Paul J. Kores

Moorpark College, Moorpark, California, United States

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Publications (15)27.66 Total impact

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  • Aliso 01/2006; 22:28-52.
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    ABSTRACT: 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.
    Proceedings of the Royal Society B: Biological Sciences 08/2005; 272(1571):1481-90. · 5.68 Impact Factor
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    ABSTRACT: An expanded plastid DNA phylogeny for Orchidaceae was generated from sequences of rbcL and matK for representatives of all five subfamilies. The data were analyzed using equally weighted parsimony, and branch support was assessed with jackknifing. The analysis supports recognition of five subfamilies with the following relationships: (Apostasioideae (Vanilloideae (Cypripedioideae (Orchidoideae (Epidendroideae))))). Support for many tribal-level groups within Epidendroideae is evident, but relationships among these groups remain uncertain, probably due to a rapid radiation in the subfamily that resulted in short branches along the spine of the tree. A series of experiments examined jackknife parameters and strategies to determine a reasonable balance between computational effort and results. We found that support values plateau rapidly with increased search effort. Tree bisection-reconnection swapping in a single search replicate per jackknife replicate and saving only two trees resulted in values that were close to those obtained in the most extensive searches. Although this approach uses considerably more computational effort than less extensive (or no) swapping, the results were also distinctly better. The effect of saving a maximal number of trees in each jackknife replicate can also be pronounced and is important for representing support accurately.
    American Journal of Botany 01/2004; 91(1):149-57. · 2.59 Impact Factor
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    ABSTRACT: Gaura (Onagraceae: Onagreae) is a small North American genus of 21 species consisting mostly of night-blooming, moth-pollinated annuals and perennials. The current infrageneric classification based on differences in habit, floral symmetry, and fruit morphology recognizes eight sections within the genus. We examine the phylogenetic relationships of all 21 species of Gaura using DNA sequence data from the internal transcribed spacer region (ITS), the external transcribed spacer region (ETS), and the plastid trnL-F region. Combined analysis of these regions indicate Gaura is monophyletic only if it includes Stenosiphon, a monotypic genus comprised of S. linifolius. Within Gaura, our studies indicate that sections Gauridium, Schizocarya, Campogaura, Stipogaura, Xenogaura, and Gaura are monophyletic, but sections Xerogaura and Pterogaura are not and should be reevaluated. In addition, molecular data provide support for the hypothesis that G. sinuata and G. drummondii arose via interspecific hybridization followed by genome doubling; their influence on phylogenetic reconstruction is discussed.
    American Journal of Botany 01/2004; 91(1):139-48. · 2.59 Impact Factor
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    ABSTRACT: Littorella (Plantaginaceae) is a disjunct, amphibious genus represented by three closely related species. Littorella uniflora occurs in Europe including Iceland and the Azores, L. americana is found in temperate North America, and L. australis grows in temperate South America. Littorella has been recognized in numerous floristic treatments, but its status as a genus has recently been questioned. Rahn (Botanical Journal of the Linnean Society 120: 145-198, 1996) proposed a new phylogeny for Plantaginaceae based on morphological, embryological, and chemical data in which he reduced Littorella to a subgenus of Plantago. This article compares the phylogeny proposed by Rahn to one based on DNA sequence data from the internal transcribed spacer (ITS) region. In our analysis, Littorella forms a strongly supported monophyletic clade sister to Plantago and its recognition at the generic rank appears warranted. Littorella australis is sister to L. americana, and this clade is sister to the European L. uniflora. This more distant relationship between L. uniflora and L. americana provides support for maintaining both taxa at the specific rank and suggests a European origin for Littorella. Our studies also indicate that the monotypic genus Bougueria is deeply nested within Plantago and that its inclusion within Plantago as proposed by Rahn appears justified.
    American Journal of Botany 03/2003; 90(3):429-35. · 2.59 Impact Factor
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    ABSTRACT: DNA sequence data from plastid matK and trnL-F regions were used in phylogenetic analyses of Diurideae, which indicate that Diurideae are not monophyletic as currently delimited. However, if Chloraeinae and Pterostylidinae are excluded from Diurideae, the remaining subtribes form a well-supported, monophyletic group that is sister to a "spiranthid" clade. Chloraea, Gavilea, and Megastylis pro parte (Chloraeinae) are all placed among the spiranthid orchids and form a grade with Pterostylis leading to a monophyletic Cranichideae. Codonorchis, previously included among Chloraeinae, is sister to Orchideae. Within the more narrowly delimited Diurideae two major lineages are apparent. One includes Diuridinae, Cryptostylidinae, Thelymitrinae, and an expanded Drakaeinae; the other includes Caladeniinae s.s., Prasophyllinae, and Acianthinae. The achlorophyllous subtribe Rhizanthellinae is a member of Diurideae, but its placement is otherwise uncertain. The sequence-based trees indicate that some morphological characters used in previous classifications, such as subterranean storage organs, anther position, growth habit, fungal symbionts, and pollination syndromes have more complex evolutionary histories than previously hypothesized. Treatments based upon these characters have produced conflicting classifications, and molecular data offer a tool for reevaluating these phylogenetic hypotheses.
    American Journal of Botany 10/2001; 88(10):1903-14. · 2.59 Impact Factor
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    ABSTRACT: Circumscriptions of Arethuseae have varied since the tribe was first described by John Lindley in 1840, containing over ninety genera among the different authors. The latest system of Arethuseae defined by Dressler, including around thirty genera, is the most commonly accepted today. The goals of this study are to assess whether Arethuseae sensu Dressler and component subtribes are monophyletic and evaluate the position(s) of Arethuseae within Orchidaceae. Sequences of two plastid genes, matK and rbcL, have been obtained for 24 representative genera of Arethuseae in Dressler's latest two taxonomic systems for the tribe, plus 46 other genera throughout Orchidaceae. Both separate and combined analyses of the matK and rbcL data indicate that the tribe may not be monophyletic, which is also true for most subtribes within Arethuseae. Furthermore, matK data suggest that this gene may be non-functional within Orchidaceae.
    Systematic Botany 01/2001; 37(1):670-695. · 1.29 Impact Factor
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    Monocots: systematics and evolution. 01/2000;
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    ABSTRACT: We present here the first molecular phylogeny of tribe Diseae (Orchidoideae: Orchidaceae). Nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequences were compared for 30 Diseae, 20 Orchideae, and four Cranichideae and Diurideae outgroups. ITS - rDNA sequences exhibited a transition:transversion ratio of 1.3 and extensive ITS length polymorphism. Phylogenetic analyses using maximum parsimony identified seven major core orchidoid groups. The branching order of the five Diseae and two Orchideae clades was weakly supported but indicated paraphyly of Diseae, with Disperis sister to the rest, followed by successive divergence of Brownleea, Disinae, Coryciinae sensu stricto (s.s.), Satyriinae, and terminated by Orchidinae plus Habenariinae. Within the monophyletic Disinae, Herschelia and Monadenia were nested within a paraphyletic Disa and clustered with D. sect. Micranthae. Within monophyletic Satyriinae, Satyridium rostratum plus Satyrium bicallosum was sister to the rest of Satyrium, and then Satyrium nepalense plus S. odorum was distinct from a cluster of six species. Coryciinae are paraphyletic because Disperis is sister to all other core orchidoids. Coryciinae s.s. are sister to Satyriinae plus Orchideae, with Pterygodium nested within Corycium. Maximum likelihood analysis supported possible affinities among Disinae, Brownleeinae, and Coryciinae but did not support monophyly of Diseae or an affinity between Disinae and Satyriinae. Morphological characters are fully congruent with the well-supported groups identified in the ITS phylogeny.
    American Journal of Botany 07/1999; 86(6):887-99. · 2.59 Impact Factor
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    ABSTRACT: Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.
    American Journal of Botany 02/1999; · 2.59 Impact Factor
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    ABSTRACT: Cladistic parsimony analyses of rbcL nucleotide sequence data from 171 taxa representing nearly all tribes and subtribes of Orchidaceae are presented here. These analyses divide the family into five primary monophyletic clades: apostasioid, cypripedioid, vanilloid, orchidoid, and epidendroid orchids, arranged in that order. These clades, with the exception of the vanilloids, essentially correspond to currently recognized subfamilies. A distinct subfamily, based upon tribe Vanilleae, is supported for Vanilla and its allies. The general tree topology is, for the most part, congruent with previously published hypotheses of intrafamilial relationships; however, there is no evidence supporting the previously recognized subfamilies Spiranthoideae, Neottioideae, or Vandoideae. Subfamily Spiranthoideae is embedded within a single clade containing members of Orchidoideae and sister to tribe Diurideae. Genera representing tribe Tropideae are placed within the epidendroid clade. Most traditional subtribal units are supported within each clade, but few tribes, as currently circumscribed, are monophyletic. Although powerful in assessing monophyly of clades within the family, in this case rbcL fails to provide strong support for the interrelationships of the subfamilies (i.e., along the spine of the tree). The cladograms presented here should serve as a standard to which future morphological and molecular studies can be compared.
    American Journal of Botany 02/1999; 86(2):208-24. · 2.59 Impact Factor
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    M Molvray, P J Kores, M W Chase
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    ABSTRACT: The nuclear encoded internal transcribed spacer (ITS) region and the plastid encoded trnL-F region were sequenced for 25 populations of Korthalsella, a genus of reduced, monoecious, Old World misletoes. The molecular study confirms the hypothesis that branch shape and cladotaxy (the arrangement of branches with respect to their parent axis) are unreliable indicators of relationship in the genus and demonstrates that many of the taxa previously recognized are not monophyletic. Both gene regions identify three major subgroups within the genus and find lower level relationships within these subgroups highly correlated with geographic distance. An analysis based upon 18S and rbcL sequences identifies Ginalloa as the sister group to Korthalsella, which together with the branching order within the genus, indicates that Korthalsella originated in Papuasia and aids in elucidating evolution of the peculiar inflorescence structure. There are problems associated with species delimitation when evolutionary units are more restricted than morphological lineages, and justification is offered for recognizing only morphologically diagnosable monophyletic lineages as species. Varying substitution rates and differing modes of inheritance in ITS and trnL-F result in complementary utility of the two regions for elucidating infrageneric relationships in Korthalsella.
    American Journal of Botany 02/1999; 86(2):249-60. · 2.59 Impact Factor
  • Mia Molvray, Paul J. Kores, Mark W. Chase
    American Journal of Botany - AMER J BOT. 01/1999; 86(2).
  • Mia Molvray, Paul J. Kores
    American Journal of Botany - AMER J BOT. 01/1995; 82(11).

Publication Stats

483 Citations
27.66 Total Impact Points

Institutions

  • 2004–2005
    • Moorpark College
      Moorpark, California, United States
  • 2001
    • University of Oklahoma
      Norman, Oklahoma, United States
  • 1999
    • Université de Montpellier 1
      Montpelhièr, Languedoc-Roussillon, France
    • Royal Botanic Gardens, Kew
      • Jodrell Laboratory
      Richmond, ENG, United Kingdom