Complete plastid genomes from \u3ci\u3eOphioglossum californicum, Psilotum nudum,\u3c/i\u3e and \u3ci\u3eEquisetum hyemale\u3c/i\u3e reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

Background: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. Results: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. Conclusions: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

Complete plastid genomes from \u3ci\u3eOphioglossum californicum, Psilotum nudum,\u3c/i\u3e and \u3ci\u3eEquisetum hyemale\u3c/i\u3e reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

Background: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. Results: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. Conclusions: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

BACKGROUND: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. RESULTS: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. CONCLUSIONS: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

T-CaST: an implementation theory comparison and selection tool

Abstract Background Theories, models, and frameworks (TMF) are foundational for generalizing implementation efforts and research findings. However, TMF and the criteria used to select them are not often described in published articles, perhaps due in part to the challenge of selecting from among the many TMF that exist in the field. The objective of this international study was to develop a user-friendly tool to help scientists and practitioners select appropriate TMF to guide their implementation projects. Methods Implementation scientists across the USA, the UK, and Canada identified and rated conceptually distinct categories of criteria in a concept mapping exercise. We then used the concept mapping results to develop a tool to help users select appropriate TMF for their projects. We assessed the tool’s usefulness through expert consensus and cognitive and semi-structured interviews with implementation scientists. Results Thirty-seven implementation scientists (19 researchers and 18 practitioners) identified four criteria domains: usability, testability, applicability, and familiarity. We then developed a prototype of the tool that included a list of 25 criteria organized by domain, definitions of the criteria, and a case example illustrating an application of the tool. Results of cognitive and semi-structured interviews highlighted the need for the tool to (1) be as succinct as possible; (2) have separate versions to meet the unique needs of researchers versus practitioners; (3) include easily understood terms; (4) include an introduction that clearly describes the tool’s purpose and benefits; (5) provide space for noting project information, comparing and scoring TMF, and accommodating contributions from multiple team members; and (6) include more case examples illustrating its application. Interview participants agreed that the tool (1) offered them a way to select from among candidate TMF, (2) helped them be explicit about the criteria that they used to select a TMF, and (3) enabled them to compare, select from among, and/or consider the usefulness of combining multiple TMF. These revisions resulted in the Theory Comparison and Selection Tool (T-CaST), a paper and web-enabled tool that includes 16 specific criteria that can be used to consider and justify the selection of TMF for a given project. Criteria are organized within four categories: applicability, usability, testability, and acceptability. Conclusions T-CaST is a user-friendly tool to help scientists and practitioners select appropriate TMF to guide implementation projects. Additionally, T-CaST has the potential to promote transparent reporting of criteria used to select TMF within and beyond the field of implementation science

Study of the sanitary condition of the swimming pool at the Lincoln High School

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Complete plastid genomes from <it>Ophioglossum californicum</it>, <it>Psilotum nudum</it>, and <it>Equisetum hyemale</it> reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

Abstract Background Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. Results In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. Conclusions Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution.</p

T-CaST: an implementation theory comparison and selection tool

Abstract Background Theories, models, and frameworks (TMF) are foundational for generalizing implementation efforts and research findings. However, TMF and the criteria used to select them are not often described in published articles, perhaps due in part to the challenge of selecting from among the many TMF that exist in the field. The objective of this international study was to develop a user-friendly tool to help scientists and practitioners select appropriate TMF to guide their implementation projects. Methods Implementation scientists across the USA, the UK, and Canada identified and rated conceptually distinct categories of criteria in a concept mapping exercise. We then used the concept mapping results to develop a tool to help users select appropriate TMF for their projects. We assessed the tool’s usefulness through expert consensus and cognitive and semi-structured interviews with implementation scientists. Results Thirty-seven implementation scientists (19 researchers and 18 practitioners) identified four criteria domains: usability, testability, applicability, and familiarity. We then developed a prototype of the tool that included a list of 25 criteria organized by domain, definitions of the criteria, and a case example illustrating an application of the tool. Results of cognitive and semi-structured interviews highlighted the need for the tool to (1) be as succinct as possible; (2) have separate versions to meet the unique needs of researchers versus practitioners; (3) include easily understood terms; (4) include an introduction that clearly describes the tool’s purpose and benefits; (5) provide space for noting project information, comparing and scoring TMF, and accommodating contributions from multiple team members; and (6) include more case examples illustrating its application. Interview participants agreed that the tool (1) offered them a way to select from among candidate TMF, (2) helped them be explicit about the criteria that they used to select a TMF, and (3) enabled them to compare, select from among, and/or consider the usefulness of combining multiple TMF. These revisions resulted in the Theory Comparison and Selection Tool (T-CaST), a paper and web-enabled tool that includes 16 specific criteria that can be used to consider and justify the selection of TMF for a given project. Criteria are organized within four categories: applicability, usability, testability, and acceptability. Conclusions T-CaST is a user-friendly tool to help scientists and practitioners select appropriate TMF to guide implementation projects. Additionally, T-CaST has the potential to promote transparent reporting of criteria used to select TMF within and beyond the field of implementation science