Chelsea Specht | University of California, Berkeley (original) (raw)

Papers by Chelsea Specht

Research paper thumbnail of Between Cancer and Capricorn: Phylogeny, evolution and ecology of the primarily tropical Zingiberales

... USA. E-mail: Chelsea I). S/> echt, Ant... more ... USA. E-mail: Chelsea I). S/> echt, Ant'York Botanical Ganlen, Plant Research l. alnmitury, Bronx, NY 10458 USA. ... 1993; Kato 1996; Sakai et al. 1999) and possibly Siamanthus as suggested by Larsen and Mood (1998). The ...

Research paper thumbnail of Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales

New Phytologist, 2010

•The MADS box transcription factor family has long been identified as an important contributor to... more •The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. Here we examine the role of GLOBOSA (GLO)-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales.•We assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. We identified GLO homologs (ZinGLO1-4) from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus and Musa basjoo.•Based on the phylogenetic data and expression results, we propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum.•Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. Here we examine the role of GLOBOSA (GLO)-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales.We assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. We identified GLO homologs (ZinGLO1-4) from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus and Musa basjoo.Based on the phylogenetic data and expression results, we propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum.Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

PLOS One, 2007

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Systematic Botany, 2004

A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variati... more A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach. DAVIS ET AL.: PHYLOGENY OF MONOCOTS FIG. 1. (continued) B. Structure of Group A from Fig. 1A.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of Flower Evolution: The Origin and Subsequent Diversification of the Angiosperm Flower

Annual Review of Ecology Evolution and Systematics, 2009

Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis a... more Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis and maize enable us to identify genes, gene families, and gene networks that are involved in the regulation of flower initiation, growth and differentiation. These genes can then function as "candidate genes" and their expression, function, and biochemical interactions can be explored in other lineages to determine if they provide a necessary and sufficient toolkit for the development of the flower. Likewise, a view to the fossil record can provide documentation of reproductive innovations occurring within gymnosperms or along the stem lineage leading to angiosperms, elucidating the transitions required for the evolution of the angiosperm flower from an ancestral reproductive strobilus. Here we discuss the origin and subsequent evolution in form of the flower, highlighting recent studies in paleobotany, morphology, evolution, and developmental genetics with the goal of outlining advances in our understanding of flower evolution. 217 Annu. Rev. Ecol. Evol. Syst. 2009.40:217-243. Downloaded from www.annualreviews.org Access provided by University of California -Berkeley on 03/23/15. For personal use only.

Research paper thumbnail of GONDWANAN VICARIANCE OR DISPERSAL IN THE TROPICS? THE BIOGEOGRAPHIC HISTORY OF THE TROPICAL MONOCOT FAMILY COSTACEAE (ZINGIBERALES

Costaceae are a pantropical family, distinguished from other families within the order Zingiberal... more Costaceae are a pantropical family, distinguished from other families within the order Zingiberales by their spiral phyllotaxy and showy labellum comprised of five fused staminodes. While the majority of Costaceae species are found in the neotropics, the pantropical distribution of the family as a whole could be due to a number of historical biogeographic scenarios, including continental-drift mediated vicariance and long-distance dispersal events. Here, the hypothesis of an ancient Gondwanan distribution followed by vicariance via continental drift as the leading cause of the current pantropical distribution of Costaceae is tested, using molecular dating of cladogenic events combined with phylogeny-based biogeographic analyses. Dispersal-Vicariance Analysis (DIVA) is used to determine ancestral distributions based upon the modern distribution of extant taxa in a phylogenetic context. Diversification ages within Costaceae are estimated using chloroplast DNA data (trnL-F and trnK) analyzed with a local clock procedure. In the absence of fossil evidence, the divergence time between Costaceae and Zingiberaceae, as estimated in an ordinal analysis of Zingiberales, is used as the calibration point for converting relative to absolute ages. The results of the temporal analysis based on extant taxa indicate that the initial diversification within Costaceae occurred approximately 65 million years ago, long after the final break up of the Gondwanan supercontinent. Considering this minimum age of diversification, potential scenarios for the current biogeographic patterns found in Costaceae are presented in a temporal and spatial context. The evolution of specialized floral forms associated with specific pollinators is also discussed within the biogeographic framework.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

PLOS One, 2007

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of Epi-illumination microscopy coupled to in situ hybridization and its utility in the study of evolution and development in non-model species

Development Genes and Evolution, 2008

Evolutionary developmental biology often combines methods for examining morphology (e.g., scannin... more Evolutionary developmental biology often combines methods for examining morphology (e.g., scanning electron microscopy, SEM) with analyses of gene expression (e.g., RNA in situ hybridization). Due to differences in tissue preparation for SEM and gene expression analyses, the same specimen cannot be used for both sets of techniques. To aid in the understanding of morphological variation, it would be particularly useful to have a high-magnification image of the very same sample in which gene expression is subsequently analyzed. To address this need, we developed a method that couples extended depth of field (EDF) epi-illumination microscopy to in situ hybridization in a sequential format, enabling both surface microscopy and gene expression analyses to be carried out on the same specimen. We first created a digital image of inflorescence apices using epi-illumination microscopy and commercially available EDF software. We then performed RNA in situ hybridizations on photographed apices to assess the expression of two developmental genes: Knotted1 (Kn1) in Zea mays (Poaceae) and a PISTILLATA (PI) homolog in Musa basjoo (Musaceae). We demonstrate that expression signal is neither altered nor reduced in the imaged apices as compared with the unphotographed controls. The demonstrated method reduces the amount of sample material necessary for developmental research, and enables individual floral development to be placed in the context of the entire inflorescence. While the technique presented here is particularly relevant to floral developmental biology, it is applicable to any research where observation and description of external features can be fruitfully linked with analyses of gene expression.

Research paper thumbnail of Dependence of rat vertex auditory evoked potentials on central muscarinic receptor activation

Brain Research, 1995

Auditory evoked potentials (AEPs) were recorded epidurally at vertex in the freely moving rat, yi... more Auditory evoked potentials (AEPs) were recorded epidurally at vertex in the freely moving rat, yielding the prominent components P18 and N40 from the averaged waveform. Both components were severely attenuated at tone presentation rates faster than 1 Hz. Dependence of the vertex AEP on central cholinergic activation was assessed by comparing the effects of subcutaneous injections of the muscarinic antagonist scopolamine (0.1-1.0 mg/kg) to methyl-scopolamine (0.5, 1.0 mg/kg) to test for peripheral effects. Scopolamine produced a significant decrease in amplitude for both the P18 and N40 components in overall tests. N40 amplitude also showed a significant decrease at each dose of scopolamine, and the magnitude of the amplitude decrement was dose dependent. At 23 h after scopolamine, only N40 amplitude remained significantly depressed. There were no effects of injection of saline, or of methyl-scopolamine. These results confirm that middle-latency vertex AEPs in the rat are attenuated by central muscarinic receptor blockade, consistent with previous findings in cats.

Research paper thumbnail of Easy trees?—Review of “Phylogenetic trees made easy: a how-to manual for molecular biologists” by Barry G. Hall

Molecular Phylogenetics and Evolution, 2003

Research paper thumbnail of Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

Science, 2011

Understanding the diversification of phenotypes through time—“descent with modification”—has been... more Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years. If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible. Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal. Such examples of homoplasy present opportunities to discover the foundations of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated exploration of the mechanisms by which similarity arises.

Research paper thumbnail of THE EVOLUTIONARY AND BIOGEOGRAPHIC ORIGIN AND DIVERSIFICATION OF THE TROPICAL MONOCOT ORDER ZINGIBERALES

... W. JOHN KRESS1 AND CHELSEA D. SPECHT2 Department of Botany, MRC-166, United States National H... more ... W. JOHN KRESS1 AND CHELSEA D. SPECHT2 Department of Botany, MRC-166, United States National Herbarium, National Museum of Natural History ... While assigning Heli-coniaceae to a separate rate class does not effect dating of the more internal nodes, the internal ...

Research paper thumbnail of A Molecular Phylogeny of Costaceae (Zingiberales

Molecular Phylogenetics and Evolution, 2001

The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gin... more The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gingers (Zingiberaceae), were investigated with a combination of two chloroplast loci (the trnL-F locus, including the trnL intron, the 3trnL exon, and the trnL-F intergenic spacer, and the trnK locus, including the trnK intron and the matK coding region) and one nuclear locus (ITS1-5.8s-ITS2). The resulting parsimony analysis of selected taxa that demonstrate the range of floral morphological variation in the family shows that the Caldavena-type floral morphology is ancestral to the group and that both Tapeinochilos species and a Monocostus ؉ Dimerocostus clade represent recent divergences. The genus Costus is broadly paraphyletic but Costus subgenus Eucostus K. Schum. represents a large monophyletic radiation that is poorly resolved. Within this clade, secondary analyses suggest that pollination syndrome, traditionally used for taxonomic and classification purposes within the genus Costus, is a relatively plastic trait of limited phylogenetic utility. This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography.

Research paper thumbnail of Systematics and Evolution of the Tropical Monocot Family Costaceae (Zingiberales): A Multiple Dataset Approach

Systematic Botany, 2006

... The nominal genus Costus is not monophyletic and its species are found in all three major cla... more ... The nominal genus Costus is not monophyletic and its species are found in all three major clades. ... The African-neotropical clade is composed entirely of the genus Costus; moreover, there is support for previously recognized subgeneric groupings within the Costus clade. ...

Research paper thumbnail of A molecular phylogeny of the wild onions ( Allium; Alliaceae) with a focus on the western North American center of diversity

Molecular Phylogenetics and Evolution, 2008

Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and... more Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and congeners were combined with 154 ITS sequences available on GenBank to develop a global Allium phylogeny with the simultaneous goals of investigating the evolutionary history (monophyly) of Allium in the Californian center of diversity and exploring patterns of adaptation to serpentine soils. Phylogenies constructed with ITS alone or ITS in combination with ETS provided sufficient resolution for investigating evolutionary relationships among species. The ITS region alone was sufficient to resolve the deeper relationships in North American species. Addition of a second marker (ETS) further supports the phylogenetic placements of the North American species and adds resolution within subgenus Amerallium, a clade containing many Californian endemics. Within the global phylogeny, the native North American species were found to be monophyletic, with the exception of Allium tricoccum and Allium schoenoprasum. All native Californian species included in the analysis fell into a monophyletic subgenus Amerallium section Lophioprason, although endemic Californian species were not monophyletic due to the inclusion of species with ranges extending beyond the California Floristic Province. The molecular phylogeny strongly supports previous morphology-based taxonomic groupings. Based on our results, serpentine adaptation appears to have occurred multiple times within section Lophioprason, while the ancestor of the Californian center of diversity may not have been serpentine-adapted.

Research paper thumbnail of E ARLY FLORAL DEVELOPMENT OF HELICONIA LATISPATHA (HELICONIACEAE), A KEY TAXON FOR UNDERSTANDING THE EVOLUTION OF FLOWER DEVELOPMENT IN THE ZINGIBERALES 1

Research paper thumbnail of Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae

Molecular Phylogenetics and Evolution, 2010

Bromeliaceae Bromelioideae ETS g3pdh Molecular phylogeny Neotropical biogeography rpb2 a b s t r ... more Bromeliaceae Bromelioideae ETS g3pdh Molecular phylogeny Neotropical biogeography rpb2 a b s t r a c t

Research paper thumbnail of Virus-Induced Gene Silencing in the Culinary Ginger (Zingiber officinale): An Effective Mechanism for Down-Regulating Gene Expression in Tropical Monocots

Molecular Plant, 2009

Virus-induced gene silencing (VIGS) has been shown to be effective for transient knockdown of gen... more Virus-induced gene silencing (VIGS) has been shown to be effective for transient knockdown of gene expression in plants to analyze the effects of specific genes in development and stress-related responses. VIGS is well established for studies of model systems and crops within the Solanaceae, Brassicaceae, Leguminaceae, and Poaceae, but only recently has been applied to plants residing outside these families. Here, we have demonstrated that barley stripe mosaic virus (BSMV) can infect two species within the Zingiberaceae, and that BSMV-VIGS can be applied to specifically down-regulate phytoene desaturase in the culinary ginger Zingiber officinale. These results suggest that extension of BSMV-VIGS to monocots other than cereals has the potential for directed genetic analyses of many important temperate and tropical crop species.

Research paper thumbnail of Molecular Analysis of the SCARECROW Gene in Maize Reveals a Common Basis for Radial Patterning in Diverse Meristems

Plant Cell, 2000

Maize and Arabidopsis root apical meristems differ in several aspects of their radial organizatio... more Maize and Arabidopsis root apical meristems differ in several aspects of their radial organization and ontogeny. Despite the large evolutionary distance and differences in root radial patterning, analysis of the putative maize ortholog of the Arabidopsis patterning gene SCARECROW ( SCR ) revealed expression localized to the endodermis, which is similar to its expression in Arabidopsis. Expression in maize extends through the quiescent center, a population of mitotically inactive cells formerly thought to be undifferentiated and to lack radial pattern information. Zea mays SCARECROW ( ZmSCR ), the putative maize SCR ortholog, was used as a molecular marker to investigate radial patterning during regeneration of the root tip after either whole or partial excision. Analysis of the dynamic expression pattern of ZmSCR as well as other markers indicates the involvement of positional information as a primary determinant in regeneration of the root radial pattern.

Research paper thumbnail of Between Cancer and Capricorn: Phylogeny, evolution and ecology of the primarily tropical Zingiberales

... USA. E-mail: Chelsea I). S/> echt, Ant... more ... USA. E-mail: Chelsea I). S/> echt, Ant'York Botanical Ganlen, Plant Research l. alnmitury, Bronx, NY 10458 USA. ... 1993; Kato 1996; Sakai et al. 1999) and possibly Siamanthus as suggested by Larsen and Mood (1998). The ...

Research paper thumbnail of Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales

New Phytologist, 2010

•The MADS box transcription factor family has long been identified as an important contributor to... more •The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. Here we examine the role of GLOBOSA (GLO)-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales.•We assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. We identified GLO homologs (ZinGLO1-4) from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus and Musa basjoo.•Based on the phylogenetic data and expression results, we propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum.•Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. Here we examine the role of GLOBOSA (GLO)-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales.We assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. We identified GLO homologs (ZinGLO1-4) from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus and Musa basjoo.Based on the phylogenetic data and expression results, we propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum.Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

PLOS One, 2007

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Systematic Botany, 2004

A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variati... more A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach. DAVIS ET AL.: PHYLOGENY OF MONOCOTS FIG. 1. (continued) B. Structure of Group A from Fig. 1A.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of Flower Evolution: The Origin and Subsequent Diversification of the Angiosperm Flower

Annual Review of Ecology Evolution and Systematics, 2009

Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis a... more Developmental genetic pathways involved in flower formation in model plants such as Arabidopsis and maize enable us to identify genes, gene families, and gene networks that are involved in the regulation of flower initiation, growth and differentiation. These genes can then function as "candidate genes" and their expression, function, and biochemical interactions can be explored in other lineages to determine if they provide a necessary and sufficient toolkit for the development of the flower. Likewise, a view to the fossil record can provide documentation of reproductive innovations occurring within gymnosperms or along the stem lineage leading to angiosperms, elucidating the transitions required for the evolution of the angiosperm flower from an ancestral reproductive strobilus. Here we discuss the origin and subsequent evolution in form of the flower, highlighting recent studies in paleobotany, morphology, evolution, and developmental genetics with the goal of outlining advances in our understanding of flower evolution. 217 Annu. Rev. Ecol. Evol. Syst. 2009.40:217-243. Downloaded from www.annualreviews.org Access provided by University of California -Berkeley on 03/23/15. For personal use only.

Research paper thumbnail of GONDWANAN VICARIANCE OR DISPERSAL IN THE TROPICS? THE BIOGEOGRAPHIC HISTORY OF THE TROPICAL MONOCOT FAMILY COSTACEAE (ZINGIBERALES

Costaceae are a pantropical family, distinguished from other families within the order Zingiberal... more Costaceae are a pantropical family, distinguished from other families within the order Zingiberales by their spiral phyllotaxy and showy labellum comprised of five fused staminodes. While the majority of Costaceae species are found in the neotropics, the pantropical distribution of the family as a whole could be due to a number of historical biogeographic scenarios, including continental-drift mediated vicariance and long-distance dispersal events. Here, the hypothesis of an ancient Gondwanan distribution followed by vicariance via continental drift as the leading cause of the current pantropical distribution of Costaceae is tested, using molecular dating of cladogenic events combined with phylogeny-based biogeographic analyses. Dispersal-Vicariance Analysis (DIVA) is used to determine ancestral distributions based upon the modern distribution of extant taxa in a phylogenetic context. Diversification ages within Costaceae are estimated using chloroplast DNA data (trnL-F and trnK) analyzed with a local clock procedure. In the absence of fossil evidence, the divergence time between Costaceae and Zingiberaceae, as estimated in an ordinal analysis of Zingiberales, is used as the calibration point for converting relative to absolute ages. The results of the temporal analysis based on extant taxa indicate that the initial diversification within Costaceae occurred approximately 65 million years ago, long after the final break up of the Gondwanan supercontinent. Considering this minimum age of diversification, potential scenarios for the current biogeographic patterns found in Costaceae are presented in a temporal and spatial context. The evolution of specialized floral forms associated with specific pollinators is also discussed within the biogeographic framework.

Research paper thumbnail of DNA Barcoding in the Cycadales: Testing the Potential of Proposed Barcoding Markers for Species Identification of Cycads

PLOS One, 2007

Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to s... more Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.

Research paper thumbnail of Epi-illumination microscopy coupled to in situ hybridization and its utility in the study of evolution and development in non-model species

Development Genes and Evolution, 2008

Evolutionary developmental biology often combines methods for examining morphology (e.g., scannin... more Evolutionary developmental biology often combines methods for examining morphology (e.g., scanning electron microscopy, SEM) with analyses of gene expression (e.g., RNA in situ hybridization). Due to differences in tissue preparation for SEM and gene expression analyses, the same specimen cannot be used for both sets of techniques. To aid in the understanding of morphological variation, it would be particularly useful to have a high-magnification image of the very same sample in which gene expression is subsequently analyzed. To address this need, we developed a method that couples extended depth of field (EDF) epi-illumination microscopy to in situ hybridization in a sequential format, enabling both surface microscopy and gene expression analyses to be carried out on the same specimen. We first created a digital image of inflorescence apices using epi-illumination microscopy and commercially available EDF software. We then performed RNA in situ hybridizations on photographed apices to assess the expression of two developmental genes: Knotted1 (Kn1) in Zea mays (Poaceae) and a PISTILLATA (PI) homolog in Musa basjoo (Musaceae). We demonstrate that expression signal is neither altered nor reduced in the imaged apices as compared with the unphotographed controls. The demonstrated method reduces the amount of sample material necessary for developmental research, and enables individual floral development to be placed in the context of the entire inflorescence. While the technique presented here is particularly relevant to floral developmental biology, it is applicable to any research where observation and description of external features can be fruitfully linked with analyses of gene expression.

Research paper thumbnail of Dependence of rat vertex auditory evoked potentials on central muscarinic receptor activation

Brain Research, 1995

Auditory evoked potentials (AEPs) were recorded epidurally at vertex in the freely moving rat, yi... more Auditory evoked potentials (AEPs) were recorded epidurally at vertex in the freely moving rat, yielding the prominent components P18 and N40 from the averaged waveform. Both components were severely attenuated at tone presentation rates faster than 1 Hz. Dependence of the vertex AEP on central cholinergic activation was assessed by comparing the effects of subcutaneous injections of the muscarinic antagonist scopolamine (0.1-1.0 mg/kg) to methyl-scopolamine (0.5, 1.0 mg/kg) to test for peripheral effects. Scopolamine produced a significant decrease in amplitude for both the P18 and N40 components in overall tests. N40 amplitude also showed a significant decrease at each dose of scopolamine, and the magnitude of the amplitude decrement was dose dependent. At 23 h after scopolamine, only N40 amplitude remained significantly depressed. There were no effects of injection of saline, or of methyl-scopolamine. These results confirm that middle-latency vertex AEPs in the rat are attenuated by central muscarinic receptor blockade, consistent with previous findings in cats.

Research paper thumbnail of Easy trees?—Review of “Phylogenetic trees made easy: a how-to manual for molecular biologists” by Barry G. Hall

Molecular Phylogenetics and Evolution, 2003

Research paper thumbnail of Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution

Science, 2011

Understanding the diversification of phenotypes through time—“descent with modification”—has been... more Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years. If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible. Similar phenotypes may be retained from common ancestry (homology), but a phylogenetic context may instead reveal that they are independently derived, due to convergence or parallel evolution, or less likely, that they experienced reversal. Such examples of homoplasy present opportunities to discover the foundations of morphological traits. A common underlying mechanism may exist, and components may have been redeployed in a way that produces the “same” phenotype. New, robust phylogenetic hypotheses and molecular, genomic, and developmental techniques enable integrated exploration of the mechanisms by which similarity arises.

Research paper thumbnail of THE EVOLUTIONARY AND BIOGEOGRAPHIC ORIGIN AND DIVERSIFICATION OF THE TROPICAL MONOCOT ORDER ZINGIBERALES

... W. JOHN KRESS1 AND CHELSEA D. SPECHT2 Department of Botany, MRC-166, United States National H... more ... W. JOHN KRESS1 AND CHELSEA D. SPECHT2 Department of Botany, MRC-166, United States National Herbarium, National Museum of Natural History ... While assigning Heli-coniaceae to a separate rate class does not effect dating of the more internal nodes, the internal ...

Research paper thumbnail of A Molecular Phylogeny of Costaceae (Zingiberales

Molecular Phylogenetics and Evolution, 2001

The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gin... more The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gingers (Zingiberaceae), were investigated with a combination of two chloroplast loci (the trnL-F locus, including the trnL intron, the 3trnL exon, and the trnL-F intergenic spacer, and the trnK locus, including the trnK intron and the matK coding region) and one nuclear locus (ITS1-5.8s-ITS2). The resulting parsimony analysis of selected taxa that demonstrate the range of floral morphological variation in the family shows that the Caldavena-type floral morphology is ancestral to the group and that both Tapeinochilos species and a Monocostus ؉ Dimerocostus clade represent recent divergences. The genus Costus is broadly paraphyletic but Costus subgenus Eucostus K. Schum. represents a large monophyletic radiation that is poorly resolved. Within this clade, secondary analyses suggest that pollination syndrome, traditionally used for taxonomic and classification purposes within the genus Costus, is a relatively plastic trait of limited phylogenetic utility. This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography.

Research paper thumbnail of Systematics and Evolution of the Tropical Monocot Family Costaceae (Zingiberales): A Multiple Dataset Approach

Systematic Botany, 2006

... The nominal genus Costus is not monophyletic and its species are found in all three major cla... more ... The nominal genus Costus is not monophyletic and its species are found in all three major clades. ... The African-neotropical clade is composed entirely of the genus Costus; moreover, there is support for previously recognized subgeneric groupings within the Costus clade. ...

Research paper thumbnail of A molecular phylogeny of the wild onions ( Allium; Alliaceae) with a focus on the western North American center of diversity

Molecular Phylogenetics and Evolution, 2008

Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and... more Nuclear ribosomal DNA (ITS and ETS) sequences from 39 native Californian (USA) Allium species and congeners were combined with 154 ITS sequences available on GenBank to develop a global Allium phylogeny with the simultaneous goals of investigating the evolutionary history (monophyly) of Allium in the Californian center of diversity and exploring patterns of adaptation to serpentine soils. Phylogenies constructed with ITS alone or ITS in combination with ETS provided sufficient resolution for investigating evolutionary relationships among species. The ITS region alone was sufficient to resolve the deeper relationships in North American species. Addition of a second marker (ETS) further supports the phylogenetic placements of the North American species and adds resolution within subgenus Amerallium, a clade containing many Californian endemics. Within the global phylogeny, the native North American species were found to be monophyletic, with the exception of Allium tricoccum and Allium schoenoprasum. All native Californian species included in the analysis fell into a monophyletic subgenus Amerallium section Lophioprason, although endemic Californian species were not monophyletic due to the inclusion of species with ranges extending beyond the California Floristic Province. The molecular phylogeny strongly supports previous morphology-based taxonomic groupings. Based on our results, serpentine adaptation appears to have occurred multiple times within section Lophioprason, while the ancestor of the Californian center of diversity may not have been serpentine-adapted.

Research paper thumbnail of E ARLY FLORAL DEVELOPMENT OF HELICONIA LATISPATHA (HELICONIACEAE), A KEY TAXON FOR UNDERSTANDING THE EVOLUTION OF FLOWER DEVELOPMENT IN THE ZINGIBERALES 1

Research paper thumbnail of Phylogenetic estimation of the core Bromelioids with an emphasis on the genus Aechmea (Bromeliaceae

Molecular Phylogenetics and Evolution, 2010

Bromeliaceae Bromelioideae ETS g3pdh Molecular phylogeny Neotropical biogeography rpb2 a b s t r ... more Bromeliaceae Bromelioideae ETS g3pdh Molecular phylogeny Neotropical biogeography rpb2 a b s t r a c t

Research paper thumbnail of Virus-Induced Gene Silencing in the Culinary Ginger (Zingiber officinale): An Effective Mechanism for Down-Regulating Gene Expression in Tropical Monocots

Molecular Plant, 2009

Virus-induced gene silencing (VIGS) has been shown to be effective for transient knockdown of gen... more Virus-induced gene silencing (VIGS) has been shown to be effective for transient knockdown of gene expression in plants to analyze the effects of specific genes in development and stress-related responses. VIGS is well established for studies of model systems and crops within the Solanaceae, Brassicaceae, Leguminaceae, and Poaceae, but only recently has been applied to plants residing outside these families. Here, we have demonstrated that barley stripe mosaic virus (BSMV) can infect two species within the Zingiberaceae, and that BSMV-VIGS can be applied to specifically down-regulate phytoene desaturase in the culinary ginger Zingiber officinale. These results suggest that extension of BSMV-VIGS to monocots other than cereals has the potential for directed genetic analyses of many important temperate and tropical crop species.

Research paper thumbnail of Molecular Analysis of the SCARECROW Gene in Maize Reveals a Common Basis for Radial Patterning in Diverse Meristems

Plant Cell, 2000

Maize and Arabidopsis root apical meristems differ in several aspects of their radial organizatio... more Maize and Arabidopsis root apical meristems differ in several aspects of their radial organization and ontogeny. Despite the large evolutionary distance and differences in root radial patterning, analysis of the putative maize ortholog of the Arabidopsis patterning gene SCARECROW ( SCR ) revealed expression localized to the endodermis, which is similar to its expression in Arabidopsis. Expression in maize extends through the quiescent center, a population of mitotically inactive cells formerly thought to be undifferentiated and to lack radial pattern information. Zea mays SCARECROW ( ZmSCR ), the putative maize SCR ortholog, was used as a molecular marker to investigate radial patterning during regeneration of the root tip after either whole or partial excision. Analysis of the dynamic expression pattern of ZmSCR as well as other markers indicates the involvement of positional information as a primary determinant in regeneration of the root radial pattern.