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1.  Trends and concepts in fern classification 
Annals of Botany  2014;113(4):571-594.
Background and Aims
Throughout the history of fern classification, familial and generic concepts have been highly labile. Many classifications and evolutionary schemes have been proposed during the last two centuries, reflecting different interpretations of the available evidence. Knowledge of fern structure and life histories has increased through time, providing more evidence on which to base ideas of possible relationships, and classification has changed accordingly. This paper reviews previous classifications of ferns and presents ideas on how to achieve a more stable consensus.
An historical overview is provided from the first to the most recent fern classifications, from which conclusions are drawn on past changes and future trends. The problematic concept of family in ferns is discussed, with a particular focus on how this has changed over time. The history of molecular studies and the most recent findings are also presented.
Key Results
Fern classification generally shows a trend from highly artificial, based on an interpretation of a few extrinsic characters, via natural classifications derived from a multitude of intrinsic characters, towards more evolutionary circumscriptions of groups that do not in general align well with the distribution of these previously used characters. It also shows a progression from a few broad family concepts to systems that recognized many more narrowly and highly controversially circumscribed families; currently, the number of families recognized is stabilizing somewhere between these extremes. Placement of many genera was uncertain until the arrival of molecular phylogenetics, which has rapidly been improving our understanding of fern relationships. As a collective category, the so-called ‘fern allies’ (e.g. Lycopodiales, Psilotaceae, Equisetaceae) were unsurprisingly found to be polyphyletic, and the term should be abandoned. Lycopodiaceae, Selaginellaceae and Isoëtaceae form a clade (the lycopods) that is sister to all other vascular plants, whereas the whisk ferns (Psilotaceae), often included in the lycopods or believed to be associated with the first vascular plants, are sister to Ophioglossaceae and thus belong to the fern clade. The horsetails (Equisetaceae) are also members of the fern clade (sometimes inappropriately called ‘monilophytes’), but, within that clade, their placement is still uncertain. Leptosporangiate ferns are better understood, although deep relationships within this group are still unresolved. Earlier, almost all leptosporangiate ferns were placed in a single family (Polypodiaceae or Dennstaedtiaceae), but these families have been redefined to narrower more natural entities.
Concluding this paper, a classification is presented based on our current understanding of relationships of fern and lycopod clades. Major changes in our understanding of these families are highlighted, illustrating issues of classification in relation to convergent evolution and false homologies. Problems with the current classification and groups that still need study are pointed out. A summary phylogenetic tree is also presented. A new classification in which Aspleniaceae, Cyatheaceae, Polypodiaceae and Schizaeaceae are expanded in comparison with the most recent classifications is presented, which is a modification of those proposed by Smith et al. (2006, 2008) and Christenhusz et al. (2011). These classifications are now finding a wider acceptance and use, and even though a few amendments are made based on recently published results from molecular analyses, we have aimed for a stable family and generic classification of ferns.
PMCID: PMC3936591  PMID: 24532607
Bibliography; classification; convergence; cryptogams; Cyatheaceae; fern family concepts; fern allies; ferns; homology; lycopods; monilophytes; Polypodiaceae; pteridophytes; history of botany
2.  Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes 
Annals of Botany  2012;110(1):71-90.
Background and aims
Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems.
The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution.
Key Results
The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years.
The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards.
PMCID: PMC3380586  PMID: 22539542
Character evolution; Diseae; evolution; food deception; Habenariinae; Orchideae; Orchidinae; pollination shifts; rpl16 intron; sexual deception
3.  Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae) 
Annals of Botany  2011;108(8):1417-1432.
Background and Aims
The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research.
DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping.
Key Results and Conclusions
Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family.
PMCID: PMC3219489  PMID: 21325340
Arecaceae; Areceae; Arecoideae; coconut; Cocos; Elaeis; incongruence; low-copy nuclear DNA; oil palm; Palmae; paralogy; phylogeny; pseudogene
5.  Five vicarious genera from Gondwana: the Velloziaceae as shown by molecules and morphology 
Annals of Botany  2011;108(1):87-102.
Background and Aims
The amount of data collected previously for Velloziaceae neither clarified relationships within the family nor helped determine an appropriate classification, which has led to huge discordance among treatment by different authors. To achieve an acceptable phylogenetic result and understand the evolution and roles of characters in supporting groups, a total evidence analysis was developed which included approx. 20 % of the species and all recognized genera and sections of Velloziaceae, plus outgroups representatives of related families within Pandanales.
Analyses were undertaken with 48 species of Velloziaceae, representing all ten genera, with DNA sequences from the atpB-rbcL spacer, trnL-trnF spacer, trnL intron, trnH-psbA spacer, ITS ribosomal DNA spacers and morphology.
Key Results
Four groups consistently emerge from the analyses. Persistent leaves, two phloem strands, stem cortex divided in three regions and violet tepals support Acanthochlamys as sister to Velloziaceae s.s., which are supported mainly by leaves with marginal bundles, transfusion tracheids and inflorescence without axis. Within Velloziaceae s.s., an African Xerophyta + Talbotia clade is uniquely supported by basal loculicidal capsules; an American clade, Barbacenia s.l. + Barbaceniopsis + Nanuza + Vellozia, is supported by only homoplastic characters. Barbacenia s.l. (= Aylthonia + Barbacenia + Burlemarxia + Pleurostima) is supported by a double sheath in leaf vascular bundles and a corona; Barbaceniopsis + Nanuza + Vellozia is not supported by an unambiguous character, but Barbaceniopsis is supported by five characters, including diclinous flowers, Nanuza + Vellozia is supported mainly by horizontal stigma lobes and stem inner cortex cells with secondary walls, and Vellozia alone is supported mainly by pollen in tetrads.
The results imply recognition of five genera (Acanthochlamys (Xerophyta (Barbacenia (Barbaceniopsis, Vellozia)))), solving the long-standing controversies among recent classifications of the family. They also suggest a Gondwanan origin for Velloziaceae, with a vicariant pattern of distribution.
PMCID: PMC3119618  PMID: 21693665
Acanthochlamys; Barbacenia; Barbaceniopsis; Gondwanian origin; morphological and molecular characters; phylogenetic analysis; Vellozia; Velloziaceae; vicarious distribution; Xerophyta
6.  Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences 
Annals of Botany  2010;106(5):775-790.
Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae.
A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades.
Key Results
The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae–Agapanthaceae–Alliaceae); (2) Asparagaceae–Laxmanniaceae–Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae–Behniaceae–Herreriaceae–Agavaceae (clades 2–5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum.
The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.
PMCID: PMC2958784  PMID: 20929900
Aphyllanthes; Asparagaceae; Convallariaceae; Dracaenaceae; Eriospermum; monocot phylogenetics; Nolinaceae; Nolinoideae
7.  Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes 
Annals of Botany  2010;106(1):37-56.
Background and Aims
Here evidence for reticulation in the pantropical orchid genus Polystachya is presented, using gene trees from five nuclear and plastid DNA data sets, first among only diploid samples (homoploid hybridization) and then with the inclusion of cloned tetraploid sequences (allopolyploids). Two groups of tetraploids are compared with respect to their origins and phylogenetic relationships.
Sequences from plastid regions, three low-copy nuclear genes and ITS nuclear ribosomal DNA were analysed for 56 diploid and 17 tetraploid accessions using maximum parsimony and Bayesian inference. Reticulation was inferred from incongruence between gene trees using supernetwork and consensus network analyses and from cloning and sequencing duplicated loci in tetraploids.
Key Results
Diploid trees from individual loci showed considerable incongruity but little reticulation signal when support from more than one gene tree was required to infer reticulation. This was coupled with generally low support in the individual gene trees. Sequencing the duplicated gene copies in tetraploids showed clearer evidence of hybrid evolution, including multiple origins of one group of tetraploids included in the study.
A combination of cloning duplicate gene copies in allotetraploids and consensus network comparison of gene trees allowed a phylogenetic framework for reticulation in Polystachya to be built. There was little evidence for homoploid hybridization, but our knowledge of the origins and relationships of three groups of allotetraploids are greatly improved by this study. One group showed evidence of multiple long-distance dispersals to achieve a pantropical distribution; another showed no evidence of multiple origins or long-distance dispersal but had greater morphological variation, consistent with hybridization between more distantly related parents.
PMCID: PMC2889800  PMID: 20525745
Allopolyploidy; consensus network; filtered supernetwork; low-copy nuclear genes; Orchidaceae; phylogenetic analysis; Polystachya; reticulate evolution
8.  Orthoptera, a new order of pollinator 
Annals of Botany  2010;105(3):355-364.
Background and Aims
Pollinator-mediated selection and evolution of floral traits have long fascinated evolutionary ecologists. No other plant family shows as wide a range of pollinator-linked floral forms as Orchidaceae. In spite of the large size of this model family and a long history of orchid pollination biology, the identity and specificity of most orchid pollinators remains inadequately studied, especially in the tropics where the family has undergone extensive diversification. Angraecum (Vandeae, Epidendroideae), a large genus of tropical Old World orchids renowned for their floral morphology specialized for hawkmoth pollination, has been a model system since the time of Darwin.
The pollination biology of A. cadetii, an endemic species of the islands of Mauritius and Reunion (Mascarene Islands, Indian Ocean) displaying atypical flowers for the genus (white and medium-size, but short-spurred) was investigated. Natural pollinators were observed by means of hard-disk camcorders. Pollinator-linked floral traits, namely spur length, nectar volume and concentration and scent production were also investigated. Pollinator efficiency (pollen removal and deposition) and reproductive success (fruit set) were quantified in natural field conditions weekly during the 2003, 2004 and 2005 flowering seasons (January to March).
Key Results
Angraecum cadetii is self-compatible but requires a pollinator to achieve fruit set. Only one pollinator species was observed, an undescribed species of raspy cricket (Gryllacrididae, Orthoptera). These crickets, which are nocturnal foragers, reached flowers by climbing up leaves of the orchid or jumping across from neighbouring plants and probed the most ‘fresh-looking’ flowers on each plant. Visits to flowers were relatively long (if compared with the behaviour of birds or hawkmoths), averaging 16·5 s with a maximum of 41·0 s. At the study site of La Plaine des Palmistes (Pandanus forest), 46·5 % of flowers had pollen removed and 27·5 % had pollinia deposited on stigmas. The proportion of flowers that set fruit ranged from 11·9 % to 43·4 %, depending of the sites sampled across the island.
Although orthopterans are well known for herbivory, this represents the first clearly supported case of orthopteran-mediated pollination in flowering plants.
PMCID: PMC2826249  PMID: 20067913
Angraecum; Mascarene Archipelago; oceanic islands; Orchidaceae; Orthoptera; plant–pollinator interactions; pollinator shifts
9.  A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences 
Annals of Botany  2009;104(3):417-430.
Background and Aims
Laeliinae are a neotropical orchid subtribe with approx. 1500 species in 50 genera. In this study, an attempt is made to assess generic alliances based on molecular phylogenetic analysis of DNA sequence data.
Six DNA datasets were gathered: plastid trnL intron, trnL-F spacer, matK gene and trnK introns upstream and dowstream from matK and nuclear ITS rDNA. Data were analysed with maximum parsimony (MP) and Bayesian analysis with mixed models (BA).
Key Results
Although relationships between Laeliinae and outgroups are well supported, within the subtribe sequence variation is low considering the broad taxonomic range covered. Localized incongruence between the ITS and plastid trees was found. A combined tree followed the ITS trees more closely, but the levels of support obtained with MP were low. The Bayesian analysis recovered more well-supported nodes. The trees from combined MP and BA allowed eight generic alliances to be recognized within Laeliinae, all of which show trends in morphological characters but lack unambiguous synapomorphies.
By using combined plastid and nuclear DNA data in conjunction with mixed-models Bayesian inference, it is possible to delimit smaller groups within Laeliinae and discuss general patterns of pollination and hybridization compatibility. Furthermore, these small groups can now be used for further detailed studies to explain morphological evolution and diversification patterns within the subtribe.
PMCID: PMC2720643  PMID: 19423551
Laeliinae; Orchidaceae; ITS; trnL intron; trnL-F spacer; matK
10.  Orchid biology: from Linnaeus via Darwin to the 21st century 
Annals of Botany  2009;104(3):359-364.
Orchidaceae are the largest family of flowering plants, with at least 24 000 species, and perhaps better than any other family of flowering plants, orchids represent the extreme specializations that are possible. As a result, they have long fascinated luminaries of the botanical world including Linnaeus and Darwin, but the size of the family has historically been an impediment to their study. Specifically, the lack of detailed information about relationships within the family made it difficult to formulate explicit evolutionary hypotheses for such a large group, but the advent of molecular systematics has revolutionized our understanding of the orchids. Their complex life histories make orchids particularly vulnerable to environmental change, and as result many are now threatened with extinction. In this Special Issue we present a series of 20 papers on orchid biology ranging from phylogenetics, floral evolutionary development, taxonomy, mycorrhizal associations, pollination biology, population genetics and conservation.
PMCID: PMC2720656  PMID: 19654223
Conservation; Darwin; evo-devo; Linnaeus; mycorrhizas; orchids; Orchidaceae; phylogenetics; pollination
11.  Floral convergence in Oncidiinae (Cymbidieae; Orchidaceae): an expanded concept of Gomesa and a new genus Nohawilliamsia 
Annals of Botany  2009;104(3):387-402.
Floral morphology, particularly the angle of lip attachment to the column, has historically been the fundamental character used in establishing generic limits in subtribe Oncidiinae (Orchidaceae), but it has also been long recognized that reliance on this character alone has produced a highly artificial set of genera. In essence, lip/column relationships reflect syndromes associated with pollinator preferences; most genera of Oncidiinae as previously defined have consisted of a single floral type. Here, the degree to which this has influenced generic delimitation in Brazilian members of the largest genus of Oncidiinae, Oncidium, which previous molecular (DNA) studies have demonstrated to be polyphyletic, is evaluated.
Phylogenetic analyses of the following multiple DNA regions were used: the plastid psbA-trnH intergenic spacer, matK exon and two regions of ycf1 exon and nuclear ribosomal DNA, comprised of the two internal transcribed spacers, ITS1 and ITS2, and the 5·8S gene. Results from all regions analysed separately indicated highly similar relationships, so a combined matrix was analysed.
Key Results
Nearly all species groups of Brazilian Oncidium are only distantly related to the type species of the genus, O. altissimum, from the Caribbean. There are two exceptions to this geographical rule: O. baueri is related to the type group and O. orthostates, an isolated species that lacks the defining tabula infrastigmata of Oncidium, is not exclusively related to any previously described genus in the subtribe. Several well-supported subclades can be observed in these results, but they do not correspond well to sections of Oncidium as previously circumscribed or to segregate genera as defined by several recent authors. In spite of their floral differences, these groups of Oncidium, formerly treated as O. sections Barbata, Concoloria pro parte, Crispa, Ranifera, Rhinocerotes, Rostrata (only O. venustum), Synsepala, Verrucituberculata pro parte and Waluewa, form a well-supported clade with Gomesa (including Rodrigueziella and Rodrigueziopsis) embedded in it. Two often recognized segregate genera, Baptistonia and Ornithophora, and the recently described Carriella are also embedded within the Brazilian clade. The level of variation within major subclades of the Gomesa clade is low and similar to that observed within other genera of Oncidiinae.
Convergence on a stereotypical syndrome of floral traits associated with pollination by oil-collecting bees has resulted in these characters not being reliable for producing monophyletic taxa, and the genus Oncidium, defined by these characters, is grossly polyphyletic. Vegetative and a few floral/inflorescence characters link these taxa with a mainly Brazilian distribution, and they were all transferred to Gomesa on this basis rather than separated from Gomesa based on their floral differences, which we hypothesize to be simple shifts in pollination strategies. Other authors have described a large number of new genera for these former members of Oncidium, but most of these are not supported by the results presented here (i.e. they are not monophyletic). A new genus, Nohawilliamsia, is described for O. orthostates because it does not fit in any currently recognized genus and is only distantly related to any other member of Oncidiinae.
PMCID: PMC2720657  PMID: 19346522
Baptistonia; Brazilian orchids; Carriella; deceit pollination; Gomesa; ITS; matK; oil-collecting bees; Oncidium; Oncidiinae; Orchidaceae
12.  Phylogenetic relationships of Cranichidinae and Prescottiinae (Orchidaceae, Cranichideae) inferred from plastid and nuclear DNA sequences 
Annals of Botany  2009;104(3):403-416.
Background and Aims
Phylogenetic relationships of subtribes Cranichidinae and Prescottiinae, two diverse groups of neotropical terrestrial orchids, are not satisfactorily understood. A previous molecular phylogenetic study supported monophyly for Cranichidinae, but Prescottiinae consisted of two clades not sister to one another. However, that analysis included only 11 species and eight genera of these subtribes. Here, plastid and nuclear DNA sequences are analysed for an enlarged sample of genera and species of Cranichidinae and Prescottiinae with the aim of clarifying their relationships, evaluating the phylogenetic position of the monospecific genera Exalaria, Ocampoa and Pseudocranichis and examining the value of various structural traits as taxonomic markers.
Approx. 6000 bp of nucleotide sequences from nuclear ribosomal (ITS) and plastid DNA (rbcL, matK-trnK and trnL-trnF) were analysed with cladistic parsimony and Bayesian inference for 45 species/14 genera of Cranichidinae and Prescottiinae (plus suitable outgroups). The utility of flower orientation, thickenings of velamen cell walls, hamular viscidium and pseudolabellum to mark clades recovered by the molecular analysis was assessed by tracing these characters on the molecular trees.
Key Results
Spiranthinae, Cranichidinae, paraphyletic Prescottia (with Pseudocranichis embedded), and a group of mainly Andean ‘prescottioid’ genera (the ‘Stenoptera clade’) were strongly supported. Relationships among these clades were unresolved by parsimony but the Bayesian tree provided moderately strong support for the resolution (Spiranthinae–(Stenoptera clade-(Prescottia/Pseudocranichis–Cranichidinae))). Three of the four structural characters mark clades on the molecular trees, but the possession of a pseudolabellum is variable in the polyphyletic Ponthieva.
No evidence was found for monophyly of Prescottiinae and the reinstatement of Cranichidinae s.l. (including the genera of ‘Prescottiinae’) is favoured. Cranichidinae s.l. are diagnosed by non-resupinate flowers. Lack of support from parsimony for relationships among the major clades of core spiranthids is suggestive of a rapid morphological radiation or a slow rate of molecular evolution.
PMCID: PMC2720660  PMID: 19136493
Cranichideae; Cranichidinae; matK-trnK; molecular phylogenetics; nrITS; Orchidaceae; Prescottiinae; resupination; trnL-trnF
13.  Molecular phylogenetics and morphological reappraisal of the Platanthera clade (Orchidaceae: Orchidinae) prompts expansion of the generic limits of Galearis and Platanthera 
Annals of Botany  2009;104(3):431-445.
Background and Aims
The Platanthera clade dominates the North American orchid flora and is well represented in eastern Asia. It has also generated some classic studies of speciation in Platanthera sections Platanthera and Limnorchis. However, it has proved rich in taxonomic controversy and near-monotypic genera. The clade is reviewed via a new molecular phylogenetic analysis and those results are combined with brief reconsideration of morphology in the group, aiming to rationalize the species into a smaller number of larger monophyletic genera and sections.
Nuclear ribosomal internal transcribed spacer (ITS) sequences were obtained from 86 accessions of 35 named taxa, supplemented from GenBank with five accessions encompassing a further two named taxa.
Key Results
Using Pseudorchis as outgroup, and scoring indels, the data matrix generated 30 most-parsimonious trees that differed in the placement of two major groups plus two closely related species. Several other internal nodes also attracted only indifferent statistical support. Nonetheless, by combining implicit assessment of morphological divergence with explicit assessment of molecular divergence (when available), nine former genera can be rationalized into four revised genera by sinking the monotypic Amerorchis, together with Aceratorchis and Chondradenia (neither yet sequenced), into Galearis, and by amalgamating Piperia, Diphylax and the monotypic Tsaiorchis into the former Platanthera section Platanthera. After further species sampling, this section will require sub-division into at least three sections. The present nomenclatural adjustments prompt five new combinations.
Resolution of major groups should facilitate future species-level research on the Platanthera clade. Recent evidence suggests that ITS sequence divergence characterizes most species other than the P. bifolia group. The floral differences that distinguished Piperia, Diphylax and Tsaiorchis from Platanthera, and Aceratorchis and Chondradenia from Galearis, reflect various forms of heterochrony (notably paedomorphosis); this affected both the perianth and the gynostemium, and may have proved adaptive in montane habitats. Floral reduction was combined with lateral expansion of the root tubers in Piperia and Diphylax (including Tsaiorchis), whereas root tubers were minimized in the putative (but currently poorly supported) Neolindleya–Galearis clade. Allopolyploidy and/or autogamy strongly influenced speciation in Platanthera section Limnorchis and perhaps also Neolindleya. Reproductive biology remains an important driver of evolution in the clade, though plant–pollinator specificity and distinctness of the species boundaries have often been exaggerated.
PMCID: PMC2720662  PMID: 19383726
Aceratorchis; Amerorchis; Chondradenia; Diphylax; Galearis; generic delimitation; internal transcribed spacer; Neolindleya; orchid; Piperia; phylogeny; Platanthera; Pseudorchis; speciation; Tsaiorchis
14.  Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics 
Annals of Botany  2008;101(6):815-823.
The evolution and biology of rDNA have interested biologists for many years, in part, because of two intriguing processes: (1) nucleolar dominance and (2) sequence homogenization. We review patterns of evolution in rDNA in the angiosperm genus Nicotiana to determine consequences of allopolyploidy on these processes.
Allopolyploid species of Nicotiana are ideal for studying rDNA evolution because phylogenetic reconstruction of DNA sequences has revealed patterns of species divergence and their parents. From these studies we also know that polyploids formed over widely different timeframes (thousands to millions of years), enabling comparative and temporal studies of rDNA structure, activity and chromosomal distribution. In addition studies on synthetic polyploids enable the consequences of de novo polyploidy on rDNA activity to be determined.
We propose that rDNA epigenetic expression patterns established even in F1 hybrids have a material influence on the likely patterns of divergence of rDNA. It is the active rDNA units that are vulnerable to homogenization, which probably acts to reduce mutational load across the active array. Those rDNA units that are epigenetically silenced may be less vulnerable to sequence homogenization. Selection cannot act on these silenced genes, and they are likely to accumulate mutations and eventually be eliminated from the genome. It is likely that whole silenced arrays will be deleted in polyploids of 1 million years of age and older.
PMCID: PMC2710217  PMID: 18310159
Diploidization; epigenetics; nucleolar dominance; polyploidy; rDNA; ribosomal DNA; sequence homogenization
15.  Cryptic Speciation in the Caesalpinia hintonii Complex (Leguminosae: Caesalpinioideae) in a Seasonally Dry Mexican Forest 
Annals of Botany  2007;100(6):1307-1314.
Backgroud and Aims
The Caesalpinia hintonii group comprises six species of endemic shrubs or trees, C. epifanioi, C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. oyamae, found in scattered patches of seasonally dry forest in the Río Balsas depression and the neighbouring Tehuacán–Cuicatlán valley, which are part of the Mexican morphotectonic province of Sierra Madre del Sur. An evaluation is made of phylogeographic patterns and genetic diversity with a phylogenetic analysis of the C. hintonii complex in order to study the dynamics of speciation in this endemic group of legumes.
A phylogeographic study based on four highly variable non-coding plastid regions (trnL intron, trnL-F intergenic spacer, trnH-psbA intergenic spacer, and accD-psaI intergenic spacer) was carried out for the Caesalpinia hintonii complex. Five of the six taxa of the C. hintonii complex were included.
Key Results and Conclusions
The plastid analyses involving multiple accessions of each taxon from throughout their ranges resolved C. epifanioi and C. hintonii as well-supported clusters, but C. oyamae has two unexpectedly divergent lineages. Two well-supported geographic clades: eastern (C. epifanioi, C. melanadenia and C. oyamae) and western (C. hintonii and C. macvaughii) were established. The analyses performed provide evidence of recent morphostatic radiation in C. oyamae resulting from isolation and local adaptation. This pattern of genetic differentiation without morphological divergence may be a model that fits many groups of tropical woody taxa inhabiting similarly dry forests subjected to shifting selection.
PMCID: PMC2759254  PMID: 17913727
Caesalpinia hintonii complex; legumes; Mesoamerica; Mexico; plant phylogeography; population differentiation; seasonally dry forest

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