432.1 JQ951746.1 0.9 Schizachyrium sanguineum 1 Schizachyrium sanguineum KM578532.1 1 Schizachyrium sanguineum KM578404.1 1 Schizachyrium sanguineum KM578376.1 1 Schizachyrium sanguineum KM578375.1 0.29 1 Schizachyrium sanguineum KM578533.1 Schizachyrium brevifolium KM578530.1 1 Andropogon gayanus KM578423.1 0.96 Andropogon gayanus KM578422.1 0.99 Andropogon gayanus KM578420.1 0.03 1 Andropogon gayanus KM578421.1 Andropogon gayanus KM578419.1 1 Hyparrhenia diplandra KM578521.1 0.99 Hyparrhenia diplandra KM578519.1 0.47 1 Hyparrhenia diplandra KM578520.1 1 Hyparrhenia diplandra KM578522.1 Hyparrhenia diplandra KM578540.1 1 0.84 Hyparrhenia hirta KM578480.1 1 Hyparrhenia hirta KM578479.1 0.66 KM578394.1 1 Hyparrhenia hirta KM578523.1 0.82 Hyparrhenia rufa 0.84 Hyparrhenia hirta KM578550.1 0.37 1 Hyparrhenia hirta KM578396.1 Hyparrhenia hirta KM578395.1 0.34 Andropogon perligulatus KM578368.1

0.62 1 Andropogon perligulatus KM578366.1 Andropogon perligulatus KM578367.1 0.7 Andropogon virginicus KM578449.1 0.06 Andropogon eucomus KM578363.1 0.68 1 Andropogon hallii KM578424.1 0.5 Andropogon gerardii KM578365.1 1 Andropogon gerardii KM578364.1 0.2 Andropogon hallii JQ951748.1 Schizachyrium sanguineum KM578374.1 1 Chasmopodium caudatum KM578497.1 0.76 Rottboellia cochinchinensis KM578414.1 Ischaemum afrum KM578397.1 0.34 Polytoca massiei KM578507.1 1 Polytoca massiei KM578505.1 0.17 0.81 Polytoca massiei KM578506.1 1 Polytoca gigantea KP243072.1 0.38 Polytoca wallichiana KP243073.1 Phacelurus digitatus JQ951747.1 0.34 Imperata tenuis KT449460.1 1 Imperata brasiliensis KT449459.1 Imperata cylindrica KM578525.1 0.55 Rottboellia lepidura JQ951743.1

0.28 1 Apluda mutica KM578483.1 Apluda mutica KM578482.1 0.87 Phacelurus huillensis KM578402.1 1 Phacelurus huillensis KM578400.1 Phacelurus huillensis KM578401.1 0.95 Chrysopogon serrulatus KM578434.1 0.56 0.97 Chrysopogon serrulatus KM578433.1 Chrysopogon gryllus KM578373.1 0.9 1 Chrysopogon gryllus JQ951750.1 0.39 Chrysopogon gryllus KM578372.1 Sorghastrum elliottii KM578552.1 0.92 Andropterum stolzii KM578418.1 0.78 1 Andropterum stolzii KM578417.1 Andropterum stolzii JQ951745.1 1 Dimeria ornithopoda KM578514.1 0.99 Dimeria chloridiformis KM578513.1

0.46 1 Dimeria chloridiformis KM578512.1 1 Dimeria chloridiformis KM578511.1 0.98 KM578551.1 1 Ischaemum santapaui KM578398.1 Ischaemum santapaui KM578399.1 1 Ischaemum muticum KM578527.1 Ischaemum muticum KM578526.1 0.81 Arundinella nepalensis KM578494.1 1 Arundinella nepalensis KM578493.1 Arundinella hirta KM578481.1 Botanical Journal of the Linnean Society Page 41 of 47 Botanical Journal of the Linnean Society C − dwarf8

1 Bothriochloa bladhii KM578219.1 1 0.89 Bothriochloa bladhii KM578218.1 Capillipedium spicigerum KM578232.1 0.38 2 0.9 Capillipedium spicigerum KM578122.1 0.770.22 Chrysopogon gryllus JQ951709.1 3 KM578231.1 1 Capillipedium spicigerum 4 Bothriochloa bladhii KM578241.1 0.9 Capillipedium spicigerum KM578123.1 0.01 subst./site 5 1 Bothriochloa insculpta KM578217.1 1 1 Bothriochloa insculpta KM578202.1 6 Bothriochloa insculpta KM578216.1 7 0.88 Bothriochloa bladhii KM578237.1 1 Bothriochloa bladhii KM578240.1 8 0.99 Bothriochloa bladhii KM578238.1 KM578239.1 1 Bothriochloa bladhii 9 0.25 Bothriochloa bladhii KM578210.1 10 0.35 Bothriochloa ischaemum KM578196.1 1 Bothriochloa ischaemum KM578194.1 11 0.93 Bothriochloa ischaemum KM578195.1 0.34 1 Bothriochloa ischaemum KM578198.1 12 Bothriochloa ischaemum KM578197.1 0.97 Bothriochloa decipiens KM578228.1 13 0.99 Bothriochloa decipiens KM578226.1 0.66 Bothriochloa decipiens KM578227.1 14 1 0.36 Bothriochloa macra KM578214.1 15 0.96 Bothriochloa macra KM578213.1 16 Bothriochloa macra KM578215.1 0.86 Bothriochloa exaristata KM578242.1 17 Bothriochloa woodrovii KM578221.1 0.97 1 Bothriochloa laguroides KM578225.1 18 0.97 Bothriochloa laguroides KM578224.1 19 1 Bothriochloa exaristata KM578243.1 Bothriochloa woodrovii KM578222.1 0.72 20 0.91 Bothriochloa barbinodis KM578212.1 1 Bothriochloa alta KM578211.1 21 1 1 Bothriochloa exaristata KM578244.1 Bothriochloa woodrovii KM578220.1 22 Bothriochloa laguroides KM578223.1 Themeda triandra KM578273.1 23 0.51 0.89 0.17 Themeda triandra KM578271.1

24 0.82 Themeda triandra KM578272.1 1 Themeda triandra KM578253.1 25 0.930.18 Themeda triandra KM578252.1

26 1 Themeda triandra KM578255.1 Themeda triandra KM578254.1 27 1 Themeda triandra KM578274.1 0.57 Themeda arundinacea KM578348.1 0.18 28 1 Themeda arundinacea KM578347.1

29 0.92 1 Themeda arundinacea KM578349.1 Themeda arundinacea KM578346.1

30 0.43 Heteropogon triticeus KM578314.1 1 Heteropogon triticeus KM578313.1 31 Heteropogon triticeus KM578315.1

32 0.66 Dichanthium foveolatum KM578353.1 1 Dichanthium foveolatum KM578351.1 33 1 Dichanthium foveolatum KM578352.1 1 Iseilema macratherum KM578193.1 34 Iseilema macratherum KM578192.1

35 0.38 Cymbopogon martinii KM578166.1 1 Cymbopogon martinii KM578164.1 0.32 36 0.37 Cymbopogon martinii KM578165.1 1 Cymbopogon martinii KM578162.1 37 Cymbopogon martinii KM578163.1

38 1 1 Cymbopogon jwarancusa subsp. olivieri KM578167.1 0.81 Cymbopogon commutatus KM578132.1 Cymbopogon citratus KM578295.1 39 0.80.31 Cymbopogon distans KM578126.1 40 Cymbopogon citratus KM578296.1 1 41 1 Cymbopogon obtectus KM578131.1 0.33 Cymbopogon obtectus KM578130.1 42 0.98 Cymbopogon obtectus KM578233.1 0.95 Cymbopogon refractus KM578134.1

43 0.14 0.97 Cymbopogon refractus KM578133.1 0.23 Cymbopogon flexuosus KM578128.1 44 0.42 0.38 Cymbopogon flexuosus JQ951710.1 45 Cymbopogon flexuosus KM578127.1 0.44 Sehima nervosum KM578149.1 46 1 Sehima nervosum KM578148.1 47 Sehima nervosum KM578150.1 0.93 Dichanthium annulatum KM578177.1 48 0.14 Dichanthium annulatum KM578176.1 0.18 Dichanthium annulatum KM578178.1

49 0.141 Dichanthium annulatum KM578181.1 Dichanthium annulatum KM578179.1 50 0.91 Dichanthium annulatum KM578180.1 1 51 Dichanthium annulatum JQ951711.1 1 Dichanthium annulatum KM578357.1 52 1 Dichanthium caricosum KM578298.1 0.54 1 Dichanthium caricosum KM578297.1 53 Dichanthium aristatum KM578136.1 54 Capillipedium assimile KM578291.1 1 Hyparrhenia hirta KM578359.1 55 0.99 Hyparrhenia hirta KM578358.1 1 Hyparrhenia hirta KM578139.1 56 0.89 Hyparrhenia hirta KM578245.1 57 1 Hyparrhenia rufa KM578319.1 0.95 Hyparrhenia hirta KM578140.1 1 Hyparrhenia hirta KM578246.1 58 0.61 0.87 Hyparrhenia hirta KM578360.1 59 Hyparrhenia hirta KM578141.1 1 60 1 Hyparrhenia diplandra KM578317.1 1 Hyparrhenia diplandra KM578316.1 1 1 Hyparrhenia diplandra KM578350.1 Hyparrhenia diplandra KM578318.1 1 Diheteropogon amplectens KM578183.1 1 Diheteropogon amplectens KM578182.1 0.48 Diheteropogon hagerupii KM578355.1 1 Andropogon hallii KM578172.1 1 Andropogon hallii KM578171.1 0.18 1 Andropogon hallii KM578173.1 Andropogon gerardii KM578120.1 0.56 Andropogon glomeratus KM578362.1 0.41 0.91 Andropogon glomeratus KM578361.1 1 Andropogon virginicus KM578209.1 Andropogon eucomus KM578119.1 1 Andropogon gayanus KM578170.1 0.3 Andropogon gayanus KM578169.1 0.31 0.3 Andropogon chinensis KM578280.1 0.78 Andropogon chinensis KM578278.1 1 Andropogon chinensis KM578277.1 0.67 Andropogon chinensis KM578279.1

1 Andropogon perligulatus KM578121.1 0.34 Schizachyrium sanguineum KM578339.1 1 Schizachyrium sanguineum KM578125.1 0.84 Schizachyrium sanguineum KM578146.1 0.81 Phacelurus digitatus JQ951714.1 1 Schizachyrium sanguineum KM578340.1 1 Schizachyrium sanguineum KM578147.1 1 Schizachyrium exile KM578155.1 Schizachyrium sanguineum KM578124.1 0.14 Eulalia villosa KM578161.1 0.15 Eulalia villosa KM578159.1

0.151 Eulalia villosa KM578160.1 0.75 Eulalia villosa KM578157.1 0.99 Eulalia villosa KM578158.1 0.99 Pseudopogonatherum quadrinerve KM578308.1 1 Pseudopogonatherum quadrinerve KM578307.1 0.36 Pseudopogonatherum quadrinerve KM578311.1 1 Pseudopogonatherum quadrinerve KM578310.1 Pseudopogonatherum quadrinerve KM578309.1 0.61 Sorghum matarankense KR493977.1 0.53 Sarga angusta KR493976.1 1 Sorghum exstans KR493975.1 0.33 Sorghum exstans KR493974.1 0.84 Sarga stipoidea KR493969.1 0.93 Sarga stipoidea KR493968.1 0.59 PDF Proof 0.19 Sorghum matarankense KR493978.1 1 Sarga plumosa KR493973.1 0.52 Sarga plumosa KR493971.1 0.331 Sarga plumosa KR493972.1 0.48 Sorghum brachypodum KR493984.1 Sorghum brachypodum KR493983.1 Sarga plumosa KR493970.1 1 Sorghum laxiflorum KR493982.1 0.97 Sorghum laxiflorum KR493981.1 0.97 Sorghum laxiflorum KR493980.1 KR493979.1 0.51 Sorghum laxiflorum 0.74 0.34 Sorghum bicolor XM_002466549.2 0.57 1 Sorghum bicolor JQ951712.1 Sorghum bicolor KM578354.1 Lasiorhachis hildebrandtii LRK2008 0.99 Saccharum villosum KP233118.1 1 Saccharum villosum KP233115.1 0.12 Saccharum villosum KP233121.1 1 Miscanthus ecklonii KM578230.1 0.05 Miscanthus ecklonii KM578229.1 KP233112.1 0.120.12 Saccharum giganteum Saccharum asperum KP233110.1 0.53 0.991 Saccharum angustifolium KP233104.1 Saccharum angustifolium KP233100.1 Saccharum asperum KP233109.1 0.91 Saccharum villosum KP233119.1 0.52 Saccharum villosum KP233113.1 Saccharum giganteum KP233111.1 0.23 0.99 Saccharum narenga KM578338.1 0.19 Saccharum narenga KM578337.1 0.69 Saccharum angustifolium KP233101.1 0.76 1 Saccharum narenga KM578336.1 0.59 1 Saccharum narenga KM578334.1 Saccharum narenga KM578335.1 0.99 Saccharum asperum KP233107.1 1 Saccharum officinarum DQ062092.1 Saccharum officinarum DQ062091.1 KM578331.1 0.51 0.82 Pseudosorghum fasciculare 1 Pseudosorghum fasciculare KM578329.1 Pseudosorghum fasciculare KM578330.1 0.97 1 Miscanthus sinensis KM578200.1 1 Miscanthus sinensis KM578199.1 Miscanthus sinensis KM578201.1 1 Tripidium arundinaceum KM578333.1 1 Tripidium arundinaceum KM578332.1 Tripidium ravennae KM578269.1 0.77 Apocopis intermedius KM578284.1 0.99 Apocopis intermedius KM578283.1 1 Apocopis intermedius KM578285.1 0.89 Germainia capitata KM578312.1 1 Apocopis intermedius KM578286.1 1 Apocopis courtallumensis KM578282.1 0.37 1 Apocopis courtallumensis KM578281.1 1 Apocopis siamensis KM578288.1 0.76 Apocopis siamensis KM578287.1 0.72 Apocopis siamensis KM578289.1 0.81 Pogonatherum paniceum KM578205.1 1 Pogonatherum paniceum KM578203.1 0.74 Pogonatherum paniceum KM578204.1 0.85 Spodiopogon sibiricus KM578344.1 0.9 Spodiopogon sibiricus KM578342.1 1 Spodiopogon sibiricus KM578343.1 0.76 0.33 Spodiopogon sibiricus KM578345.1 Spodiopogon sibiricus KM578341.1 1 Imperata tenuis KT449491.1 1 Imperata brasiliensis KT449490.1 0.99 Imperata cylindrica KM578321.1 0.76 Imperata cylindrica KM578320.1 0.99 Kerriochloa siamensis KM578326.1 0.86 Kerriochloa siamensis KM578325.1 1 Kerriochloa siamensis KM578327.1 Kerriochloa siamensis KM578328.1 1 1 0.51 Polytrias indica KM578207.1 1 Polytrias indica KM578206.1 1 Eulalia aurea KM578247.1 Polytrias indica KM578208.1 0.1 Eriochrysis cayennensis KT449482.1 0.02 Eriochrysis cayennensis KT449462.1 0.1 Eriochrysis cayennensis KT449481.1 0.09 Eriochrysis cayennensis KT449461.1 0.990.09 Eriochrysis cayennensis KT449480.1 Eriochrysis cayennensis KT449463.1 0.32 Eriochrysis cayennensis KT449464.1 Eriochrysis villosa KT449486.1 0.930.88 0.47 Eriochrysis villosa KT449484.1 0.08 1 Eriochrysis villosa KT449488.1 Eriochrysis villosa KT449485.1 Eriochrysis warmingiana KT449489.1 KT449478.1 0.31 0.99 Eriochrysis laxa 0.9 Eriochrysis laxa KT449474.1 0.13 Eriochrysis laxa KT449479.1 1 Eriochrysis pallida KM578138.1 0.031 Eriochrysis pallida KM578137.1 0.1 Eriochrysis holcoides KT449467.1 Eriochrysis holcoides KT449466.1 Eriochrysis holcoides KT449465.1 1 Apluda mutica KM578251.1 0.78 Apluda mutica KM578250.1 0.44 Dimeria ornithopoda KM578305.1 0.99 Dimeria ornithopoda KM578303.1 1 Dimeria ornithopoda KM578304.1 1 Dimeria kurzii KM578306.1 1 Dimeria chloridiformis KM578302.1 1 Dimeria chloridiformis KM578301.1 1 Dimeria chloridiformis KM578300.1 Dimeria chloridiformis KM578299.1 0.35 Polytrias indica KM578324.1 1 1 1 Polytrias indica KM578322.1 Polytrias indica KM578323.1 0.86 0.54 Ischaemum rugosum KM578356.1 1 1 1 Ischaemum santapaui KM578143.1 Ischaemum santapaui KM578144.1 1 Andropterum stolzii KM578168.1 Andropterum stolzii JQ951707.1 Ischaemum afrum KM578142.1 1 Coix lacryma−jobi KM578175.1 1 Coix lacryma−jobi KM578174.1 Coix gasteenii KM578293.1 1 0.99 Chasmopodium caudatum KM578276.1 1 Chasmopodium caudatum KM578275.1 Rottboellia cochinchinensis KM578156.1 0.22 Zea mexicana FJ708399.1 0.31 Zea mays subsp. parviglumis AY514608.1 0.83 Zea mexicana FJ708391.1 0.15 Zea mexicana FJ708397.1 0.05 Zea mays subsp. parviglumis AY514612.1 0.11 Zea mexicana FJ708400.1 0.17 Zea mexicana FJ708395.1 0.8 Zea mexicana FJ708393.1 0.36 Zea mays subsp. parviglumis AY514609.1 0.57 Zea luxurians FJ708406.1 0.06 0.49 Zea luxurians FJ708402.1 0.96 Zea luxurians FJ708407.1 0.02 0.74 Zea mexicana FJ708396.1 Zea mays subsp. parviglumis AY514604.1 0.01 Zea luxurians FJ708404.1 0.08 Zea mexicana FJ708394.1 0.02 Zea mays subsp. parviglumis AY514610.1 1 Zea mays subsp. parviglumis AY514613.1 0.06 0.12 Zea mays AF377633.1 Zea mays AF377635.1 Zea mays AF377626.1 0.06 0.52 Zea mays AF377622.1 Zea mays AF377636.1 Zea mays subsp. parviglumis AY514602.1 0.3 0.86 0.47 Zea mays AF377631.1 0.56 Zea mays subsp. parviglumis AY514607.1 0.47 AY103865.1 0.67 Zea mays Zea mays NM 001367464.1 0.73 Zea mays subsp. parviglumis AY514606.1 0.92 Zea mays subsp. parviglumis AY514614.1 Tripsacum dactyloides AF377646.1 0.76 1 Zea mays NM 001309851.1 1 Zea mays DQ903074.1 1 0.96 Zea mays subsp. parviglumis AY514605.1 Tripsacum dactyloides KM578154.1 1 Polytoca gigantea KP233123.1 0.43 1 Polytoca massiei KM578292.1 0.44 Polytoca wallichiana KP233124.1 1 Phacelurus huillensis KM578145.1 Rottboellia lepidura JQ951708.1 1 Arthraxon prionodes KM578257.1 1 Arthraxon prionodes KM578256.1 Arthraxon lanceolatus KM578290.1 0.31 Chrysopogon zizanioides KM578263.1 0.08 Chrysopogon zizanioides KM578259.1 0.13 Chrysopogon zizanioides KM578262.1 KM578261.1 0.111 Chrysopogon zizanioides Chrysopogon zizanioides KM578260.1 1 Chrysopogon zizanioides KM578258.1 Chrysopogon serrulatus KM578184.1 0.99 Arundinella hirta KM578249.1 1 Arundinella hirta KM578248.1 Arundinella nepalensis KM578270.1 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 42 of 47 D − ep2−7

1 Hyparrhenia hirta KM578118.1 0.9 Hyparrhenia hirta KM577948.1 1 0.92 Hyparrhenia hirta KM577950.1 KM578025.1 2 1 Hyparrhenia hirta 0.7 Hyparrhenia hirta KM578116.1 3 1 1 Hyparrhenia hirta KM577949.1 KM578112.1 0.01 subst./site 1 Hyparrhenia hirta 4 Hyparrhenia rufa KM578080.1

5 0.47 Hyparrhenia rufa KM578081.1 0.62 Diheteropogon hagerupii KM578111.1 6 1 Diheteropogon hagerupii KM578110.1 1 Diheteropogon amplectens KM577987.1 7 Diheteropogon amplectens KM577986.1

8 0.97 Schizachyrium sanguineum KM578100.1 1 1 Schizachyrium sanguineum KM577961.1 9 0.94 Schizachyrium sanguineum KM577931.1 1 Schizachyrium exile KM577969.1 1 10 Schizachyrium sanguineum KM577932.1 1 Schizachyrium sanguineum KM578098.1 11 1 Schizachyrium sanguineum KM577960.1 12 0.33 Schizachyrium brevifolium KM578097.1 0.21 0.85 Schizachyrium brevifolium KM578096.1 13 1 Schizachyrium brevifolium KM578095.1 14 Schizachyrium sanguineum KM578099.1 1 Andropogon gayanus KM577982.1 15 0.45 Andropogon gayanus KM577981.1 Andropogon chinensis KM578053.1 0.2 16 0.21 1 Andropogon gerardii KM577923.1 1 Andropogon hallii JQ951705.1 17 0.52 Schizachyrium sanguineum JQ951704.1

18 1 Andropogon perligulatus KM577925.1 Andropogon perligulatus KM577924.1 1 19 1 Hyparrhenia diplandra KM578107.1 20 1 Hyparrhenia diplandra KM578079.1 Hyparrhenia diplandra KM578078.1 KM577983.1 21 0.28 1 Andropogon hallii 1 Andropogon gerardii KM577922.1 22 1 Andropogon virginicus KM578001.1 23 Andropogon eucomus KM577921.1 1 Spodiopogon sibiricus KM578102.1

24 0.23 Spodiopogon sibiricus KM578101.1 0.64 Themeda triandra KM578044.1 25 0.62 Themeda triandra KM578030.1 26 1 Themeda triandra KM578045.1 1 Themeda triandra KM578032.1 0.35 27 1 Themeda triandra KM578031.1 0.92 Themeda villosa KM578106.1 28 1 Themeda arundinacea KM578104.1 29 Themeda villosa KM578105.1 1 Heteropogon triticeus KM578077.1 30 Heteropogon triticeus KM578076.1 0.34 Capillipedium spicigerum KM578015.1 31 0.97 Capillipedium spicigerum KM577926.1 1 Bothriochloa bladhii KM578021.1 32 KM578014.1 0.99 0.95 Capillipedium spicigerum 33 Capillipedium spicigerum KM577927.1 0.11 Bothriochloa bladhii KM578002.1 34 1 Dichanthium caricosum KM578068.1 1 Dichanthium aristatum KM577946.1 35 Capillipedium assimile KM578062.1 Bothriochloa insculpta KM577997.1 36 1 0.08 0.99 1 Bothriochloa insculpta KM577996.1 Bothriochloa insculpta KM578003.1 37 0.95 1 Bothriochloa insculpta KM577995.1 0.11 38 0.43 Bothriochloa insculpta KM578004.1 39 0.04 Bothriochloa decipiens KM578009.1 1 Bothriochloa woodrovii KM578007.1 40 Bothriochloa woodrovii KM578006.1 Bothriochloa exaristata KM578024.1 41 0.52 0.21 Bothriochloa bladhii KM578010.1 42 0.21 Dichanthium annulatum KM577945.1 1 Dichanthium annulatum KM577984.1 43 0.34 Dichanthium annulatum JQ951701.1 1 0.84 Dichanthium annulatum KM577985.1 1 44 Dichanthium annulatum KM578115.1 45 Bothriochloa bladhii KM578011.1 1 1 Bothriochloa exaristata KM578023.1 46 1 Bothriochloa exaristata KM578022.1 0.36 Bothriochloa woodrovii KM578008.1 47 0.81 Dichanthium foveolatum KM578108.1 48 Iseilema macratherum KM577992.1 1 Cymbopogon obtectus KM578017.1

49 0.26 Cymbopogon obtectus KM578016.1 0.21 Cymbopogon refractus KM577944.1 50 1 Cymbopogon obtectus KM577941.1 1 Cymbopogon flexuosus KM577940.1 51 1 Cymbopogon flexuosus JQ951700.1 1 52 Cymbopogon citratus KM578066.1 0.99 Cymbopogon martinii KM577975.1 53 1 Cymbopogon martinii KM577973.1 54 Cymbopogon martinii KM577974.1 0.21 Cymbopogon distans KM577936.1 55 0.36 0.21 Cymbopogon distans KM577934.1 0.96 Cymbopogon distans KM577938.1 56 1 Cymbopogon distans KM577939.1 1 Cymbopogon distans KM577935.1 57 0.99 1 0.82 1 Cymbopogon jwarancusa subsp. olivieri KM577977.1 Cymbopogon jwarancusa subsp. olivieri KM577976.1 58 1 Cymbopogon citratus KM578067.1 59 Cymbopogon commutatus KM577942.1

60 Cymbopogon commutatus KM577943.1 0.34 Sorghum propinquum KR494008.1 1 Sorghum bicolor JQ951703.1 0.11 Sorghum bicolor XM_021453233.1 0.04 Sorghum halepense KR494020.1 0.1 Sorghum halepense KR494021.1 0.52 Sorghum halepense KR494018.1 0.36 10.11 Sorghum halepense KR494017.1 Sorghum bicolor KM578109.1 0.21 Sorghum propinquum KR494007.1

0.94 PDF SorghumProof macrospermum KR494012.1 1 1 Sorghum macrospermum KR494011.1 Sorghum laxiflorum KR494014.1 1 0.25 Lasiorhachis perrieri NOP140 Lasiorhachis hildebrandtii LRK2008 1 1 Sorghum laxiflorum KR494013.1 Sorghum macrospermum KR494009.1 1 Pseudopogonatherum quadrinerve KM578074.1 1 Pseudopogonatherum quadrinerve KM578073.1 0.94 Pseudopogonatherum quadrinerve KM578072.1 0.12 Eulalia villosa KM577972.1 0.56 Andropterum stolzii KM577979.1 1 Andropterum stolzii KM577978.1 0.38 Andropterum stolzii KM577980.1 Andropterum stolzii JQ951698.1 1 Phacelurus digitatus KM577959.1 Phacelurus digitatus JQ951702.1 0.16 Sorghum exstans KR493995.1 0.15 Sarga plumosa KR493991.1 Sarga intrans KR493997.1 0.990.15 Sorghum matarankense KR493989.1 0.34 Sarga intrans KR493996.1 0.99 Sarga angusta KR494004.1 0.35 Sarga stipoidea KR494005.1 0.99 Sarga angusta KR494003.1

0.38 Sarga plumosa KR493992.1 1 Sorghum brachypodum KR494000.1 1 Sorghum brachypodum KR493999.1 0.94 Sorghum exstans KR493994.1 1 Sorghum interjectum KR493987.1 1 Sorghum interjectum KR493986.1 0.37 0.98 Sarga plumosa KR493993.1 0.98 Sorghum ecarinatum KR493998.1 Sorghum matarankense KR493988.1 1 Sorghum ecarinatum KR494025.1 0.34 Sarga leioclada KR494001.1 1 0.98 Sarga plumosa KR493990.1 Sarga leioclada KR494002.1 Sarga purpureosericea KR493985.1 1 Saccharum villosum KP242921.1 0.14 Saccharum villosum KP242919.1 0.15 Miscanthus ecklonii KM578012.1 KP242904.1 0.161 Saccharum asperum Saccharum angustifolium KP242897.1 Saccharum asperum KP242906.1 0.81 1 1 Saccharum narenga KM578093.1 0.98 Saccharum narenga KM578092.1 1 Saccharum narenga KM578091.1 0.7 Saccharum officinarum KP242908.1 Saccharum officinarum KP242907.1 KP242920.1 0.31 1 Saccharum villosum 0.19 0.23 Saccharum villosum KP242918.1 0.2 Saccharum asperum KP242905.1

10.81 Saccharum villosum KP242917.1 Saccharum villosum KP242915.1 0.2 0.81 Saccharum angustifolium KP242896.1 1 Miscanthus sinensis KM577994.1 0.89 Saccharum narenga KM578094.1 0.2 Miscanthus ecklonii KM578013.1 Pseudosorghum fasciculare KM578089.1 0.87 Miscanthus sinensis KM577993.1 0.97 Microstegium vimineum KM578051.1 0.38 Microstegium vimineum KM578049.1 0.68 Microstegium vimineum KM578047.1 1 Microstegium vimineum KM578052.1 1 Microstegium vimineum KM578050.1 0.27 Microstegium vimineum KM578048.1 1 Kerriochloa siamensis KM578087.1 0.16 Kerriochloa siamensis KM578086.1 1 Polytrias indica KM578000.1 1 Polytrias indica KM577999.1 0.74 Eulalia aurea KM578027.1 0.97 0.21 Ischaemum afrum KM577954.1 1 Ischaemum afrum KM577952.1 0.7 0.32 0.21 Ischaemum afrum KM577953.1 Ischaemum afrum KM577951.1 Sorghastrum nutans KM577963.1 Sehima nervosum KM577962.1 1 Dimeria kurzii KM578071.1 1 Dimeria chloridiformis KM578070.1 0.36 Dimeria chloridiformis KM578069.1 0.93 KM578085.1 0.36 Ischaemum muticum 0.78 Ischaemum santapaui KM577957.1 1 Ischaemum santapaui KM577956.1 1 1 Ischaemum rugosum KM578113.1 Ischaemum santapaui KM577955.1 1 Polytrias indica KM578084.1 Polytrias indica KM578083.1 0.76 1 Arthraxon prionodes KM578036.1 1 Arthraxon prionodes KM578035.1 1 Arthraxon prionodes KM578034.1 Arthraxon lanceolatus KM578061.1 1 Chrysopogon gryllus KM577928.1 0.07 1 Chrysopogon gryllus JQ951699.1 0.99 Chrysopogon serrulatus KM577988.1 KM578038.1 1 1 Chrysopogon zizanioides Chrysopogon zizanioides KM578037.1 1 Chrysopogon gryllus KM577929.1 Thelepogon elegans KM578103.1 0.17 1 Rottboellia cochinchinensis KM577971.1 1 Rottboellia cochinchinensis KM577970.1 1 Chasmopodium caudatum KM578046.1 0.24 Coix gasteenii KM578065.1 1 Tripidium arundinaceum KM578090.1 0.72 Tripidium ravennae KM578042.1 0.32 1 Zea mays NM 001360287.1 Tripsacum dactyloides KM577967.1 1 Polytoca massiei KM578064.1 1 Polytoca massiei KM578063.1 0.94 Polytoca gigantea KP242922.1 Polytoca wallichiana KP242923.1 0.83 0.67 Apocopis siamensis KM578060.1 1 Apocopis siamensis KM578059.1 Apocopis siamensis KM578058.1 1 1 Apocopis intermedius KM578057.1 1 1 Apocopis intermedius KM578056.1 Apocopis courtallumensis KM578054.1 0.79 Apocopis intermedius KM578055.1 1 Pogonatherum crinitum KM578088.1 1 Pogonatherum paniceum KM577998.1 1 Imperata tenuis KT449513.1 1 Imperata brasiliensis KT449512.1 Imperata cylindrica KM578082.1 0.34 Eriochrysis cayennensis KT449493.1 1 0.98 Eriochrysis cayennensis KT449492.1 0.99 Eriochrysis cayennensis KT449504.1 KT449510.1 1 Eriochrysis villosa 0.21 Eriochrysis laxa KT449502.1 0.98 0.2 Eriochrysis laxa KT449501.1 KT449498.1 1 Eriochrysis laxa Eriochrysis holcoides KT449494.1 Eriochrysis pallida KM577947.1 1 Zea mays XM_008672356.3 1 Tripsacum dactyloides KM577968.1 Phacelurus huillensis KM577958.1 Rottboellia lepidura JQ951697.1 0.93 Arundinella hirta KM578029.1 1 Arundinella hirta KM578028.1 Arundinella nepalensis KM578043.1 Botanical Journal of the Linnean Society Page 43 of 47 Botanical Journal of the Linnean Society E − ep2−8

0.96 Bothriochloa bladhii KM577791.1

1 0.95 Bothriochloa bladhii KM577790.1 0.33 Bothriochloa bladhii KM577800.1 1 2 Bothriochloa ischaemum KM577777.1 1 Bothriochloa bladhii KM577817.1

3 0.83 Bothriochloa insculpta KM577797.1 1 Bothriochloa insculpta KM577798.1 4 0.01 subst./site 0.96 Bothriochloa insculpta KM577784.1 0.96 5 0.97 Bothriochloa insculpta KM577783.1 Bothriochloa insculpta KM577782.1 6 0.15 Capillipedium spicigerum KM577812.1

7 0.14 Capillipedium spicigerum KM577811.1 0.13 Bothriochloa bladhii KM577799.1 8 Capillipedium spicigerum KM577712.1 1 1 Bothriochloa decipiens KM577802.1 9 0.98 Bothriochloa macra KM577796.1 0.96 Bothriochloa exaristata KM577819.1 10 0.34 0.99 Bothriochloa barbinodis KM577794.1 11 Bothriochloa barbinodis KM577793.1 0.21 Bothriochloa woodrovii KM577801.1 0.91 12 0.96 Bothriochloa decipiens KM577804.1 1 Bothriochloa decipiens KM577803.1 13 0.24 1 Bothriochloa decipiens KM577805.1 Bothriochloa macra KM577795.1 14 1 Capillipedium spicigerum KM577711.1 15 1 Dichanthium caricosum KM577861.1 0.26 Dichanthium aristatum KM577726.1 16 Capillipedium assimile KM577855.1

17 1 Iseilema macratherum KM577776.1 Iseilema macratherum KM577775.1 0.46 18 0.33 Dichanthium annulatum KM577766.1 0.92 Dichanthium annulatum JQ951688.1 19 0.66 Dichanthium annulatum KM577725.1 20 0.84 1 Dichanthium annulatum KM577912.1 Bothriochloa ischaemum KM577829.1 21 0.99 Dichanthium foveolatum KM577904.1 1 1 Dichanthium foveolatum KM577903.1 22 0.34 Dichanthium foveolatum KM577905.1 23 Dichanthium foveolatum KM577902.1 1 Bothriochloa exaristata KM577820.1 24 0.67 Bothriochloa barbinodis KM577792.1 0.2 Themeda triandra KM577841.1 25 0.2 Themeda triandra KM577840.1 26 1 Themeda triandra KM577827.1 Themeda triandra KM577828.1 1 0.99 27 0.89 Themeda villosa KM577899.1 0.99 Themeda arundinacea KM577897.1 28 Themeda villosa KM577898.1

29 0.35 Heteropogon triticeus KM577873.1 1 Heteropogon triticeus KM577872.1

30 1 Heteropogon triticeus KM577874.1 Heteropogon triticeus KM577871.1 31 0.15 Cymbopogon citratus KM577860.1 0.16 Cymbopogon flexuosus KM577719.1 32 Cymbopogon obtectus KM577720.1 0.990.14 33 0.74 Cymbopogon flexuosus JQ951689.1 0.99 Cymbopogon obtectus KM577813.1 34 0.34 Cymbopogon martinii KM577761.1 1 Cymbopogon martinii KM577760.1 35 0.54 Cymbopogon martinii KM577762.1

36 0.73 Cymbopogon jwarancusa subsp. olivieri KM577763.1 0.82 Cymbopogon commutatus KM577721.1 1 37 1 Cymbopogon citratus KM577859.1

38 Cymbopogon citratus KM577858.1 1 Cymbopogon commutatus KM577723.1 39 0.32 Cymbopogon commutatus KM577722.1 1 Pseudopogonatherum quadrinerve KM577869.1 40 0.91 Pseudopogonatherum quadrinerve KM577868.1 41 1 Eulalia villosa KM577759.1 1 Pseudopogonatherum quadrinerve KM577867.1 42 Pseudopogonatherum quadrinerve KM577866.1 0.33 Andropogon chinensis KM577850.1 43 0.85 Andropogon chinensis KM577848.1

44 0.16 Andropogon chinensis KM577849.1 1 Andropogon perligulatus KM577710.1 45 0.15 Andropogon perligulatus KM577709.1 1 Andropogon gerardii KM577708.1 46 0.470.82 Andropogon gerardii KM577707.1 Schizachyrium sanguineum JQ951695.1 47 Andropogon gayanus KM577765.1

48 1 0.15 Andropogon glomeratus KM577919.1 0.37 0.15 Andropogon glomeratus KM577917.1 Andropogon glomeratus KM577920.1 49 0.151 Andropogon glomeratus KM577916.1 0.9 50 Andropogon glomeratus KM577918.1 51 1 Andropogon virginicus KM577789.1 1 Andropogon eucomus KM577706.1

52 0.98 Andropogon eucomus KM577705.1 0.97 Schizachyrium sanguineum KM577746.1 53 1 Schizachyrium sanguineum KM577745.1 54 0.38 Schizachyrium sanguineum KM577747.1 1 Schizachyrium sanguineum KM577894.1 1 55 Schizachyrium brevifolium KM577893.1 Schizachyrium sanguineum KM577748.1 1 1 56 Schizachyrium sanguineum KM577717.1

57 1 Schizachyrium exile KM577757.1 Schizachyrium sanguineum KM577716.1

58 0.99 Hyparrhenia hirta KM577908.1

0.21 1 Hyparrhenia hirta KM577734.1 59 0.92 Hyparrhenia hirta KM577913.1 0.82 Hyparrhenia hirta KM577914.1 60 0.99 Hyparrhenia hirta KM577732.1 0.2 Hyparrhenia hirta KM577915.1 0.98 0.2 Hyparrhenia hirta KM577822.1

0.99 Hyparrhenia hirta KM577733.1 Hyparrhenia hirta KM577821.1 1 0.75 Hyparrhenia hirta KM577735.1 1 Hyparrhenia rufa KM577876.1 1 Hyparrhenia rufa KM577875.1

0.2 1 Hyparrhenia diplandra KM577901.1 Hyparrhenia diplandra KM577900.1 Andropogon hallii JQ951694.1 1 Diheteropogon hagerupii KM577907.1 Diheteropogon amplectens KM577768.1 0.99 Saccharum giganteum KP242955.1 0.13 Saccharum giganteum KP242953.1 0.05 Saccharum villosum KP242958.1 0.99 Saccharum villosum KP242970.1 0.12 Saccharum villosum KP242968.1 1 Saccharum asperum KP242951.1 KP242949.1 0.121 Saccharum asperum 1 Saccharum asperum KP242947.1

0.95 Saccharum asperum KP242945.1 Saccharum angustifolium KP242935.1 1 1 Miscanthus ecklonii KM577810.1 PDF Proof 0.98 Miscanthus ecklonii KM577809.1 Saccharum narenga KM577892.1 0.43 0.47 Saccharum narenga KM577891.1

0.77 Pseudosorghum fasciculare KM577886.1 0.63 Miscanthus sinensis KM577779.1 0.99 Miscanthus sinensis KM577778.1 Miscanthus sinensis KM577780.1 0.34 Saccharum villosum KP242975.1 0.97 Saccharum villosum KP242959.1 0.09 KP242963.1 0.83 Saccharum villosum Saccharum asperum KP242950.1 0.02 1 Miscanthus ecklonii KM577807.1 1 Miscanthus ecklonii KM577806.1 0.1 0.1 Miscanthus ecklonii KM577808.1 Saccharum asperum KP242952.1 0.33 0.97 Saccharum angustifolium KP242940.1 10.1 Saccharum angustifolium KP242936.1 Saccharum giganteum KP242954.1 1 1 Saccharum asperum KP242948.1 Saccharum asperum KP242946.1 Miscanthus sinensis KM577781.1 1 Saccharum officinarum KP242957.1 Saccharum officinarum KP242956.1 0.17 0.99 Ischaemum muticum KM577883.1 1 Ischaemum muticum KM577882.1 KM577881.1 1 Ischaemum muticum 0.9 Polytrias indica KM577880.1 1 Polytrias indica KM577879.1 Polytrias indica KM577878.1 1 1 Dimeria ornithopoda KM577864.1 1 Dimeria chloridiformis KM577863.1

1 Dimeria chloridiformis KM577862.1 1 Ischaemum rugosum KM577910.1 1 Ischaemum santapaui KM577738.1 Ischaemum santapaui KM577737.1 0.14 Sorghum halepense KR493963.1 0.18 Sorghum halepense KR493962.1 0.17 0.14 Sorghum halepense KR493964.1 0.77 Sorghum propinquum KR493932.1 0.03 0.33 Sorghum bicolor XM_021453233.1 1 0.68 Sorghum bicolor JQ951693.1 Sorghum halepense KR493967.1 0.34 Sorghum propinquum KR493933.1 KR493960.1 0.5 0.99 Sorghum macrospermum Sorghum macrospermum KR493957.1

0.49 0.72 Sorghum laxiflorum KR493956.1 Sorghum laxiflorum KR493955.1 0.97 Lasiorhachis perrieri NOP140 1 Lasiorhachis hildebrandtii LRK2008 KR493958.1 0.95 0.76 Sorghum macrospermum 0.47 Sorghum laxiflorum KR493953.1 0.61 0.83 Sorghum macrospermum KR493959.1 Sorghum laxiflorum KR493954.1 1 Andropterum stolzii KM577764.1 Andropterum stolzii JQ951690.1 1 Microstegium vimineum KM577847.1 1 Microstegium vimineum KM577845.1 1 Microstegium vimineum KM577846.1 KM577844.1 0.19 Microstegium vimineum 0.98 Polytrias indica KM577788.1 1 Polytrias indica KM577787.1 Eulalia aurea KT449542.1 0.96 1 Sehima nervosum KM577750.1 0.66 Sehima nervosum KM577749.1 0.72 Ischaemum afrum KM577736.1 KM577911.1 0.19 1 Sorghastrum elliottii Sorghastrum nutans KM577751.1 Kerriochloa siamensis KM577884.1 0.36 Tripidium arundinaceum KM577890.1 0.74 Tripidium arundinaceum KM577887.1 1 Tripidium arundinaceum KM577889.1 0.62 Tripidium arundinaceum KM577888.1 Tripidium ravennae KM577837.1 0.84 1 Zea mays NM 001360287.1 0.99 Zea mays BT041563.1 1 EU949885.1 0.21 Zea mays Tripsacum dactyloides KM577755.1 0.01 1 Phacelurus huillensis KM577740.1 0.96 Phacelurus huillensis KM577739.1 Rottboellia lepidura JQ951692.1 0.18 Eriochrysis pallida KM577730.1 0.15 Eriochrysis pallida KM577729.1 Eriochrysis pallida KM577728.1 0.990.15 Eriochrysis pallida KM577727.1 0.21 Eriochrysis pallida KM577731.1 0.96 Eriochrysis holcoides KT449521.1 0.2 Eriochrysis holcoides KT449519.1 Eriochrysis warmingiana KT449541.1 1 0.34 Eriochrysis cayennensis KT449532.1 1 Eriochrysis cayennensis KT449515.1 Eriochrysis cayennensis KT449516.1 0.98 1 Eriochrysis cayennensis KT449514.1 0.97 Eriochrysis villosa KT449536.1 Eriochrysis laxa KT449530.1 1 Apocopis siamensis KM577853.1 0.58 1 Apocopis siamensis KM577852.1 1 Germainia capitata KM577870.1 1 Apocopis intermedius KM577851.1 0.34 Pogonatherum crinitum KM577885.1 1 Pogonatherum paniceum KM577785.1 1 Pogonatherum paniceum KM577786.1 0.34 Imperata brasiliensis KT449543.1 0.71 1 Imperata cylindrica KM577877.1 Imperata tenuis KT449544.1 1 Apluda mutica KM577826.1 Apluda mutica KM577825.1 0.02 0.98 Sorghum exstans KR493943.1 0.52 0.15 Sorghum exstans KR493942.1 0.15 Sarga intrans KR493940.1 KR493952.1 0.970.15 Sarga plumosa Sorghum matarankense KR493946.1 0.82 Sarga intrans KR493941.1 0.12 Sarga purpureosericea KR493937.1 0.96 Sorghum matarankense KR493947.1 0.14 Sorghum ecarinatum KR493939.1 Sorghum brachypodum KR493945.1 0.03 0.97 0.980.14 Sorghum brachypodum KR493944.1 Sarga angusta KR493935.1 0.34 Sarga plumosa KR493951.1 10.97 Sorghum ecarinatum KR493938.1 Sarga leioclada KR493936.1 Sarga stipoidea KR493934.1 1 Arthraxon prionodes KM577831.1 1 Arthraxon prionodes KM577830.1 0.26 Arthraxon lanceolatus KM577854.1 0.06 1 Polytoca gigantea KP242976.1 Polytoca massiei KM577856.1 1 Chrysopogon zizanioides KM577833.1 0.53 Chrysopogon zizanioides KM577832.1 1 Chrysopogon serrulatus KM577769.1 1 Chrysopogon gryllus KM577715.1 1 Chrysopogon gryllus KM577713.1 0.94 1 Chrysopogon gryllus JQ951687.1 Chrysopogon gryllus KM577714.1 1 Thelepogon elegans KM577896.1 0.08 Thelepogon elegans KM577895.1 KM577843.1 0.28 0.89 Chasmopodium caudatum 1 Chasmopodium caudatum KM577842.1 1 Rottboellia cochinchinensis KM577758.1 Coix gasteenii KM577857.1 0.15 Phacelurus digitatus KM577743.1 0.2 Phacelurus digitatus KM577742.1 Phacelurus digitatus KM577744.1 0.151 Phacelurus digitatus JQ951691.1 1 Phacelurus digitatus KM577741.1 Zea mays XM_008672356.3 1 Zea mays AY104462.2 Tripsacum dactyloides KM577756.1 Polytoca wallichiana KP242977.1 0.97 Arundinella nepalensis KM577839.1 1 Arundinella nepalensis KM577838.1 1 Arundinella hirta KM577824.1 Arundinella hirta KM577823.1 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 44 of 47 F − floricaula

0.98 Zea mays AY789603.1 1 0.14 Zea mays subsp. parviglumis AY789039.1 0.01 subst./site 0.15 Zea mays subsp. parviglumis AY789048.1 AY789598.1 2 0.18 Zea diploperennis Zea mays subsp. parviglumis AY789036.1 0.77 3 Zea mays subsp. parviglumis AY789037.1 0.2 Zea luxurians AY789597.1 4 0.82 Zea mays subsp. parviglumis AY789043.1 0.18 Zea mays subsp. parviglumis AY789042.1 0.64 5 Zea mays subsp. parviglumis AY789044.1

6 0.7 Zea mays subsp. parviglumis AY789047.1 0.340.54 Zea mays subsp. parviglumis AY789041.1 7 Zea mays subsp. parviglumis AY789040.1 1 Zea mays subsp. parviglumis AY789045.1 8 1 Tripsacum zopilotense AY789602.1 9 1 AY789601.1 Tripsacum andersonii AY789600.1

10 0.98 PDF Proof1 Tripsacum dactyloides AY789596.1 0.63 Tripsacum latifolium AY789592.1 11 1 Tripsacum zopilotense AY789591.1 0.98 Tripsacum floridanum AY789590.1 0.47 12 0.92 1 Zea mays NM 001111731.1 13 Zea luxurians AY789594.1 Elionurus muticus AY789605.1

14 0.26 Polytoca gigantea AY789614.1 Phacelurus digitatus AY789613.1 15 1 Sorghum bicolor XM_021462255.1 0.43 Sorghum bicolor AY789623.1 0.36 16 0.79 Lasiorhachis perrieri NOP140 Sarga versicolor AY789621.1 17 0.31 1 Cleistachne sorghoides AY789619.1 0.31 Saccharum officinarum AY789622.1 18 0.51 Apluda mutica AY789607.1 0.26 19 0.37 Ischaemum afrum AY789620.1

0.24 1 Coix lacryma−jobi AY789624.1 20 Coix aquatica AY789609.1 21 Elionurus tripsacoides AY789604.1 1 Rottboellia selloana AY789608.1 22 0.38 0.66 Rottboellia aurita AY789606.1 Chrysopogon fulvus AY789611.1 23 1 Capillipedium parviflorum AY789618.1 0.97 Bothriochloa bladhii AY789616.1 24 0.97 Cymbopogon distans AY789610.1 25 0.34 Cymbopogon flexuosus AY789617.1 0.68 Heteropogon contortus AY789612.1 26 Hyparrhenia hirta AY789615.1

27 Arundinella hirta AY789625.1 28 Botanical Journal of the Linnean Society 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 45 of 47 Botanical Journal of the Linnean Society G − GBSSI

0.07 Zea mays subsp. parviglumis EF539712.1

1 0.01 Zea mays subsp. parviglumis EF539686.1 0.07 Zea mays subsp. parviglumis EF539719.1 2 0.01 Zea mays subsp. parviglumis EF539674.1 0.01 subst./site 0.09 Zea mexicana FJ708436.1 3 Zea mays subsp. parviglumis EF539724.1 0.07 4 0.95 Zea diploperennis AF329737.1 0.33 Zea diploperennis AF329736.1 5 0.94 Zea perennis AF329744.1 0.06 Zea perennis AF329752.1 6 0.49 0.92 Zea mays subsp. parviglumis EF539679.1 7 Zea mays subsp. parviglumis EF539649.1 0.5 Zea mays subsp. parviglumis EF539699.1 8 0.71 Zea mexicana AF079260.1 EF539722.1 0.15 0.53 Zea mays subsp. parviglumis 9 0.44 Zea mays X03935.1

10 Zea mays BT016675.1 0.27 Zea mays subsp. parviglumis FJ708473.1 0.23 11 0 Zea mexicana FJ708427.1 0.99 Zea mays subsp. parviglumis EF539702.1 12 Zea mays subsp. parviglumis AF079261.1 0.98 Zea mays subsp. parviglumis EF539683.1 13 0.04 Zea mays subsp. parviglumis EF539673.1 14 Zea mays AY109531.1 0.24 Zea mays subsp. parviglumis EF539713.1 15 0 0.46 Zea mays subsp. parviglumis EF539711.1 0.32 Zea mays subsp. parviglumis EF539708.1 16 Zea mays AF267643.1 0.44 17 0.18 Zea mays XM_023301364.1 0.19 0.18 Zea mays AF488416.1 EF539685.1 18 0.1 Zea mays subsp. parviglumis 0 Zea mays subsp. parviglumis EF539671.1 19 0 Zea luxurians FJ708445.1

20 0.04 Zea perennis AF329755.1 Zea diploperennis AF329739.1 0.88 Zea mays subsp. parviglumis EF539723.1 21 0.02 0.04 Zea mays subsp. parviglumis EF539703.1 22 0 Zea mays subsp. parviglumis EF539659.1 0.04 Zea mays subsp. parviglumis EF539720.1 23 0.58 Zea mays subsp. parviglumis EF539696.1

24 0.04 Zea mays subsp. parviglumis EF539705.1 Zea mays subsp. parviglumis EF539665.1 25 1 Zea perennis AF329754.1 1 Zea perennis AF329749.1 26 0.96 Zea perennis AF329746.1 27 0.23 Zea perennis AF329748.1 0.35 Zea perennis AF329756.1 0.54 28 Zea diploperennis AF329743.1 0.84 Diheteropogon amplectens JN560725.1 29 0.56 Andropogon gayanus JN560722.1 30 0.28 0.52 Andropogon gerardii AF079235.1 0.99 Schizachyrium scoparium AF079256.1 31 Hyparrhenia hirta AF079254.1 0.52 Miscanthus floridulus AF446083.1 32 Microstegium nudum AF446082.1

33 0.5 Cymbopogon obtectus AF079246.1 0.99 Cymbopogon flexuosus AF079243.1 0.82 34 0.04 Cymbopogon refractus AF079249.1 0.96 Cymbopogon martinii AF079245.1 35 1 Cymbopogon schoenanthus AF079250.1 0.99 Cymbopogon jwarancusa AF079244.1 36 AF079248.1 0.79 0.96 Cymbopogon pospischilii 37 Cymbopogon commutatus AF079247.1 0.88 Sehima nervosum JN560734.1 38 Heteropogon contortus AF079253.1 0.41 PDF Proof 39 1 Dichanthium annulatum KC469421.1 1 Dichanthium annulatum KC469420.1

40 1 Dichanthium annulatum KC469419.1 0.98 Dichanthium annulatum KC469418.1 41 1 Capillipedium parviflorum AF079239.1 0.89 Bothriochloa bladhii AF079238.1 42 Bothriochloa bladhii KC469417.1

43 0.19 Sorghum halepense KC469387.1 0.18 Sorghum halepense KC469386.1 Sarga versicolor KC469369.1 44 0.82 0.85 Sorghum × drummondii KC469358.1 0.18 45 Sarga leioclada KC469371.1 0.14 Sorghum virgatum KC469381.1 46 0.950.19 Sorghum bicolor U23945.1 47 Sorghum bicolor AF488412.1 Sarga leioclada KC469370.1 48 Sorghum halepense KC469364.1 1 0.33 49 0.96 Sorghum halepense KC469363.1 0.86 Sorghum halepense KC469366.1 0.48 50 1 Sorghum halepense KC469362.1 0.94 Sorghum halepense KC469360.1 51 Sorghum halepense KC469361.1

52 0.98 Lasiorhachis perrieri NOP140 0.04 Lasiorhachis hildebrandtii LRK2008

53 0.44 0.19 Sorghum macrospermum KC469357.1 0.84 Sorghum macrospermum KC469354.1 54 0.19 Sorghum macrospermum KC469356.1 1 55 Sorghum macrospermum KC469353.1 1 Sorghum laxiflorum KC469378.1 56 0.52 Sorghum laxiflorum KC469376.1 0.94 Cleistachne sorghoides KC469412.1 57 1 Cleistachne sorghoides AF446081.1

58 Cleistachne sorghoides KC469413.1 0.2 Sorghum exstans KC469352.1

59 0.2 Sorghum interjectum KC469350.1 Sarga angusta KC469346.1 0.95 0.96 60 Sarga angusta KC469344.1 0.41 0.12 Sarga intrans KC469351.1 0.34 Sarga timorensis KC469349.1 0.91 Sarga timorensis KC469348.1 0.12 Sarga timorensis KC469347.1 0.34 Sorghum matarankense KC469331.1 0.91 Sorghum matarankense KC469329.1 0.06 Sorghum matarankense KC469328.1 0.25 Sorghum nitidum EF600040.1 0.84 Sarga leioclada EF600038.1

0.19 0.15 Sarga stipoidea KC469340.1 0.15 Sarga stipoidea KC469337.1 0.15 Sarga stipoidea KC469339.1 10.15 Sarga stipoidea KC469336.1 1 0.86 Sarga stipoidea KC469342.1 0.37 Sorghum matarankense KC469335.1 Sorghum matarankense KC469333.1 0.34 Sorghum nitidum KC469327.1 0.06 1 Sorghum nitidum KC469325.1 Sorghum nitidum KC469324.1 Saccharum officinarum AF446084.1 0.98 Microstegium vimineum KC469401.1 1 Microstegium vimineum KC469400.1 1 Microstegium vimineum KC469399.1 1 Microstegium vimineum KC469398.1 Microstegium vimineum KC469397.1 0.98 0.53 0.33 Sorghastrum nutans KC469415.1 0.88 Sorghastrum nutans KC469414.1 1 Sorghastrum nutans AF079257.1 1 Cleistachne sorghoides KC469411.1 Cleistachne sorghoides KC469410.1 0.33 Chrysopogon serrulatus KC469407.1 0.97 Chrysopogon serrulatus KC469405.1 0.34 Chrysopogon serrulatus KC469406.1 1 Chrysopogon serrulatus KC469404.1 0.28 0.99 Chrysopogon serrulatus KC469409.1 1 Chrysopogon fulvus AF079240.1 0.53 Chrysopogon gryllus AF079241.1 Eulalia villosa JN560727.1 Coix lacryma−jobi EU041672.1 0.58 Coix lacryma−jobi var. lacryma−jobi AB700120.1 1 1 Coix aquatica AF079242.1 Phacelurus digitatus AF318769.1 0.96 Dimeria lawsonii JN560726.1 Ischaemum santapaui AF079255.1

0.88 1 Hemarthria compressa JN560729.1 0.63 Hemarthria altissima JN560728.1 1 Rottboellia selloana JN560724.1 Rottboellia afraurita JN560723.1 1 rottboellioides JN560733.1 1 Heteropholis sulcata JN560730.1 Oxyrhachis gracillima JN560731.1 1 Arundinella nepalensis AF079237.1 Arundinella hirta AF079236.1 Botanical Journal of the Linnean Society Botanical Journal of the Linnean Society Page 46 of 47 H − phyB

0.96 Sorghum bicolor AY466085.1 1 0.13 Sorghum bicolor AF182394.1 0.01 subst./site 0.13 Sorghum arundinaceum AY466097.1 AY466090.1 2 0.340.11 Sorghum bicolor Sorghum bicolor AY466087.1 0.4 3 Sorghum bicolor AY466088.1 0.2 Sorghum halepense AF137326.1 4 1 Sorghum arundinaceum AY466093.1 0.2 Sorghum propinquum AY466100.1 5 1 Sorghum arundinaceum AY466098.1

6 1 Lasiorhachis perrieri NOP140 0.24 Lasiorhachis hildebrandtii LRK2008 7 0.3 Dimeria lawsonii JN560782.2

8 0.35 Ischaemum afrum AF443812.1 0.29 Sehima nervosum JN560789.2 9 Apluda mutica AF443799.1 0.06 0.54 Schizachyrium scoparium AF443817.1 10 0.44 Hyparrhenia hirta AF443811.1 0.53 Diheteropogon amplectens JN560781.2 PDF Proof1 11 Andropogon ternarius AF443798.1 12 0.29 Andropogon gayanus JN560778.2 0.07 Dichanthium aristatum AF443808.1

13 0.16 Heteropogon contortus AF443810.1 Cymbopogon flexuosus AF443807.1 14 0.02 0.82 Phacelurus huillensis JN560787.2 1 Rottboellia afraurita JN560779.2 15 0.5 Rottboellia selloana AF443805.1 Hemarthria compressa JN560785.2 16 0.36 1 Hemarthria altissima JN560784.2 0.22 Elionurus muticus AF443809.1 17 0.1 1 Zea mays NM 001174606.1 18 Zea mays DQ307620.1 0.09 Coix aquatica AF443806.1 0.04 19 0.99 Zea mays NM 001176339.1 20 1 Zea mays AF137332.1 1 Zea mays DQ307579.1 21 Tripsacum dactyloides AF443818.1 0.22 0.88 Eulalia villosa JN560783.2 22 0.98 Cleistachne sorghoides AF443804.1 0.18 Microstegium nudum AF443813.1 23 Miscanthus sinensis AF137311.1 0.1 24 1 Chrysopogon gryllus AF443803.1 0.25 Chrysopogon fulvus AF443802.1

25 0.47 digitatum JN560790.2 0.47 Rhytachne rottboellioides JN560788.2 26 Oxyrhachis gracillima JN560786.2 1 Bothriochloa bladhii AF443800.1 27 Capillipedium parviflorum AF137296.1

28 0.89 Phacelurus digitatus AF443815.1 Polytoca gigantea AF443801.1 29 Arundinella hirta AF137293.1 30 Botanical Journal of the Linnean Society 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 Page 47 of 47 Botanical Journal of the Linnean Society I − rep1

0.36 Hyparrhenia hirta KM578736.1 1 1 Hyparrhenia hirta KM578667.1 Hyparrhenia hirta KM578579.1 1 2 0.87 Hyparrhenia hirta KM578578.1 0.79 Hyparrhenia hirta KM578577.1 3 0.01 subst./site 1 Hyparrhenia hirta KM578740.1

4 0.97 Hyparrhenia rufa KM578710.1 1 Hyparrhenia rufa KM578709.1 5 0.64 Hyparrhenia rufa KM578711.1 1 Hyparrhenia rufa KM578708.1 6 1 Hyparrhenia rufa KM578707.1 0.990.43 Hyparrhenia rufa KM578706.1 7 Andropterum stolzii KM578609.1

8 1 Hyparrhenia diplandra KM578731.1 0.44 1 Hyparrhenia diplandra KM578704.1 9 Hyparrhenia diplandra KM578705.1 1 Diheteropogon amplectens KM578616.1 10 1 Diheteropogon amplectens KM578615.1 11 Diheteropogon hagerupii KM578735.1 1 Schizachyrium sanguineum KM578565.1 12 1 Schizachyrium sanguineum JQ951633.1 0.95 0.56 Andropogon gerardii KM578557.1 13 KM578612.1 0.98 1 Andropogon hallii 14 Andropogon hallii JQ951634.1 Andropogon gerardii KM578556.1 0.49 15 0.33 Andropogon virginicus KM578635.1 1 Andropogon eucomus KM578555.1 16 0.6 Andropogon glomeratus KM578741.1 0.55 17 1 Andropogon perligulatus KM578559.1 0.22 Andropogon perligulatus KM578558.1 18 1 Andropogon chinensis KM578688.1 1 Andropogon chinensis KM578687.1 19 Andropogon gayanus KM578610.1

20 1 Coix gasteenii KM578695.1 0.93 Coix gasteenii KM578694.1 21 0.12 0.91 Coix lacryma−jobi KM578613.1 1 Chasmopodium caudatum KM578684.1 22 0.14 Rottboellia cochinchinensis KM578601.1

23 1 Zea mays NM 001196163.1 0.23 Tripsacum dactyloides KM578596.1 24 Rottboellia lepidura JQ951635.1 0.07 1 Iseilema macratherum KM578626.1 25 Iseilema macratherum KM578625.1

26 1 Polytoca massiei KM578693.1 1 Polytoca massiei KM578692.1 27 1 Polytoca gigantea KP243025.1 KP243026.1 0.42 Polytoca wallichiana 28 1 Microstegium vimineum KM578686.1 0.94 Microstegium vimineum KM578685.1 29 Apluda mutica KM578670.1

30 1 Chrysopogon serrulatus KM578619.1 0.99 Chrysopogon serrulatus KM578618.1 31 0.54 Chrysopogon serrulatus KM578617.1 1 Chrysopogon zizanioides KM578676.1 0.68 32 0.19 Chrysopogon gryllus KM578561.1 Chrysopogon gryllus KM578562.1 33 1 0.99 Chrysopogon gryllus JQ951636.1 34 0.76 1 Thelepogon elegans KM578728.1 Thelepogon elegans KM578726.1 35 Phacelurus huillensis KM578586.1 0.08 36 0.88 Heteropogon triticeus KM578702.1 1 Heteropogon triticeus KM578701.1 37 0.4 Heteropogon triticeus KM578703.1 0.09 1 Themeda villosa KM578730.1 38 Themeda villosa KM578729.1

39 1 Arthraxon lanceolatus KM578689.1 0.61 Arthraxon prionodes KM578672.1 40 1 Andropterum stolzii JQ951631.1 0.28 Tripsacum dactyloides KM578600.1 41 0.47 Tripsacum dactyloides KM578597.1 42 0.96 Tripsacum dactyloides KM578599.1 1 Tripsacum dactyloides KM578598.1 43 Zea mays EU971416.1 Zea mays BT061081.1 44 0.35 Saccharum villosum KP243018.1 0.07 0.79 Saccharum villosum KP243016.1 45 1 1 Saccharum villosum KP243023.1 46 Saccharum villosum KP243008.1 0.98 Saccharum villosum KP243019.1 47 0.2 Saccharum angustifolium KP242993.1 0.2 Saccharum angustifolium KP242991.1 48 Saccharum angustifolium KP242987.1 1 49 1 Saccharum asperum KP243001.1 0.21 Saccharum asperum KP242999.1 50 Saccharum asperum KP242997.1 0.26 0.21 1 Saccharum asperum KP242995.1 51 Saccharum giganteum KP243003.1 PDF Proof 52 0.52 0.5 Miscanthus ecklonii KM578655.1 Miscanthus ecklonii KM578654.1 53 0.9 Saccharum narenga KM578725.1 1 Saccharum narenga KM578724.1 54 Saccharum narenga KM578723.1

55 0.16 Saccharum villosum KP243015.1 0.14 Saccharum villosum KP243009.1 56 0.14 0.26 Saccharum villosum KP243011.1 0.99 57 Saccharum villosum KP243007.1 0.7 0.090.99 Saccharum villosum KP243020.1 58 Saccharum villosum KP243017.1 0.02 Saccharum asperum KP242996.1

59 0.090.12 Saccharum villosum KP243024.1 Saccharum angustifolium KP242988.1 60 0.870.09 Saccharum giganteum KP243004.1 Saccharum asperum KP243002.1 0.520.96 Saccharum giganteum KP243005.1

0.39 Saccharum asperum KP242998.1 0.08 Miscanthus ecklonii KM578656.1 0.45 Pseudosorghum fasciculare KM578716.1 Saccharum narenga KM578722.1 0.25 Tripidium arundinaceum KM578721.1 0.27 Tripidium arundinaceum KM578719.1 1 Tripidium arundinaceum KM578720.1 0.96 Tripidium arundinaceum KM578718.1 1 0.11 Tripidium arundinaceum KM578717.1 0.29 1 Tripidium ravennae KM578682.1 Tripidium ravennae KM578681.1 Phacelurus digitatus JQ951637.1 Imperata cylindrica KM578712.1 0.32 1 Sorghastrum nutans KM578592.1 0.34 Sorghastrum nutans KM578591.1 1 Sorghastrum elliottii KM578738.1 Sorghastrum elliottii KM578737.1 1 Kerriochloa siamensis KM578714.1 0.37 Kerriochloa siamensis KM578713.1 0.98 Sorghum bicolor XM_002460157.2 0.14 Sorghum bicolor JQ951638.1 0.17 Sorghum bicolor KM578593.1 KM578633.1 0.211 Polytrias indica Sorghum bicolor KM578595.1 0.92 Polytrias indica KM578634.1 1 Lasiorhachis perrieri NOP140 Lasiorhachis hildebrandtii LRK2008 1 Bothriochloa insculpta KM578644.1 0.31 Bothriochloa insculpta KM578629.1 0.81 Bothriochloa insculpta KM578630.1 1 Bothriochloa insculpta KM578643.1 0.92 Bothriochloa bladhii KM578645.1

0.331 Bothriochloa bladhii KM578663.1 Bothriochloa ischaemum KM578628.1 0.42 Bothriochloa ischaemum KM578627.1 1 Dichanthium caricosum KM578700.1 1 Dichanthium caricosum KM578699.1 0.3 0.99 Dichanthium aristatum KM578576.1 0.57 Bothriochloa ischaemum KM578671.1 0.55 Dichanthium annulatum JQ951630.1 1 Dichanthium annulatum KM578739.1 1 Bothriochloa bladhii KM578653.1 1 Bothriochloa exaristata KM578666.1 0.33 Bothriochloa exaristata KM578665.1 0.92 Bothriochloa alta KM578637.1 0.99 Bothriochloa woodrovii KM578646.1 Bothriochloa barbinodis KM578640.1 0.2 Bothriochloa exaristata KM578664.1 0.18 Bothriochloa woodrovii KM578647.1 0.37 0.94 Bothriochloa barbinodis KM578639.1 0.96 Bothriochloa barbinodis KM578638.1 1 Bothriochloa decipiens KM578651.1 0.77 Bothriochloa macra KM578641.1 1 0.5 Bothriochloa laguroides KM578649.1 1 Bothriochloa bladhii KM578662.1 0.96 Bothriochloa bladhii KM578652.1 0.8 0.99 1 Bothriochloa decipiens KM578650.1 Bothriochloa macra KM578642.1 0.94 Bothriochloa bladhii KM578636.1 0.35 Capillipedium spicigerum KM578560.1 1 Capillipedium spicigerum KM578657.1 1 Capillipedium assimile KM578691.1 Capillipedium assimile KM578690.1 1 Ischaemum santapaui KM578584.1 Ischaemum santapaui KM578582.1 0.94 Pogonatherum paniceum KM578632.1 1 Pogonatherum paniceum KM578631.1 0.31 Pogonatherum crinitum KM578715.1 1 Eulalia villosa KM578603.1 0.38 Eulalia villosa KM578602.1 0.21 1 Sehima nervosum KM578590.1 1 Sehima nervosum KM578588.1 Sehima nervosum KM578589.1 0.99 Cymbopogon obtectus KM578658.1 1 Cymbopogon refractus KM578574.1 1 Cymbopogon obtectus KM578571.1 KM578570.1 1 1 Cymbopogon flexuosus Cymbopogon flexuosus JQ951632.1 0.42 Cymbopogon citratus KM578697.1 0.19 Cymbopogon citratus KM578696.1 0.6 Cymbopogon commutatus KM578572.1

0.39 0.92 Cymbopogon citratus KM578698.1 0.97 Cymbopogon jwarancusa subsp. olivieri KM578608.1 0.33 Cymbopogon distans KM578567.1 0.98 Cymbopogon distans KM578566.1 0.96 Cymbopogon distans KM578568.1 0.38 Cymbopogon martinii KM578607.1 1 Cymbopogon martinii KM578606.1 0.35 1 Cymbopogon martinii KM578604.1 Cymbopogon martinii KM578605.1 1 Ischaemum afrum KM578581.1 Ischaemum afrum KM578580.1 1 Dichanthium foveolatum KM578733.1 Dichanthium foveolatum KM578732.1 1 Arundinella hirta KM578669.1 Arundinella hirta KM578668.1 Botanical Journal of the Linnean Society