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PLoS Curr. 2010 November 22; 2: RRN1197.
PMCID: PMC2989831
Tree of Life

New insights into the phylogeny and historical biogeography of the Lellingeria myosuroides clade (Polypodiaceae)

Abstract

Grammitid ferns are a well-supported clade of ~900 primarily tropical epiphytic species. Recent phylogenetic studies have found support for a distinctive, geographically diverse group of 24 species referred to as the Lellingeria myosuroides clade and have provided evidence for a variety of phylogenetic relationships within the group, as well as hypotheses of historical processes that have produced current biogeographical patterns. We present new data and analyses that support the following primary conclusions: 1) the L. myosuroides clade is monophyletic and pantropical; 2) that clade is sister to a more species rich clade of entirely Neotropical species (Lellingeria s.s.); 3) we infer two independent dispersal events from the Neotropics to Pacific islands, five independent dispersal events from the Neotropics to the Paleotropics, and two separate dispersal events from mainland tropical America to the West Indies.

Introduction

Grammitid ferns comprise a well-supported clade of ~900 primarily epiphytic, tropical species of the widespread family Polypodiaceae [1] (Parris, unpublished data). One of the long-standing questions in the study of grammitid ferns has been the circumscription of genera, with some authors recognizing a single genus [2] and others up to 24 [3]. The first broad molecular phylogenetic study of grammitids provided new insights and some clarification of generic delimitations. Ranker et al. [4] found that only six of 12 genera for which more than one species was sampled were recovered as monophyletic. Large genera in both the Paleotropics (e.g., Ctenopteris Blume ex Kunze s.l., Grammitis Sw. s.l.) and the Neotropics (e. g., Lellingeria A. R. Sm. & R. C. Moran, Terpsichore A. R. Sm.) were found to be polyphyletic. Ranker et al. [4] cited convergent evolution and the use of homoplastic characters by taxonomists to account for the problems in generic circumscription. That study has been followed by more intensive studies of particular grammitid groups (e.g., [5] [6] [7]), some of which have led to nomenclatural changes, including the recognition of new genera [8] [9] [10] [11] [12] [13] [14].

      We focus here on the Lellingeria myosuroides (Sw.) A.R. Sm. & R.C. Moran group recognized by Smith et al. [15]. Phylogenetic studies of molecular and morphological data provide strong support for the monophyly of this group [16] [5] [4] [7] and its sister relationship to a clade containing all remaining species of Lellingeria (the Lellingeria s.s. clade of Labiak et al., [5]). The group includes 24 species, which are distinguished from Lellingeria s.s by segments with a single unbranched vein, the fertile veins with dark sclerenchyma visible beneath the sporangia, linear hydathodes, and a single sorus per segment (Fig. 1) and will be recognized as a new genus by Labiak [10]. Unlike Lellingeria s.s., which is restricted to the Neotropics, the L. myosuroides clade has a pantropical distribution, and is found in the Neotropics (West Indies, Mexico to Bolivia, and Brazil), Hawaiian Islands, French Polynesia, Africa, Madagascar, and La Réunion Island [5]. Estimations of relationships within the L. myosuroides clade, including attempts to explain biogeographical patterns, however, have varied across studies. For example, the focus of the work of Geiger et al. [16] was to use molecular phylogenetics to explore the geographical origins of multiple Hawaiian fern lineages, including the Hawaiian endemic L. saffordii (Maxon) A. R. Sm. & R. C. Moran (Fig. 1e, 1f). Their results supported a sister relationship between L. saffordii and the French Polynesian endemic L. subcoriacea (Copel.) A.R. Sm. & R.C. Moran, with that clade being sister to the Neotropical L. limula (Christ) A.R. Sm. & R.C. Moran. The clade of those three species was embedded in a larger clade of Neotropical species. Thus, Geiger et al. [16] inferred a single dispersal event from the Neotropics of the common ancestor of the two Pacific species. By contrast, Labiak et al. [5] and Sundue et al. [7] included additional species of Lellingeria in their analyses, although the latter did not include L. subcoriacea. Both of those studies provided robust support for a sister relationship between the Hawaiian L. saffordii and the Mexican L. hellwigii (Mickel & Beitel) A.R. Sm. & R.C. Moran. Although the analysis of Labiak et al. [5] could not resolve the exact relationships of L. subcoriacea, it was clearly not sister to L. saffordii or even the L. saffordii-L. hellwigii clade. Thus, they hypothesized two independent dispersal events of the ancestors of L. saffordii and L. subcoriacea from the Neotropics.

      We present new evidence of relationships and biogeographical affinities among members of the L. myosuroides clade based on phylogenetic analyses of plastid DNA sequences.

figure ranker-et-al.-figure-1-small
Figure 1. Examples of species in the Lellingeria myosuroides clade. A. Habit of L. pumila (Brazil). B. Segments and sori of L. limula, showing the green spores inside the sporangia (Costa Rica). C. Habit of L. wittigiana ...


Materials and Methods

Taxonomic sampling — Outgroup sampling included 18 species (19 accessions) including species of Lellingeria s.s., Melpomene A. R. Sm. & R. C. Moran, the Terpsichore anfractuosa clade, and the Terpsichore subscabra clade. These were chosen because they have been recovered as the closest relatives to the Lellingeria myosuroides clade in previously published studies [4] [5] [7]. The ingroup is represented by 13 species (24 accessions), representing 54% of the known species. Voucher information is listed in Appendix 1.

DNA extraction, amplifications and sequencing — Genomic DNA was isolated following the protocol detailed in Ranker et al. [17]. The three plastid DNA markers used for the analyses (atpB, rbcL, and trnL-trnF) were amplified by PCR following the protocols detailed in Ranker et al. [17]. All 28 newly obtained consensus sequences have been submitted to GenBank (Appendix 1).

Alignment and phylogenetic analyses — Consensus sequences were automatically aligned using the program Muscle v3.6 [18], and the resulting alignment was manually checked and revised when necessary. Following alignment, we coded the resulting gaps for the trnL-trnF region following the simple coding model as suggested by Simmons and Ochoterena [19], using the program 2xread [20]. Data matrices were constructed using the program ASADO [21] and analyzed using equally weighted maximum parsimony (MP), and Bayesian inference (BI). Maximum parsimony analyses were performed using the program TNT v1.1 [22]. For all MP analyses, heuristic searches were performed with 10,000 parsimony ratchet replicates ([23]; 200 iteration ratchet, the up and down weights set to 5% each), holding 20 trees per ratchet, followed by tree-bisection-reconnection (TBR)-max branch swapping. Support for nodes for the combined data set analysis was calculated by bootstrap analyses (BS), with 1000 replicates doing 10 ratchets per replicate, holding 20 trees per ratchet, and keeping only the strict consensus. The best performing evolutionary model was obtained by the Akaike information criterion (AIC; [24]), using the program jModeltest v.0.1.1 [25]. Bayesian analyses (BI) were performed using the program MrBayes v.3.1.2 [26] [27] on the freely available Bioportal ( www.bioportal.uio.no ). The coded gap characters (for trnL-trnF) were included and analyzed separately from the rest of the sequence data, being set to follow the model implemented in MrBayes for binary data: “lset coding = variable”. The partition strategy included the models for each marker, separate codon positions for atpB and rbcL, and the binary model for the coded gap characters. Three independent runs were started from random trees, consisting of four chains each, one cold and three hot, with the temperature parameter set to 0.2. The analyses were run for 10 million generations, sampling every 1000th generations. To assess whether the Markov chain Monte Carlo (MCMC) reached stationarity after the “burn-in” period, we compared the standard deviation of split frequencies, and by looking at the posterior probability of each clade, as suggested by Huelsenbeck et al. [28], using the online program AWTY [29]. Our data file has been submitted to TreeBase under study number S11022 (http://purl.org/phylo/treebase/phylows/study/TB2:S11022).

   Nomenclatural novelties ― The new species mentioned in the text are not intended to be formal proposals. They will be validly published in subsequent articles.

Results and Discussion

      We report here only the results of the analyses of the combined dataset, the resulting phylogenetic trees of which were more resolved and statistically more strongly supported than each tree resulting from the three separate data matrices. The MP analysis recovered three equally parsimonious trees, with L = 628, CI = 0.64, and RI = 0.87. These collapsed at three nodes in a Nelson strict consensus tree. Bootstrap support values (BS) are shown on the strict consensus tree (Fig. 2). Convergence between the three runs of the Bayesian analysis was satisfactorily achieved


figure ranker-et-al-figure-2
Figure 2. Strict consensus tree from parsimony analysis of the combined dataset. Numbers above branches are bootstrap values. Names in black text are of Neotropical species. Other text colors represent the geographical areas ...

according to a plot of the log likelihood (lnL) and analyses performed using AWTY [29]. The 50% majority-rule consensus phylogram from the Bayesian analysis is shown in Fig. 3, which shows the posterior probability (PP) support of the resolved branches. Generally, our results support the relationships discovered by the analyses of Labiak et al. [5] and we will not comment on most of them. As with previous studies, the L. myosuroides clade was strongly supported as monophyletic (100 BS, 1.00 PP). Parsimony and Bayesian analyses also strongly supported the sister-taxon status of the Hawaiian L. saffordii and the Mexican L. hellwigii (100 BS, 1.00 PP). The relationships of the French Polynesian L. subcoriacea were not resolved in either analysis but it was clearly not sister to L. saffordii or even the L. saffordii-L. hellwigii clade. Thus, these results support the hypothesis of Labiak et al. [5] of two independent dispersal events to Pacific islands, probably from the Neotropics, and not the single-dispersal hypothesis of Geiger et al. [16]. Our results also suggest that there were five independent dispersal events from the Neotropics to the Paleotropics, and two separate dispersal events from mainland tropical America to the West Indies.

figure ranker-et-al-figure-3
Figure 3. Fifty percent majority-rule consensus phylogram from the Bayesian analysis of the combined dataset. Numbers to the right of or below branches are posterior probabilities. Names in black text are of Neotropical species. ...

      The parsimony analysis also found strong support (100 BS) for a sister-taxon relationship between the L. saffordii-L. hellwigii clade and what had been called the L. myosuroides clade, as had Labiak et al. [5], but with some significant differences because of the addition of two new accessions. Labiak et al. [5] included data from six South American/Andean accessions labeled L. myosuroides, however, recent observations [10] have shown that these Andean specimens should be referred to Xiphopteris jamesonii Hook., a species that has been considered as a synonym of L. myosuroides by recent authors (e.g., [15] [30]. This species occurs in Central America and the Andes and is morphologically and geographically distinct from L. myosuroides, which is restricted to the Antilles. Our dataset included all of the sequence data used by Labiak et al. [5], plus a new accession of true L. myosuroides from the Dominican Republic. We also included a new accession from La Réunion Island in the Indian Ocean, which had originally been identified as L. myosuroides but will be described soon as a new species, and that is restricted to La Réunion (Parris, unpublished data). We tentatively refer to it as L. reunionensis Parris sp. nov. ined. Table 1 presents some of the key differences among X. jamesonii, L. myosuroides, and L. reunionensis. Our parsimony and Bayesian analyses placed both L. myosuroides and L. reunionensis within the X. jamesonii clade, rendering X. jamesonii paraphyletic. Lellingeria myosuroides was supported as sister to an accession of X. jamesonii (98 BS, 1.00 PP) and L. reunionensis was placed with 100 BS and 1.00 PP support as a member of a distinct clade with four other accessions of X. jamesonii. One interpretation of this is that X. jamesonii is the ancestral taxon for L. myosuroides and L. reunionensis, both of which diverged from X. jamesonii subsequent to independent long-distance dispersals away from the Andes. Alternatively, there could be multiple cryptic species within this clade for which distinctive characters have yet to be discovered.

     Another interesting pattern is the fact that the L. myosuroides clade is geographically highly diverse, having both Neotropical and Paleotropical species, including some extremely localized endemics, whereas its sister clade (Lellingeria s.s.) is more species rich but restricted entirely to the Neotropics. We suggest that detailed studies of life history and other attributes may be of value in helping to explain this phenomenon.

Table 1. Key characters distinguishing X. jamesonii, L. myosuroides, and L. reunionensis.

Table thumbnail

Acknowledgements

We thank Robbin Moran for use of the L. limula photo.

Funding information

Funding for this project was provided in part by grants to Tom Ranker from the US National Science Foundation (DEB-0344522) and the National Geographic Society. Michael Sundue's research was supported in part by the Burkill Fellowship at the Singapore Botanic Garden.Paulo Labiak's research was partially funded by the Brazilian government (CNPq/PDE n° 201782/2008–1).

Competing interests

The authors have declared that no competing interests exist.

Appendix 1

 Accession information of species in analyses.  nd = no data

Table thumbnail

References

  • Schneider, H., A. R. Smith, R. Cranfill, T. E. Hildebrand, C. H. Haufler, T. A. Ranker. 2004. Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae & Grammitidaceae): exploring aspects of the diversification of epiphytic plants. Molecular Phylogenetics and Evolution 31: 1041–1063. [PubMed]
  • Tryon, R. M. and A. F. Tryon. 1982. Ferns and allied plants: with special reference to tropical America. New York: Springer-Verlag.
  • Parris, B. S. 2009. New genera of Malesian Grammitidaceae (Monilophyta). Blumea 54: 217–219.
  • Ranker, T. A., A. R. Smith, B. S. Parris, J. M. O. Geiger, C. H. Haufler, S. C. K. Straub, and H. Schneider. 2004. Phylogeny and evolution of grammitid ferns (Grammitidaceae): a case of rampant morphological homoplasy. Taxon 53: 415–428.
  • Labiak, P. H., M. Sundue, and G. Rouhan. 2010a. Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae). American Journal of Botany 97: 1354–1364. [PubMed]
  • Lehnert, M., M. Kessler, A. N. Schmidt-Lebuhn, S. A. Klimas, S. D. Fehlberg, T. A. Ranker. 2009. Phylogeny of the fern genus Melpomene (Polypodiaceae) inferred from morphology and chloroplast DNA analysis. Systematic Botany 34: 17–27.
  • Sundue, M. A., M. B. Islam, and T. A. Ranker. 2010. Systematics of grammitid ferns (Polypodiaceae): using morphology and plastid sequence data to resolve the circumscription of Melpomene and portions of the polyphyletic genera Lellingeria and Terpsichore. Systematic Botany 35: 701–715.
  • Kessler, M., A. L. Moguel Velázquez, M. A. Sundue, and P. H. Labiak. In press. Alansmia, a new genus of grammitid ferns (Polypodiaceae) segregated from Terpsichore. Brittonia.
  • Labiak, P. H. and F. B. Matos. 2007. A new hybrid and two new combinations in neotropical grammitid ferns. Brittonia 59: 182–185.
  • Labiak, P. H. In press. Stenogrammitis, a new genus of grammitid ferns segregated from Lellingeria (Polypodiaceae). Brittonia.
  • Labiak, P. H., M. Sundue, and G. Rouhan. 2010b. Phylogeny and taxonomy of Leucotrichum (Polypodiaceae), a new genus of the grammitid ferns from the neotropics. Taxon 59: 911–921.
  • Parris, B. S. 2007. Five new genera and three new species of Grammitidaceae (Filicales) and the re-establishment of Oreogrammitis. Gardens’ Bulletin Singapore 58: 233–274.
  • Ranker, T. A. 2008. A new combination in Adenophorus (Polypodiaceae). 2008. American Fern Journal 98: 170–171.
  • Sundue, M. A. In press. A monograph of Ascogrammitis, a new genus of grammitid ferns (Polypodiaceae). Brittonia.
  • Smith, A. R., R. C. Moran, and L. E. Bishop. 1991. Lellingeria, a new genus of Grammitidaceae. American Fern Journal 81: 76–88.
  • Geiger, J. M. O., T. A. Ranker, J. M. Ramp Neale, and S. T. Klimas. 2007. Molecular biogeography and origins of the Hawaiian fern flora. Brittonia 59: 142–158.
  • Ranker, T. A., J. M. O. Geiger, S. C. Kennedy, A. R. Smith, C. H. Haufler, and B. S. Parris. 2003. Molecular phylogenetics and evolution of the endemic Hawaiian genus Adenophorus (Grammitidaceae). Molecular Phylogenetics and Evolution 26: 337–347. [PubMed]
  • Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792–1797. [PMC free article] [PubMed]
  • Simmons, M. P., and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369–381. [PubMed]
  • Little, D.P. 2005. 2xread: a simple indel coding tool. Program distributed by the author.
  • Nixon, K. C. 2004. ASADO version 1.5 Beta. Program and documentation distributed by the author. Ithaca, New York, USA.
  • Goloboff, P. A., J. S. Farris, and K. C. Nixon. 2008. TNT, a free program for phylogenetic analysis. Cladistics 24: 774–786.
  • Nixon, K. C. 1999. The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis. Cladistics 15: 407–414.
  • Akaike, H. 1973. Information theory as an extension of the maximum likelihood principle. In: B. N. Petrov and F. Csaki (Eds.), Second International Symposium on Information Theory. Budapest: Akademiai Kiado, pp. 267–281.
  • Posada, D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253–1256. [PubMed]
  • Huelsenbeck, J.P., and Ronquist, F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755. [PubMed]
  • Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. [PubMed]
  • Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Evolution – Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 2310–2314. [PubMed]
  • Wilgenbusch, J. C., D. L. Warren, and D. L. Swofford. 2004. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available at <http://ceb.csit.fsu.edu/awty>. [PubMed]
  • Labiak, P. H. and J. Prado. 2005. The species of Melpomene and Micropolypodium (Grammitidaceae – Pteridophyta) in Brazil. Boletim de Botânica da Universidade de São Paulo. 23: 51–69.

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