Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data

Generic delimitations in the Ficinia Clade of tribe Cypereae are revisited. In particular, we aim to establish the placement of annual species currently included in Isolepis of which the phylogenetic position is uncertain. Phylogenetic inference is based on two nuclear markers (ETS, ITS) and five plastid markers (the genes matK, ndhF, rbcL and rps16, the trnL intron and trnL-F spacer) data, analyzed using model based methods. Topologies based on nuclear and plastid data show incongruence at the backbone. Therefore, the results are presented separately. The monophyly of the smaller genera (Afroscirpoides, Dracoscirpoides, Erioscirpus, Hellmuthia, Scirpoides) is confirmed. However, Isolepis is paraphyletic as Ficinia is retrieved as one of its clades. Furthermore, Ficinia is paraphyletic if I. marginata and allies are excluded. We take a pragmatic approach based on the nuclear topology, driven by a desire to minimize taxonomic changes, to recircumscribe Ficinia to include the annual Isolepis species characterized by cartilaginous glumes and formally include all the Isolepis species inferred outside the core Isolepis clade. Consequently, the circumscription of Isolepis is narrowed to encompass only those species retrieved as part of the core Isolepis clade. Five new combinations are made (Ficinia neocapensis, Ficinia hemiuncialis, Ficinia incomtula, Ficinia leucoloma, Ficinia minuta). We present nomenclatural summary at genus level, identification keys and diagnostic features.


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A unique 3 base-pair insertion in ITS2 further supports the uniqueness of the core 246 Isolepis. This insertion is missing in I. hemiuncialis, I. incomtula as well as the species in the I. 247 marginata clade, and can therefore be used as a synapomorphy for the core Isolepis clade. 248 Similar use of indels, located at the 5.8S gene of the nuclear ribosomal DNA, as synapomorphies 249 has been suggested for the Cypereae (Yano et al., 2012) and Cyperaceae (Starr et al., 2007). 250 A number of the genera in the ingroup can be distinguished unambiguously based on one 251 or few characters (Table 1). The presence and type perianth segments, even though perhaps 252 arising independently, are unique in Dracoscirpoides (scabrid bristles; Muasya et al., 2012), 253 Erioscirpus (cotton-like bristles; Yano et al., 2012) and in Hellmuthia (scale-like; Vrijdaghs et 254 al., 2006). Among the taxa lacking perianth segments, Afroscirpoides and Scirpoides have 255 densely tufted culms which have reduced leaf blades (>5 mm, but some Scirpoides have well 256 developed leaf blades), with the former having dioecious individuals whereas the later has 257 bisexual florets. Ficinia is most similar in gross morphology and ecology to Afroscirpoides and 258 Scirpoides, diagnosed by the presence of a cupular disk (gynophore; Vrijdaghs et al., 2005) at 259 the base of the nutlets (except in several species where the trait is lost; Muasya et al., 2014). 260 Isolepis is most similar to Ficinia, sharing presence of bisexual florets and glumes with well 261 defined parallel veins, but differing in Isolepis lacking the gynophore. The glume texture appears 262 to offer additional separation, being chartaceous to hyaline (herbaceous; Muasya & Simpson, 263 2002) in Isolepis but cartilaginous (or coriaceious) in Ficinia. 264 Generic boundaries within Isolepis and Ficinia have been noted as problematic. 265 Eleogiton, still recognized as distinct in some floras (e.g. Germany, Kadereit et al., 2016) based 266 on possessing multiple internodes and peduncle termination in a single terminal spikelet, is 267 confirmed to be a clade in Isolepis (subgenus Fluitantes; Muasya et al., 2001;Muasya & 268 Simpson, 2002). In Ficinia, Sickmania Nees has been previously recognized based on a capitate 269 inflorescence with multiple leaf-like bracts (F. radiata) whereas Desmoschoenus has primary 270 bracts adnate to axis and covering congested spikelets) (Goetghebeur, 1998). The phylogenetic 271 inference showing I. maginata and other annual species that lack a gynophore being closer to 272 Ficinia further blurs the generic boundaries.

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Cyperaceae has experienced shifting generic classification in the last two decades. The 274 paradigm shift to recognize monophyletic genera (Humphries & Linder, 2009) accompanied by 275 the use of DNA sequence data have enabled disentangling phylogenetic relatedness of taxa 276 obscured by extreme morphological modification. Several highly diversified lineages appear to 277 have been split into genera based on one of few characters, at times such characters arising 278 independently. This phenomenon was epitomized Cyperus, now recognized as a single genus 279 (Larridon et al. 2011a(Larridon et al. , b, 2013(Larridon et al. , 2014Bauters et al. 2014), where 13 segregate genera were 280 diagnosed based on morphology of reproductive structures (spikelet size and organization, nutlet 281 orientation, style branching; Muasya et al., 2009a). This study supports a further refinement 282 within the Cypereae, recognizing the core Isolepis and an enlarged Ficinia at generic level. 283 We speculate that the Ficinia clade evolved in southern Africa, given that majority of 284 lineages and species occur in the region. Diversification in Isolepis and Ficinia has occurred 285 since the Miocene (Besnard et al., 2009), perhaps ecologically driven by aridification associated 286 with onset of the Mediterranean climate (Linder & Verboom, 2015), where emerging traits 287 include annual life form, colonization of permanently wet habitats, sprouting regeneration driven 288 by the frequent fires in sclerophyllous habitats, and ant dispersal of seeds (gynophore in Ficinia; 289 Bond & Slingsby, 1983). Within southern Africa, the Ficinia Clade members are predominantly 290 occurring in the Greater Cape Flora and exhibit the typical diversification pattern whereby 291 lineages in the Fynbos are older than those in the Succulent Karoo biome (Verboom et al., 2009). 292 Dispersal out of the Cape appears to be predominantly to other similar habitats, especially in 293 Mediterranean Eurasia (Erioscirpus, Isolepis, Scirpoides), within temperate zones of high 294 mountains in tropical Africa (Dracoscirpoides, Ficinia, Isolepis, Scirpoides) and austral 295 temperate areas (Ficinia, Isolepis). Dispersal to Australasia in Isolepis has been accompanied by 296 hybridization in Isolepis (Ito et al., 2016). 297 298 Taxonomic treatment 299 The current generic classification is supported for the smaller genera (Afroscirpoides, 300 Dracoscirpoides, Erioscirpus, Hellmuthia, Scirpoides). However, Isolepis is paraphyletic as 301 Ficinia is one of its clades as well as Ficinia is paraphyletic if I. marginata and allies are 302 excluded. We acknowledge the conflicting topology between the nuclear and plastid 303 phylogenies, particularly regarding the position of I. hemiuncialis and I. incomtula, opting to 304 follow the nuclear phylogeny. We take a phragmatic approach, to recognize clades that will 305 minimize nomenclatural changes, by adopting a classification framework based on the nuclear 306 phylogeny (Figure 2). We therefore recognize an expanded concept of Ficinia, to include annual 307 species with mostly cartilaginous glumes and lacking a gynophore (occasionally a gynophore is 308 observed among Australian I. marginata, see Figure 3F). As a consequence, Isolepis is now 309 considered in a narrower concept which encompasis the core Isolepis and excludes the seven  Two species of perennial hemicryptophytes, diagnosed on presence of cotton-like 341 perianth. Taxonomic revision as part of regional flora, e.g. Flora of Pakistan 342 (http://www.tropicos.org/Project/Pakistan).

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Distributed in Asia, from Iran to China, occurring in shallow soil and rocky crevices, at 344 700-2300 m.  Three species of perennial hemicryptophytes or rhizomatous geophytes, taxonomy 349 revised in Muasya et al. 2012. 350 Restricted to southern Africa, occurring in montane grasslands.   Monotypic, densely tufted hemicryptophytes or rhizomatous geophytes, diagnosed by 362 dioecious flowers borne in dense globose inflorescences whose bract terminates in a sharp-363 pointed tip.

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About 90 species are recognized here, including the annual species transferred from 384 Isolepis. Majority of species are perennial hemicryptophytes or rhizomatous geophytes, adapted 385 to survive frequest fires in the Fynbos biomes, but also few annual and pyrophytic short-lived 386 perrenials. The most comprehensive taxonomic study of Ficinia was part of the Flora Capensis 387 (Clarke, 1897-98) and recent synopsis of the Cape Flora (Archer & Muasya, 2012). Ongoing 388 studies reveal existence of undescribed species and the Ficinia is among the highest priority 389 Cypeaceae for taxonomic revision in southern Africa.

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Predominantly occurring in southern Africa in the Cape Flora and extending into 391 montane areas of tropical Africa. Two species occur in Australasia, among which F. nodosa is 392 nearly circumpolar.  Manuscript to be reviewed