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Full-Text Articles in Life Sciences

In Situ Muscle Power Differs Without Varying In Vitro Mechanical Properties In Two Insect Leg Muscles Innervated By The Same Motor Neuron, Anna N. Ahn, Kenneth Meijer, Robert J. Full Sep 2006

In Situ Muscle Power Differs Without Varying In Vitro Mechanical Properties In Two Insect Leg Muscles Innervated By The Same Motor Neuron, Anna N. Ahn, Kenneth Meijer, Robert J. Full

All HMC Faculty Publications and Research

The mechanical behavior of muscle during locomotion is often predicted by its anatomy, kinematics, activation pattern and contractile properties. The neuromuscular design of the cockroach leg provides a model system to examine these assumptions, because a single motor neuron innervates two extensor muscles operating at a single joint. Comparisons of the in situ measurements under in vivo running conditions of muscle 178 to a previously examined muscle (179) demonstrate that the same inputs (e.g. neural signal and kinematics) can result in different mechanical outputs. The same neural signal and kinematics, as determined during running, can result in different mechanical ...


An Optimal Brain Can Be Composed Of Conflicting Agents, Adi Livnat, Nicholas Pippenger Jan 2006

An Optimal Brain Can Be Composed Of Conflicting Agents, Adi Livnat, Nicholas Pippenger

All HMC Faculty Publications and Research

Many behaviors have been attributed to internal conflict within the animal and human mind. However, internal conflict has not been reconciled with evolutionary principles, in that it appears maladaptive relative to a seamless decision-making process. We study this problem through a mathematical analysis of decision-making structures. We find that, under natural physiological limitations, an optimal decision-making system can involve “selfish” agents that are in conflict with one another, even though the system is designed for a single purpose. It follows that conflict can emerge within a collective even when natural selection acts on the level of the collective only.


Word Association Tests Of Associative Memory And Implicit Processes: Theoretical And Assessment Issues, Alan W. Stacy, Susan L. Ames, Jerry L. Grenard Jan 2006

Word Association Tests Of Associative Memory And Implicit Processes: Theoretical And Assessment Issues, Alan W. Stacy, Susan L. Ames, Jerry L. Grenard

CGU Faculty Publications and Research

Word association is one of the most commonly used measures of association in cognitive science. These tests have been used to infer association parameters in normative studies, to derive cues and primes used in diverse paradigms (semantic priming, cued recall, illusory memory), to test implicit memory in experimental studies, and to suggest the operation of implicit processes in nonexperimental work. This chapter briefly outlines some of the historical routes and current controversies about association and summarizes basic cognitive research applying associative tests. The authors then describe benefits and limitations of the tests, as well as implications for theory and interventions ...


Speciation In Duckweeds (Lemnaceae): Phylogenetic And Ecological Inferences, Daniel J. Crawford, Elias Landolt, Donald H. Les, Rebecca T. Kimball Jan 2006

Speciation In Duckweeds (Lemnaceae): Phylogenetic And Ecological Inferences, Daniel J. Crawford, Elias Landolt, Donald H. Les, Rebecca T. Kimball

Aliso: A Journal of Systematic and Evolutionary Botany

Species of duckweeds (Letnnaceae) that were resolved as sister taxa in a phylogeny based on combined molecular and non-molecular data were compared for morphological, physiological, and ecological attributes to infer factors important in the initial divergence leading to speciation. The ability to survive extreme conditions such as desiccation and cold temperatures is the most common difference identified between species. Two morphological characters facilitating survival in extreme environments are production of special resting buds called turions and increased seed production. The prevalent geographic pattern for species pairs consists of one restricted species occurring on the periphery of a more widespread taxon ...


Systematics Of Xanthorrhoeaceae Sensu Lato, With An Emphasis On Bulbine, Dion S. Devey, Ilia Leitch, J. Chris Pires, Yohan Pillon, Mark W. Chase Jan 2006

Systematics Of Xanthorrhoeaceae Sensu Lato, With An Emphasis On Bulbine, Dion S. Devey, Ilia Leitch, J. Chris Pires, Yohan Pillon, Mark W. Chase

Aliso: A Journal of Systematic and Evolutionary Botany

We provide here results of a combined analysis of plastid genes rbcL, matK, and ndhF for Xanthorrhoeaceae s.l., the Asphodelaceae/Xanthorrhoeaceae/Hemerocallidaceae clade, which are well supported by the DNA data. Xanthorrhoea (often treated as the sole member of Xanthorrhoeaceae) is sister to the hemerocallid clade (former Hemerocallidaceae); and the asphodelid clade (formerly Asphodelaceae) is sister to them both. For additional species of Bulbine and Jodrellia (both Asphodeloideae), we also collected rps16 intron and ITS nuclear ribosomal DNA sequences to better assess their relationships. Bulbine, with Jodrellia, embedded are sister to the collective genera of ...


Phylogenetics Of The "Tiger-Flower" Group (Tigridieae: Iridaceae): Molecular And Morphological Evidence, Aaron Rodriguez, Kenneth J. Sytsma Jan 2006

Phylogenetics Of The "Tiger-Flower" Group (Tigridieae: Iridaceae): Molecular And Morphological Evidence, Aaron Rodriguez, Kenneth J. Sytsma

Aliso: A Journal of Systematic and Evolutionary Botany

The phylogenetic relationships among 23 species of the tribe Tigridieae (lridaceae) were inferred using morphological data and nucleotide sequences from nuclear ITS and three intergenic spacers of the cpDNA: psbA-trnH, trnT-trnL, and trnL-trnF. Although all data sets supported a monophyletic Mexican-Guatemalan Tigridiinae including two taxa usually placed in Cipurinae (Cardiostigma longispatha and Nemastylis convoluta), neither morphology, cpDNA, nor ITS resolved phylogenetic relationships within this lineage. A graphical tree of trees analysis showed the cladograms derived from morphology to be the most topologically distinct within the set of all trees examined and ...


Phylogenetics Of Lilliales, Michael F. Fay, Mark W. Chase, Nina Rønsted, Dion S. Devey, Yohan Pillon, J. Chris Pires, Gitte Peterson, Ole Seberg, Jerrold I. Davis Jan 2006

Phylogenetics Of Lilliales, Michael F. Fay, Mark W. Chase, Nina Rønsted, Dion S. Devey, Yohan Pillon, J. Chris Pires, Gitte Peterson, Ole Seberg, Jerrold I. Davis

Aliso: A Journal of Systematic and Evolutionary Botany

In order to investigate interfamilial relationships of Liliales we analyzed a combined matrix of plastid rbcL, trnL intron, trnL-F intergenic spacer, matK, and ndhF, and mitochondrial atp1 DNA sequences. The results are generally congruent with previous broad analyses and provide higher bootstrap support for many relationships. Important changes relative to previous studies are the recognition of Petermanniaceae distinct from Colchicaceae and the tentative inclusion of Corsiaceae in the order. This brings the number of families in the order from nine to eleven. The additional data presented here strengthen the case for including Uvulariaceae in ...


Missing Links Between Disjunct Populations Of Androcymbium (Colchicaceae) In Africa Using Chloroplast Dna Noncoding Sequences, Alberto Del Hoyo, Joan Pedrola-Monfort Jan 2006

Missing Links Between Disjunct Populations Of Androcymbium (Colchicaceae) In Africa Using Chloroplast Dna Noncoding Sequences, Alberto Del Hoyo, Joan Pedrola-Monfort

Aliso: A Journal of Systematic and Evolutionary Botany

With the objective of clarifying some aspects of the biogeography, phylogeny, and taxonomy of the genus Androcymbium, we sequenced three chloroplastic DNA noncoding regions (trnL intron, trnL-trnF IGS, and trnY-trnD IGS). These data were analyzed with maximum parsimony and the ancestral areas methods following Bremer. Results show that Androcymbium is not monophyletic and that the origin of its distribution and speciation is situated in western South Africa. Later, it dispersed to North Africa, going first to eastern South Africa. Androcymbium austrocapense and A. roseum allow us to phylogenetically connect the species of western ...


Further Evidence For Seed Size Variation In The Genus Zostera: Exploratory Studies With Z. Japonica And Z. Asiatica, Sandy Wyllie-Echeverria, Victoria R. Wyllie-Echeverria, Algernon C. Churchill, Paul A. Cox Jan 2006

Further Evidence For Seed Size Variation In The Genus Zostera: Exploratory Studies With Z. Japonica And Z. Asiatica, Sandy Wyllie-Echeverria, Victoria R. Wyllie-Echeverria, Algernon C. Churchill, Paul A. Cox

Aliso: A Journal of Systematic and Evolutionary Botany

Recent studies found seed size variation within the seagrass Zostera marina, one of nine species in the genus Zostera. The objectives of this study were to determine if variation also exists in the seeds of two other species Zostera japonica and Zostera asiatica within this genus. Results indicate that: (1) length and weight varied between two populations (one indigenous population from Akkeshi-Ko, Japan, and one exotic population from Willapa Bay, Washington, USA) of the small-bodied intertidal seagrass species Z. japonica, and (2) seed-size classes were discernable. Preliminary investigations were also initiated with a Japanese population of Z. asiatica, a large-bodied ...


Stem Anatomy Of Climbing Palms In Relation To Long-Distance Water Transport, P. Barry Tomlinson Jan 2006

Stem Anatomy Of Climbing Palms In Relation To Long-Distance Water Transport, P. Barry Tomlinson

Aliso: A Journal of Systematic and Evolutionary Botany

Palms lack secondary growth so their primary vascular system is long-lived and must be minimally vulnerable to dysfunction. For water movement, the axial xylem must be well defended against cavitation. Climbing palms can be very long and represent a maximum solution to transport problems. How is this demonstrated in their anatomy? This article contrasts stem vascular anatomy in a canelike "tree palm" (Rhapis excelsa) with that in the American climbing palm Desmoncus and the Old World rattan genus Calamus. Rhapis, representing the basic classical palm vasculature, has a continuously integrated vascular system determined by branching of the axial (stem) system ...


Genomic Resources For Asparagales, Michael J. Havey, Kenneth C. Sink, Maria Jenderek, Christopher D. Town Jan 2006

Genomic Resources For Asparagales, Michael J. Havey, Kenneth C. Sink, Maria Jenderek, Christopher D. Town

Aliso: A Journal of Systematic and Evolutionary Botany

Enormous genomic resources have been developed for plants in the monocot order Poales; however, it is not known how useful these resources will be for other economically important monocots. Asparagales are a monophyletic order sister to class Commelinanae that carries Poales, and is the second most economically important monocot order. Development of genomic resources for and their application to Asparagales are challenging because of huge nuclear genomes and the relatively long generation times required to develop segregating families. We synthesized a normalized eDNA library of onion (Allium cepa) and produced II ,008 unique expressed sequence tags (ESTs) for comparative genomic ...


Pollination Biology And Adaptive Radiation Of Agavaceae, With Special Emphasis On The Genus Agave, Martha Rocha, Sara V. Good-Ávila, Fracisco Molina-Freaner, Hector T. Arita, Amanda Castillo, Abisaí García-Mendoza, Arturo Silva-Montellano, Brandon S. Gaut, Valeria Souza, Luis E. Eguiarte Jan 2006

Pollination Biology And Adaptive Radiation Of Agavaceae, With Special Emphasis On The Genus Agave, Martha Rocha, Sara V. Good-Ávila, Fracisco Molina-Freaner, Hector T. Arita, Amanda Castillo, Abisaí García-Mendoza, Arturo Silva-Montellano, Brandon S. Gaut, Valeria Souza, Luis E. Eguiarte

Aliso: A Journal of Systematic and Evolutionary Botany

Agavaceae are an American family that comprises nine genera and ca. 300 species distributed in arid and semiarid environments, mainly in Mexico. The family is very successful and displays a wide array of ecological, reproductive, and morphological adaptations. Many of its members play important roles as keystone species, because they produce abundant resources during the reproductive season. In this paper we analyze the current knowledge about the pollination ecology of the different genera in the family and the role that pollination systems have played in the ecological and phylogenetic success of the group. After providing an overview of each of ...


Phylogeny Of Iridaceae Subfamily Crocoideae Based On A Combined Multigene Plastid Dna Analysis, Peter Goldblatt, T. Jonathan Davies, John C. Manning, Michelle Van Der Bank, Vincent Savolainen Jan 2006

Phylogeny Of Iridaceae Subfamily Crocoideae Based On A Combined Multigene Plastid Dna Analysis, Peter Goldblatt, T. Jonathan Davies, John C. Manning, Michelle Van Der Bank, Vincent Savolainen

Aliso: A Journal of Systematic and Evolutionary Botany

The phylogeny of Crocoideae, the largest of four subfamilies currently recognized in Tridaceae, has eluded resolution until sequences of two more plastid DNA regions were added here to a previously published matrix containing sequences from four DNA plastid regions. Sister to the core Nivenioideae, the woody Klattia, Nivenia, and Witsenia, Crocoideae are a climax group in lridaceae, comprising some 995 species, slightly more than half of the total in the family. Synapomorphies of Crocoideae include pollen exine perforate, pollen aperture operculate, ovule campylotropous (or hypotropous), root xylem vessels with simple perforations, cormous rootstock, inflorescence a spike, and plants deciduous. The ...


A Comparison And Combination Of Plastid Atpb And Rbcl Gene Sequences For Inferring Phylogenetic Relationships Within Orchidaceae, Kenneth M. Cameron Jan 2006

A Comparison And Combination Of Plastid Atpb And Rbcl Gene Sequences For Inferring Phylogenetic Relationships Within Orchidaceae, Kenneth M. Cameron

Aliso: A Journal of Systematic and Evolutionary Botany

Parsimony analyses of DNA sequences from the plastid genes atpB and rbcL were completed for 173 species of Orchidaceae (representing 150 different genera) and nine genera from outgroup families in Asparagales. The atpB tree topology is similar to the rbcL tree, although the atpB data contain less homoplasy and provide greater jackknife support than rbcL alone. In combination, the two-gene tree recovers five monophyletic clades corresponding to subfamilies within Orchidaceae, and fully resolves them with moderate to high jackknife support as follows: Epidendroideae are sister to Orchidoideae, followed by Cypripedioideae, then Vanilloideae, and with ...


The Good, The Bad, The Ugly: Using Naturally Occurring Terata To Distinguish The Possible From The Impossible In Orchid Floral Evolution, Richard M. Bateman, Paula J. Rudall Jan 2006

The Good, The Bad, The Ugly: Using Naturally Occurring Terata To Distinguish The Possible From The Impossible In Orchid Floral Evolution, Richard M. Bateman, Paula J. Rudall

Aliso: A Journal of Systematic and Evolutionary Botany

We interpret extensive field observations of terata in the context of recent insights into monocot phylogeny and evolutionary-developmental genetics to explore the evolution of the orchid flower. Our arguably typological classification of floral terata focuses on natural occurrences of three contrasting modes of peloria (restoration of actinomorphy in a formerly zygomorphic perianth) and three contrasting modes of pseudopeloria (lessening of the degree of zygomorphy shown by the evolutionarily preceding perianth). Dynamic evolutionary transitions in floral morphology are assigned to recently revised concepts of heterotopy (including homeosis: evolutionary transitions in position of expression) and heterochrony (evolutionary transitions in timing of expression ...


Species Boundaries And Population Divergence In The Pyrenean Endemic Relict Genus Borderea (Dioscoreaceae) As Revealed By Microsatellite (Ssr) And Other Hypervariable Markers, José Gabriel Segarra-Moragues, Pilar Catalan Jan 2006

Species Boundaries And Population Divergence In The Pyrenean Endemic Relict Genus Borderea (Dioscoreaceae) As Revealed By Microsatellite (Ssr) And Other Hypervariable Markers, José Gabriel Segarra-Moragues, Pilar Catalan

Aliso: A Journal of Systematic and Evolutionary Botany

Microsatellite alleles were used to delimit the genetic boundaries and divergence of the two relictual endemic Pyrenean taxa Borderea chouardii and B. pyrenaica (Dioscoreaceae), and to infer the different life histories followed by each species. Our study was conducted on the same populations previously analyzed with allozymes and RAPD markers. The three studied data sets were congruent in the inference of a single evolutionary scenario for the split of the two Borderea taxa from a common Tertiary ancestor in the Prepyrenees, thus supporting their taxonomic treatment as separate species. However, the more variable SSR and RAPD data provided better resolution ...


A Synopsis Of Melanthiaceae (Liliales) With Focus On Character Evolution In Tribe Melanthieae, Wendy B. Zomlefer, Walter S. Judd, W. Mark Whitten, Norris H. Williams Jan 2006

A Synopsis Of Melanthiaceae (Liliales) With Focus On Character Evolution In Tribe Melanthieae, Wendy B. Zomlefer, Walter S. Judd, W. Mark Whitten, Norris H. Williams

Aliso: A Journal of Systematic and Evolutionary Botany

Melanthiaceae s.l. comprises five tribes: Chionographideae, Heloniadeae, Melanthieae, Parideae, and Xerophylleae—each defined by distinctive autapomorphies. The most morphologically diverse tribe Melanthieae, now with seven genera, had not been subject to rigorous phylogenetic character study prior to the current series of investigations that also include an overview of the family. Data from our publications and studies underway are here assessed and integrated, providing a useful overview of Melanthiaceae, and especially of Melanthieae. The results of parsimony analyses of ITS (nuclear ribosomal) and trnL-F (plastid) DNA sequence data correlate with potentially synapomorphic phenotypic characters for genera of Melanthieae, including ...


Phylogenetic Relationships Of Monocots Based On The Highly Informative Plastid Gene Ndhf, Thomas J. Givnish, J. Chris Pires, Sean W. Graham, Marc A. Mcpherson, Linda M. Prince, Thomas B. Patterson, Hardeep S. Rai, Eric H. Roalson, Timothy M. Evans, William J. Hahn, Kendra C. Millam, Alan W. Meerow, Mia Molvray, Paul J. Kores, Heath W. O'Brien, Jocelyn C. Hall, W. John Kress, Kenneth J. Sytsma Jan 2006

Phylogenetic Relationships Of Monocots Based On The Highly Informative Plastid Gene Ndhf, Thomas J. Givnish, J. Chris Pires, Sean W. Graham, Marc A. Mcpherson, Linda M. Prince, Thomas B. Patterson, Hardeep S. Rai, Eric H. Roalson, Timothy M. Evans, William J. Hahn, Kendra C. Millam, Alan W. Meerow, Mia Molvray, Paul J. Kores, Heath W. O'Brien, Jocelyn C. Hall, W. John Kress, Kenneth J. Sytsma

Aliso: A Journal of Systematic and Evolutionary Botany

We used ndhF sequence variation to reconstruct relationships across 282 taxa representing 78 monocot families and all 12 orders. The resulting tree is highly resolved and places commelinids sister to Asparagales, with both sister to Liliales—Pandanales in the strict consensus; Pandanales are sister to Dioscoreales in the bootstrap majority-rule tree, just above Petrosaviales. Acorales are sister to all other monocots, with Alismatales sister to all but Acorales. Relationships among the four major clades of commelinids remain unresolved. Relationships within orders are consistent with those based on rbcL, alone or in combination with atpB and 18S nrDNA ...


Multigene Analyses Of Monocot Relationships, Mark W. Chase, Michael F. Fay, Dion S. Devey, Oliver Maurin, Nina Rønsted, T. Jonathan Davies, Yohan Pillon, Gitte Peterson, Minoru N. Tamura, Conny B. Asmussen, Khidir Hilu, Thomas Borsch, Jerrold I. Davis, Dennis W. Stevenson, J. Chris Pires, Thomas J. Givnish, Kenneth J. Systma, Marc A. Mcpherson, Sean W. Graham, Hardeep S. Rai Jan 2006

Multigene Analyses Of Monocot Relationships, Mark W. Chase, Michael F. Fay, Dion S. Devey, Oliver Maurin, Nina Rønsted, T. Jonathan Davies, Yohan Pillon, Gitte Peterson, Minoru N. Tamura, Conny B. Asmussen, Khidir Hilu, Thomas Borsch, Jerrold I. Davis, Dennis W. Stevenson, J. Chris Pires, Thomas J. Givnish, Kenneth J. Systma, Marc A. Mcpherson, Sean W. Graham, Hardeep S. Rai

Aliso: A Journal of Systematic and Evolutionary Botany

We present an analysis of supra-familial relationships of monocots based on a combined matrix of nuclear I8S and partial 26S rDNA, plastid atpB, matK, ndhF, and rbcL, and mitochondrial atp1 DNA sequences. Results are highly congruent with previous analyses and provide higher bootstrap support for nearly all relationships than in previously published analyses. Important changes to the results of previous work are a well-supported position of Petrosaviaceae as sister to all monocots above Acorales and Alismatales and much higher support for the commelinid clade. For the first time, the spine of the monocot tree has ...


Placing The Monocots: Conflicting Signal From Trigenomic Analyses, Melvin R. Duvall, Sarah Matthews, Neill Mohammad, Tammy Russel Jan 2006

Placing The Monocots: Conflicting Signal From Trigenomic Analyses, Melvin R. Duvall, Sarah Matthews, Neill Mohammad, Tammy Russel

Aliso: A Journal of Systematic and Evolutionary Botany

Despite recent significant advances in understanding angiosperm phylogeny, the position of monocots remains uncertain. We present here a phylogeny inferred from four genes that unambiguously unite monocots with eumagnoliids. A well-supported position for the monocots was obtained only after we replaced the available nuclear 18S rDNA sequence data with data from phytochrome C in a matrix that also included plastid rbcL and ndhF and mitochondrial atp1. Over 5000 base pairs of sequence data from 42 taxa were analyzed using Bayesian inference. The results of these analyses united monocots with the eumagnoliids in a well-supported clade. Although the ...


Fleshy Fruits In Liliflorous Monocots, Finn N. Rasmussen, Signe Frederikson, Bo Johansen, Lise Bolt Jørgenson, Gitte Peterson Jan 2006

Fleshy Fruits In Liliflorous Monocots, Finn N. Rasmussen, Signe Frederikson, Bo Johansen, Lise Bolt Jørgenson, Gitte Peterson

Aliso: A Journal of Systematic and Evolutionary Botany

Fleshy fruits occur in several monocot orders and families, and it is generally assumed that they have been derived from capsular fruits many times during the evolution of monocot lineages. Huber hypothesized in 1969 that most capsules in Asparagales are derived secondarily from berries and that this transformation was correlated with the evolution of phytomelan-coated seeds, a pivotal character in his circumscription of Asparagales as part of reclassifying Liliaceae s.l. Dahlgren and co-workers suggested several parallel derivations and "reversals" in this character, e.g., the transformation sequence trifollicular fruits → capsules → berries→ capsules→ berries. Mapping of fleshy fruits on a ...


Molecular Basis Of Development In Petaloid Monocot Flowers, Bo Johansen, Signe Frederikson Jan 2006

Molecular Basis Of Development In Petaloid Monocot Flowers, Bo Johansen, Signe Frederikson

Aliso: A Journal of Systematic and Evolutionary Botany

and several studies have confirmed the extended ABC model as the molecular background of flower development in this plant group. The core eudicots are characterized as having one copy of each of the B-class genes and at least two copies of A-class genes: one is expressed in floral meristems, the other in inflorescence meristems. In monocots and non-core eudicots the validity of the ABC model is under discussion. Generally, more than one functional copy is found of at least one of the B-class genes. The A-class genes apparently are expressed in meristems of both flower and inflorescence. Morphologically petaloid stamens ...


Aperture Pattern And Microsporogenesis In Asparagales, Sophie Nadot, Laurent Penet, Leanne D. Dreyer, Arlette Forchioni, Adrienne Ressayre Jan 2006

Aperture Pattern And Microsporogenesis In Asparagales, Sophie Nadot, Laurent Penet, Leanne D. Dreyer, Arlette Forchioni, Adrienne Ressayre

Aliso: A Journal of Systematic and Evolutionary Botany

The aperture pattern of pollen grains is a character defined as the number, shape, and position of apertures. Although this character is highly variable in angiosperms, two states are particularly widespread. Pollen grains with one polar aperture occur frequently in basal angiosperms and monocots while tricolpate pollen is a synapomorphy of the eudicots. Many morphological characters are the result of a compromise between selective forces (acting on morphology) and developmental constraints (limiting the range of possible morphologies). To investigate what are the respective roles of development and selection in the determination of aperture pattern in angiosperms, we have chosen to ...


Analyzing Dna Microarrays With Undergraduate Statisticians, Johanna S. Hardin, Laura Hoopes, Ryan Murphy '06 Jan 2006

Analyzing Dna Microarrays With Undergraduate Statisticians, Johanna S. Hardin, Laura Hoopes, Ryan Murphy '06

Pomona Faculty Publications and Research

With advances in technology, biologists have been saddled with high dimensional data that need modern statistical methodology for analysis. DNA microarrays are able to simultaneously measure thousands of genes (and the activity of those genes) in a single sample. Biologists use microarrays to trace connections between pathways or to identify all genes that respond to a signal. The statistical tools we usually teach our undergraduates are inadequate for analyzing thousands of measurements on tens of samples. The project materials include readings on microarrays as well as computer lab activities. The topics covered include image analysis, filtering and normalization techniques, and ...


Robust Inference Of Monocot Deep Phylogeny Using An Expanded Multigene Plastid Data Set, Sean W. Grahan, Jessie M. Zgurski, Marc A. Mcpherson, Donna M. Cherniawsky, Jeffery M. Saarela, Elvira F. C. Horne, Selena Y. Smith, Winson A. Young, Heath E. O'Brien, Vincent L. Brown, J. Chris Pires, Richard G. Olmstead, Mark W. Chase, Hardeep S. Rai Jan 2006

Robust Inference Of Monocot Deep Phylogeny Using An Expanded Multigene Plastid Data Set, Sean W. Grahan, Jessie M. Zgurski, Marc A. Mcpherson, Donna M. Cherniawsky, Jeffery M. Saarela, Elvira F. C. Horne, Selena Y. Smith, Winson A. Young, Heath E. O'Brien, Vincent L. Brown, J. Chris Pires, Richard G. Olmstead, Mark W. Chase, Hardeep S. Rai

Aliso: A Journal of Systematic and Evolutionary Botany

We use multiple photosynthetic, chlororespiratory, and plastid translation apparatus loci and their associated noncoding regions (ca. 16 kb per taxon, prior to alignment) to make strongly supported inferences of the deep internal branches of monocot phylogeny. Most monocot relationships are robust (an average of ca. 91 % bootstrap support per branch examined), including those poorly supported or unresolved in other studies. Our data strongly support a sister-group relationship between Asparagales and the commelinid monocots, the inclusion of the orchids in Asparagales, and the status of Petrosaviaceae as the sister group of all monocots except Acorus and Alismatales. The latter finding supports ...


Systematic Floral Anatomy Of Pontederiaceae, Michael G. Simpson, Darren H. Burton Jan 2006

Systematic Floral Anatomy Of Pontederiaceae, Michael G. Simpson, Darren H. Burton

Aliso: A Journal of Systematic and Evolutionary Botany

Twenty species of Pontederiaceae and six species of the outgroup families Haemodoraceae and Philydraceae were investigated with regard to floral anatomy, using standard histological methods and graphic reconstructions. Variation is described in several features, including functional carpel number, the distribution of floral aerenchyma, the presence of unusual floral epithelial cells, the presence, type, and distribution of tannin cells, crystal type and distribution, aspects of placentation, ovule number, number of ovule rows per carpel, and septal nectary presence. In order to better assess character homology, one of these features, placentation, was divided into three discrete characters: septal fusion, placenta position, and ...


Gondwanan Vicariance Or Dispersal In The Tropics? The Biogeographic History Of The Tropical Monocot Family Costaceae (Zingiberales), Chelsea D. Specht Jan 2006

Gondwanan Vicariance Or Dispersal In The Tropics? The Biogeographic History Of The Tropical Monocot Family Costaceae (Zingiberales), Chelsea D. Specht

Aliso: A Journal of Systematic and Evolutionary Botany

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 ...


Mitochondrial Data In Monocot Phylologenetics, Gitte Peterson, Ole Seberg, Jerrold I. Davis, Douglas H. Goldman, Dennis W. Stevenson, Lisa M. Campbell, Fabian A. Michaelangeli, Chelsea D. Specht, Mark W. Chase, Michael E. Fay, J. Chris Pires, John V. Freudenstein, Christopher R. Hardy, Mark P. Simmons Jan 2006

Mitochondrial Data In Monocot Phylologenetics, Gitte Peterson, Ole Seberg, Jerrold I. Davis, Douglas H. Goldman, Dennis W. Stevenson, Lisa M. Campbell, Fabian A. Michaelangeli, Chelsea D. Specht, Mark W. Chase, Michael E. Fay, J. Chris Pires, John V. Freudenstein, Christopher R. Hardy, Mark P. Simmons

Aliso: A Journal of Systematic and Evolutionary Botany

Mitochondrial sequences are an important source of data in animal phylogenetics, equivalent in importance to plastid sequences in plants. However, in recent years plant systematists have begun exploring the mitochondrial genome as a source of phylogenetically useful characters. The plant mitochondrial genome is renowned for its variability in size, structure, and gene organization, but this need not be of concern for the application of sequence data in phylogenetics. However, the incorporation of reverse transcribed mitochondrial genes ("processed paralogs") and the recurring transfer of genes from the mitochondrion to the nucleus are evolutionary events that must be taken into account. RNA ...


Gondwanan Origin Of Major Monocot Groups Inferred From Dispersal-Vicariance Analysis, Kåre Bremer, Thomas Janssen Jan 2006

Gondwanan Origin Of Major Monocot Groups Inferred From Dispersal-Vicariance Analysis, Kåre Bremer, Thomas Janssen

Aliso: A Journal of Systematic and Evolutionary Botany

Historical biogeography of major monocot groups was investigated by biogeographical analysis of a dated phylogeny including 79 of the 81 monocot families using the Angiosperm Phylogeny Group II (APG II) classification. Five major areas were used to describe the family distributions: Eurasia, North America, South America, Africa including Madagascar, and Australasia including New Guinea, New Caledonia, and New Zealand. In order to investigate the possible correspondence with continental breakup, the tree with its terminal distributions was fitted to the geological area cladogram ((Eurasia, North America), (Africa, (South America, Australasia)) and to alternative area cladograms using the TreeFitter program. The results ...


Perianth Development In The Basal Monocot Triglochin Maritima (Juncaginaceae), Matyas Buzgo, Douglas E. Soltis, Pamela S. Soltis, Sangtae Kim, Hong Ma, Bernard A. Hauser, Jim Lebens-Mack, Bo Johansen Jan 2006

Perianth Development In The Basal Monocot Triglochin Maritima (Juncaginaceae), Matyas Buzgo, Douglas E. Soltis, Pamela S. Soltis, Sangtae Kim, Hong Ma, Bernard A. Hauser, Jim Lebens-Mack, Bo Johansen

Aliso: A Journal of Systematic and Evolutionary Botany

Basal monocots exhibit considerable variation in inflorescence and floral structure. In some cases, such as Triglochin maritima, it is not clear whether the lateral and terminal structures of the inflorescence are flowers or pseudanthia, or where the limits between flowers and inflorescence lie. To address these questions, morphological studies were carried out, and the results show that in T. maritima both terminal and lateral structures are flowers, not pseudanthia. The terminal flower of T. maritima develops from the apical inflorescence meristem, suggesting that the apical meristem identity changes from "inflorescence" to "flower" during inflorescence development. In addition, distal flowers of ...