Publications by authors named "Michael F Fay"

63 Publications

Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae).

Ann Bot 2021 Feb 18. Epub 2021 Feb 18.

Royal Botanic Gardens, Kew, Richmond, UK.

Background And Aims: Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution.

Methods: DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum.

Key Results: On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes.

Conclusions: The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.
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http://dx.doi.org/10.1093/aob/mcab005DOI Listing
February 2021

Effective double-digest RAD sequencing and genotyping despite large genome size.

Mol Ecol Resour 2021 May 9;21(4):1037-1055. Epub 2021 Jan 9.

Royal Botanic Gardens, Kew, Richmond, Surrey, UK.

Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double-digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set-specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.
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http://dx.doi.org/10.1111/1755-0998.13314DOI Listing
May 2021

Lost and Found: and , the Forgotten Coffee Crop Species of West Africa.

Front Plant Sci 2020 19;11:616. Epub 2020 May 19.

Department of Agriculture, Health and Environment, Faculty of Engineering and Science, Natural Resources Institute, University of Greenwich, Medway, United Kingdom.

(Arabica) and (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: and . We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of ; (2) identify new accessions of ; (3) refute hybrid status for ; (4) identify accessions confused with ; (5) show that and are closely related, and possibly a single species; (6) substantiate the hybrid × ; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in ; (8) infer that is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa species (Coffee Crop Wild Relative Priority Groups I and II). and may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.
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http://dx.doi.org/10.3389/fpls.2020.00616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248357PMC
May 2020

Conservation of the Threatened Species, Pulsatilla vulgaris Mill. (Pasqueflower), is Aided by Reproductive System and Polyploidy.

J Hered 2019 08;110(5):618-628

Royal Botanic Gardens, Kew, Richmond, UK.

Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using 10 nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations are not as evident as expected from demographic trends. Restored populations show genetic variation comparable to their source populations and, in general, to the wild ones. Genetic homogeneity is observed in regeneration trials, although some alleles not captured in source populations are detected. We infer that polyploidy, longevity, and clonal reproduction have provided P. vulgaris with the standing genetic variation necessary to make the species resilient to the effects of demographic decline, suggesting that the use of multiple sources for reintroduction may be beneficial to mimic natural gene flow and the availability of multiple allele copies typical of polyploid species.
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http://dx.doi.org/10.1093/jhered/esz035DOI Listing
August 2019

Apomixis and Hybridization Drives Reticulate Evolution and Phyletic Differentiation in L.: Implications for Conservation.

Front Plant Sci 2018 13;9:1796. Epub 2018 Dec 13.

Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.

Hybridization and polyploidy are major forces in the evolution of plant diversity and the study of these processes is of particular interest to understand how novel taxa are formed and how they maintain genetic integrity. is an example of a genus where active diversification and speciation are ongoing and, as such, represents an ideal model to investigate the roles of hybridization, polyploidy and apomixis in a reticulate evolutionary process. To elucidate breeding systems and evolutionary origins of a complex of closely related taxa, we assessed genotypic diversity and population structure within and among taxa, combining data from nuclear DNA microsatellite markers and flow cytometry. Clonal analysis and low genotypic diversity within the polyploid taxa suggest apomixis is obligate. However, genetic variation has led to groups of 'clone-mates' within apomictic taxa that strongly suggest mutation is responsible for the genotypic diversity of these apomictic lineages. In addition, microsatellite profiles and site demographics suggest hybridization events among apomictic polyploid may have contributed to the extant diversity of recognized taxa in this region. This research demonstrates that both macro- and micro-evolutionary processes are active within this reticulate complex. Conservation measures should be aimed at maintaining this process and should therefore be prioritized for those areas of species richness where the potential for interspecific gene flow is greatest.
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http://dx.doi.org/10.3389/fpls.2018.01796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300497PMC
December 2018

Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization.

BMC Genomics 2018 Aug 2;19(1):578. Epub 2018 Aug 2.

School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.

Background: Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA.

Results: SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific.

Conclusions: We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
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http://dx.doi.org/10.1186/s12864-018-4956-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6090851PMC
August 2018

Orchid conservation: how can we meet the challenges in the twenty-first century?

Authors:
Michael F Fay

Bot Stud 2018 Jun 5;59(1):16. Epub 2018 Jun 5.

Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.

With c. 28,000 species, orchids are one of the largest families of flowering plants, and they are also one of the most threatened, in part due to their complex life history strategies. Threats include habitat destruction and climate change, but many orchids are also threatened by unsustainable (often illegal and/or undocumented) harvest for horticulture, food or medicine. The level of these threats now outstrips our abilities to combat them at a species-by-species basis for all species in such a large group as Orchidaceae; if we are to be successful in conserving orchids for the future, we will need to develop approaches that allow us to address the threats on a broader scale to complement focused approaches for the species that are identified as being at the highest risk.
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http://dx.doi.org/10.1186/s40529-018-0232-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988927PMC
June 2018

Isolation and characterization of microsatellite loci in and cross-amplification in and (Rosaceae).

Appl Plant Sci 2017 Feb 14;5(2). Epub 2017 Feb 14.

Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom; School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia.

Premise Of The Study: Southwestern Britain is an emblematic hotspot of polyploid diversity of whitebeams ( agg.; Rosaceae) with ca. 30 polyploid endemic species. The tetraploid is postulated as one of the parents of most of these endemics, along with the sexual diploid s. str. and the tetraploid .

Methods And Results: We isolated 16 nuclear microsatellite loci from and characterized them on 45 trees representing the three putative parental species. Eleven loci were polymorphic, and eight of them exhibited species-specific alleles. Allele numbers ranged from one to 11, and observed heterozygosity ranged from 0.40 to 1.00. The intraspecific levels of variation were very low, in agreement with the facultative apomictic reproduction hypothesized for this species.

Conclusions: The species-specific alleles will be useful for tracing the origin of the narrowly distributed taxa. In addition, the assessment of diversity levels will help design a conservation strategy for the polyploid complex.
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http://dx.doi.org/10.3732/apps.1600150DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5315384PMC
February 2017

Orchid conservation: further links.

Authors:
Michael F Fay

Ann Bot 2016 07;118(1):89-91

Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia

Background: Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here.

Conclusions: The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use.
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http://dx.doi.org/10.1093/aob/mcw147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4934403PMC
July 2016

Valproate in Adjuvant Glioblastoma Treatment.

J Clin Oncol 2016 09 13;34(25):3105-7. Epub 2016 Jun 13.

University of Newcastle; Calvary Mater Hospital, Newcastle, New South Wales; University of Queensland, Brisbane, Queensland, Australia.

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http://dx.doi.org/10.1200/JCO.2016.67.2162DOI Listing
September 2016

Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula.

Am J Bot 2016 04 7;103(4):677-91. Epub 2016 Apr 7.

Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom.

Premise Of The Study: Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation.

Methods: Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis.

Key Results: Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes.

Conclusions: Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators.
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http://dx.doi.org/10.3732/ajb.1500252DOI Listing
April 2016

Orchid conservation: making the links.

Ann Bot 2015 Sep;116(3):377-9

Department of Environment and Agriculture, Curtin University, Kent Street, Bentley, Perth, Western Australia, 6102, Australia.

Orchidaceae, one of the largest families of flowering plants, present particular challenges for conservation, due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees. In this Highlight, we present seven papers focusing on orchids and their interactions and other factors relating to their conservation.
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http://dx.doi.org/10.1093/aob/mcv142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549965PMC
September 2015

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

New Phytol 2015 Oct 8;208(2):596-607. Epub 2015 Jun 8.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK.

Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.
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http://dx.doi.org/10.1111/nph.13471DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4744688PMC
October 2015

Beyond the EDGE with EDAM: Prioritising British Plant Species According to Evolutionary Distinctiveness, and Accuracy and Magnitude of Decline.

PLoS One 2015 27;10(5):e0126524. Epub 2015 May 27.

Department of Life Sciences, Imperial College London, Ascot, Berkshire, United Kingdom; Centre for Ecology and Hydrology, Wallingford, Oxfordshire, United Kingdom; Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK.

Conservation biologists have only finite resources, and so must prioritise some species over others. The EDGE-listing approach ranks species according to their combined evolutionary distinctiveness and degree of threat, but ignores the uncertainty surrounding both threat and evolutionary distinctiveness. We develop a new family of measures for species, which we name EDAM, that incorporates evolutionary distinctiveness, the magnitude of decline, and the accuracy with which decline can be predicted. Further, we show how the method can be extended to explore phyogenetic uncertainty. Using the vascular plants of Britain as a case study, we find that the various EDAM measures emphasise different species and parts of Britain, and that phylogenetic uncertainty can strongly affect the prioritisation scores of some species.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0126524PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446313PMC
April 2016

Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data.

PLoS One 2014 20;9(11):e113207. Epub 2014 Nov 20.

Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain.

The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113207PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4239036PMC
January 2016

Evolutionary relationships in the medicinally important genus Fritillaria L. (Liliaceae).

Mol Phylogenet Evol 2014 Nov 11;80:11-9. Epub 2014 Aug 11.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK. Electronic address:

Fritillaria (Liliaceae) is a genus of approximately 140 species of bulbous perennial plants that includes taxa of both horticultural and medicinal importance. As well as being commercially valuable, Fritillaria species have attracted attention because of their exceptionally large genome sizes, with all values recorded to date in excess of 30Gb. Despite such interest in the genus, phylogenetic relationships between the majority of species have remained untested. Here we present the first phylogenetic reconstruction of relationships to encompass most of the currently recognised species diversity in the genus. Three regions of the plastid genome were sequenced in 117 individuals of Fritillaria, representing 92 species (c. 66% of the genus) and in representatives of nine other genera of Liliaceae. Eleven low-copy nuclear gene regions were also screened in selected species for their potential utility. Phylogenetic analysis of a combined plastid dataset using maximum parsimony and Bayesian inference provided support for the monophyly of the majority of currently recognised subgenera. However, subgenus Fritillaria, which is by far the largest of the subgenera and includes the most important species used in traditional Chinese medicine, is found to be polyphyletic. Moreover, several taxa that were represented by multiple individuals show evidence of species non-monophyly. The Japanese endemic subgenus Japonica, which contains the species with the largest recorded genome size for any diploid plant, is resolved as sister to the predominantly Middle Eastern and Central Asian subgenus Rhinopetalum. Whilst relationships between most of the major Fritillaria lineages can now be resolved, our results also highlight the need for data from additional independently evolving loci; an endeavour that may be particularly challenging in light of the huge nuclear genomes found in these plants.
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http://dx.doi.org/10.1016/j.ympev.2014.07.024DOI Listing
November 2014

Phylogenetics, ancestral state reconstruction, and a new infrafamilial classification of the pantropical Ochnaceae (Medusagynaceae, Ochnaceae s.str., Quiinaceae) based on five DNA regions.

Mol Phylogenet Evol 2014 Sep 23;78:199-214. Epub 2014 May 23.

Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.

Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.
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http://dx.doi.org/10.1016/j.ympev.2014.05.018DOI Listing
September 2014

Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil.

BMC Evol Biol 2014 Mar 15;14(1):49. Epub 2014 Mar 15.

Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado, Avenida Miguel Estéfano 3687, 04301-012 São Paulo, SP, Brazil.

Background: Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as most of them display a marked ecological isolation from the surrounding area. The isolation of these rock outcrops is reflected in the high number of recorded endemic species and the strong floristic differences between individual inselbergs and adjacent habitats. We examined the genetic connectivity of orchids Epidendrum cinnabarinum and E. secundum adapted to Neotropical inselbergs of northeastern Brazil. Our goals were to identify major genetic divergences or disjunctions across the range of the species and to investigate potential demographic and evolutionary mechanisms leading to lineage divergence in Neotropical mountain ecosystems.

Results: Based on plastid markers, high genetic differentiation was found for E. cinnabarinum (FST = 0.644) and E. secundum (FST = 0.636). Haplotypes were not geographically structured in either taxon, suggesting that restricted gene flow and genetic drift may be significant factors influencing the diversification of these inselberg populations. Moreover, strong differentiation was found between populations over short spatial scales, indicating substantial periods of isolation among populations. For E. secundum, nuclear markers indicated higher gene flow by pollen than by seeds.

Conclusions: The comparative approach adopted in this study contributed to the elucidation of patterns in both species. Our results confirm the ancient and highly isolated nature of inselberg populations. Both species showed similar patterns of genetic diversity and structure, highlighting the importance of seed-restricted gene flow and genetic drift as drivers of plant diversification in terrestrial islands such as inselbergs.
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http://dx.doi.org/10.1186/1471-2148-14-49DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4004418PMC
March 2014

A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae.

New Phytol 2014 Mar 2;201(4):1484-97. Epub 2013 Dec 2.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.

• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.
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http://dx.doi.org/10.1111/nph.12617DOI Listing
March 2014

Phylogeographic structure and outbreeding depression reveal early stages of reproductive isolation in the neotropical orchid Epidendrum denticulatum.

Evolution 2013 Jul 21;67(7):2024-39. Epub 2013 Mar 21.

Instituto de Botânica, São Paulo, Brazil.

Phylogeographic studies provide an important framework for investigating the mechanisms operating during the earliest stages of speciation, as reproductive barriers can be examined among divergent lineages in a geographic context. We investigated the evolution of early stages of intrinsic postmating isolation among different populations and lineages of Epidendrum denticulatum, a Neotropical orchid distributed across different biomes in South America. We estimated genetic diversity and structure for both nuclear and plastid markers, using a haplotype network, differentiation tests, Bayesian assignment analysis, and divergence time estimates of the main lineages. Reproductive barriers among divergent lineages were examined by analyzing seed viability following reciprocal crossing experiments. Strong plastid phylogeographic structure was found, indicating that E. denticulatum was restricted to multiple refuges during South American forest expansion events. In contrast, significant phylogeographic structure was not found for nuclear markers, suggesting higher gene flow by pollen than by seeds. Large asymmetries in seed set were observed among different plastid genetic groups, suggesting the presence of polymorphic genic incompatibilities associated with cytonuclear interactions. Our results confirm the importance of phylogeographic studies associated with reproductive isolation experiments and suggest an important role for outbreeding depression during the early stages of lineage diversification.
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http://dx.doi.org/10.1111/evo.12085DOI Listing
July 2013

Evidence-based guideline for the written radiology report: methods, recommendations and implementation challenges.

J Med Imaging Radiat Oncol 2013 Feb 28;57(1):1-7. Epub 2012 Dec 28.

Department of Diagnostic Imaging, Southern Health, Monash University, Sydney, Australia.

The written radiology report is the dominant method by which radiologists communicate the results of diagnostic and interventional imaging procedures. It has an important impact on decisions about further investigation and management. Its form and content can be influential in reducing harm to patients and mitigating risk for practitioners but varies markedly with little standardisation in practice. Until now, the Royal Australian and New Zealand College of Radiologists has not had a guideline for the written report. International guidelines on this subject are not evidence based and lack description of development methods. The current guideline seeks to improve the quality of the written report by providing evidence-based recommendations for good practice. The following attributes of the report are addressed by recommendations: Content Clinical information available to the radiologist at the time the report was created Technical details of the procedure Examination quality and limitations Findings (both normal and abnormal) Comparison with previous studies Pathophysiological diagnosis Differential diagnoses Clinical correlation and/or answer to the clinical question Recommendations, particularly for further imaging and other investigations Conclusion/opinion/impression Format Length Format Language Confidence and certainty Clarity Readability Accuracy Communication of discrepancies between an original verbal or written report and the final report Proofreading/editing of own and trainee reports.
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http://dx.doi.org/10.1111/1754-9485.12014DOI Listing
February 2013

Cytotype diversity in the Sorbus complex (Rosaceae) in Britain: sorting out the puzzle.

Ann Bot 2012 Nov 23;110(6):1185-93. Epub 2012 Aug 23.

Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.

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.
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http://dx.doi.org/10.1093/aob/mcs185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3478048PMC
November 2012

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes.

Am J Bot 2012 May 26;99(5):875-89. Epub 2012 Apr 26.

Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark.

Premise Of The Study: The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial.

Methods: Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated.

Key Results: The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent.

Conclusions: Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
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http://dx.doi.org/10.3732/ajb.1100468DOI Listing
May 2012

Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography.

Mol Phylogenet Evol 2012 Jul 2;64(1):177-89. Epub 2012 Apr 2.

Universidade Federal do Rio Grande do Norte, Departamento de Botânica, Ecologia e Zoologia, Natal, Rio Grande do Norte, Brazil.

The genus Alcantarea comprises near 30 species endemic to rocky outcrops from eastern Brazil. Most species are ornamental and several are threatened due to habitat loss and over collection. In this paper we examine the phylogenetics of Alcantarea and its relationship with the Brazilian members of Vriesea, a genus of which Alcantarea has been treated as a subgenus. We discuss the morphological evolution of the stamen position and its implication for pollination and the occurrence of Alcantarea in the Espinhaço mountain range rocky savanna-like habitat vegetation. DNA sequence data derived from two plastid markers (trnK-rps16, trnC-petN) and from a low copy nuclear gene (Floricaula/Leafy) together with 20 nuclear microsatellite loci were the data source to perform analyses and construct phylogenetic and Neighbor Joining trees for the genus. Alcantarea is well supported as monophyletic in both Bayesian and parsimony analyses, but sections of Vriesea, represented by the eastern Brazilian species, appear paraphyletic. Microsatellites delimit geographically isolated species groups. Nevertheless individuals belonging to a single species may appear related to distinct clusters of species, suggesting that hybridization and/or homoplasy and/or incomplete lineage sorting are also influencing the analysis based on such markers and may be the reasons for some unexpected results. Alcantarea brasiliana is hypothesized as putative hybrid between A. imperialis and A. geniculata. Spreading stamens, a morphological floral characteristic assumed to be related to Chiropterophily, apparently evolved multiple times within the genus, and invasion of rocky savanna-like habitat vegetation by Atlantic rainforest ancestors seems to have occurred multiple times as well.
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http://dx.doi.org/10.1016/j.ympev.2012.03.015DOI Listing
July 2012

Challenges in the DNA barcoding of plant material.

Methods Mol Biol 2012 ;862:23-33

Jodrell Laboratory, Royal Botanic Gardens, Richmond, Surrey, UK.

DNA barcoding, using a short gene sequence from a standardized region of the genome, is a species identification tool which would not only aid species discovery but would also have applications ranging from large-scale biodiversity surveys through to identification of a single fragment of material in forensic contexts. To fulfill this vision a universal, relatively cheap, scalable system needs to be in place. The mitochondrial locus being used for many animal groups and algae is not suitable for use in land plants, and an appropriate alternative is needed.Progress has been made in the selection of two alternative regions for plant DNA barcoding. There are however many challenges in finding a solution that fulfills all the requirements of a successful, universally applicable barcode, and in the short term a pragmatic solution that achieves as much as possible and has payoffs in most areas has been chosen. Research continues in areas ranging from the technicalities of sequencing the regions to data analysis and the potential improvements that may result from the developing technology and data analysis systems.The ultimate success of DNA barcoding as a plant identification tool for all occasions depends on the building of a reference database and it fulfilling the requirements of potential users such that they are able to achieve valid results through its use, that would be more time consuming and costly, and less reliable using other techniques.
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http://dx.doi.org/10.1007/978-1-61779-609-8_3DOI Listing
August 2012

Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae).

Mol Phylogenet Evol 2012 Feb 17;62(2):624-39. Epub 2011 Nov 17.

Royal Botanic Gardens, Kew, Richmond TW9 3AB, UK.

For the 12 named taxa in the Gagea reticulata species complex, 609 cloned sequences of the low-copy nuclear gene malate synthase (MS) were used to investigate species relationships, using standard phylogenetic tools and network analyses. Three (homologous) copies of MS locus were present in each individual analyzed, and multiple alleles were present at most of these loci. Duplication of MS occurred after divergence of the G. reticulata complex. After comparisons, 591 sequence types (i.e. haplotypes) were identified, requiring implementation of novel statistical analyses to group haplotypes in a smaller number of groups/lineages to enable further study. Haplotype groups/lineages are not fully congruent with species limits with some widely present among species. MS genotypes at the root of the network are those of G. setifolia from central Iran, with more derived sequences in this species found in the west and northwest. Presence of ancestral genotypes in several other taxa may indicate either the retention of "ancestral" polymorphisms, more recent introgressive hybridization, or both. The relative DNA content of specimens was estimated with flow cytometry (FCM). The FCM analyses revealed two levels of DNA content (putatively "diploid" and "tetraploid"), but no correlation between number of MS gene copies and ploidy was found.
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http://dx.doi.org/10.1016/j.ympev.2011.11.003DOI Listing
February 2012

Parental divergence and hybrid speciation in angiosperms revisited.

Taxon 2011 Oct;60(5):1241-1244

Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, A-1030, Austria.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605764PMC
October 2011

Sympatric bromeliad species (Pitcairnia spp.) facilitate tests of mechanisms involved in species cohesion and reproductive isolation in Neotropical inselbergs.

Mol Ecol 2011 Aug 15;20(15):3185-201. Epub 2011 Jun 15.

Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey, UK.

The roles of intra- and interspecific gene flow in speciation and species evolution are topics of great current interest in molecular ecology and evolutionary biology. Recent modelling studies call for new empirical data to test hypotheses arising from the recent shift from a 'whole-genome reproductive isolation' view to a 'genic' view of species and speciation. Particularly scarce (and thus of particular interest) are molecular genetic data on recently radiated, naturally hybridizing species in strongly structured and species-rich environments. Here, we studied four sympatric plant species (Pitcairnia spp.; Bromeliaceae) adapted to Neotropical inselbergs (isolated outcrops resembling habitat 'islands' in tropical rainforests) using nuclear and plastid DNA. Patterns of plastid DNA haplotype sharing and nuclear genomic admixture suggest the presence of both, incomplete lineage sorting and interspecific gene flow over extended periods of time. Integrity and cohesion of inselberg species of Pitcairnia are maintained despite introgression and in the face of extremely low within-species migration rates (N(e)m < 1 migrant per generation). Cross-evaluation of our genetic data against published pollination experiments indicate that species integrity is maintained by the simultaneous action of multiple prezygotic barriers, including flowering phenology, pollinator isolation and divergent mating systems. Postzygotic Bateson-Dobzhansky-Muller incompatibilities appear to contribute to isolation, as suggested by asymmetric introgression rates of single loci. Our results suggest that incomplete lineage sorting, hybridization and introgression form integral aspects of adaptive radiation in Neotropical inselberg 'archipelagos'. Inselbergs with multiple closely related co-occurring species should be of special interest to students of speciation in mountain systems, and to ongoing conservation programmes in the Atlantic Rainforest biodiversity hotspot.
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http://dx.doi.org/10.1111/j.1365-294X.2011.05143.xDOI Listing
August 2011

Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae).

BMC Evol Biol 2011 Apr 26;11:113. Epub 2011 Apr 26.

Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg, Austria.

Background: Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a polyploid complex formed through unidirectional (and, in the first two cases, recurrent) hybridization between the widespread diploids D. fuchsii and D. incarnata. Differing considerably in geographical extent and ecological tolerance, the three allopolyploids together provide a useful system to explore genomic responses to allopolyploidization and reveal their role in adaptation to contrasting environments.

Results: Analyses of cDNA-AFLPs show a significant increase in the range of gene expression of these allopolyploid lineages, demonstrating higher potential for phenotypic plasticity than is shown by either parent. Moreover, allopolyploid individuals express significantly more gene variants (including novel alleles) than their parents, providing clear evidence of increased biological complexity following allopolyploidization. More genetic mutations seem to have accumulated in the older D. majalis compared with the younger D. traunsteineri since their respective formation.

Conclusions: Multiple origins of the polyploids contribute to differential patterns of gene expression with a distinct geographic structure. However, several transcripts conserved within each allopolyploid taxon differ between taxa, indicating that habitat preferences shape similar expression patterns in these independently formed tetraploids. Statistical signals separate several transcripts - some of them novel in allopolyploids - that appear correlated with adaptive traits and seem to play a role favouring the persistence of individuals in their native environments. In addition to stabilizing the allopolyploid genome, genetic and epigenetic alterations are key determinants of adaptive success of the new polyploid species after recurrent allopolyploidization events, potentially triggering reproductive isolation between the resulting lineages.
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http://dx.doi.org/10.1186/1471-2148-11-113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3112086PMC
April 2011