cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5235994.v1
title: Handouts - Ten Lectures on the Elaboration of Cognitive Grammar

description: This book reviews the basic claims and descriptive constructs of Cognitive Grammar, outlines major themes in its ongoing development, and applies these notions to central problems in grammatical analysis. The initial review covers conceptual semantics, the conceptual characterization of grammatical categories, grammatical constructions, and the architecture of a unified theory of language structure. Main themes in the framework’s development include the dynamicity of language structure, grammar as the implementation of semantic functions, systems of opposing elements to serve those functions, and organization in strata representing successive elaborations of a baseline structure. The descriptive application of these notions centers on nominal and clausal structure, with special emphasis on nominal grounding.
DOI: 10.6084/m9.figshare.5236006.v1
title: Hesselmann 2017 (CFS priming data)

description: Data and R code from CFS priming experiments.<br>
DOI: 10.6084/m9.figshare.5235979.v2
title: Handouts - Ten Lectures on the Basics of Cognitive Grammar

description: These lectures provide a basic introduction to the linguistic theory known as Cognitive Grammar. It is argued that a conceptualist semantics, well motivated in its own terms, provides the basis for a symbolic view of grammar. Consisting in the structuring and symbolization of conceptual content, grammar is inherently meaningful, and basic grammatical notions have conceptual characterizations. An account is given of grammatical categories, markings, and constructions. A number of central topics are examined in detail, including subjects, possessives, locatives, voice, and impersonals.
DOI: 10.6084/m9.figshare.5235979.v1
title: Handouts - Ten Lectures on the Basics of Cognitive Grammar

description: These lectures provide a basic introduction to the linguistic theory known as Cognitive Grammar. It is argued that a conceptualist semantics, well motivated in its own terms, provides the basis for a symbolic view of grammar. Consisting in the structuring and symbolization of conceptual content, grammar is inherently meaningful, and basic grammatical notions have conceptual characterizations. An account is given of grammatical categories, markings, and constructions. A number of central topics are examined in detail, including subjects, possessives, locatives, voice, and impersonals.
DOI: 10.6084/m9.figshare.5235922
title: Table S6 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235931
title: Table S3 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235922.v1
title: Table S6 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235931.v1
title: Table S3 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235910
title: Table S5 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235910.v1
title: Table S5 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235895
title: Table S8 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235892
title: Bending calculations from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Calculation of bending resistance in three small metapodials vs. a single larger one of the same total mass
DOI: 10.6084/m9.figshare.5235886
title: SI Table 1: List of all specimens included in the study. Juvenile: 0-3 months, before the eruption of all deciduous teeth, sub-adult: 3-15 months, and adult: over 15months, after deciduous teeth being replaced by permanent teeth. from A test for paedomorphism in domestic pig cranial morphology

description: Juvenile: 0-3 months, before the eruption of all deciduous teeth, sub-adult: 3-15 months, and adult: over 15months, after deciduous teeth being replaced by permanent teeth.
DOI: 10.6084/m9.figshare.5235892.v1
title: Bending calculations from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Calculation of bending resistance in three small metapodials vs. a single larger one of the same total mass
DOI: 10.6084/m9.figshare.5235895.v1
title: Table S8 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235883
title: Bending results from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Full output of beam bending analysis
DOI: 10.6084/m9.figshare.5235877
title: SI Table 2: Description of landmarks used, and of the sub-regions of the crania. from A test for paedomorphism in domestic pig cranial morphology

description: See SI - Figure 1 for a visual location of the landmarks.
DOI: 10.6084/m9.figshare.5235886.v1
title: SI Table 1: List of all specimens included in the study. Juvenile: 0-3 months, before the eruption of all deciduous teeth, sub-adult: 3-15 months, and adult: over 15months, after deciduous teeth being replaced by permanent teeth. from A test for paedomorphism in domestic pig cranial morphology

description: Juvenile: 0-3 months, before the eruption of all deciduous teeth, sub-adult: 3-15 months, and adult: over 15months, after deciduous teeth being replaced by permanent teeth.
DOI: 10.6084/m9.figshare.5235874
title: Supplementary methods and results from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Details on specimens, TRI, and beam bending, as well as extra results.
DOI: 10.6084/m9.figshare.5235877.v1
title: SI Table 2: Description of landmarks used, and of the sub-regions of the crania. from A test for paedomorphism in domestic pig cranial morphology

description: See SI - Figure 1 for a visual location of the landmarks.
DOI: 10.6084/m9.figshare.5235883.v1
title: Bending results from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Full output of beam bending analysis
DOI: 10.6084/m9.figshare.5235865
title: Specimen metadata from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Specimen numbers, geometry, and beam bending variables
DOI: 10.6084/m9.figshare.5235874.v1
title: Supplementary methods and results from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Details on specimens, TRI, and beam bending, as well as extra results.
DOI: 10.6084/m9.figshare.5235859
title: Table S7 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235865.v1
title: Specimen metadata from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Specimen numbers, geometry, and beam bending variables
DOI: 10.6084/m9.figshare.5235856
title: TRI Data from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Proximal phalanx lengths used to calculate TRI
DOI: 10.6084/m9.figshare.5235859.v1
title: Table S7 from Rapid functional and evolutionary changes follow gene duplication in yeast

description: Duplication of genes or genomes provides the raw material for evolutionary innovation. After duplication a gene may be lost, recombine with another gene, have its function modified, or be retained in an unaltered state. The fate of duplication is usually studied by comparing extant genomes and reconstructing the most likely ancestral states. Valuable as this approach is, it may miss the most rapid evolutionary events. Here, we engineered strains of <i>Saccharomyces cerevisiae</i> carrying tandem and non-tandem duplications of the singleton gene <i>IFA38</i> to monitor (i) the fate of the duplicates in different conditions, including timescale and asymmetry of gene loss and (ii) the changes in fitness and transcriptome of the strains immediately after duplication and after experimental evolution. We found that the duplication brings widespread transcriptional changes but a fitness advantage is only present in fermentable media. In respiratory conditions, the yeast strains consistently lose the non-tandem <i>IFA38</i> gene copy in a surprisingly short time, within only few generations. This gene loss appears to be asymmetric and dependent on genome location since the original <i>IFA38</i> copy and the tandem duplicate are retained. Overall, this work shows for the first time that gene loss can be extremely rapid and context dependent.
DOI: 10.6084/m9.figshare.5235856.v1
title: TRI Data from Mechanics of evolutionary digit reduction in fossil horses (Equidae)

description: Proximal phalanx lengths used to calculate TRI
DOI: 10.6084/m9.figshare.5235832
title: North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae): alignment files and results of phylogenetic analyses

description: Data from Prous et al. (2017). The zip file contains three alignment files of COI (cox1_BINs.fas), nuclear (nuc_122.fas, NaK + TPI), and combined (prist3_113.fas, COI + nuclear) genes. Results of phylogenetic analyses from CIPRES Science Gateway V. 3.3 are in folders Cipres_Data_cox1_BINs and Cipres_Data_prist3_113. Alignment file "nuc_122.fas" was used to calculate net synonymous divergence between species. Trace files of <i>Pristiphora friesei</i> DEI-GISHym11558 COI sequence that containes a frameshift mutation are also included.<br>Prous M, Kramp K, Vikberg V, Liston A (2017) North-Western Palaearctic species of <i>Pristiphora</i> (Hymenoptera, Tenthredinidae). Journal of Hymenoptera Research 59: 1–190. https://doi.org/10.3897/jhr.59.12656<br>
DOI: 10.6084/m9.figshare.5235835
title: North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae): studied specimens

description: Data from Prous et al. (2017). The excel file includes collection data of the studied specimens and GenBank accession numbers.<br>Prous M, Kramp K, Vikberg V, Liston A (2017) North-Western Palaearctic species of <i>Pristiphora</i> (Hymenoptera, Tenthredinidae). Journal of Hymenoptera Research 59: 1–190. https://doi.org/10.3897/jhr.59.12656<br>
DOI: 10.6084/m9.figshare.5235832.v1
title: North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae): alignment files and results of phylogenetic analyses

description: Data from Prous et al. (2017). The zip file contains three alignment files of COI (cox1_BINs.fas), nuclear (nuc_122.fas, NaK + TPI), and combined (prist3_113.fas, COI + nuclear) genes. Results of phylogenetic analyses from CIPRES Science Gateway V. 3.3 are in folders Cipres_Data_cox1_BINs and Cipres_Data_prist3_113. Alignment file "nuc_122.fas" was used to calculate net synonymous divergence between species. Trace files of <i>Pristiphora friesei</i> DEI-GISHym11558 COI sequence that containes a frameshift mutation are also included.<br>Prous M, Kramp K, Vikberg V, Liston A (2017) North-Western Palaearctic species of <i>Pristiphora</i> (Hymenoptera, Tenthredinidae). Journal of Hymenoptera Research 59: 1–190. https://doi.org/10.3897/jhr.59.12656<br>
DOI: 10.6084/m9.figshare.5235835.v1
title: North-Western Palaearctic species of Pristiphora (Hymenoptera, Tenthredinidae): studied specimens

description: Data from Prous et al. (2017). The excel file includes collection data of the studied specimens and GenBank accession numbers.<br>Prous M, Kramp K, Vikberg V, Liston A (2017) North-Western Palaearctic species of <i>Pristiphora</i> (Hymenoptera, Tenthredinidae). Journal of Hymenoptera Research 59: 1–190. https://doi.org/10.3897/jhr.59.12656<br>