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Sean Graham

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Sean Graham's Recent Papers (as indexed by PubMed)

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Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

PLoS One. 2008;3(7):e2802

Authors: Fazekas AJ, Burgess KS, Kesanakurti PR, Graham SW, Newmaster SG, Husband BC, Percy DM, Hajibabaei M, Barrett SC

A universal barcode system for land plants would be a valuable resource, with potential utility in fields as diverse as ecology, floristics, law enforcement and industry. However, the application of plant barcoding has been constrained by a lack of consensus regarding the most variable and technically practical DNA region(s). We compared eight candidate plant barcoding regions from the plastome and one from the mitochondrial genome for how well they discriminated the monophyly of 92 species in 32 diverse genera of land plants (N = 251 samples). The plastid markers comprise portions of five coding (rpoB, rpoC1, rbcL, matK and 23S rDNA) and three non-coding (trnH-psbA, atpF-atpH, and psbK-psbI) loci. Our survey included several taxonomically complex groups, and in all cases we examined multiple populations and species. The regions differed in their ability to discriminate species, and in ease of retrieval, in terms of amplification and sequencing success. Single locus resolution ranged from 7% (23S rDNA) to 59% (trnH-psbA) of species with well-supported monophyly. Sequence recovery rates were related primarily to amplification success (85-100% for plastid loci), with matK requiring the greatest effort to achieve reasonable recovery (88% using 10 primer pairs). Several loci (matK, psbK-psbI, trnH-psbA) were problematic for generating fully bidirectional sequences. Setting aside technical issues related to amplification and sequencing, combining the more variable plastid markers provided clear benefits for resolving species, although with diminishing returns, as all combinations assessed using four to seven regions had only marginally different success rates (69-71%; values that were approached by several two- and three-region combinations). This performance plateau may indicate fundamental upper limits on the precision of species discrimination that is possible with DNA barcoding systems that include moderate numbers of plastid markers. Resolution to the contentious debate on plant barcoding should therefore involve increased attention to practical issues related to the ease of sequence recovery, global alignability, and marker redundancy in multilocus plant DNA barcoding systems.

PMID: 18665273 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Multiple multilocus DNA barcodes from the plastid genome discriminate plant species equally well.

How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set.

Mol Phylogenet Evol. 2008 Jun;47(3):1232-7

Authors: Zgurski JM, Rai HS, Fai QM, Bogler DJ, Francisco-Ortega J, Graham SW

PMID: 18424186 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: How well do we understand the overall backbone of cycad phylogeny? New insights from a large, multigene plastid data set.

Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree.

Nature. 2007 Mar 15;446(7133):312-5

Authors: Saarela JM, Rai HS, Doyle JA, Endress PK, Mathews S, Marchant AD, Briggs BG, Graham SW

Although the relationship of angiosperms to other seed plants remains controversial, great progress has been made in identifying the earliest extant splits in flowering-plant phylogeny, with the discovery that the New Caledonian shrub Amborella trichopoda, the water lilies (Nymphaeales), and the woody Austrobaileyales constitute a basal grade of lines that diverged before the main radiation in the clade. By focusing attention on these ancient lines, this finding has re-written our understanding of angiosperm structural and reproductive biology, physiology, ecology and taxonomy. The discovery of a new basal lineage would lead to further re-evaluation of the initial angiosperm radiation, but would also be unexpected, as nearly all of the approximately 460 flowering-plant families have been surveyed in molecular studies. Here we show that Hydatellaceae, a small family of dwarf aquatics that were formerly interpreted as monocots, are instead a highly modified and previously unrecognized ancient lineage of angiosperms. Molecular phylogenetic analyses of multiple plastid genes and associated noncoding regions from the two genera of Hydatellaceae identify this overlooked family as the sister group of Nymphaeales. This surprising result is further corroborated by evidence from the nuclear gene phytochrome C (PHYC), and by numerous morphological characters. This indicates that water lilies are part of a larger lineage that evolved more extreme and diverse modifications for life in an aquatic habitat than previously recognized.

PMID: 17361182 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree.

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny.

Proc Biol Sci. 2005 Jul 22;272(1571):1481-90

Authors: Givnish TJ, Pires JC, Graham SW, McPherson MA, Prince LM, Patterson TB, Rai HS, Roalson EH, Evans TM, Hahn WJ, Millam KC, Meerow AW, Molvray M, Kores PJ, O'Brien HE, Hall JC, Kress WJ, Sytsma KJ

We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence (p<10(-9)), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats (p<10(-13)-10(-29)). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.

PMID: 16011923 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny.

Patterns of genetic variation in Phialocephala fortinii across a broad latitudinal transect in Canada.

Mycol Res. 2004 Aug;108(Pt 8):955-64

Authors: Piercey MM, Graham SW, Currah RS

Dark septate root endophytes (DSE) are an artificial assemblage of fungi that have darkly pigmented, septate hyphae and that are frequent or distinctive intracellular associates of roots of apparently healthy plants. Based on isolates obtained from the roots of Salix spp., the distribution of a common DSE fungus, Phialocephala fortinii, was examined along a latitudinal transect in Canada running from the high arctic to the 49 degrees N parallel. Non-sporulating isolates were provisionally identified as P. fortinii through analysis of DNA sequence data of the ITS2 region of rDNA. P. fortinii was isolated frequently from boreal and arctic habitats, but rarely from grassland habitats. Patterns of genetic variation were examined through analysis of amplified fragment length polymorphisms (AFLP). All AFLP profiles were unique with the majority of genetic variation occurring among individuals within the collecting sites at each latitude. Neighbour-joining analysis of genetic distances yielded eight well-supported clusters, three of which included individuals from more than one latitude. Some linkage disequilibrium, possibly due to partial clonality, was detected.

PMID: 15449601 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Patterns of genetic variation in Phialocephala fortinii across a broad latitudinal transect in Canada.

The imbalanced supertree of flowering-plant phylogeny.

Genome Biol. 2004;5(8):236

Authors: Graham SW, Cronk QC

Two contrasting approaches have been used to construct the overall tree of life from molecular data: one involves the analysis of single large datasets, while the other involves joining many independent smaller analyses into a supertree. A recent study uses the latter approach to produce the most complete phylogeny yet of flowering plant families.

PMID: 15287967 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: The imbalanced supertree of flowering-plant phylogeny.

Inference of higher-order relationships in the cycads from a large chloroplast data set.

Mol Phylogenet Evol. 2003 Nov;29(2):350-9

Authors: Rai HS, O'Brien HE, Reeves PA, Olmstead RG, Graham SW

We investigated higher-order relationships in the cycads, an ancient group of seed-bearing plants, by examining a large portion of the chloroplast genome from seven species chosen to exemplify our current understanding of taxonomic diversity in the order. The regions considered span approximately 13.5 kb of unaligned data per taxon, and comprise a diverse range of coding sequences, introns and intergenic spacers dispersed throughout the plastid genome. Our results provide substantial support for most of the inferred backbone of cycad phylogeny, and weak evidence that the sister-group of the cycads among living seed plants is Ginkgo biloba. Cycas (representing Cycadaceae) is the sister-group of the remaining cycads; Dioon is part of the next most basal split. Two of the three commonly recognized families of cycads (Zamiaceae and Stangeriaceae) are not monophyletic; Stangeria is embedded within Zamiaceae, close to Zamia and Ceratozamia, and not closely allied to the other genus of Stangeriaceae, Bowenia. In contrast to the other seed plants, cycad chloroplast genomes share two features with Ginkgo: a reduced rate of evolution and an elevated transition:transversion ratio. We demonstrate that the latter aspect of their molecular evolution is unlikely to have affected inference of cycad relationships in the context of seed-plant wide analyses.

PMID: 13678689 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Inference of higher-order relationships in the cycads from a large chloroplast data set.

Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots.

Mol Biol Evol. 2002 Oct;19(10):1769-81

Authors: Graham SW, Olmstead RG, Barrett SC

Phylogenetic rooting experiments demonstrate that two chloroplast genes from commelinoid monocot taxa that represent the closest living relatives of the pickerelweed family, Pontederiaceae, retain measurable signals regarding the position of that family's root. The rooting preferences of the chloroplast sequences were compared with those for artificial sequences that correspond to outgroups so divergent that their signal has been lost completely. These random sequences prefer the three longest branches in the unrooted ingroup topology and do not preferentially root on the branches favored by real outgroup sequences. However, the rooting behavior of the artificial sequences is not a simple function of branch length. The random outgroups preferentially root on long terminal ingroup branches, but many ingroup branches comparable in length to those favored by random sequences attract no or few hits. Nonterminal ingroup branches are generally avoided, regardless of their length. Comparisons of the ease of forcing sequences onto suboptimal roots indicate that real outgroups require a substantially greater rooting penalty than random outgroups for around half of the least-parsimonious candidate roots. Although this supports the existence of nonrandomized signal in the real outgroups, it also indicates that there is little power to choose among the optimal and nearly optimal rooting possibilities. A likelihood-based test rejects the hypothesis that all rootings of the subtree using real outgroup sequences are equally good explanations of the data and also eliminates around half of the least optimal candidate roots. Adding genes or outgroups can improve the ability to discriminate among different root locations. Rooting discriminatory power is shown to be stronger, in general, for more closely related outgroups and is highly correlated among different real outgroups, genes, and optimality criteria.

PMID: 12270903 [PubMed - indexed for MEDLINE]

Link to abstract on PubMed: Rooting phylogenetic trees with distant outgroups: a case study from the commelinoid monocots.

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