Polyphyly of the fern family Tectariaceae sensu Ching: insights from cpDNA sequence data

Tectariaceae are a pantropical fern family of about 20 genera, among which 8 are distributed in China. The morphological distinctiveness of the family is widely recognized, yet relatively little systematic research has been conducted on members of Tectariaceae. Phylogenetic analyses of chloroplast DNA sequence data (rbcL and atpB) from 15 species representing all 8 genera in China were carried out under parsimony criteria and Bayesian inference. The phylogenetic reconstructions indicated that the fern family Tectariaceae as traditionally circumscribed are polyphyletic. Ctenitis, Dryopsis, Lastreopsis clustered with and should be included within the newly-defined Dryopteridaceae, and Pleocnemia is also tentatively assigned to it. A narrowly monophyletic Tectariaceae is identified, which includes Ctenitopsis, Hemigramma, Pteridrys, Quercifilix, and Tectaria. In the single rbcL analysis, Arthropteris clustered with the above-mentioned monophyletic Tectariaceae. Although further investigations are still needed to identify infrafamilial relationships within the monophyletic Tectariaceae and to redefine several problematic genera, we propose a working concept here that better reflects the inferred evolutionary history of this group.     

Towards the natural classification of tectarioid ferns: Confirming the phylogenetic relationships of Pleocnemia and Pteridrys (eupolypods I)

The phylogenetic relationships of the two derived fern genera Pleocnemia and Pteridrys were considered ambiguous even with molecular evidence from previous studies. In the present study we determined the phylogenetic position based on five plastid DNA regions, namely atpA, atpB, rbcL, the rps4 + rps4–trnS intergenic spacer, and the trnL-F region, and an expanded taxonomic coverage including several accessions of each of the two genera. Our results showed that the monophyletic genus Pleocnemia belonged to the Dryopteridaceae and was not related to the Tectariaceae, as it had been in the past. Pleocnemia was found to be closely related to the bolbitidoid and lastreopsioid ferns. The monophyletic genus Pteridrys was found to be sister to a clade comprising Triplophyllum and Tectarias.l. Thus, the placement of this genus into Tectariaceae was confirmed. The sinus teeth, the unique similarity shared by Pleocnemia and Pteridrys, evolved independently in the two genera. Both genera appeared to have diverged from their closest extant relatives at least since the Eocene, whereas the crown group ages indicated radiation events in the Late Miocene for both genera.     

Phylogenetic relationships of Salix (Salicaceae) based on rbcL sequence data

Nucleotide sequences of the chloroplast-encoded rbcL gene were used to examine phylogenetic relationships of the genus Salix together with other allied genera of the family Salicaceae. Phylogenetic analyses of rbcL sequences strongly suggest the monophyly of three commonly recognized genera (Chosenia, Salix, and Toisusu). Two monophyletic groups are recognized within the larger monophyletic group. They do not correspond with any infrageneric taxa proposed so far. With regard to character evolution, it is thought that the reduction of stamen number from more than two stamens to two might occur in at least three lineages and that fused bud scales evolved several times and/or the reverse evolution occurred from fused to free. Some types of pollen surfaces are considered to have evolved independently.     

Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective

Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes--while playing an essential role in fern colonization and reproduction--generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNA-identifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distance-based analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology.     

Pteridryaceae: A new fern family of Polypodiineae (Polypodiales) including taxonomic treatments

We undertook phylogenetic analyses to resolve the relationships of Pteridrys and related taxa based on six plastidmarkers (atpA, atpB, matK& rps16-matK, rbcL, rps4& rps4-trnS, and trnL & trnL-F) and nuclear pgiC.We included 195 accessions representing approximately 147 species in 38 genera, and seven of the nine families in Polypodiineae (eupolypods I). Tectariaceae s.l. (i.e., Arthropteris, Draconopteris, Hypoderris, Malaifilix, Pteridrys, Tectaria, and Triplophyllum in addition to Polydictyum) is recovered asmonophyletic (97% maximum likelihood bootstrap value), but with low (<50%) maximum parsimony jackknife value. The family Tectariaceae s.l. is therefore the only family in ferns without a corresponding non-parametric-based strong support in spite of our data totaling 9616 aligned base pairs. Tectariaceae s.l. can not be unambiguously recognized by any of the 13morphological characters analyzed. However, if the clade composed of Draconopteris, Malaifilix, Polydictyum, and Pteridrys (DMPP) is recognized as a distinct family, at least four morphological characters enable the distinction of the DMPP clade from its sister clade. Considering the uncertainty in the monophyly, the diagnosability, and the deep divergence, we propose to establish a new family, Pteridryaceae, to accommodate the DMPP clade. Species of Pteridryaceae share mostly the following characteristics: erect to suberect rhizomes, reduced basal pinnae, anastomosing or free venation, absence of catenate hairs at the leaf surface, and perine ornamentation lacking spines or spinules. Identification keys are provided for the four genera and 31 species of the DMPP clade (or Pteridryaceae). Reflecting the presented results, the recognition of Arthropteridaceae is the preferred taxonomic status of the Arthropteris clade.     

海南尖峰岭自然保护区蕨类植物区系分析

对海南尖峰岭国家级自然保护区的蕨类植物区系进行了分析。结果表明：自然保护区内共有蕨类植物165种,隶属于41科84属,优势科有7科,分别为水龙骨科、铁角蕨科、金星蕨科、蹄盖蕨科、叉蕨科、膜蕨科、鳞毛蕨科,含5种以上的优势属有7属,分别为铁角蕨属Asplenium、卷柏属Selaginella、观音座莲属Angiopteris、鳞始蕨属Lindsaea、凤尾蕨属Pteris、短肠蕨属Allantodia、鳞毛蕨属Dryopteris;根据植物的现代地理分布,本区蕨类植物科、属、种的热带成分分别占非世界分布的96.6%、90.4%、72.2%,表明本区蕨类植物区系具有较强的热带性质;本区蕨类植物的属内种类贫乏,含1种的属占63.1%,含2～3种的属占21.4%;生态类型多样,主要有土生蕨类、石生和附生蕨类;苏铁蕨Brainea insignis、水蕨Certopteris thalictroides、金毛狗Cibotium barometz、桫椤Alsophila spinulosa、黑桫椤Gymnasphaera podophylla、大叶黑桫椤Gymnasphaera gigantea是本区国家重点二级保护珍稀濒危蕨类植物,应采取措施加强保护。     

里白科植物的系统发育和分歧时间估计——基于叶绿体三个基因序列的证据

里白科(Gleicheniaceae)是古老的真蕨类植物,最早的化石记录可追溯到石炭纪。现存类群的属级分类和系统演化关系一直存在很大的分歧,为了进一步探讨该类群的起源演化,文中运用最大简约法和贝叶斯演绎方法对18种代表现存里白科植物全部6属(包括新测的12种)的叶绿体3个编码基因序列(atpB,rbcL和rps4)进行分析,探讨其主要分类群(属级)的系统演化关系。结果显示,里白科植物为一个单系群,由3个分支构成:里白属(Diplopterygium Nakai)和Gleichenia japonica构成一个分支;芒萁属(Dicranopteris Bernh.)和Gleichenella pec-tinata构成另一个分支;假芒萁属(Sticherus C.Presl)与单种属Stromatopteris Mettenius及Gleichenia dicarpa构成第三个分支。用宽松分子钟方法推测里白科主要类群的起源时间为:现代里白科植物起源于早白垩世(111—140Ma),其主要分支类群随后发生多样性分化,里白属和芒萁属的快速辐射演化均发生在古近纪(40—64Ma,36—50Ma)。起源时间的估算结果暗示化石种三叠里白Diplopterygium triassica不应归入现代里白属,其归属需要重新考虑。     

New insights on the phylogeny of Tectaria (Tectariaceae), with special reference to Polydictyum as a distinct lineage

The fern genus Tectaria (Tectariaceae) Cav. is morphologically diverse and difficult in terms of recognizing species and species groups. To infer the systematic positions of some species and identity-unknown collections with special morphological characters, we undertook phylogenetic analyses based on sequences of five plastid regions (atpB, ndhF + ndhF-trnL, rbcL, rps16-matK + matK, and trnL-F). Three analysis methods (maximum parsimony, maximum likelihood, and Bayesian inference) were used to reconstruct the phylogeny of Tectaria. The most surprising result is that T. menyanthidis (C. Presl) Copel., T. ternata (Baker) Copel., and T. variabilis Tardieu & Ching are revealed to represent a distinct lineage from Tectaria, which should be called Polydictyum C. Presl, and is supported as sister to Pteridrys C. Chr. & Ching. Other accessions of Tectaria are well resolved into four major clades, which is consistent with the results of previous studies. Of the four clades, Clade II (T. subtriphylla (Hook. & Arn.) Copel. group) is unpredictable, with morphologically very diverse species clustered there, and is supposed to be a minor evolutionary line within Tectaria in the Old World. In addition, the position of the climbing genus Arthropteris J. Sm. and the utility of molecular data in recognizing species of Tectaria are briefly discussed. As a conclusion, we formally reinstate the genus Polydictyum by providing diagnostic characters, key to species, nomenclature, and information of detailed distribution and habitat for the currently known three species.     

Origin of Hawaiian Polystichum (Dryopteridaceae) in the context of a world phylogeny

A genus-wide molecular phylogeny for Polystichum and allied genera (Dryopteridaceae) was reconstructed to address the biogeographic origin and evolution of the three Hawaiian Polystichum species, all endemic there. The analysis was based on the cpDNA sequences rbcL and the trnL-F spacer from a taxonomically and geographically diverse sample. Parsimony and Bayesian phylogenetic analyses of the combined data support a monophyletic Polystichum and corroborate recent hypotheses as to membership and sequence of origin of the major groups within the genus. The Hawaiian Polystichum species are polyphyletic; two separate lineages appear to have arrived independently from the Old World. The provenance of the diploid Polystichum hillebrandii is continental eastern Asia, while the source of the polyploid lineage comprising tetraploid P. haleakalense and octoploid P. bonseyi is likely continental Asia. From our results, the origin of the Hawaiian species of Polystichum, like many Hawaiian fern genera with several species, is the result of multiple migrations to the islands, rather than single migrations yielding nearly all the local diversity as in the angiosperms. This emerging pattern provides a modern test of the premise that propagule vagility has a central role in determining pattern of evolution.     

Origin and evolution of the colonial volvocales (Chlorophyceae) as inferred from multiple, chloroplast gene sequences

A combined data set of DNA sequences (6021 bp) from five protein-coding genes of the chloroplast genome (rbcL, atpB, psaA, psaB, and psbC genes) were analyzed for 42 strains representing 30 species of the colonial Volvocales (Volvox and its relatives) and 5 related species of green algae to deduce robust phylogenetic relationships within the colonial green flagellates. The 4-celled family Tetrabaenaceae was robustly resolved as the most basal group within the colonial Volvocales. The sequence data also suggested that all five volvocacean genera with 32 or more cells in a vegetative colony (all four of the anisogamous/oogamous genera, Eudorina, Platydorina, Pleodorina, and Volvox, plus the isogamous genus Yamagishiella) constituted a large monophyletic group, in which 2 Pleodorina species were positioned distally to 3 species of Volvox. Therefore, most of the evolution of the colonial Volvocales appears to constitute a gradual progression in colonial complexity and in types of sexual reproduction, as in the traditional volvocine lineage hypothesis, although reverse evolution must be considered for the origin of certain species of Pleodorina. Data presented here also provide robust support for a monophyletic family Goniaceae consisting of two genera: Gonium and Astrephomene.     

Clarification of the relationship beteen Apiaceae and Araliaceae based on matK and rbcL sequence data

Apiaceae and Araliaceae (Apiales) represent a particularly troublesome example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. Previous studies based on rbcL sequence data provided insights at higher levels, but were unable to resolve fully the family-pair relationship. In this study, sequence data from a more rapidly evolving gene, matK, was employed to provide greater resolution. In Apiales, matK sequences evolve an average of about two times faster than rbcL sequences. Results of phylogenetic analysis of matK sequences were first compared to those obtained previously from rbcL data; the two data sets were then combined and analyzed together. Molecular analyses confirm the polyphyly of apiaceous subfamily Hydrocotyloideae and suggest that some members of this subfamily are more closely related to Araliaceae than to other Apiaceae. The remainder of Apiaceae forms a monophyletic group with well-defined subclades corresponding to subfamilies Apioideae and Saniculoideae. Both the matK and the combined rbcL-matK analyses suggest that most Araliaceae form a monophyletic group, including all araliads sampled except Delarbrea and Mackinlaya. The unusual combination of morphological characters found in these two genera and the distribution of matK and rbcL indels suggest that these taxa may be the remnants of an ancient group of pro-araliads that gave rise to both Apiaceae and Araliaceae. Molecular data indicate that the evolutionary history of the two families is more complex than simple derivation of Apiaceae from within Araliaceae. Rather, the present study suggests that there are two well-defined "families," both of which may have been derived from a lineage (or lineages) or pro-araliads that may still have extant taxa.     

Family-level relationships of Onagraceae based on chloroplast rbcL and ndhF data

Despite intensive morphological and molecular studies of Onagraceae, relationships within the family are not fully understood. One drawback of previous analyses is limited sampling within the large tribe Onagreae. In addition, the monophyly of two species-rich genera in Onagreae, Camissonia and Oenothera, has never been adequately tested. To understand relationships within Onagraceae, test the monophyly of these two genera, and ascertain the affinities of the newly discovered genus Megacorax, we conducted parsimony and maximum likelihood analyses with rbcL and ndhF sequence data for 24 taxa representing all 17 Onagraceae genera and two outgroup Lythraceae. Results strongly support a monophyletic Onagraceae, with Ludwigia as the basal lineage and a sister-taxon relationship between Megacorax and Lopezia. Gongylocarpus is supported as sister to Epilobieae plus the rest of Onagreae, although relationships within the latter clade have limited resolution. Thus, we advocate placement of Gongylocarpus in a monogeneric tribe, Gongylocarpeae. Most relationships within Onagreae are weakly resolved, suggesting a rapid diversification of this group in western North America. Neither Camissonia nor Oenothera appears to be monophyletic; however, increased taxon sampling is needed to clarify those relationships. Morphological characters generally agree with the molecular data, providing further support for relationships.     

Major evolutionary events in the origin and diversification of the fern genus Polystichum (Dryopteridaceae)

Recent advances in molecular systematics of the ferns make it possible to address long-standing questions about classification of the major fern genera, such as the worldwide genus Polystichum (Dryopteridaceae), comprising at least 200 species. In this study we examined rbcL sequences and morphological characters from 55 fern taxa: 34 were from Polystichum and 21 were from other genera in the Dryopteridaceae. We found that Phanerophlebia, possibly including Polystichopsis, is the sister group to Polystichum sensu lato (s.l.), including Cyrtomium. Polystichum as commonly recognized is paraphyletic. Our results lead us to suggest recognizing the clade of earliest diverging Polystichum species as a distinct genus (Cyrtomidictyum) and to continue to recognize Cyrtomium as a separate genus, leaving a monophyletic Polystichum sensu stricto (s.s.). We resolved a tropical American clade and an African clade within Polystichum s.s. However, the resemblance between the once-pinnate, bulb-bearing calciphilic species found in Asia and the West Indies appears to be the result of convergent evolution. Optimizing our morphological character transformations onto the combined phylogeny suggests that the common ancestor of Polystichum s.l. and Phanerophlebia had evolved the common features of the alliance, including ciliate petiole-base scales, once-pinnate fronds, ultimate segments with scarious tips, peltate indusia, and microscales.     

Phylogenetic analyses and chromosome evolution in Convallarieae (Ruscaceae sensu lato), with some taxonomic treatments

The tribe Convallarieae, comprising 10 genera and 95 species, has recently been transferred from its own family to Ruscaceae sensu lato. In this study, sequence data from trnK and rbcL were analyzed for 19 species in 8 genera, and chromosome morphology was analyzed for 17 species in 7 genera. The parsimony analysis of trnK and rbcL sequences showed that Convallarieae are monophyletic. Although early branches did not receive strong bootstrap support, Convallaria diverged at the first branch, followed by Speirantha. The rest of the tribe was split into three, well-supported clades: one with Reineckea, the second with Campylandra and Rohdea, and the third with Tupistra, Tricalistra, and Aspidistra. Two monotypic genera, Rohdea and Tricalistra, were embedded in a clade of Campylandra and of Tupistra, respectively. Three karyotypes were distinguished in the tribe on the basis of the basic number and morphology of metaphase chromosomes: Convallaria type (with x=19 and unimodal chromosome length), Tupistra type (with x=19 and trimodal chromosome length), and Aspidistra-elatior type (with x=18 and trimodal chromosome length). The character-state distribution in the molecular tree showed that the Convallaria type is plesiomorphic, from which was derived the Tupistra type and subsequently the Aspidistra-elatior type. Taxonomic treatments to transfer Campylandra to Rohdea and Tricalistra to Tupistra are also given.     

A new taxonomic system of the Campanulaceae s.s.

The Campanulaceae s.s. have been proved to be monophyletic, but the subdivision of the family is still controversial among authors. To investigate the intrafamilial structure of the Campanulaceae s.s., four chloroplast DNA fragments, atpB, matK, rbcL, and petD with the petB-petD spacer region, were chosen for molecular phylogenetic analysis, and 90 taxa representing 36 genera of this family were sampled. The result shows that the Campanulaceae s.s. consist of three strongly supported monophyletic clades. This result is highly correlated with the data from palynology and external morphology. Therefore, we propose to establish a new three tribal classification system of Campanulaceae s.s. The Cyanantheae is characterized by colpate or colporate pollen with elongate apertures and a loculicidal capsule which is dehiscent by apical valves, or a berry. The other two tribes have porate pollen with poroid apertures, but the Campanuleae possesses a poricidal capsule which is dehiscent by lateral pores or valves, or a dry indehiscent fruit, whereas the Wahlenbergieae possesses a loculicidal capsule which is dehiscent by apical valves, pores, or opercula. In the Cyanantheae, we recognize 6 subtribes and 10 genera. In addition, keys to tribes of Campanulaceae s.s. and to subtribes and genera of the Cyanantheae are presented.     

金佛山自然保护区蕨类植物资源与区系初步研究

金佛山自然保护区共计有野生蕨类植物46科107属458种(含亚种和变种)。在科的区系成分中单种科14个,少型科(2~5种)16个,多种科(包含6~19种)12个,大科(20~49种)1个,特大科(50种以上)3个,分别占金佛山蕨类植物总科数的30.43%、34.78%、26.09%、2.17%和6.53%;其中热带分布占总科数的54.35%;在属的区系成分中,具12个分布区类型,单种属和少种属数量多;热带成分丰富,包含55属,占总属数的51.40%;特有现象明显,地方特有种十分丰富;属的区系与武陵山和大巴山关系最为密切,与九华山、化龙山、齐云山和云山关系疏远;东亚分布、世界广布、热带亚洲至热带非洲间断分布及北温带分布型对该区系性质的影响最大,热带亚洲分布型和东亚北美间断分布型的影响最小;该区系具有古老、孑遗和原始性等特点,验证了金佛山地区处于我国三大特有现象中心之一的鄂西—川东特有现象中心的观点。     

Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences

Phylogenetic analyses of Meliaceae, including representatives of all four currently recognized subfamilies and all but two tribes (32 genera and 35 species, respectively), were carried out using DNA sequence data from three regions: plastid genes rbcL, matK (partial), and nuclear 26S rDNA (partial). Individual and combined phylogenetic analyses were performed for the rbcL, matK, and 26S rDNA data sets. Although the percentage of informative characters is highest in the segment of matK sequenced, rbcL provides the greatest number of informative characters of the three regions, resulting in the best resolved trees. Results of parsimony analyses support the recognition of only two subfamilies (Melioideae and Swietenioideae), which are sister groups. Melieae are the only tribe recognized previously that are strongly supported as monophyletic. The members of the two small monogeneric subfamilies, Quivisianthe and Capuronianthus, fall within Melioideae and Swietenioideae, respectively, supporting their taxonomic inclusion in these groups. Furthermore, the data indicate a close relationship between Aglaieae and Guareeae and a possible monophyletic origin of Cedreleae of Swietenioideae. For Trichilieae (Melioideae) and Swietenieae (Swietenioideae) lack of monophyly is indicated.     

A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide

Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.     

A MOLECULAR PHYLOGENY OF THE GELIDIALES (RHODOPHYTA) BASED ON ANALYSIS OF PLASTID rbcL NUCLEOTIDE SEQUENCES1

Parsimony analyses of rbcL nucleotide. sequences were used to develop hypotheses of relationships among taxa in the taxonomically difficult order Celidiales including species from seven currently recognized genera: Capreolia, Gelidiella, Gelidium, Onikusa, Pterocladia, Ptilophora, and Suhria. Nucleotide. sequences of rbcL from red algae are variable and provide a large number of informative characters for phylogenetic analysis, yet the absence of insertion/deletion mutations allows for the unambiguous alignment of sequences. Species were resolved into 10 well-.supported major clades representing genera and species complexes. The topological positions of these 10 clades within trees are also well supported and indicate that Gelidium and Pterocladia as currently circumscribed are not monophyletic. These results call for a revision of the classification of the Gelidiales .