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Molecular and Evolution 81 (2014) 195–206

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Molecular Phylogenetics and Evolution

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Global phylogeny and biogeography of grammitid () ⇑ Michael A. Sundue a,c, , Barbara S. Parris b, Tom A. Ranker c, Alan R. Smith d, Erin L. Fujimoto c, Delia Zamora-Crosby a, Clifford W. Morden c, Wen-Liang Chiou e, Cheng-Wei Chen f, Germinal Rouhan g, Regina Y. Hirai h, Jefferson Prado h a The Pringle Herbarium, Department of Biology, The University of Vermont, 27 Colchester Ave., Burlington, VT 05405, USA b Research Foundation, 21 James Kemp Place, Kerikeri, Bay of Islands, 0230, New Zealand c Department of Botany, University of Hawaii, 3190 Maile Way, Honolulu, HI 96822, USA d University Herbarium, 1001 Valley Life Sciences Bldg. # 2465, University of California, Berkeley, CA 94720-2465, USA e Division of Botanical Garden, Taiwan Forestry Research Institute, 53 Nan-Hai Rd., Taipei 100, Taiwan f Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan g Muséum national d’Histoire naturelle, UMR CNRS 7205 ‘Origine, Structure et Evolution de la Biodiversité, Botanique, 16 rue Buffon CP 39, 75005 Paris, France h Instituto de Botânica, Caixa Postal 68041, CEP 04045-972 São Paulo, SP, article info abstract

Article history: We examined the global historical biogeography of grammitid ferns (Polypodiaceae) within a phyloge- Received 23 April 2014 netic context. We inferred phylogenetic relationships of 190 representing 31 of the 33 currently Revised 13 August 2014 recognized genera of grammitid ferns by analyzing DNA sequence variation of five plastid DNA regions. Accepted 15 August 2014 We estimated the ages of cladogenetic events on an inferred phylogeny using secondary calibration Available online 27 August 2014 points. Historical biogeographical patterns were inferred via ancestral area reconstruction. Our results supported four large-scale phylogenetic and biogeographic patterns: (1) a monophyletic grammitid Keywords: that arose among Neotropical polypod ancestors about 31.4 Ma; (2) a paraphyletic assemblage of Polypodiaceae distributed in the Neotropics and the Afro-Malagasy region; (3) a large clade distributed throughout the Epiphytes Phylogeny Asia–Malesia–Pacific region that originated about 23.4 Ma; and, (4) an Australian or New Zealand origin Grammitid ferns of the circumaustral Notogrammitis. Most genera were supported as monophyletic except for Biogeography , Oreogrammitis, Radiogrammitis, and Zygophlebia. Grammitid ferns are a well-supported mono- phyletic group with two biogeographically distinct lineages: a primarily Neotropical grade exhibiting several independent successful colonizations to the Afro-Malagasy region and a primarily Paleotropical clade exhibiting multiple independent dispersals to remote Pacific islands and temperate, austral regions. Ó 2014 Elsevier Inc. All rights reserved.

1. Introduction 2012) treated in 33 genera, the grammitids comprise close to two-thirds of the diversity in the family; the non-grammitid Poly- With close to 1500 species, the cosmopolitan Polypodiaceae are podiaceae (referred to here as the polypods) include some 450 spe- among the largest families of ferns (Smith et al., 2006; unpubl.). cies treated in 40 genera (Smith et al., 2006; unpubl.). Whereas the Most species are epiphytes and represent the fourth largest family polypods are characterized by often round exindusiate sori, reni- of epiphytic vascular (Gentry and Dodson, 1987). The fam- form, monolete spores usually lacking chlorophyll at maturity, usu- ily’s prominence was established during a Cenozoic radiation in ally scaly leaves, and dorsiventral with well-developed which leptosporangiate ferns diversified into new niches in other- phyllopodia, synapomorphies for the grammitid clade include a wise angiosperm-dominated forests (Schuettpelz and Pryer, 2009). reduction in the number of cells in the middle of the sporangial The family includes a large monophyletic clade referred to as the stalk from three to one (Wilson, 1959), a reduction in the number ‘‘grammitids’’, which were often treated as a separate family of vascular bundles in the from several (like most eupolypod (Grammitidaceae) prior to molecular phylogenetic evidence I ferns) to a single bundle or two that fuse above the base (Parris, (Schneider et al., 2004). With ca. 900 species (Perrie and Parris, 1990; Sundue, 2010a), and globose, trilete spores that contain fully developed chlorophyll at maturity (Parris, 1990; Sundue, 2010a). Although both groups often have minute branched hairs (c. ⇑ Corresponding author at: The Pringle Herbarium, Department of Plant Biology, 0.1 mm long), polypods most often have broad basifixed or peltate The University of Vermont, 27 Colchester Ave., Burlington, VT 05405, USA. scales whereas grammitids do not have these scales but have E-mail address: [email protected] (M.A. Sundue). http://dx.doi.org/10.1016/j.ympev.2014.08.017 1055-7903/Ó 2014 Elsevier Inc. All rights reserved. 196 M.A. Sundue et al. / and Evolution 81 (2014) 195–206 pluricellular uniseriate setae (Sundue et al., 2010). Occasional confined to the tropics, although some groups extend to the tem- intermediates between scales and setae suggest that these two perate zones, reaching 40°N and 56°S(Parris, 2003). types of indument may in fact be homologous (Sundue, unpub- Parris (2003) assigned grammitid distributions to two major lished). Perhaps owing to their relatively larger size, ease of cultiva- phytogeographic zones: (1) Neotropics–Africa–Madagascar (includ- tion, and conspicuous adaptations (e.g., myrmecophily, detritus ing also the Mascarenes, Seychelles, and Comoros) where there are catching leaves, desiccation tolerance), it is the polypods, as defined about 300 species, and (2) Asia–Malesia–Pacific with about 450 above, that have received most attention in the literature. The species. Current species counts are c. 400 species for Neotropics– grammitids, which are generally small, inconspicuous, and not Africa–Madagascar, and c. 500 for Asia–Malesia–Pacific (Parris, amenable to cultivation, are less well known. This has begun to unpubl.), reflecting the progress in grammitid systematics in the last change recently, with grammitids becoming the focus of many sys- decade. Dispersal within each zone appears to be common; all but tematic studies. one of the genera present in Africa–Madagascar also occur in the Polypodiaceae have undergone massive generic re-circumscrip- Neotropics, and at least three species are found in both places tion following molecular phylogenetic studies (e.g., Ranker et al., (Moran and Smith, 2001). Likewise, the Asian, Malesian, and Pacific 2004; Schneider et al., 2004; Kreier et al., 2008; Wang et al., areas contain overlapping diversity. Phylogenetic analyses further 2010), which demonstrated that many genera were not monophy- corroborate these two phytogeographic zones, with both Ranker letic. Within the grammitids, the classical genera Grammitis, Xip- et al. (2004) and Sundue et al. (2010) finding evidence that most hopteris, and Ctenopteris were largely based on blade dissection, a species from the Asia, Malesia, and the Pacific belong to a single character that has proven nearly useless in defining monophyletic clade. Migration between these two zones is rare. As currently clades. More recently described genera such as A.R. Sm. understood, only four genera cross these phytogeographic zones: and A.R. Sm. & R.C. Moran, have relied instead on suites (1) Stenogrammitis, a primarily Neotropical genus that reaches of morphological characters including microscopic and anatomical Africa–Madagascar, the Hawaiian Islands, and a few south-Pacific features (Smith et al., 1991; Smith, 1993). These characters have islands (Labiak, 2011; Ranker et al., 2010); (2) , a mainly more reliably defined monophyletic groups, but are still subject Malesian Pacific genus that extends to Africa (Parris, 2007); (3) Noto- to cases of morphological homoplasy resulting in polyphyletic gen- grammitis, an austral genus most diverse in Australia and New Zea- era (Ranker et al., 2004; Labiak et al., 2010b). Consequently, the land that reaches South Africa and southern South America, and (4) of Lellingeria R.C. Moran & A.R. Sm. (Labiak et al., Grammitis s.s., ranging from the western Pacific through the Neo- 2010b) and Terpsichore A.R. Sm. (Ranker et al., 2004; Sundue tropics to Africa, Madagascar, and the Mascarenes. Notably the et al., 2010) has led to the segregation of Kessler et al. Hawaiian Islands represent an area of overlap, appearing to have (Kessler et al., 2011), Ascogrammitis Sundue (Sundue, 2010b), been colonized via migrations from both phytogeographic zones Galactodenia Sundue & Labiak (Sundue et al., 2012), (Geiger et al., 2007). Labiak (Labiak et al., 2010a), Moranopteris R.Y. Hirai & J. Prado The historical biogeography of ferns includes examples of both (Hirai et al., 2011), Mycopteris Sundue (Sundue, 2013), and Steno- vicariance and long-distance dispersal, and discerning between grammitis Labiak (Labiak, 2011). these has been a goal of biogeographic research (Barrington, Similarly, our understanding of Paleotropical grammitids has 1993; Wolf et al., 2001; Korall and Pryer, 2014; Labiak et al., changed radically. Two names that had been widely applied are 2014). Copeland (1939, 1952) hypothesized that Grammitis s.l. now recognized as synonyms of other genera: Ctenopteris Blume (including all species with simple and entire leaves) were ances- ex Kunze = Prosaptia C. Presl (Price, 1982, 1987), and trally Antarctic in distribution, attaining their present distribution Kaulf. = Kaulf. (Bishop, 1978). Moreover, an under- via migration through New Zealand, South Africa and Madagascar, standing that traditional generic boundaries were not well defined and the southern Andes. While this austral source for the origin of (Parris, 1977, 1984), and the determinations of polyphyly of such grammitids cannot be ruled out, migration via all three routes con- large historically recognized genera as Grammitis Sw. (in the strict flicts with current inferences. Based on the results of Schuettpelz sense including only those species with a distinct black, sclerified and Pryer (2009), it appears that the Polypodiaceae diverged from leaf margin, sensu Parris, 2007), Ctenopteris, and Xiphopteris, which Paleotropical ancestors 55.8 Ma, and migrated into the Neotrop- were defined mainly on the basis of blade dissection, led to the ics 43 Ma. Grammitids appear to have evolved from these Neo- recent coining of Archigrammitis Parris (Parris, 2013), Chrysogramm- tropical polypod ancestors 30.6 Ma. Subsequent migration to itis Parris (Parris, 1998a), Dasygrammitis Parris (Parris, 2007), Asia/Africa occurred later, and must have operated via long- Notogrammitis Parris (Perrie and Parris, 2012), Radiogrammitis Par- distance dispersal, at least at the intercontinental level, because ris (Parris, 2007), Themelium (T. Moore) Parris (Parris, 1997), and the continents have not moved appreciably since the clade Tomophyllum (E. Fourn.) Parris (Parris, 2007), and the reinstatement evolved. Long-distance dispersal of spores by wind was also of Oreogrammitis Copel. (Parris, 2007). With the exception of invoked by Moran and Smith (2001) to explain floristic similarities Notogrammitis, which Perrie and Parris (2012) distinguished from between the Neotropics and Africa/Madagascar. The timing and Grammitis s.l. using plastid DNA markers, the circumscription of patterns of these dispersals remain largely unknown, but puta- Paleotropical genera has not had the benefit of densely sampled tively, it would seem that they are quite recent; some of the same molecular phylogenetic studies. Consequently, phylogenetic species occur in both areas, and there is very little diversification in relationships among Paleotropical grammitids remain largely several of the genera that migrated to Africa, namely uncertain. A.R. Sm. & R.C. Moran, Alansmia, Cochlidium, Leucotrichum, and Grammitids are found most abundantly in montane forests L.E. Bishop. The pattern is similar in some other genera, (Parris, 2005; Parris et al., 1992). At higher elevations they can be such as Zygophlebia L.E. Bishop, Baker, Stenogrammitis, an important component of the fern flora, for example, on Mt. and Grammitis s.s., but in these genera more diversification has Kinabalu (Sabah, Malaysia) grammitid ferns constitute 25–35% of occurred in Africa and Madagascar. The origin of the Asian– total fern diversity between 2000–4000 m (Kessler et al., 2001). Malesian–Pacific grammitids; however, is particularly unclear. Likewise, Notogrammitis crassior occurs up to 2600 m in New Zea- With these issues in mind, we undertook a phylogenetic study land (Parris and Given, 1976), higher than any other fern species of grammitid ferns aiming establishing a global picture of phylog- there. Among vascular epiphytes, the two species thought to grow eny and historical biogeography. Our sampling included 50% of at highest recorded elevations both belong to Melpomene Paleotropical species and 31 of the 33 currently recognized genera (Sylvester et al., 2014). The majority of grammitid diversity is (Archigrammitis Parris and Luisma M.T. Murillo & A.R. Sm. remain M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206 197 unsampled). We addressed two primary questions: Are the Neo- Table 1 tropical and Afro-Malagasy floras closely related as hypothesized Type species of grammitid genera sampled. by Parris (2003)? Do the Asian–Malesian–Pacific species constitute Genus Species Sampled p a single clade, or is this Old World diversity the result of multiple exaltatus (Copel.) Copel. = friderici-et-pauli migrations? (Christ) Copel tripinnatifidus Gaudich – p Alansmia lanigera (Desv.) Moguel & M. Kessler 2. Materials and methods Archigrammitis friderici-et-pauli (Christ) Parris – p Ascogrammitis athyrioides (Hook.) Sundue cucullatus (Nees & Blume) C. Presl – 2.1. DNA extraction and amplification p Ceradenia curvata (Sw.) L.E. Bishop p Chrysogrammitis glandulosa (J. Sm.) Parris Ingroup sampling included 190 species (202 accessions) from Cochlidium graminoides (Sw.) Kaulf – Ctenopterella blechnoides (Grev.) Parris – 31 of the 33 currently recognized genera; samples of Archigramm- p itis and Luisma were unavailable. Sampling included the type spe- Dasygrammitis mollicoma (Nees & Blume) Parris Enterosora campbellii Baker – cies for 20 genera (Table 1). Outgroups included five species of p Galactodenia delicatula (M. Martens & Galeotti) Sundue & Neotropical polypods found to be closely related in previous stud- Labiak ies (e.g., Schuettpelz and Pryer, 2009). This choice was further Grammitis marginella (Sw.) Sw – p informed by our unpublished analysis of available sequences in Lellingeria apiculata (Kunze ex Klotzsch) A.R. Sm. & R.C. Moran GenBank that also find these Neotropical polypods as the closest p Leucotrichum organense (Gardner) Labiak relative of the grammitid clade. Sequences not generated by us Lomaphlebia linearis (Sw.) J. Sm. = graminea (Sw.) Parris – were downloaded from GenBank. DNA extraction and PCR amplifi- Luisma bivascularis M.T. Murillo & A.R. Sm – p cation protocols followed those of Labiak et al. (2010b). We PCR- Melpomene moniliformis (Lagasca ex Sw.) A.R. Sm. & R.C. Moran amplified five plastid DNA markers: the atpß and rbcL coding p pseudotrichomanoides (Hayata) regions, and the trnL-trnF, rps4-trnS, and trnG-trnR intergenic spac- Hayata = okuboi (Yatabe) Hayata ers, and generated 67, 71, 106, 92, and 71 sequences of each, Moranopteris basiattenuata (Jenman) R.Y. Hirai & J. Prado – p respectively. DNA sequencing was performed at the Greenwood Mycopteris taxifolia (L.) Sundue p Molecular Biology Facility at the University of Hawai’i at Ma¯noa, Notogrammitis billardierei (Willd.) Parris Oreogrammitis clemensiae Copel – and all sequences were submitted to GenBank (Appendix 1). p Prosaptia contigua (G. Forst.) C. Presl p Radiogrammitis setigera (Blume) Parris p Scleroglossum pusillum (Blume) Alderw 2.2. Alignment and analyses p Stenogrammitis myosuroides (Sw.) Labiak p Terpsichore asplenifolia (L.) A.R. Sm Sequences were edited and contigs were produced using Themelium tenuisectum (Blume) Parris – Geneious 6.17 (Biomatters Ltd., San Francisco, CA), and the MAAFT Tomophyllum subsecundodissectum (Zoll.) Parris – p Xiphopterella hieronymusii (C. Chr.) Parris plug-in was used to produce alignments (Katoh, 2013). Alignments p were visually inspected and no areas appeared to be aligned Zygophlebia sectifrons (Kunze ex Mett.) L.E. Bishop ambiguously. For each aligned marker, optimal data partitioning and models of substitution evolution were estimated using AICc in PartitionFinder (Lanfear et al., 2012). We provided PartitionFind- er with subsets for each marker, and for the three coding regions except that rates were allowed to vary among loci (ratepr = vari- we provided subsets for each nucleotide position. The resulting able). The posterior was sampled every 1000 generations, and best scheme was a single GTR + I + G model for the dataset. This the first 25% discarded as ‘‘burn-in’’. Convergence was estimated was implemented in the Bayesian and likelihood tree searches. by examining the standard deviation of split frequencies, plotting We conducted tree searches using maximum parsimony (MP), the output parameters in TRACER v 1.5 (Rambaut et al., 2013), maximum likelihood (ML) and Bayesian (BI) analyses. Maximum and examining tree files in AWTY (Wilgenbush et al., 2004; parsimony tree searches were performed using TNT (Goloboff Nylander et al., 2008). et al., 2008) employing two approaches. First, we conducted tradi- tional heuristic searches with 1000 parsimony ratchet replicates 2.3. Fossil calibration (Nixon, 1999) (200 iteration ratchet, the up and down weights set to 5% each), holding 20 trees per ratchet, followed by tree- Known fossil calibration points for the Polypodiaceae are lim- bisection-reconnection (TBR)-max branch swapping. We then ited. Consequently, we chose to calibrate our chronogram using implemented a New Tech search strategy set at level 15 imple- node ages generated by a fossil-calibrated analysis of all leptospo- menting tree fusing, sectorial search, and the parsimony ratchet rangiate ferns (Schuettpelz and Pryer, 2009). Grammitis succinea finding the minimum length tree 10 times. In each case, support L.D. Gómez, a fossil in Dominican amber, is the only known fossil for nodes was calculated by bootstrap analyses (BS), with 1000 that appears to belong to the grammitids (Gómez, 1982). While replicates using the same methods. Maximum likelihood tree purported to have several synapomorphies for the grammitids searches were conducted using RAxML (Stamatakis, 2006) through (namely, stiff, erect uniseriate, pluricellular setae and uniseriate the CIPRES portal (Miller et al., 2010). Five independent searches sporangial stalks), this fossil is relatively young (approximately for the ‘best tree’ and 10,000 BS replicates were generated 25 Ma) and cannot be placed with confidence in any clade within implementing the best partition scheme determined by Partition- grammitids; consequently, it was not useful to our study. Finder. Bayesian tree searches were conducted using MrBayes We estimated divergence times using a relaxed molecular clock (Huelsenbeck and Ronquist, 2001; Ronquist and Huelsenbeck, as implemented in BEAST, using a Markov chain Monte Carlo strat- 2003) through the Oslo Lifeportal (https://lifeportal.uio.no/root). egy (Drummond et al., 2006, 2013; Drummond and Rambaut, We conducted five runs implementing the best partition scheme 2007). We partitioned the dataset by plastid DNA region, and spec- determined by PartitionFinder for 10 million generations. Each ified the optimal model for each region as determined by Partition- run included four chains (one cold, three heated) with unlinked Finder. We implemented a Yule speciation tree prior and an parameters, and chain temperature set to 0.2. Priors were uniform uncorrelated lognormal model of rate change, with clock models 198 M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206

Table 2 Table 3 Dispersal constraints (Q matrix). Summary of molecular sequences.

ABCDEF Region Aligned Variable Parsimony No. of bases bases informative samples A 1 0.25 0.01 0.25 0.01 0.25 characters B 0.25 1 0.25 0.25 0.01 0.01 C 0.01 0.25 1 0.25 0.01 0.01 atpB 1174 394(34%) 295(25%) 173 D 0.25 0.25 0.25 1 0.01 0.01 rbcL 1329 503(38%) 320(24%) 200 E 0.01 0.01 0.01 0.01 1 0.01 rps4-trnS 778 537(69%) 393(51%) 144 F 0.25 0.01 0.01 0.01 0.01 1 trnG-trnR 1572 877(56%) 652(41%) 117 trnL-trnF 661 419(61%) 305(45%) 178 Total 5514 2730(49%) 1974(35%) 207 unlinked between partitions and a GTR + G substitution model in all cases. We used the following calibration points from Schuettpelz and Pryer (2009) with normal distribution priors: the ML and Bayesian analyses. One minor difference was that the most recent common ancestor (MRCA) of the grammitid clade Grammitis s.s. was recovered as monophyletic, but without strong (31.2 Ma, 3.12 s.d.), the MRCA of the large Neotropical clade branch support. Best ML trees resulting from RAxML shared an including Mycopteris–Stenogrammitis (23.3 Ma, 2.33 s.d.), the large overall topology identical to that of the Bayesian trees and there- primarily Paleotropical clade including Moranopteris–Oreogramm- fore are not discussed in further detail. Results from the Bayesian itis (23.4 Ma, 2.34 s.d.), and the MRCA of A.R. Sm. analyses were generally well resolved and well supported (Fig. 1). (15.5 Ma, 1.55 s.d.). The clade corresponding to each calibration Results from our analyses supported grammitids as monophy- point was constrained to be monophyletic. Three analyses were letic (Fig. 1). The overall topology can be explained in general as run, each for 30,000,000 generations, with parameters sampled a monophyletic tropical Asian clade nested within a primarily Neo- every 1000 generations. The program LogCombiner was used to tropical and African grade (Fig. 2). Our results support the Neotrop- pool the resulting files. Tracer v1.5 (Drummond and Rambaut, ical genus Moranopteris as sister to this tropical Asian clade, and 2007) was used to examine the posterior distribution of all param- the tropical Asian genus Chrysogrammitis, which has been difficult eters and their associated statistics including estimated sample to resolve in previous analyses, as sister to the remainder of the sizes (ESS) and 95% highest posterior density (HPD) intervals. The tropical Asian clade. program TreeAnnotator v2.0.2 (Drummond and Rambaut, 2007) Relationships within the Neotropical and African grade are gen- was used to summarize the post burn-in trees and produce a max- erally congruent with previous studies, but with improved resolu- imum clade credibility chronogram showing mean divergence tion. Well-supported relationships not previously reported time estimates with 95% HPD intervals. include: (1) Zygophlebia is paraphyletic with Enterosora nested Historical Biogeography – Ancestral area reconstruction (AAR) within it; (2) Ceradenia is resolved as two clades corresponding was conducted using the dispersal-cladogenesis (DEC) model as to Bishop’s (1988) subgenera Ceradenia and Filicipecten; and (3) implemented in the program Lagrange (Ree and Smith, 2008). Lomaphlebia J. Sm. is sister to the clade comprising Grammitis s.s. We defined the following geographic areas: (A) Neotropical, (B) and Cochlidium. In previous studies (e.g., Sundue et al., 2010), Terp- Africa–Madagascar and islands of the Atlantic (Ascension and St. sichore was resolved as sister to all other grammitids, but here it is Helena) and Indian Oceans (Comoros, Réunion, Mauritius, Sey- sister to the clade of Adenophorus Gaudich., Cochlidium, Grammitis chelles), (C) tropical Asia and the Pacific including Bougainville, s.s., and Lomaphlebia. These five genera instead compose a clade Solomon Islands and Vanuatu, as well as NE Australia and New Cal- sister to all other grammitids. of Grammitis s.s. with edonia and Micronesia (Palau, Pohnpei, Kosrae), (D) a temperate respect to Cochlidium is also a novel result supported by our Bayes- circumaustral region south of 28°S, (E) Hawaiian Islands and the ian and likelihood results. central and eastern South Pacific, and (F) Nearctic. Distributions The remaining tropical Asian genera resolve in two main were assigned to each species based upon known records of her- clades, one comprising Calymmodon C. Presl, Dasygrammitis, barium specimens, and species with broad ranges were scored as Micropolypodium Hayata, Scleroglossum Alderw., Tomophyllum, polymorphic. These occurred in Alansmia, Cochlidium, and Steno- and Xiphopterella, and the other comprising Acrosorus, Ctenopterel- grammitis. Given the recent age of grammitid ferns, and vagility la, Notogrammitis, Oreogrammitis, Prosaptia, Radiogrammitis, Theme- of their spores, we made no restrictions in the adjacency matrix. lium, and four species currently combined in Grammitis (listed in Dispersal constraints (Q matrix) between these regions were Figs. 1 and 2 as ‘‘Grammitis’’) that are not placed within current scored as uncommon (0.25) or very uncommon (0.01) and are pre- generic concepts. sented in Table 2; maximum range size was set at 2. Most Paleotropical genera were supported as monophyletic, including Calymmodon, Chrysogrammitis, Dasygrammitis, Micropo- lypodium, Notogrammitis, Prosaptia, Tomophyllum, Scleroglossum, 3. Results and Xiphopterella. In contrast, Oreogrammitis and Radiogrammitis are polyphyletic. The three species of Themelium included were 3.1. Phylogenetic analyses resolved as monophyletic, but nested within the large clade com- prising Oreogrammitis and Radiogrammitis. Ctenopterella and Acros- The final aligned dataset included 5569 sites of which 1974 orus included only one species each, so the monophyly of those (35%) were parsimony informative (Table 3). During Bayesian anal- genera remains untested. yses, runs converged after the first 1 million generations, ESS val- ues of each parameter were all well above the recommended threshold of 200, and the traces of corresponding parameters in 3.2. Analyses of divergence times and diversification rates independent runs converged to the same optimum. Maximum par- simony tree searches with TNT found shortest trees of 10,761 BEAST analyses estimated the MRCA of the grammitids at steps. In a strict consensus, these MP trees retained all backbone 31.4 Ma and the MRCA of the large Paleotropical clade at 23.4 Ma relationships, except for one large polytomy forming in the crown (Fig. 2a, b). While stem ages varied among Paleotropical genera, group of Oreogrammitis, Radiogrammitis, and Themelium. The over- many of them began to diversify within the last 8.4 Ma, including all topology of the MP trees was very similar to that resulting from Acrosorus, Calymmodon, Chrysogrammitis, Dasygrammitis, M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206 199

Micropolypodium, Prosaptia, Scleroglossum, and Xiphopterella. The diversity of the clade (e.g., Tryon and Tryon, 1982; Christenhusz large predominantly Neotropical clades were estimated to origi- and Chase, 2014). Most recent authors; however, have restricted nate from 18 to 23 Ma, with subsequent diversification occurring it to include the ca. 25 species with simple, entire leaves that have as early as 14.5 Ma for Ascogrammitis and as recently as 3.8 Ma in black sclerotic margins. The decision to adopt a broad Grammitis Melpomene. The stem age of the Hawaiian Island endemic Adeno- comprising the entire grammitid lineage by Tryon and Tryon phorus was estimated as 22.5 Ma, and subsequent diversification (1982) was conservative, but justified by their understanding that of the genus was estimated at 10.6 Ma. the other two widely applied names at that time, Ctenopteris and Xiphopteris, were patently artificial. However, the problems in gen- 3.3. Ancestral area reconstruction eric circumscription that Tryon and Tryon (1982) faced have now largely been resolved by subsequent studies. Nonetheless, Lagrange analyses reconstructed a Neotropical ancestral area Christenhusz and Chase (2014) recently advocated treating all for the entire grammitid clade (Fig. 2a). The majority of early grammitid genera at the subgeneric rank within a single genus, diverging lineages are distributed in the Neotropics, and a Neo- Grammitis, and the clade as a tribe Polypodieae within an unwieldy tropical ancestral area was retained throughout the first six back- mega-family Polypodiaceae, subfamily . We view bone nodes of the tree. The present distribution of grammitids in this decision as retrogressive, uninformative to the goals of tropical Asia was explained by a single transition to tropical Asia biological systematics, and contrary to all other recent advances at 23.4 Ma (25.0–20.7 Ma). Subsequent backbone nodes after this in depiction of the relationships of ferns. It is also inconsistent with transition were reconstructed as having a tropical Asian ancestral their proposed treatment of the remainder of the family. Their clas- area as well. There was a single transition from within the tropical sification has the effect of obscuring understanding rather than Asian clade to the austral region at 14.7 Ma (21.0–8.6) by the genus clarifying it. A more informative classification can be found in Notogrammitis. Smith et al. (2008). Based on our sampling, the present distribution of grammitids Surprisingly, our results do not support the monophyly of in Africa and Madagascar is explained by at least six separate Grammitis s.s., the black-margined group. Instead, it is paraphylet- migrations from the Neotropics: (1) the Grammitis cryptophlebia ic, with a Neotropical clade and an Afro-Malagasy clade, and the clade 6.8 Ma [11.9–3.0]; (2) Alansmia elastica 4.9 Ma [9.9–2.0]; genus Cochlidium sister to the latter (Fig. 1). Cochlidium differs mor- (3) Melpomene flabelliformis 0.3 Ma [2.3–0.002]; (4) Stenogrammitis phologically from Grammitis s.s. by having veins usually ending in oosora 5.59 Ma [8.9–2.6]; and (5) Zygophlebia 12.6 Ma [22.1–7.5]. hydathodes, lacking the dark sclerotic margin, and in some cases Migrations of the Grammitis cryptophlebia clade and Zygophlebia by having a coenosorus (Bishop, 1978). The coenosorus is often differ from the others by involving more than a single species. sunken into a thickened lamina, giving Cochlidium a very different The former is a single event followed by a small radiation of three appearance from Grammitis s.s., in spite of having a large number species. The Zygophlebia migration involves two species (three of similarities that include radially symmetrical rhizomes, conco- accessions) that comprise the first two bifurcations of the Zygo- lorous scales, and the loss of laminar setae. These results, together phlebia-Enterosora clade. This could be interpreted as a single with the presence of Grammitis cryptophlebia (Baker) Copel., which migration followed by a subsequent migration back to the Neo- lacks a black sclerotic lamina margin, as sister to G. melanoloma tropics, or as two separate migrations to Africa–Madagascar. (Cordemoy) Tardieu, which has a black margin, indicate that the The present distribution of grammitids in the Hawaiian Islands black sclerotic lamina margin, previously considered to be a unique was explained by three migrations, two from the Neotropics (Sten- character, may in fact be homoplastic. However, our sampling of ogrammitis 1.5 Ma [4.7–0.38]; Adenophorus 22.5 [29.0–14.1]); and Grammitis s.s. is limited, and denser sampling is needed to accu- one from tropical Asia (Oreogrammitis hookeri + O. forbesiana rately estimate the evolution of that character. Sister to all of these 2.3 Ma [7.08–0.36]). is Lomaphlebia turquina (Maxon) Sundue and Ranker (Appendix 2), one of two species in the genus endemic to the and which has not been included in previous molecular phylogenetic 4. Discussion analyses. Its position here is supported by its general morphology in that it is very similar to Grammitis s.s., but lacks the black scle- 4.1. Phylogenetic results rotic lamina margin and has a submarginal commissural vein.

4.1.1. Overall results 4.1.3. Ceradenia, Enterosora, and Zygophlebia Our sampling included 31 of the 33 currently recognized gram- Our results support a monophyletic Ceradenia as sister to a mitid genera. We find that 24 of them are monophyletic (Fig. 1); clade of Zygophlebia with Enterosora nested within the latter however, these monophyletic genera are nested within other gen- (Fig. 1). These largely agree with previous results; however, era in three cases. Ctenopterella (14 spp.) and Acrosorus (11 spp.) Sundue et al. (2010) found Zygophlebia nested within Enterosora, are each represented by a single species, and so their monophyly or sister to it. Bishop (1988) anticipated the close relationship remains untested. Monophyly among the predominantly Neotrop- between Ceradenia and Zygophlebia and subsequent studies have ical lineages is not surprising as many of these genera were questioned their circumscription (Rakotondrainibe and Deroin, recently circumscribed following results of molecular phylogenetic 2006). In contrast, the distinction between Enterosora and studies. Our finding that most Paleotropical genera are monophy- Zygophlebia has received less attention. The two genera share a letic is surprising. Most of these generic concepts were based on number of characters, and the most prominent character used to morphological characters alone, which had been shown to be separate them, spongiose mesophyll, is homoplastic throughout prone to homoplasy among Neotropical lineages (Ranker et al., grammitids (Bishop and Smith, 1992; Sundue, 2010a). These 2004; Sundue, 2010a,b; Sundue et al., 2010). results suggest that maintaining the two as separate genera may not be tenable. 4.1.2. Cochlidium, Grammitis s.s., and Lomaphlebia Ceradenia is resolved into two clades that correspond with Circumscription of Grammitis, typified by G. marginella, a Neo- Bishop’s subgenera: subg. Ceradenia and subg. Filicipecten (Fig. 1). tropical species not included in our analyses (Bishop, 1977), has Although several of the species included here were described after been a central problem in the systematics of grammitid ferns. Bishop’s (1988) classification, the morphological characters he One extreme has been to use it to include all or nearly all of the used still apply. Subgenus Ceradenia is characterized by radially 200 M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206

Fig. 1. Fifty-percent majority rule consensus phylogram from the Bayesian analysis using the combined dataset. Numbers represent the posterior probability (PP) values of each branch. The scale bar indicates the number of substitutions per site. The dotted lines indicate where the two portions of the tree are connected. M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206 201

Fig. 2. Biogeographical hypothesis for the grammitid ferns inferred by the DEC model using the maximum clade credibility chronogram from the BEAST analysis. Blue bars depict the median divergence time estimates with 95% HPD intervals of each node age. The most likely ancestral areas are indicated at each node by colored squares corresponding to areas indicated on the map. Two colored squares are present when ancestral ranges include two regions. Numbers at each node represent the probabilities of ancestral ranges. Areas depicted are: Neotropical (dark blue), Africa–Madagascar and islands of the Atlantic and Indian Oceans (purple), tropical Asia and the Pacific (red), a temperate circumaustral region south of 28°S (orange), Hawaiian Islands and the central and eastern South Pacific (green), and the Nearctic (light blue). Scale bar indicates divergence times in millions of years. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.) symmetrical rhizomes, short or absent petioles, and white wax-like Scleroglossum, Tomophyllum, Micropolypodium, Xiphopterella, and glandular hairs upon the laminar surfaces and paraphyses. Dorsi- Calymmodon (Fig. 1). Parris (2007) argued that Dasygrammitis ventral rhizomes, elongate petioles, and white wax-like glandular was closely allied with Tomophyllum, Scleroglossum, and Calymm- hairs restricted to paraphyses characterize subg. Filicipecten. odon based in part upon this character, and she indicated that Xiphopterella was also likely to be related. Parris (2007) also noted 4.1.4. Phylogenetic relationships within the tropical Asian clade the morphological similarity between Micropolypodium and Xiph- A novel relationship revealed here is support of a large clade of opterella in some characters, including radial . Radially species with radially symmetrical rhizomes comprising c. 140 spp. symmetrical rhizomes occur frequently among grammitids (Parris, unpublished) belonging to six genera: Dasygrammitis, (Sundue et al., 2010), particularly in Alansmia, Leucotrichum, and 202 M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206

Fig. 2 (continued)

Radiogrammitis, but the clade of six tropical Asian genera resolved across the family, the change from dorsiventral to radially sym- here is by far the largest group of taxa sharing this morphology. metrical rhizomes is likely to be a derived trait that arose multiple Polypods, in contrast, exhibit only dorsiventral rhizomes. Thus, times within the grammitid clade. We speculate that this change is M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206 203 coincident with the reduction in size and with higher niche spe- morphological definition of the genus. Two of these species, cialization of grammitids compared to polypods. Grammitis deplanchei and G. pseudaustralis, are endemic to New Caledonia. The third, G. diminuta, is endemic to Lord Howe Island. 4.1.5. Oreogrammitis, Radiogrammitis, and Themelium Similar phylogenetic relationships were found by Perrie and Parris Copeland (1917) described Oreogrammitis to accommodate a (2012), who argued to exclude these species from Notogrammitis single species from Mt. Kinabalu, Borneo, and cited its confluent because they depart morphologically and because they lacked suf- sori as unique. Christensen and Holttum (1934) maintained the ficient support values for those nodes to justify their inclusion in genus, but noted that its validity was problematical. Parris (1983, that genus. Parris is the fourth unplaced 1990) initially sunk the genus into Grammitis because confluent taxon. In our analyses, it forms a clade with Ctenopterella denticu- sori occur in other unrelated grammitids, but later resurrected it, lata and the three accessions of Acrosorus friderici-et-pauli. Gramm- making combinations for 107 species when it became apparent itis stenophylla is an Australian endemic that was previously that a broadly circumscribed Grammitis was untenable (Parris, thought to be related to species now included in Notogrammitis 2007). The closely related Radiogrammitis was simultaneously (Parris, 1998b). Perrie and Parris (2012) concluded that it was described and distinguished by its radially symmetrical rhizomes unrelated to Notogrammitis, but did not have sufficient sampling that sometimes lack scales. By contrast, the rhizomes of Oreo- to resolve its phylogenetic placement. Its position is well resolved grammitis are uniformly dorsiventral and scaly. Our results find here as sister to Acrosorus and Ctenopterella (Fig. 1), from which it that Oreogrammitis is polyphyletic and nested in three places departs strongly morphologically, and which themselves have little within Radiogrammitis (Fig. 1). In some ways, this result is not sur- in common with each other. Long branches lead to each of these prising since the two genera were distinguished using essentially a genera, and this may indicate poor sampling in this clade. Acrosorus single character – rhizome symmetry. It is a bit unexpected; how- comprises nine species (Parris, unpubl.) and Ctenopterella has 20 ever, because rhizome symmetry effectively circumscribes many species (Parris, unpubl.). genera of grammitid ferns (Ranker et al., 2004; Sundue et al., 2010). The number of changes in rhizome symmetry within this 4.2. Historical biogeography clade suggests that there may be an increased rate of change for this character relative to other grammitid lineages. Further sam- 4.2.1. General patterns pling is needed to address that issue, however. There are 153 spe- Based on the result of our divergence estimates and ancestral cies of Oreogrammitis and 36 species of Radiogrammitis (Parris, area reconstructions, we hypothesize that the grammitid lineage unpubl.), thus the apparently large number of transitions seen in evolved in the Neotropics toward the end of the Eocene (37– our results may be an artifact of relatively low sampling of both 44.9 Ma) close to the Oligocene boundary (Fig. 2a), when the Ant- Oreogrammitis and Radiogrammitis. arctic ice sheet began to expand rapidly. Subsequent lineages Relationships within Oreogrammitis are further complicated by remained Neotropical through the end of the Oligocene. Frequent Themelium (27 species; Parris, unpubl.), which nests within it migration to Africa–Madagascar, and infrequent migration to the (Fig. 1). Themelium is similar to Oreogrammitis in its dorsiventral Hawaiian Islands and eastern Pacific occur among these lineages, rhizome with glabrous rhizome scales, but differs in having gla- beginning in the Miocene. Toward the end of the Oligocene, a sin- brous sporangia and usually subclathrate to clathrate rhizome gle lineage migrated to tropical Asia. Currently, this lineage com- scales. Radiogrammitis has small leaves that are uniformly simple prises well over half of grammitid diversity. Like the Neotropical and entire (or repand) and those of Oreogrammitis are usually also lineages, migration of the tropical Asian lineage continued during simple and entire (or repand, or even pinnate in a few species). the Miocene, but these migrations were to the Hawaiian Islands Some species of Themelium also have simple laminae; however, and Australasian regions. Further migrations from this lineage most are pinnate or twice-pinnate, sometimes with rigid sclerified did not occur to Africa–Madagascar. Our evidence does not support axes and reduced laminar tissue (Parris 1997, 2004, 2010). This Copeland’s (1939) hypothesis of an Antarctic migration of Gramm- transition from simple to compound leaves is surprising, but not itis s.l. to each of the austral continents. Instead, we reconstruct an unique. Laminar blade dissection among the 10 species of Adeno- austral lineage as being derived from tropical Asian ancestors. phorus alone ranges from simple to tripinnate (Ranker et al., 2003), in Ceradenia it ranges from simple to bipinnate (Bishop, 4.2.2. Origin of the Afro-Malagasy grammitid flora 1988), and in Notogrammitis it ranges from simple to bipinnatifid We infer that migrations to Africa and Madagascar occurred at (Perrie and Parris, 2012). These transitions occur outside of the least six times in our analyses, all within the last 14 Ma (21 Ma) grammitids as well, one example being that of Elaphoglossum sect. including the genera Alansmia, Cochlidium, Grammitis s.s., Melpom- Squamipedia Mickel & Atehortúa (Vasco et al., 2013) in comparison ene, Stenogrammitis, and Zygophlebia (Fig. 2a). Considering the to most other Elaphoglossum spp. that have simple, entire leaves. results of other studies and of species not sampled here, we expect This is among the largest and least well sampled clades of gram- that the total number of long-distance migrations from the Neotrop- mitids. With an estimated 216 species, our sampling represents ics to Africa–Madagascar will be considerably higher and will only 10% of the diversity. Our results suggest that generic recir- include species of Ceradenia, Enterosora, and Leucotrichum, as well cumscription is necessary within this clade, but denser sampling, as other species of Grammitis s.s., Stenogrammitis, and Zygophlebia including the types of all three genera, is warranted before making (Ranker et al., 2010; Labiak et al., 2010a; Rouhan et al., 2012). taxonomic changes. If a single genus is to be retained, Oreogramm- Because of their recent age, these are best explained by long- itis has nomenclatural priority, but would require alteration of its distance dispersal. Thus, as hypothesized by Moran and Smith morphological definition. (2001), the entire African-Malagasy grammitid flora appears to be the product of recent migration from the Neotropics, based on cur- 4.1.6. Orphan species rent sampling. Two of the migrations to Africa and/or Madagascar Notwithstanding the problems involving the circumscription of have led to radiations of species, including Stenogrammitis with 14 Oreogrammitis, Radiogrammitis, and Themelium, current generic species in the Neotropics and 13 species in the African-Malagasy concepts accommodate all but four species included in our analy- region (Parris, unpublished), and Zygophlebia with seven species in ses. Three of these species reside in a clade sister to Notogrammitis the Neotropics (Bishop, 1989) and nine species in Africa–Madagas- and could potentially be accommodated within an expanded con- car (Bishop, 1989; Parris, 2003; Rakotondrainibe and Deroin, 2006). cept of that genus. That would require, however, alteration of the The other large genera in the region, Ceradenia and Grammitis s.s., 204 M.A. Sundue et al. / Molecular Phylogenetics and Evolution 81 (2014) 195–206 are each represented by eight species, respectively (Bishop, 1988; Stenogrammitis) and tropical Asia (Oreogrammitis). These results Parris, 2003). There is currently no phylogenetic evidence that spe- agree with the results of Geiger et al. (2007). Two of these migra- cies have migrated from tropical Asia to Africa–Madagascar or vice tions have resulted in local radiations resulting in three species of versa. However, our sampling does not include any of the six species Oreogrammitis (only two sampled here), and 10 species of Adeno- of Ctenopterella from Africa, Madagascar, the Comoros or the Masca- phorus. The migration of Oreogrammitis to the Hawaiian Islands is renes (Parris, 2007, 2012; Parris, unpubl.). If Ctenopterella is mono- part of a larger pattern of tropical Asian species moving into the phyletic, these species would have been derived from tropical central and eastern Pacific to Rarotonga (Radiogrammitis cheesema- Asian ancestors; however, monophyly of Ctenopterella remains to nii and the Marquesas Islands (O. uapensis). A species from the be tested. Moluccas and New Guinea (R. parva) also resides within this clade Over half of the diversity in Zygophlebia resides in Madagascar, in our BEAST analysis (Fig. 2), complicating the larger pattern. We and our study is the first to sample taxa from that region (two spp., interpret our results as evidence for multiple migrations from trop- three accessions). Their relationships, resolved here as a grade sis- ical Asia to the eastern Pacific, rather than a reversal in direction, ter to the remainder of the clade, could be interpreted as evidence and this result is supported by our Bayesian analysis that supports for migration to Africa–Madagascar followed by a subsequent O. uapensis further outside of this clade (Fig. 1). More sampling is migration back to the Neotropics (Fig. 2a), a result not otherwise needed to clarify the pattern. Nonetheless, there is no indication supported by our results. This result could also be derived from that grammitids have migrated from the Hawaiian Islands to other two subsequent dispersal events. The latter explanation is consis- regions such as the Neotropics. tent with what appears to be the predominant direction of migra- Our estimated stem age of the Adenophorus clade of 22.5 Ma tion via long-distance dispersal of spores from West to East in our (29.0–14.1) is effectively identical to what Schneider et al. (2005) results. estimated for the Hawaiian endemic diellia clade of Asplenium L. Africa has also received migrants from the austral region. South of 24.3 Ma (27.0–21.5). Both of these ages effectively coincide with Africa is home to Notogrammitis angustifolia, which, along with N. the estimate of the renewal of Hawaiian terrestrial life at c. 23 Ma crassior on islands to the SW and SE of Africa, is part of a southern (Clague, 1996; Price and Clague, 2002) after a 10 Ma lull in new migration out of tropical Asia. Our results, and those of Perrie and island production by the Hawaiian volcanic hotspot. This suggests Parris (2012), suggest that N. angustifolia and N. crassior evolved that these two fern lineages were among the first to colonize suc- from ancestors residing in Australia or New Zealand, and not the cessfully the newly emerging islands in the early Miocene. As with Americas. the diellia lineage of Asplenium, the Adenophorus lineage is consid- erably older than any of the current, high Hawaiian Islands (i.e., 4.2.3. Origin of the tropical Asian and temperate austral grammitid Kaua‘i is the oldest at c. 5.2 Ma) and extant or ancestral species floras have arrived at the current islands by dispersing along the island The tropical Asian grammitid flora is best explained by a single chain as new islands have been produced. Interestingly, the Adeno- migration from the Neotropics to tropical Asia, an event estimated phorus clade at 22.5 Ma and only 10 species is nearly the same age to have occurred 24.5 Ma (22.4–27.3 Ma) (Fig. 2b). Because of its as the large, species-rich Paleotropical clade at 24.5 Ma and c. 500 recent age, this distribution pattern is likely the result of long- species (Parris, unpubl.). distance dispersal. The historical biogeography of grammitid ferns in tropical Asia is quite different than that in Hawai’i and Africa– Acknowledgments Madagascar, which are both explained by multiple long-distance dispersal events. Tropical Asia is home to the greatest diversity We thank the Curators of the following herbaria for making of grammitid species, with c. 490 species (Parris, unpubl.), and a facilities available for examination of material and/or loans: A, single origin of this diversity is a remarkable finding. Grammitids AK, B, BISH, BM, BO, BR, BRI, CANB, CGE, CHR, E, FI, GH, K, KEP, of tropical Asian origin have migrated to the Hawaiian Islands KLU, L, LAE, M, MEL, MO, NHT, NSW, NY, P, PAP, PDA, PE, PTBG, and other islands of the central and eastern Pacific, but there is S, SAN, SAR, SING, TAIF, TI, UC, US, VT, WAG, WELT, and Ewen no indication that they have migrated to Africa–Madagascar, or Cameron (AK) for organizing loans to Barbara Parris. We thank back to the Neotropics. One important migration out of tropical the University of Oslo Lifeportal for their computational resources Asia is that of Notogrammitis (12 spp.), which dominates the gram- and the Willi Hennig Society for freely providing TNT. This material 0 mitid flora in the southern hemisphere south of 35°30 S(Perrie and is based upon work supported by the National Science Foundation Parris, 2012). Notogrammitis is estimated to have entered austral of the United States under Grant No. DEB-1119695 to T.A. Ranker regions 14.7 Ma (21.0–8.6 Ma) (Fig. 2b). Range expansion was and C.W. Morden. Michael Sundue was also supported by the likely through rather than migration across the H.M. Burkill Fellowship provided by the Singapore Botanic Garden. Australian plate via the Sahul Shelf, because the to Notogrammitis comprises species currently distributed on New Cal- edonia and Lord Howe Island. Notogrammitis has also migrated Appendix A. Supplementary material around the southern hemisphere to South Africa and southern South America and oceanic islands, including Tristan da Cunha, Supplementary data associated with this article can be found, in Gough, Amsterdam, Marion, Crozet, Kerguelen, Falklands, and the online version, at http://dx.doi.org/10.1016/j.ympev.2014. South Georgia Islands. It is the only Paleotropical lineage that has 08.017. re-established itself in the Americas. 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