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1.  Cytotype diversity in the Sorbus complex (Rosaceae) in Britain: sorting out the puzzle 
Annals of Botany  2012;110(6):1185-1193.
Background and Aims
Large-scale ploidy surveys using flow cytometry have become an essential tool to study plant genome dynamics and to gain insight into the mechanisms and genetic barriers framing ploidy diversity. As an ideal complement to traditional techniques such as chromosome counting, the analysis of cytotype diversity in plant systems such as Sorbus provides primary investigation into the potential patterns and evolutionary implications of hybrid speciation.
Methods
Ploidy was assessed by means of relative nuclear DNA content using propidium iodide flow cytometry in 474 Sorbus samples collected from 65 populations in southern Wales and South-West England. Statistical tests were applied to evaluate the utility of this technique to confidently discriminate ploidy in the genus.
Key Results
Flow cytometric profiles revealed the presence of four cytotypes (2x, 3x, 4x and 5x), confirming in many cases chromosome counts previously reported and demonstrating cytotype heterogeneity within specific Sorbus aggregates. Diploid cytotypes were restricted to the potential parental species and homoploid hybrids. Most of the samples processed were polyploid. The occurrence of the pentaploid cytotype had previously only been reported from a single specimen; it is now confirmed for two taxa occurring at different sites.
Conclusions
Flow cytometry results obtained have proved useful in shedding light on the taxonomy of several controversial taxa and in confirming the presence of cytoypes which occur at very low frequencies. Notably, the coexistence of several cytotypes in Sorbus populations has probably been facilitated by the overlapping distribution of many of the species studied, which might also explain the high incidence of potential hybrid apomictic polyploids. These results will provide a solid baseline for molecular research aiming to better understand the genetic pathways controlling the formation and establishment of polyploid Sorbus.
doi:10.1093/aob/mcs185
PMCID: PMC3478048  PMID: 22922587
Apomixis; cytotype mixture; flow cytometry; genome size; hybridization; ploidy; polyploidy; whitebeam
2.  Diversity, phylogeny, and evolution in the monocotyledons 
Annals of Botany  2011;108(5):vi-vii.
doi:10.1093/aob/mcr213
PMCID: PMC3177686
3.  Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement 
Annals of Botany  2010;107(1):1-37.
Background and Aims
The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed.
Methods
Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters.
Key Results
Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily.
Conclusions
On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and Trimelopter. Each of these has a particular syndrome of morphological characters. As a result, 105 new combinations are made and two new names are proposed to accommodate the taxa studied in the new arrangement. A short morphological diagnosis, synonymy, details of distribution and an identification key are presented.
doi:10.1093/aob/mcq207
PMCID: PMC3002468  PMID: 21163815
Ornithogaloideae; Hyacinthaceae; Asparagaceae; Scilloideae; molecular systematics; taxonomy
4.  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.
Background
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.
Methods
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.
Conclusions
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.
doi:10.1093/aob/mcq167
PMCID: PMC2958784  PMID: 20929900
Aphyllanthes; Asparagaceae; Convallariaceae; Dracaenaceae; Eriospermum; monocot phylogenetics; Nolinaceae; Nolinoideae
5.  The names of plants, 4th edn 
Annals of Botany  2010;106(1):viii.
doi:10.1093/aob/mcq099
PMCID: PMC2889806
6.  Micropropagation of orchids, 2 volume set, 2nd edn 
Annals of Botany  2010;105(4):vi-vii.
doi:10.1093/aob/mcq019
PMCID: PMC2850803
7.  Genetic structure and systematic relationships within the Ophrys fuciflora aggregate (Orchidaceae: Orchidinae): high diversity in Kent and a wind-induced discontinuity bisecting the Adriatic 
Annals of Botany  2009;104(3):483-495.
Background and Aims
A recent phylogenetic study based on multiple datasets is used as the framework for a more detailed examination of one of the ten molecularly circumscribed groups identified, the Ophrys fuciflora aggregate. The group is highly morphologically variable, prone to phenotypic convergence, shows low levels of sequence divergence and contains an unusually large proportion of threatened taxa, including the rarest Ophrys species in the UK. The aims of this study were to (a) circumscribe minimum resolvable genetically distinct entities within the O. fuciflora aggregate, and (b) assess the likelihood of gene flow between genetically and geographically distinct entities at the species and population levels.
Methods
Fifty-five accessions sampled in Europe and Asia Minor from the O. fuciflora aggregate were studied using the AFLP genetic fingerprinting technique to evaluate levels of infraspecific and interspecific genetic variation and to assess genetic relationships between UK populations of O. fuciflora s.s. in Kent and in their continental European and Mediterranean counterparts.
Key Results
The two genetically and geographically distinct groups recovered, one located in England and central Europe and one in south-eastern Europe, are incongruent with current species delimitation within the aggregate as a whole and also within O. fuciflora s.s. Genetic diversity is higher in Kent than in the rest of western and central Europe.
Conclusions
Gene flow is more likely to occur between populations in closer geographical proximity than those that are morphologically more similar. Little if any gene flow occurs between populations located in the south-eastern Mediterranean and those dispersed throughout the remainder of the distribution, revealing a genetic discontinuity that runs north–south through the Adriatic. This discontinuity is also evident in other clades of Ophrys and is tentatively attributed to the long-term influence of prevailing winds on the long-distance distribution of pollinia and especially seeds. A cline of gene flow connects populations from Kent and central and southern Europe; these individuals should therefore be considered part of an extensive meta-population. Gene flow is also evident among populations from Kent, which appear to constitute a single metapopulation. They show some evidence of hybridization, and possibly also introgression, with O. apifera.
doi:10.1093/aob/mcp039
PMCID: PMC2720644  PMID: 19251716
AFLP; conservation; gene flow; Kent; migration; Ophrys fuciflora; prevailing winds; pseudocopulation; speciation; species delimitation
8.  Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range 
Annals of Botany  2008;104(3):507-516.
Background and Aims
Species may occur over a wide geographical range within which populations can display large variation in reproductive success and genetic diversity. Neotinea maculata is a rare orchid of conservation concern at the edge of its range in Ireland, where it occurs in small populations. However, it is relatively common throughout the Mediterranean region. Here, factors that affect rarity of N. maculata in Ireland are investigated by comparing Irish populations with those found in Italy, where it is more common.
Methods
Vegetation communities, breeding system and genetic diversity were compared using three amplified fragment length polymorphism (AFLP) primer pairs in populations in Ireland and Italy. Vegetation was quantified using quadrats taken along transects in study populations, and hand pollination experiments were performed to assess reliance of N. maculata on pollinators in both Irish and Italian populations.
Key Results
Neotinea maculata occupies different vegetation communities in Italian and Irish populations. Breeding system experiments show that N. maculata is 100 % autogamous, and there are no differences in fruit and seed production in selfed, outcrossed and unmanipulated plants. AFLP markers revealed that Irish and Italian populations have similar genetic diversity and are distinct from each other.
Conclusions
Neotinea maculata does not suffer any negative effects of autogamous reproduction; it self-pollinates and sets seed readily in the absence of pollinators. It occupies a variety of habitats in both Ireland and Italy; however, Irish populations are small and rare and should be conserved. This could be due to climatic factors and the absence of suitable soil mycorrhizas to allow recruitment from seed.
doi:10.1093/aob/mcn200
PMCID: PMC2720646  PMID: 18940852
Neotinea maculata; AFLP; autogamy; conservation; genetic diversity; Lusitanian species; pollination
9.  Genetic diversity in Cypripedium calceolus (Orchidaceae) with a focus on north-western Europe, as revealed by plastid DNA length polymorphisms 
Annals of Botany  2009;104(3):517-525.
Background and Aims
Cypripedium calceolus, although widespread in Eurasia, is rare in many countries in which it occurs. Population genetics studies with nuclear DNA markers on this species have been hampered by its large nuclear genome size. Plastid DNA markers are used here to gain an understanding of variation within and between populations and of biogeographical patterns.
Methods
Thirteen length-variable regions (microsatellites and insertions/deletions) were identified in non-coding plastid DNA. These and a previously identified complex microsatellite in the trnL-trnF intergenic spacer were used to identify plastid DNA haplotypes for European samples, with sampling focused on England, Denmark and Sweden.
Key Results
The 13 additional length-variable regions identified were two homopolymer (polyA) repeats in the rps16 intron and a homopolymer (polyA) repeat and ten indels in the accD-psa1 intergenic spacer. In accD-psa1, most of these were in an extremely AT-rich region, and it was not possible to design primers in the flanking regions; therefore, the whole intergenic spacer was sequenced. Together, these new regions and the trnL-trnF complex microsatellite allowed 23 haplotypes to be characterized. Many were found in only one or a few samples (probably due to low sampling density), but some commoner haplotypes were widespread. Most of the genetic variation was found within rather than between populations (83 vs. 18%, respectively). Two haplotypes occurred from the Spanish Pyrenees to Sweden.
Conclusions
Plastid DNA data can be used to gain an understanding of patterns of genetic variation and seed-mediated gene flow in orchids. Although these data are less information-rich than those for nuclear DNA, they present a useful option for studying species with large genomes. Here they support the hypothesis of long-distance seed dispersal often proposed for orchids.
doi:10.1093/aob/mcp116
PMCID: PMC2720647  PMID: 19454594
Biogeography; Cypripedium calceolus; genome size; plastid microsatellites; population genetics; seed dispersal
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.
doi:10.1093/aob/mcp190
PMCID: PMC2720656  PMID: 19654223
Conservation; Darwin; evo-devo; Linnaeus; mycorrhizas; orchids; Orchidaceae; phylogenetics; pollination
11.  Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical ‘inselbergs’: Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae) 
Annals of Botany  2009;103(1):65-77.
Background and Aims
Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’ in neotropical rain forests have been identified as suitable plant models for studying population divergence and speciation during continental plant radiations. Little is known about genetic relationships and variation in reproductive strategies within and among inselberg-adapted species, yet knowledge of these parameters is important for understanding divergence processes and for conservation planning.
Methods
Nuclear microsatellites were used to assess the role of clonal reproduction, estimate genetic diversity and explore genetic relationships and variation in reproductive strategies for a total of 15 populations of four closely related Alcantarea inselberg species in south-eastern Brazil: A. glaziouana, A. regina, A. geniculata and A. imperialis.
Key Results
Clonal propagation is frequent in coastal populations of A. glaziouana and A. regina, but absent in the high-altitude species A. geniculata and A. imperialis. Considerable variation in clonal diversity, gene diversity (He), allelic richness, and Wright's inbreeding coefficient (FIS) exists within and between species of Alcantarea. A Bayesian analysis of coastal inselberg species indicated pronounced genetic structure. A neighbor-joining analysis grouped populations of each species together with moderate bootstrap support, except for the high altitude species A. imperialis.
Conclusions
The coastal inselberg species A. glaziouana and A. regina tend to propagate asexually via vegetative clonal growth, and both reproductive strategies and breeding systems vary greatly between populations and species of Alcantarea. The microsatellite data indicate a history of hybridization and reticulation involving the high-altitude species A. geniculata and A. imperialis in areas of co-occurrence. The results highlight the need to understand similarities and differences in reproductive strategies both within and between related species for conservation planning and as a basis for understanding evolutionary processes in tropical radiations.
doi:10.1093/aob/mcn226
PMCID: PMC2707295  PMID: 19074451
Alcantarea; Atlantic Rainforest; Bromeliaceae; clonality; gene flow; inselberg; microsatellites; reproductive strategy
12.  Friends or Relatives? Phylogenetics and Species Delimitation in the Controversial European Orchid Genus Ophrys 
Annals of Botany  2008;101(3):385-402.
Background and Aims
Highly variable, yet possibly convergent, morphology and lack of sequence variation have severely hindered production of a robust phylogenetic framework for the genus Ophrys. The aim of this study is to produce this framework as a basis for more rigorous species delimitation and conservation recommendations.
Methods
Nuclear and plastid DNA sequencing and amplified fragment length polymorphism (AFLP) were performed on 85 accessions of Ophrys, spanning the full range of species aggregates currently recognized. Data were analysed using a combination of parsimony and Bayesian tree-building techniques and by principal co-ordinates analysis.
Key Results
Complementary phylogenetic analyses and ordinations using nuclear, plastid and AFLP datasets identify ten genetically distinct groups (six robust) within the genus that may in turn be grouped into three sections (treated as subgenera by some authors). Additionally, genetic evidence is provided for a close relationship between the O. tenthredinifera, O. bombyliflora and O. speculum groups. The combination of these analytical techniques provides new insights into Ophrys systematics, notably recognition of the novel O. umbilicata group.
Conclusions
Heterogeneous copies of the nuclear ITS region show that some putative Ophrys species arose through hybridization rather than divergent speciation. The supposedly highly specific pseudocopulatory pollination syndrome of Ophrys is demonstrably ‘leaky’, suggesting that the genus has been substantially over-divided at the species level.
doi:10.1093/aob/mcm299
PMCID: PMC2701817  PMID: 18184645
AFLP; DNA sequencing; hybridization; introgression; Ophrys; pseudocopulation; species delimitation; systematics
13.  Towards a Phylogeny for Coffea (Rubiaceae): Identifying Well-supported Lineages Based on Nuclear and Plastid DNA Sequences 
Annals of Botany  2007;100(7):1565-1583.
Background and Aims
The phylogenetic relationships between species of Coffea and Psilanthus remain poorly understood, owing to low levels of sequence variation recovered in previous studies, coupled with relatively limited species sampling. In this study, the relationships between Coffea and Psilanthus species are assessed based on substantially increased molecular sequence data and greatly improved species sampling.
Method
Phylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions [trnL–F intron, trnL–F intergenic spacer (IGS), rpl16 intron and accD–psa1 IGS], and the internal transcribed spacer (ITS) region of nuclear rDNA (ITS 1/5·8S/ITS 2). Supported lineages in Coffea are discussed within the context of geographical correspondence, biogeography, morphology and systematics.
Key Results
Several major lineages with geographical coherence, as identified in previous studies based on smaller data sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for the first time. Coffea subgenus Baracoffea is shown to be monophyletic, but Coffea subgenus Coffea is paraphyletic. Sequence data do not substantiate the monophyly of either Coffea or Psilanthus. Low levels of sequence divergence do not allow detailed resolution of relationships within Coffea, most notably for species of Coffea subgenus Coffea occurring in Madagascar. The origin of C. arabica by recent hybridization between C. canephora and C. eugenioides is supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferred based on sequence data from Coffea.
doi:10.1093/aob/mcm257
PMCID: PMC2759236  PMID: 17956855
Africa; accD–psa1 IGS; Coffea; coffee; Indian Ocean Islands; ITS; Madagascar; molecular phylogeny; rpl16 intron; Rubiaceae; trnL–F intron; trnL–F IGS

Results 1-13 (13)