Publications by authors named "Lynn Clark"

35 Publications

Notes on leaf micromorphology of the rare herbaceous bamboo Pilg. (Olyreae, Poaceae) from New Guinea and its taxonomic implications.

PhytoKeys 2021 19;172:135-143. Epub 2021 Feb 19.

Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil Universidade Estadual de Feira de Santana Feira de Santana Brazil.

We present notes on the leaf micromorphology of , a rare species from New Guinea and included in Buergersiochloinae, one of three subtribes of the herbaceous bamboos (tribe Olyreae). We used scanning electron microscopy and light microscopy to analyze the microcharacters of both adaxial and abaxial leaf surfaces. Within the Olyreae, saddle-shaped silica bodies in both the costal and intercostal zones are considered unique to Buergersiochloinae. Simple, circular and very small papillae are observed on the adaxial surface, and for the first time, branched papillae on the abaxial surface are observed in . On the abaxial surface, there are papillae on long cells associated with the stomatal complexes. Bicellular microhairs are the only trichomes present and they are found almost exclusively on the abaxial surface. The saddle-shaped silica bodies are the most taxonomically important among the microcharacters observed on the leaf surface of .
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http://dx.doi.org/10.3897/phytokeys.172.59506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7910262PMC
February 2021

Draft genome of the herbaceous bamboo Raddia distichophylla.

G3 (Bethesda) 2021 02;11(2)

Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.

Bamboos are important nontimber forest plants widely distributed in the tropical and subtropical regions of Asia, Africa, America, and Pacific islands. They comprise the Bambusoideae in the grass family (Poaceae), including approximately 1700 described species in 127 genera. In spite of the widespread uses of bamboo for food, construction, and bioenergy, the gene repertoire of bamboo still remains largely unexplored. Raddia distichophylla (Schrad. ex Nees) Chase, belonging to the tribe Olyreae (Bambusoideae, Poaceae), is a diploid herbaceous bamboo with only slightly lignified stems. In this study, we report a draft genome assembly of the ∼589 Mb whole-genome sequence of R. distichophylla with a contig N50 length of 86.36 Kb. Repeat sequences account for ∼49.08% of the genome assembly, of which LTR retrotransposons occupy ∼35.99% of the whole genome. A total of 30,763 protein-coding genes were annotated in the R. distichophylla genome with an average transcript size of 2887 bp. Access to this herbaceous bamboo genome sequence will provide novel insights into biochemistry, molecular marker-assisted breeding programs, and germplasm conservation for bamboo species worldwide.
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http://dx.doi.org/10.1093/g3journal/jkaa049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022951PMC
February 2021

3D shape analysis of grass silica short cell phytoliths: a new method for fossil classification and analysis of shape evolution.

New Phytol 2020 10 1;228(1):376-392. Epub 2020 Jul 1.

University of Washington Biology Department, Life Sciences Building, Seattle, WA, 98105, USA.

Fossil grass silica short cell phytoliths (GSSCP) have been used to reconstruct the biogeography of Poaceae, untangle crop domestication history and detect past vegetation shifts. These inferences depend on accurately identifying the clade to which the fossils belong. Patterns of GSSCP shape and size variation across the family have not been established and current classification methods are subjective or based on a 2D view that ignores important 3D shape variation. Focusing on Poaceae subfamilies Anomochlooideae, Pharoideae, Pueliodieae, Bambusoideae and Oryzoideae, we observed in situ GSSCP to establish their orientation and imaged isolated GSSCP using confocal microscopy to produce 3D models. 3D geometric morphometrics was used to analyze GSSCP shape and size. Classification models were applied to GSSCP from Eocene sediments from Nebraska, USA, and Anatolia, Turkey. There were significant shape differences between nearly all recognized GSSCP morphotypes and between clades with shared morphotypes. Most of the Eocene GSSCP were classified as woody bamboos with some distinctive Nebraska GSSCP classified as herbaceous bamboos. 3D morphometrics hold great promise for GSSCP classification. It accounts for the complete GSSCP shape, automates size measurements and accommodates the complete range of morphotypes within a single analytical framework.
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http://dx.doi.org/10.1111/nph.16677DOI Listing
October 2020

Phylogenetic relationships within Parianinae (Poaceae: Bambusoideae: Olyreae) with emphasis on Eremitis: Evidence from nuclear and plastid DNA sequences, macromorphology, and pollen ectexine patterns.

Mol Phylogenet Evol 2019 10 19;139:106541. Epub 2019 Jun 19.

Iowa State University, Dept. of Ecology, Evolution, and Organismal Biology, Ames, IA 50011-4009, USA. Electronic address:

Eremitis, Pariana, and Parianella are herbaceous bamboos (tribe Olyreae) included in the subtribe Parianinae, which is characterized by the presence of fimbriae at the apex of the leaf sheaths and exclusively spiciform synflorescences. We analyzed 43 samples of herbaceous and woody bamboos in order to infer relationships within the Parianinae, based on combined data from the nuclear ribosomal internal transcribed spacer (ITS) and plastid DNA (rpl32-trnL and trnD-trnT spacers). Bayesian inference, maximum likelihood, and maximum parsimony methods were applied, and macro- and micromorphological aspects were also analyzed, including the ectexine patterns of pollen grains. Parianinae is represented by three well-supported lineages in our analyses: (1) Parianella, endemic to southern Bahia, Brazil; (2) Pariana sensu stricto with a broad distribution in southern Central America and northern South America, especially in the Amazon region; and (3) Eremitis, endemic to the Brazilian Atlantic Forest, from the states of Pernambuco to Rio de Janeiro, including one species previously described as a member of Pariana. Our molecular phylogeny showed that Pariana, as historically circumscribed, is not monophyletic, by recovering Pariana sensu stricto as strongly supported and sister to Eremitis + Pariana multiflora, with Parianella sister to the Pariana-Eremitis clade. Morphological features of their synflorescences and differences in ectexine patterns characterize each lineage. Based on all these characters and the phylogenetic results, Pariana multiflora, endemic to the state of Espírito Santo, Brazil, is transferred to Eremitis.
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http://dx.doi.org/10.1016/j.ympev.2019.106541DOI Listing
October 2019

Leaf shape and size track habitat transitions across forest-grassland boundaries in the grass family (Poaceae).

Evolution 2019 05 26;73(5):927-946. Epub 2019 Mar 26.

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50011.

Grass leaf shape is a strong indicator of their habitat with linear leaves predominating in open areas and ovate leaves distinguishing forest-associated grasses. This pattern among extant species suggests that ancestral shifts between forest and open habitats may have coincided with changes in leaf shape or size. We tested relationships between habitat, climate, photosynthetic pathway, and leaf shape and size in a phylogenetic framework to evaluate drivers of leaf shape and size variation over the evolutionary history of the family. We also estimated the ancestral habitat of Poaceae and tested whether forest margins served as transitional zones for shifts between forests and grasslands. We found that grass leaf shape is converging toward different shape optima in the forest understory, forest margins, and open habitats. Leaf size also varies with habitat. Grasses have smaller leaves in open and drier areas, and in areas with high solar irradiance. Direct transitions between linear and ovate leaves are rare as are direct shifts between forest and open habitats. The most likely ancestral habitat of the family was the forest understory and forest margins along with an intermediate leaf shape served as important transitional habitat and morphology, respectively, for subsequent shifts across forest-grassland biome boundaries.
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http://dx.doi.org/10.1111/evo.13722DOI Listing
May 2019

Fusoid cells in the grass family Poaceae (Poales): a developmental study reveals homologies and suggests new insights into their functional role in young leaves.

Ann Bot 2018 11;122(5):833-848

Universidade Estadual Paulista - UNESP, Departamento de Botânica, São Paulo, Brazil.

Background And Aims: In mature grass leaf blades as seen in cross-section, oblong cell-like structures have been interpreted most recently as intercellular gas spaces delimited by successive collapsed fusoid cells. These cells have been reported in at least seven of 12 subfamilies of Poaceae and are considered a synapomorphy for the family; however, no developmental work has been performed to verify their meristematic origin or to assess possible homologies within the graminid clade (= Flagellariaceae + [(Joinvilleaceae + Ecdeiocoleaceae) + Poaceae]) or among subfamilies of Poaceae. A developmental study was therefore carried out, including 20 species in three families (Flagellariaceae, Joinvilleaceae and Poaceae), representing the earlier-diverging and derived branches within the graminid clade and Poaceae.

Methods: Light microscopy was combined with scanning electron microscopy, cryoscanning electron microscopy and transmission electron microscopy to study the development of leaves taken from the shoot apex of young plants. Mature leaf blades also were taken from living or dried plants and the mid-portion was studied.

Key Results: Developmental results show that, in mature leaf blades as seen in cross-section, one apparent fusoid cell is typically a cavity resulting from the collapse of the initial fusoid cell and its internal divisions, which are herein interpreted as derivative cells with formation of cell plates only. Each cavity is delimited by successive collapsed fusoid cells arranged perpendicularly to the veins. Fusoid cells in all studied Poaceae members originate from the ground meristem, as do the colourless cells in Joinvillea ascendens (Joinvilleaceae). These two types of mesophyll cell have a strongly similar ontogeny, distinguished mainly by the collapse of the fusoid cells in Poaceae, which is not observed in the colourless cells in J. ascendens.

Conclusions: Within the Poaceae, the meristematic origin of fusoid cells is the same in the early-diverging lineages, BOP clade and Panicoideae, and thus they are homologous within the family. The same topography and meristematic origin suggest that fusoid cells in Poaceae and colourless cells in Joinvilleaceae are homologous. The results also suggest that the role played by the fusoid cells in young grass leaves is related to synthesis and storage of starch granules at early stages of development.
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http://dx.doi.org/10.1093/aob/mcy025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6215035PMC
November 2018

A refined method for digitally modeling small and complex plant structures in 3D: An example from the grasses (Poaceae).

Appl Plant Sci 2018 Aug 27;6(8):e01177. Epub 2018 Aug 27.

Department of Ecology, Evolution, and Organismal Biology Iowa State University 2200 Osborn Drive Ames Iowa 50011 USA.

Premise Of The Study: A refined procedure is described for modeling small, intricate plant structures using computer-aided design software. The procedure facilitates the study of wind pollination in the family Poaceae and provides virtual biological illustrations for public outreach.

Methods And Results: Spikelets were fixed in gFAA, dehydrated using ethanol and xylene, embedded in paraffin wax, and then sectioned with a rotary microtome. Images of serial sections were used as a reference for modeling the shape of bracts with splines in a computer-aided design program. Virtual models produced by this method have many potential uses; examples include geometric morphometric analyses and simulations of computational fluid dynamics.

Conclusions: This protocol is a synthesis of modern biological illustration and engineering technology. Virtual models facilitate quantitative experiments that may address questions about reproductive biology, conditions shaping the form of anatomical support, or the morphological evolution of structures of biomechanical interest.
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http://dx.doi.org/10.1002/aps3.1177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110240PMC
August 2018

Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace.

Front Plant Sci 2018 25;9:553. Epub 2018 Apr 25.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States.

Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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http://dx.doi.org/10.3389/fpls.2018.00553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996898PMC
April 2018

Priming as a Motivating Factor in Sociophonetic Variation and Change.

Authors:
Lynn Clark

Top Cogn Sci 2018 10 24;10(4):729-744. Epub 2018 Apr 24.

Linguistics, University of Canterbury.

Understanding how and why pronunciations vary and change has been a dominant theme in variationist sociolinguistics (Labov, , ). Linguistic variability has also been an area of focus in psychology and cognitive science. Work from these two fields has shown that where variation exists in language, an alternative form, once used, persists in working memory and has a greater chance of reuse (Bock, ; Bock & Loebell, ; Branigan, Pickering, & Cleland, ). While there have been efforts to connect priming research with sociolinguistics at the level of grammar (Poplack, ; Travis, ), there has been less work which explicitly considers the potential role of priming as a motivating factor in accent variation and change. This paper explores the role of priming in a socially conditioned sound change. There are two main findings: (a) phonetic variants with the same voicing tend to cluster together in naturally occurring speech and (b) repetition of phonetic form interacts with widely attested sociolinguistic predictors of variation. I argue that there are benefits to both cognitive science and sociolinguistics from this synergy: Incorporating research from cognitive science into sociolinguistics provides us with a better understanding of the factors underpinning a sound change in progress; incorporating insights from sociolinguistics into cognitive science shows that priming does not always operate in the same way for all speakers.
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http://dx.doi.org/10.1111/tops.12338DOI Listing
October 2018

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.

PeerJ 2018 2;6:e4299. Epub 2018 Feb 2.

Plant Molecular and Bioinformatics Center, Biological Sciences, Northern Illinois University, DeKalb, IL, USA.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.
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http://dx.doi.org/10.7717/peerj.4299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798404PMC
February 2018

Digital Media, Participatory Politics, and Positive Youth Development.

Pediatrics 2017 Nov;140(Suppl 2):S127-S131

Department of Family and Community Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina.

Research on the social implications of adolescent technology use often focuses on identifying and preventing risk. However, adolescence is also a time of rapidly expanding capacities, expectations of autonomy, and identity exploration. In this article, we highlight findings from research in the field of youth civic development, which point to the importance of youth civic engagement during adolescence for later adult civic engagement as well as for promoting positive developmental outcomes. Researchers suggest that certain forms of Internet use (such as information seeking, social network site use, media production, and participation in online communities) promote civic engagement and that digital tools play an important role in youth empowerment efforts. In this article, we suggest a need for greater attention to efforts to promote digital media competencies among adolescents and for greater coordination of research on adolescent risk and adolescent autonomy and empowerment related to Internet use.
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http://dx.doi.org/10.1542/peds.2016-1758QDOI Listing
November 2017

Phylogenomics and Plastome Evolution of Tropical Forest Grasses (: Poaceae).

Front Plant Sci 2016 27;7:1993. Epub 2016 Dec 27.

Department of Biological Sciences, Northern Illinois University, DeKalb IL, USA.

Studies of complete plastomes have proven informative for our understanding of the molecular evolution and phylogenomics of grasses. In this study, a plastome phylogenomic analysis sampled species from lineages of deeply diverging grasses including (Anomochlooideae), , and . (both Pharoideae). Plastomes from next generation sequences for three species were assembled by methods. The unambiguously aligned coding and non-coding sequences of the entire plastomes were aligned with those from 43 other grasses and the outgroup . Outgroup sampling of grasses has previously posed a challenge for plastome phylogenomic studies because of major rearrangements of the plastome. Here, over 81,000 bases of homologous sequence were aligned for phylogenomic and divergence estimation analyses. Rare genomic changes, including persistently long ψ and ψ loci, the loss of the intron, and a 21 base tandem repeat insert in the coding sequence for defined branch points in the grass phylogeny. Marked differences were seen in the topologies inferred from the complete plastome and two gene matrices, and mean maximum likelihood support values for the former were 10% higher. In the full plastome phylogenomic analyses, the two species of Anomochlooideae were monophyletic. and were found to be reciprocally monophyletic, with the estimated divergence of two species preceding those of by over 14 Ma, consistent with historical biogeography. Our estimates for deep divergences among grasses were older than previous such estimates, likely influenced by more complete taxonomic and molecular sampling and the use of recently available or previously unused fossil calibration points.
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http://dx.doi.org/10.3389/fpls.2016.01993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5186769PMC
December 2016

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae).

BMC Plant Biol 2016 06 18;16(1):140. Epub 2016 Jun 18.

Department of Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL, 60115-2861, USA.

Background: Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lack resolution and/or robust support for certain tribal and subtribal groups. This study aims to resolve these relationships, as well as characterize a putative mitochondrial insert in one linage.

Results: 35 newly sequenced Panicoideae plastomes were combined in a phylogenomic study with 37 other species: 15 Panicoideae and 22 from outgroups. A robust Panicoideae topology largely congruent with previous studies was obtained, but with some incongruences with previously reported subtribal relationships. A mitochondrial DNA (mtDNA) to plastid DNA (ptDNA) transfer was discovered in the Paspalum lineage.

Conclusions: The phylogenomic analysis returned a topology that largely supports previous studies. Five previously recognized subtribes appear on the topology to be non-monophyletic. Additionally, evidence for mtDNA to ptDNA transfer was identified in both Paspalum fimbriatum and P. dilatatum, and suggests a single rare event that took place in a common progenitor. Finally, the framework from this study can guide larger whole plastome sampling to discern the relationships in Cyperochloeae, Steyermarkochloeae, Gynerieae, and other incertae sedis taxa that are weakly supported or unresolved.
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http://dx.doi.org/10.1186/s12870-016-0823-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912804PMC
June 2016

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis.

Mol Phylogenet Evol 2016 08 7;101:111-121. Epub 2016 May 7.

Department of Ecology Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, United States. Electronic address:

We explored phylogenetic relationships among the twelve lineages of the temperate woody bamboo clade (tribe Arundinarieae) based on plastid genome (plastome) sequence data. A representative sample of 28 taxa was used and maximum parsimony, maximum likelihood and Bayesian inference analyses were conducted to estimate the Arundinarieae phylogeny. All the previously recognized clades of Arundinarieae were supported, with Ampelocalamus calcareus (Clade XI) as sister to the rest of the temperate woody bamboos. Well supported sister relationships between Bergbambos tessellata (Clade I) and Thamnocalamus spathiflorus (Clade VII) and between Kuruna (Clade XII) and Chimonocalmus (Clade III) were revealed by the current study. The plastome topology was tested by taxon removal experiments and alternative hypothesis testing and the results supported the current plastome phylogeny as robust. Neighbor-net analyses showed few phylogenetic signal conflicts, but suggested some potentially complex relationships among these taxa. Analyses of morphological character evolution of rhizomes and reproductive structures revealed that pachymorph rhizomes were most likely the ancestral state in Arundinarieae. In contrast leptomorph rhizomes either evolved once with reversions to the pachymorph condition or multiple times in Arundinarieae. Further, pseudospikelets evolved independently at least twice in the Arundinarieae, but the ancestral state is ambiguous.
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http://dx.doi.org/10.1016/j.ympev.2016.05.008DOI Listing
August 2016

Simple Web-based interactive key development software (WEBiKEY) and an example key for Kuruna (Poaceae: Bambusoideae).

Appl Plant Sci 2016 Apr 20;4(4). Epub 2016 Apr 20.

Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011 USA.

Premise Of The Study: Programs that are user-friendly and freely available for developing Web-based interactive keys are scarce and most of the well-structured applications are relatively expensive. WEBiKEY was developed to enable researchers to easily develop their own Web-based interactive keys with fewer resources.

Methods And Results: A Web-based multiaccess identification tool (WEBiKEY) was developed that uses freely available Microsoft ASP.NET technologies and an SQL Server database for Windows-based hosting environments. WEBiKEY was tested for its usability with a sample data set, the temperate woody bamboo genus Kuruna (Poaceae).

Conclusions: WEBiKEY is freely available to the public and can be used to develop Web-based interactive keys for any group of species. The interactive key we developed for Kuruna using WEBiKEY enables users to visually inspect characteristics of Kuruna and identify an unknown specimen as one of seven possible species in the genus.
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http://dx.doi.org/10.3732/apps.1500128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850057PMC
April 2016

Resolving deep relationships of PACMAD grasses: a phylogenomic approach.

BMC Plant Biol 2015 Jul 11;15:178. Epub 2015 Jul 11.

Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois, 60115-2861, U.S.A.

Background: Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats.

Results: New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya.

Conclusions: Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.
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http://dx.doi.org/10.1186/s12870-015-0563-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498559PMC
July 2015

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes.

AoB Plants 2015 May 4;7. Epub 2015 May 4.

Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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http://dx.doi.org/10.1093/aobpla/plv046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480051PMC
May 2015

Evolution of the bamboos (Bambusoideae; Poaceae): a full plastome phylogenomic analysis.

BMC Evol Biol 2015 Mar 18;15:50. Epub 2015 Mar 18.

Biological Sciences, Northern Illinois University, 1425 W Lincoln Hwy, DeKalb, 60115-2861, IL, USA.

Background: Bambusoideae (Poaceae) comprise three distinct and well-supported lineages: tropical woody bamboos (Bambuseae), temperate woody bamboos (Arundinarieae) and herbaceous bamboos (Olyreae). Phylogenetic studies using chloroplast markers have generally supported a sister relationship between Bambuseae and Olyreae. This suggests either at least two origins of the woody bamboo syndrome in this subfamily or its loss in Olyreae.

Results: Here a full chloroplast genome (plastome) phylogenomic study is presented using the coding and noncoding regions of 13 complete plastomes from the Bambuseae, eight from Olyreae and 10 from Arundinarieae. Trees generated using full plastome sequences support the previously recovered monophyletic relationship between Bambuseae and Olyreae. In addition to these relationships, several unique plastome features are uncovered including the first mitogenome-to-plastome horizontal gene transfer observed in monocots.

Conclusions: Phylogenomic agreement with previous published phylogenies reinforces the validity of these studies. Additionally, this study presents the first published plastomes from Neotropical woody bamboos and the first full plastome phylogenomic study performed within the herbaceous bamboos. Although the phylogenomic tree presented in this study is largely robust, additional studies using nuclear genes support monophyly in woody bamboos as well as hybridization among previous woody bamboo lineages. The evolutionary history of the Bambusoideae could be further clarified using transcriptomic techniques to increase sampling among nuclear orthologues and investigate the molecular genetics underlying the development of woody and floral tissues.
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http://dx.doi.org/10.1186/s12862-015-0321-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4389303PMC
March 2015

Pediatric migraine: common, yet treatable.

Nurse Pract 2014 Nov;39(11):22-31; quiz 31-2

Alicia Harding is a nurse practitioner at Children's Medical Center, Dallas, Tex. Lynn Clark is a nurse practitioner, Manager Pain Management and Palliative Care at Children's Medical Center, Dallas, Tex.

Migraine headache is a common problem among children and adolescents that is now recognized as a significant and often debilitating condition in this population. Improved recognition and management of pediatric migraine in primary care is necessary, as there is a knowledge gap in understanding the unique features of this condition and a general reluctance to treat children.
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http://dx.doi.org/10.1097/01.NPR.0000454980.88918.f0DOI Listing
November 2014

Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos.

New Phytol 2014 Oct 7;204(1):66-73. Epub 2014 Aug 7.

Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013-7012, USA.

The objectives of the current study were to investigate the origin of polyploidy in the woody bamboos and examine putative hybrid relationships in one major lineage (the temperate woody bamboos, tribe Arundinarieae). Phylogenetic analyses were based on sequence data from three nuclear loci and 38 species in 27 genera. We identify six ancestral genome donors for contemporary bamboo lineages: temperate woody bamboos (tribe Arundinarieae) contain genomes A and B, tropical woody bamboos (tribe Bambuseae) contain genomes C and D, and herbaceous bamboos (tribe Olyreae) contain genome H; some hexaploid paleotropical bamboos contain genome E in addition to C and D. Molecular data indicate that allopolyploidy arose independently in temperate (AABB) and tropical woody lineages (CCDD and CCDDEE), and speciation occurred subsequent to polyploidization. Moreover, hybridization has played a surprising and recurrent role in bamboo evolution, generating allohexaploid species in the paleotropical clade and intergeneric hybrids among the allotetraploid temperate bamboos. We suggest this complex history of reticulate evolution is at least partially responsible for the taxonomic difficulty associated with the woody bamboos. This newly-resolved phylogenetic framework reflects a major step forward in our understanding of bamboo biodiversity and has important implications for the interpretation of bamboo phylogenomics.
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http://dx.doi.org/10.1111/nph.12988DOI Listing
October 2014

A molecular phylogeny of Raddia and its allies within the tribe Olyreae (Poaceae, Bambusoideae) based on noncoding plastid and nuclear spacers.

Mol Phylogenet Evol 2014 Sep 5;78:105-17. Epub 2014 May 5.

Universidade Estadual de Feira de Santana, Departamento de Ciências Biológicas, Av. Transnordestina s.n., Feira de Santana, Bahia 44031-460, Brazil. Electronic address:

The plastid spacer trnD-trnT and the nuclear ribosomal internal transcribed spacer (ITS) were sequenced for 37 samples of herbaceous bamboos (Poaceae: Olyreae), including all Raddia species and allied genera, as well as two members of the woody bamboos (tribes Bambuseae and Arundinarieae), in order to examine their relationships. The sequences were analyzed using maximum parsimony and Bayesian inference. Both the individual and combined analyses of ITS and trnD-trnT supported Olyreae as a monophyletic group. All species of Raddia also formed a well-supported monophyletic group, and combined datasets allowed us to outline some relationships within this group. Individual analyses indicated incongruence regarding the sister group of Raddia, with ITS data weakly indicating Raddiella malmeana whereas trnD-trnT data supported Sucrea maculata in this position. However, the combined analysis supported Sucrea as sister to Raddia, although the monophyly of Sucrea is not well supported. Parodiolyra is paraphyletic to Raddiella in all analyses; Olyra is also paraphyletic, with species of Lithachne, Arberella and Cryptochloa nested within it. Eremitis and Pariana appeared as an isolated clade within Olyreae, and the position of the New Guinean Buergersiochloa remains uncertain within this tribe.
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http://dx.doi.org/10.1016/j.ympev.2014.04.012DOI Listing
September 2014

Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited.

Am J Bot 2014 05 7;101(5):886-91. Epub 2014 May 7.

Department of Biological Sciences, 1425 W. Lincoln Hwy, Northern Illinois University, DeKalb, Illinois 60115-2861 USA.

Unlabelled: •

Premise Of The Study: New World Bambusoideae have only recently been studied in a phylogenomic context. Plastome sequences were determined and analyzed from Arundinaria appalachiana, A. tecta, and Olyra latifolia, to refine our knowledge of their evolution and historical biogeography. A correction is noted regarding an error in an earlier report on the biogeography of Cryptochloa•

Methods: Single-end DNA libraries were prepared and sequenced on the Illumina platform. Complete plastomes were assembled and analyzed with 13 other Poaceae.•

Key Results: Complete sampling in Arundinaria and an additional species of Olyreae gave a more detailed picture of their evolution/historical biogeography. Phylogenomic analyses indicated that the first major divergence in Arundinaria occurred around 2.3 to 3.2 mya and that Arundinaria tecta and A appalachiana diverged from their common ancestor around 0.57 to 0.82 mya. Estimates of the divergence of Olyra latifolia from Cryptochloa strictiflora ranged from 14.6 to 20.7 mya. The age of the stem node of Olyreae ranged from an estimated 26.9 to 38.2 mya.•

Conclusions: Estimates of divergences in Arundinaria can be correlated with paleoclimatic events including an early Pliocene warming, subsequent cooling, and North American glaciations. Discriminating between alternate evolutionary/biogeographic scenarios in Olyreae is challenging.
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http://dx.doi.org/10.3732/ajb.1400063DOI Listing
May 2014

Molecular phylogeny of the arthrostylidioid bamboos (Poaceae: Bambusoideae: Bambuseae: Arthrostylidiinae) and new genus Didymogonyx.

Mol Phylogenet Evol 2012 Oct 6;65(1):136-48. Epub 2012 Jun 6.

Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA.

We present the first multi-locus chloroplast phylogeny of Arthrostylidiinae, a subtribe of neotropical woody bamboos. The morphological diversity of Arthrostylidiinae makes its taxonomy difficult and prior molecular analyses of bamboos have lacked breadth of sampling within the subtribe, leaving internal relationships uncertain. We sampled 51 taxa, chosen to span the range of taxonomic diversity and morphology, and analyzed a combined chloroplast DNA dataset with six chloroplast regions: ndhF, trnD-trnT, trnC-rpoB, rps16-trnQ, trnT-trnL, and rpl16. A consensus of maximum parsimony and Bayesian inference analyses reveals monophyly of the Arthrostylidiinae and four moderately supported lineages within it. Six previously recognized genera were monophyletic, three polyphyletic, and two monotypic; Rhipidocladum sect. Didymogonyx is here raised to generic status. When mapped onto our topology, many of the morphological characters show homoplasy.
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http://dx.doi.org/10.1016/j.ympev.2012.05.033DOI Listing
October 2012

Incidence, correlates, and interventions used for pressure ulcers of the ear.

Medsurg Nurs 2011 Sep-Oct;20(5):241-6; quiz 247

St. Elizabeth Health Center, Youngstown, OH, USA.

Skin prevalence audits revealed annual increases in incidence of pressure ulcers of the ear. A research study was conducted to assess correlates of the problem. Study results guided clinical practice changes that reduced the incidence to zero.
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January 2012

Pain management in the pediatric population.

Authors:
Lynn Clark

Crit Care Nurs Clin North Am 2011 Jun;23(2):291-301

Pain Management Department, Children's Medical Center Dallas, TX 75235, USA.

Pain management is an important part of health care. During childhood, the prevalence of pain depends on the child's ongoing health status. Most healthy children receive more than 20 immunizations before 2 years of age. If the child is born with health concerns and is required to spend time in the neonatal intensive care unit, the number of painful encounters can reach into the hundreds. To optimally treat children with pain, nurses must realize that appropriately assessing and treating pain in children is a necessary part of their care.
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http://dx.doi.org/10.1016/j.ccell.2011.04.003DOI Listing
June 2011

Phylogeny and a new tribal classification of the Panicoideae s.l. (Poaceae) based on plastid and nuclear sequence data and structural data.

Am J Bot 2010 Oct 22;97(10):1732-48. Epub 2010 Sep 22.

Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apdo. Postal 70-233, México D.F. 04510, Mexico.

Unlabelled:

Premise Of The Study: The subfamily Panicoideae (Poaceae) encompasses nearly one-third of the diversity of grass species, including important crops such as maize and sugarcane. Previous analyses recovered strong support for a Panicoideae+Centothecoideae lineage within the diverse Panicoideae+Arundinoideae+Chloridoideae+Micrairoideae+Aristidoideae+Danthonioideae (PACMAD) clade, although support for internal relationships was inconsistent. The objectives of this research were to (1) further test the monophyly of each subfamily and previously recovered clades within the Panicoideae+Centothecoideae lineage, (2) establish phylogenetic relationships among these groups, and (3) propose a new tribal classification for this lineage based explicitly on the phylogeny. •

Methods: Maximum parsimony and Bayesian inference analyses of 37 taxa were based on previously published sequences (ndhF and rpl16 intron) and on new plastid and nuclear (rbcL and granule-bound starch synthase I) sequence data as well as structural data. • Key results. The Panicoideae+Centothecoideae lineage and a majority of the clades identified in previous analyses continue to be robustly supported, but resolution along the backbone of the topology remains elusive. Support for the monophyly of both subfamilies was lacking although support values for some clades increased. The tribes Centotheceae and Arundinelleae were confirmed as polyphyletic. •

Conclusions: Subfamily Centothecoideae is formally submerged into the Panicoideae, and a new tribal classification for the expanded Panicoideae is proposed based explicitly on the phylogeny. This classification includes 12 tribes of which Chasmanthieae and Zeugiteae are segretated from the Centotheceae; Tristachyideae is segregated from Arundinelleae, and a new tribe, Cyperochloeae, is validated to accommodate two isolated genera. A key to the tribes is provided.
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http://dx.doi.org/10.3732/ajb.1000024DOI Listing
October 2010

Emerging battery-ingestion hazard: clinical implications.

Pediatrics 2010 Jun 24;125(6):1168-77. Epub 2010 May 24.

National Capital Poison Center, 3201 New Mexico Ave, Suite 310, Washington, DC 20016, USA.

Objectives: Recent cases suggest that severe and fatal button battery ingestions are increasing and current treatment may be inadequate. The objective of this study was to identify battery ingestion outcome predictors and trends, define the urgency of intervention, and refine treatment guidelines.

Methods: Data were analyzed from 3 sources: (1) National Poison Data System (56535 cases, 1985-2009); (2) National Battery Ingestion Hotline (8648 cases, July 1990-September 2008); and (3) medical literature and National Battery Ingestion Hotline cases (13 deaths and 73 major outcomes) involving esophageal or airway button battery lodgment.

Results: All 3 data sets signal worsening outcomes, with a 6.7-fold increase in the percentage of button battery ingestions with major or fatal outcomes from 1985 to 2009 (National Poison Data System). Ingestions of 20- to 25-mm-diameter cells increased from 1% to 18% of ingested button batteries (1990-2008), paralleling the rise in lithium-cell ingestions (1.3% to 24%). Outcomes were significantly worse for large-diameter lithium cells (> or = 20 mm) and children who were younger than 4 years. The 20-mm lithium cell was implicated in most severe outcomes. Severe burns with sequelae occurred in just 2 to 2.5 hours. Most fatal (92%) or major outcome (56%) ingestions were not witnessed. At least 27% of major outcome and 54% of fatal cases were misdiagnosed, usually because of nonspecific presentations. Injuries extended after removal, with unanticipated and delayed esophageal perforations, tracheoesophageal fistulas, fistulization into major vessels, and massive hemorrhage.

Conclusions: Revised treatment guidelines promote expedited removal from the esophagus, increase vigilance for delayed complications, and identify patients who require urgent radiographs.
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http://dx.doi.org/10.1542/peds.2009-3037DOI Listing
June 2010

Preventing battery ingestions: an analysis of 8648 cases.

Pediatrics 2010 Jun 24;125(6):1178-83. Epub 2010 May 24.

National Capital Poison Center, 3201 New Mexico Ave, Suite 310, Washington, DC 20016, USA.

Objectives: Outcomes of pediatric button battery ingestions have worsened substantially, predominantly related to the emergence of the 20-mm-diameter lithium cell as a common power source for household products. Button batteries lodged in the esophagus can cause severe tissue damage in just 2 hours, with delayed complications such as esophageal perforation, tracheoesophageal fistulas, exsanguination after fistulization into a major blood vessel, esophageal strictures, and vocal cord paralysis. Thirteen deaths have been reported. The objective of this study was to explore button battery ingestion scenarios to formulate prevention strategies.

Methods: A total of 8648 battery ingestions that were reported to the National Battery Ingestion Hotline were analyzed.

Results: Batteries that were ingested by children who were younger than 6 years were most often obtained directly from a product (61.8%), were loose (29.8%), or were obtained from battery packaging (8.2%). Of young children who ingested the most hazardous battery, the 20-mm lithium cell, 37.3% were intended for remote controls. Adults most often ingested batteries that were sitting out, loose, or discarded (80.8%); obtained directly from a product (4.2%); obtained from battery packaging (3.0%); or swallowed within a hearing aid (12.1%). Batteries that were intended for hearing aids were implicated in 36.3% of ingestions. Batteries were mistaken for pills in 15.5% of ingestions, mostly by older adults.

Conclusions: Parents and child care providers should be taught to prevent battery ingestions. Because 61.8% of batteries that were ingested by children were obtained from products, manufacturers should redesign household products to secure the battery compartment, possibly requiring a tool to open it.
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http://dx.doi.org/10.1542/peds.2009-3038DOI Listing
June 2010

Phylogenetic relationships and natural hybridization among the North American woody bamboos (Poaceae: Bambusoideae: Arundinaria).

Am J Bot 2010 Mar 12;97(3):471-92. Epub 2010 Feb 12.

Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020 USA.

In spite of the ecological and economic importance of temperate bamboos, relatively little is known about their population biology or evolutionary history. Recently, hybridization has emerged as a potential source of diversity in this group, as well as an underlying cause of taxonomic problems. As part of a broader phylogenetic study of the temperate bamboos, we report the results of an analysis of the North American Arundinaria gigantea species complex, including estimates of genetic variation and molecular evidence of natural hybridization among A. gigantea, A. tecta, and A. appalachiana. The study involved a comparative analysis of amplified fragment length polymorphisms (AFLPs) and chloroplast DNA sequences representing diversity within and among all three species plus individuals with intermediate or unusual morphological characteristics (putative hybrids). Molecular results support the recognition of three species previously defined on the basis of morphology, anatomy, and ecology, with most of the molecular variance accounted for by among-species variation. Molecular evidence also demonstrates that A. tecta and A. appalachiana are sister species, forming a clade that is significantly divergent from A. gigantea. The role of hybridization in the phylogenetic history of Arundinaria is discussed along with implications for the evolution and taxonomy of the temperate woody bamboos.
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http://dx.doi.org/10.3732/ajb.0900244DOI Listing
March 2010

A voxel-based morphometric MRI study in men with borderline personality disorder: preliminary findings.

Crim Behav Ment Health 2009 ;19(1):64-72

Section of Forensic Mental Health, Division of Psychiatry, University of Nottingham, UK.

Objective: There is increasing evidence for subtle changes in brain morphology and function in patients with borderline personality disorder (BPD). Structural brain imaging studies show lower volume in frontal, temporal and parietal brain regions than in healthy controls. The aim of our preliminary study of men with BPD was to investigate structural brain changes and their relationship with a measure of impulsivity.

Methods: We examined seven male patients with BPD and six control men using voxel-based morphometry. Analysis of covariance was carried out to assess regionally specific differences in grey and white matter (WM) volumes. Correlations between trait impulsivity as measured using the Impulsiveness-Venturesomeness-Empathy scale and brain volumes were studied.

Results: Compared with healthy men, men with BPD had similar WM volumes but smaller grey matter (GM) volumes in frontal, temporal and parietal cortices. The latter were negatively correlated with trait impulsivity.

Conclusions: Our findings fit with previous reports of smaller regional GM volumes reported in women with BPD, and suggest that in men there may be an association between smaller GM volumes and impulsivity.
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http://dx.doi.org/10.1002/cbm.716DOI Listing
May 2009
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