Systematics of Amaryllidaceae based on cladistic analysis of plastid sequence data

Cladistic analyses of plastid DNA sequences rbcL and trnL-F are presented separately and combined for 48 genera of Amaryllidaceae and 29 genera of related asparagalean families. The combined analysis is the most highly resolved of the three and provides good support for the monophyly of Amaryllidaceae and indicates Agapanthaceae as its sister family. Alliaceae are in turn sister to the Amaryllidaceae/Agapanthaceae clade. The origins of the family appear to be western Gondwanaland (Africa), and infrafamilial relationships are resolved along biogeographic lines. Tribe Amaryllideae, primarily South African, is sister to the rest of Amaryllidaceae; this tribe is supported by numerous morphological synapomorphies as well. The remaining two African tribes of the family, Haemantheae and Cyrtantheae, are well supported, but their position relative to the Australasian Calostemmateae and a large clade comprising the Eurasian and American genera, is not yet clear. The Eurasian and American elements of the family are each monophyletic sister clades. Internal resolution of the Eurasian clade only partially supports currently accepted tribal concepts, and few conclusions can be drawn on the relationships of the genera based on these data. A monophyletic Lycorideae (Central and East Asian) is weakly supported. Galanthus and Leucojum (Galantheae pro parte) are supported as sister genera by the bootstrap. The American clade shows a higher degree of internal resolution. Hippeastreae (minus Griffinia and Worsleya) are well supported, and Zephyranthinae are resolved as a distinct subtribe. An Andean clade marked by a chromosome number of 2n = 46 (and derivatives thereof) is resolved with weak support. The plastid DNA phylogenies are discussed in the context of biogeography and character evolution in the family.     

Systematics of the genus Capra inferred from mitochondrial DNA sequence data

Traditional classification in the genus Capra is based mainly on horn morphology. However, previous investigations based on allozyme data are not consistent with this classification. We thus reexamined the evolutionary history of the genus by analyzing mitochondrial DNA (mtDNA) sequence variation. We collected bone samples from museums or dead animals found in the field. Thirty-four individuals were successfully sequenced for a portion of the mtDNA cytochrome b gene and control region (500 bp in total). We obtained a star-like phylogeny supporting a rapid radiation of the genus. In accordance with traditional classification, mtDNA data support the presence of two clades in the Caucasus and the hypothesis of a domestication event in the Fertile Crescent. However, in conflict with morphology, we found that C. aegagrus and C. ibex are polyphyletic species, and we propose a new scenario for Capra immigration into Europe.     

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data

The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.     

Phylogenetic relationships in Cyperaceae subfamily Mapanioideae inferred from pollen and plastid DNA sequence data

Cyperaceae are the third largest monocotyledon family, with considerable economic and conservation importance. In subfamily Mapanioideae there is particular specialization of the inflorescence into units termed spicoids. The structural homology of the spicoid is difficult to interpret, making determination of intrafamilial relationships problematic. To address this, pollen from eight species in Mapanioideae was investigated using light microscopy and scanning and transmission electron microscopy. Pollen development was also examined to identify the type of pollen present in these species. We also analyzed DNA sequence data using the trnL-F and rps16 regions from 25 genera and 35 species of Cyperaceae, Juncaceae, and Thurniaceae. Two types of pollen, Mapania-type and pseudomonad, were identifed. Analysis of combined DNA and pollen data resolved a clade sister to the rest of Cyperaceae, corresponding to Mapanioideae. Within this, two further clades were resolved. One comprised taxa assigned to tribe Hypolytreae, which had Mapania-type pollen. The other comprised taxa mainly assigned to tribe Chrysitricheae, but included two taxa from Hypolytreae, Capitularina and Exocarya. All taxa in this clade had pseudomonad pollen. Thus new groupings within the subfamily have been discovered based on the specialization of some taxa in terms of their pollination biology.     

Phylogenetic studies of Ophioglossaceae: evidence from rbcL and trnL-F plastid DNA sequences and morphology

Ophioglossaceae are a putatively ancient lineage of ferns in which the aerial portion of the plant is composed of a single leaf. The simplicity of foliar morphology has limited the number of characters available for constructing classifications and contributed to taxonomic difficulties at nearly every level of classification within the family. Analysis of plastid DNA rbcL sequences from 36 species representing the diversity of Ophioglossaceae supported the monophyly of the family. Intrafamilial relationships were examined using rbcL and trnL-F plastid DNA sequences and morphological data. Individual and combined analyses of the three data sets revealed two main clades within the family, here termed ophioglossoid and botrychioid. In the botrychioid clade, Helminthostachys was sister to a broadly defined Botrychium, within which Botrychium in the narrow sense of some authors and Sceptridium were sister. Botrypus was paraphyletic, with Botrypus virginianus sister to Botrychium plus Sceptridium, and with Botrypus strictus sister to all other botrychioid species except Helminthostachys. In the ophioglossoid clade, Ophioglossum in the narrow sense was sister to Cheiroglossa plus Ophioderma, but relationships within Ophioglossum were not well supported.     

Molecular identification of Grateloupia elliptica and G. lanceolata (Rhodophyta) inferred from plastid rbcL and mitochondrial COI genes sequence data

The marine red algae Grateloupia is the largest genus in the family Halymeniaceae and widely distributed from tropical to warm temperate regions of the world. In the genus Grateloupia, especially G. elliptica and G. lanceolata have common features of bladelike thalli with leather in texture and cruciately divided tetrasporangia. Due to this similar morphology, G. elliptica and G. lanceolata are frequently confused and resulted in considerable difficulty distinguishing these two taxa. We have reassessed the relationships between two species using molecular identification including plastid rbcL and mitochondrial COI genes to more accurately define their genetic diversity owing to the confusion of identification. As a result, the chloroplast-encoded rbcL sequence analyses support the distinction of two species, G. elliptica and G. lanceolata collected from Jeju Island, Korea and Japan at the species level, with interspecific divergence of 3.7-4.6 %. The genetic diversity of COI gene within species are estimated to be 0–0.3 % in G. elliptica and 0–1.0 % in G. lanceolata, respectively. The effectiveness of mtDNA COI barcoding in the identification for two species demonstrates in this study.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

Phylogenetic position and generic differentiation of Epithemateae (Gesneriaceae) inferred from plastid DNA sequence data

The systematic position and generic differentiation of the morphologically and geographically outstanding tribe Epithemateae (Gesneriaceae) was analyzed using the rbcL/atpB-spacer and trnL-F intron-spacer regions of chloroplast DNA. In our analysis Epithemateae forms a strongly supported monophyletic clade (bootstrap [BS] = 100%; jackknife [JK] = 100%; decay index [DI] = 12) and appears as sister to the rest of the paleotropical Gesneriaceae (= subfamily Cyrtandroideae). The paleotropical Gesneriaceae form a monophyletic group (BS = 88%; JK = 85%; DI = 3) that is sister to the neotropical Gesneriaceae (subfamily Gesnerioideae) plus Austral Gesneriaceae (subfamily Coronantheroideae) (BS = 99%; JK = 98%; DI = 10). Within Epithemateae Rhynchoglossum is sister to the remaining Epithemateae (BS = 97%; JK = 96%; DI = 12), in which Epithema is sister to a clade of two genera: Loxonia/Stauranthera (BS = 68%; JK = 64%; DI = 1), which form, together with Epithema, a sister clade (BS = 85%; JK = 83%; DI = 2) to Whytockia and Monophyllaea. While the support for Loxonia and Stauranthera is moderate, the relationship of Whytockia and Monophyllaea is very strongly supported (BS = 100%; JK = 100%; DI = 13). Apart from the somewhat surprising (but well-substantiated) isolated position of Rhynchoglossum, the results are in perfect accordance with the relationships worked out earlier on grounds of architectural and floral characters. Especially remarkable is the predicted coherence between the morphologically and geographically different genera Whytockia and Monophyllaea.     

Phylogenetic relationships of Combretaceae inferred from nuclear and plastid DNA sequence data: implications for generic classification

The putative complexity of Combretaceae and lack of information on phylogenetic relationships within the family led us to explore relationships between genera of Combretaceae by means of combined analyses of plastid and nuclear sequences. We collected DNA sequence data from the nuclear ribosomal internal transcribed spacer region and plastid rbcL, psaA‐ycf3 spacer and psbA‐trnH spacer for 14 of the 17 genera of Combretaceae. The current classification of the family into two subfamilies, Strephonematoideae and Combretoideae, is corroborated. Within Combretoideae, division into two tribes, Laguncularieae and Combreteae, is strongly supported. Within Combreteae subtribe Terminaliinae, relationships between genera are largely unresolved. Terminalia is not supported as monophyletic and two groups were identified, one containing mainly African species and another of mostly Asian species. Pteleopsis, Buchenavia and Anogeissus are embedded within Terminalia, and we suggest that all genera of Terminaliinae, with the exception of Conocarpus, should be included in an expanded circumscrition of Terminalia. Within subtribe Combretinae, a clade formed by the two monotypic genera Guiera and Calycopteris is sister to the rest of the subtribe. Groupings in Combretinae are consistent with recent results based on morphological data. Combretum is currently divided into three subgenera: Apethalanthum, Cacoucia and Combretum. The last two were included in this study and supported as monophyletic if Quisqualis is included within subgenus Cacoucia. Meiostemon is sister to subgenus Combretum. We recommend that subgenus Combretum should be expanded to include Meiostemon and subgenus Cacoucia to include Quisqualis. The sectional classification within Combretum proposed in earlier morphological studies is confirmed except for the exclusion of C. imberbe from section Hypocrateropsis in a separate and monotypic section and the inclusion of C. zeyheri (section Spathulipetala) in section Macrostigmatea. In order to accommodate C. imberbe, a new section is suggested. The reinstatement of previously recognized sections Grandiflora and Trichopetala, both of which had been sunk into subgenus Cacoucia section Poivrea, is proposed. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 453–476.     

A phylogenetic analysis of the Arecoid Line of palms based on plastid DNA sequence data

A phylogenetic analysis of the Arecoid Line (sensu Moore) of palms was conducted using 7 kb of coding and noncoding plastid DNA sequence data. Recovered maximum-parsimony and maximum-likelihood phylogenies support monophyly for the Arecoid Line relative to the rest of the family but paraphyly for subfamily Arecoideae and polyphyly for subfamily Ceroxyloideae (sensu Dransfield and Uhl). Tribes Cocoeae, Geonomeae, Hyophorbeae, and Iriarteae and subfamily Phytelephantoideae were identified as monophyletic as were subfamily Phytelephantoideae + Ravenea (tribe Ceroxyleae of Ceroxyloideae), Podococcus (tribe Podococceae of Arecoideae) + Pseudophoenix (tribe Cyclospatheae of Ceroxyloideae), Reinhardtia (tribe Malortieinae) + tribe Cocoeae (both of Arecoideae), and a clade containing all IndoPacific pseudomonomerous genera of tribe Areceae (Arecoideae). A few taxa show spurious resolution with noncoding plastid DNA data but noncoding data are generally congruent with protein-coding data. Biogeographic interpretation suggests a Gondwanan origin for the Arecoid Line with several lineages found on more than one fragment of the former supercontinent and primary diversification in these groups possibly due to continental breakup vicariance. Three groups involving Cocos, Orania, and the IndoPacific clade demonstrate independent dispersals into the IndoPacific region from a Gondwanan origin.     

Phylogenetic relationships between Juncaceae and Cyperaceae: insights from rbcL sequence data

Among the commelinid monocots, phylogenetic relationships involving Juncaceae and Cyperaceae have been difficult to resolve because of parallel and convergent evolution of morphological features. Using comparative sequencing of the chloroplast gene rbcL, hypotheses of relationships between these two families were tested. Sequences from 13 taxa were obtained for this study and analyzed using parsimony with 15 previously published sequences. Results of this analysis suggest that two genera of Juncaceae, Oxychloë and Prionium, are not closely related to the other genera of this family. Further, Cyperaceae appear to be more closely related to Juncaceae than to Poaceae, with which Cyperaceae are sometimes classified. In fact, Cyperaceae appear to be derived from within Juncaceae. The progenitor-derivative relationship of Juncaceae and Cyperaceae suggested by this study reveals an additional example of paraphyletic families which presents a series of taxonomic dilemmas.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Phylogeny and diversification of Chinese Araliaceae based on nuclear and plastid DNA sequence data

Chinese Araliaceae consist of 20 genera and ca. 175 species. To assess the evolutionary relationships of Araliaceae and their biogeographic diversification in China, the phylogeny of Chinese Araliaceae was constructed by sampling 96 accessions representing 20 genera and 50 species of Chinese Araliaceae and 45 closely related taxa using sequences of the nuclear ribosomal internal transcribed spacer (ITS) region and six plastid regions (the ndhF gene, the trnL-trnF region, the rps16intron, the atpB-rbcL intergenic spacer, the rpl16 intron, and the psbA-trnH intergenic spacer). Phylogenetic analyses of the combined plastid and ITS data supported the results of the previously studies that the Chinese members of Araliaceae were scattered within the Asian Palmate group and the Aralia-Panax group withOsmoxylon at the base of core Araliaceae. The generic status of Pentapanax and Tupidanthus is not supported. Our analysis clearly places them in Aralia and AsianSchefflera, respectively. In a broader phylogenetic framework of Araliaceae, based on the fossil-calibrated Bayesian dating, Chinese Araliaceae was inferred to have originated in Asia and underwent a rapid radiation in its evolutionary history. Its diversification is hypothesized to have been driven largely by the orogenies in Asia during the Cenozoic. In China, the distribution pattern of the phylogenetic diversity of Araliaceae corresponds with its taxonomic diversity across the entire region.     

A phylogenetic analysis of Diurideae (Orchidaceae) based on plastid DNA sequence data

DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.     

Circumscription of the Malvales and relationships to other Rosidae: evidence from rbcL sequence data

The order Malvales remains poorly circumscribed, despite its seemingly indisputable core constituents: Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae. We conducted a two-step parsimony analysis on 125 rbcL sequences to clarify the composition of Malvales, to determine the relationships of some controversial families, and to identify the placement of the Malvales within Rosidae. We sampled taxa that have been previously suggested to be within, or close to, Malvales (83 sequences), plus additional rosids (26 sequences) and nonrosid eudicots (16 sequences) to provide a broader framework for the analysis. The resulting trees strongly support the monophyly of the core malvalean families, listed above. In addition, these data serve to identify a broader group of taxa that are closely associated with the core families. This expanded malvalean clade is composed of four major subclades: (1) the core families (Bombacaceae, Malvaceae, Sterculiaceae, Tiliaceae); (2) Bixaceae, Cochlospermaceae, and Sphaerosepalaceae (Rhopalocarpaceae); (3) Thymelaeaceae sensu lato (s.l.); and (4) Cistaceae, Dipterocarpaceae s.l., Sarcolaenaceae (Chlaenaceae), and Muntingia. In addition, Neurada (Neuradaceae or Rosaceae) falls in the expanded malvalean clade but not clearly within any of the four major subclades. This expanded malvalean clade is sister to either the expanded capparalean clade of Rodman et al. or the sapindalean clade of Gadek et al. Members of Elaeocarpaceae, hypothesized by most authors as a sister group to the four core malvalean families, are shown to not fall close to these taxa. Also excluded as members of, or sister groups to, the expanded malvalean clade were the families Aextoxicaceae, Barbeyaceae, Cannabinaceae, Cecropiaceae, Dichapetalaceae, Elaeagnaceae, Euphorbiaceae s.l., Huaceae, Lecythidaceae, Moraceae s.l., Pandaceae, Plagiopteraceae, Rhamnaceae, Scytopetalaceae, Ulmaceae, and Urticaceae.