cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7694546
title: A facile forward-genetic screen for <i>Arabidopsis</i> autophagy mutants reveals twenty-one loss-of-function mutations disrupting six <i>ATG</i> genes

description: Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (<i>ATG</i>) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved <i>ATG</i> genes in plants, only a few <i>atg</i> mutants have emerged from forward-genetic screens in <i>Arabidopsis thaliana</i>. We developed a screen that consistently recovers <i>Arabidopsis atg</i> mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. <i>Arabidopsis lon2</i> mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a <i>lon2</i> suppressor screen to expedite recovery of additional <i>atg</i> mutants. After screening mutagenized <i>lon2-2</i> seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 <i>ATG</i> genes: <i>ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230</i>, and <i>ATG18a/At3g62770</i>. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional <i>atg11</i>/<i>At4g30790</i> allele incompletely suppresses <i>lon2</i> defects. Finally, we show that NBR1 is not necessary for autophagy of <i>lon2</i> peroxisomes and that <i>NBR1</i> overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that <i>Arabidopsis</i> can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation. <b>Abbreviations:</b> ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type
DOI: 10.6084/m9.figshare.7694534
title: Table S2 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: List of estimated body masses for the cetartiodactyl taxa included in the parsimony reconstruction based on the phylogeny simplified from Lihoreau et al. (2015; cf figure 3).
DOI: 10.6084/m9.figshare.7694537
title: Table S3 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: List of ratio for mandibular (Md) size and associated data on the investigated cetartiodactyl taxa (cf figure 4).
DOI: 10.7284/118840
title: Meteorological Station data collected during research cruise AT31C using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7694531
title: Table S1 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: Details of the dental eruption sequence for each cetartiodactyl species investigated, and corresponding specimens of interest.
DOI: 10.6084/m9.figshare.7694537.v1
title: Table S3 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: List of ratio for mandibular (Md) size and associated data on the investigated cetartiodactyl taxa (cf figure 4).
DOI: 10.6084/m9.figshare.7694531.v1
title: Table S1 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: Details of the dental eruption sequence for each cetartiodactyl species investigated, and corresponding specimens of interest.
DOI: 10.6084/m9.figshare.7694534.v1
title: Table S2 from Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

description: List of estimated body masses for the cetartiodactyl taxa included in the parsimony reconstruction based on the phylogeny simplified from Lihoreau et al. (2015; cf figure 3).
DOI: 10.7284/118838
title: Multibeam Echosounder data collected during research cruise AT31C using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7694546.v2
title: A facile forward-genetic screen for <i>Arabidopsis</i> autophagy mutants reveals twenty-one loss-of-function mutations disrupting six <i>ATG</i> genes

description: Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (<i>ATG</i>) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved <i>ATG</i> genes in plants, only a few <i>atg</i> mutants have emerged from forward-genetic screens in <i>Arabidopsis thaliana</i>. We developed a screen that consistently recovers <i>Arabidopsis atg</i> mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. <i>Arabidopsis lon2</i> mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a <i>lon2</i> suppressor screen to expedite recovery of additional <i>atg</i> mutants. After screening mutagenized <i>lon2-2</i> seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 <i>ATG</i> genes: <i>ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230</i>, and <i>ATG18a/At3g62770</i>. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional <i>atg11</i>/<i>At4g30790</i> allele incompletely suppresses <i>lon2</i> defects. Finally, we show that NBR1 is not necessary for autophagy of <i>lon2</i> peroxisomes and that <i>NBR1</i> overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that <i>Arabidopsis</i> can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation. <b>Abbreviations:</b> ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type
DOI: 10.7284/118841
title: Radiometer data collected during research cruise AT31C using a Eppley PIR instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7694513
title: Ranking cows’ methane emissions under commercial conditions with sniffers versus respiration chambers

description: This study assessed the ranking of dairy cows using individual-level correlations for methane (CH<sub>4</sub>) emission on-farm using sniffers and in respiration chambers. In total 20 lactating dairy cows, ten Holstein and ten Jerseys were recorded using sniffers installed in milking robots for three weeks of lactation and subsequently in respiration chambers (RC) where they were each recorded on three occasions within the RC. Bivariate linear mixed models were used to determine the individual-level correlations (r<sub>I</sub>) between sniffer and RC phenotypes as proxies for genetic correlations. Despite differences in feeding and management, the predicted CH<sub>4</sub> production from sniffers correlated highly with RC CH<sub>4</sub> production r<sub>I</sub> = 0.77 ± 0.18 and CH<sub>4</sub> breath concentration correlated nearly as well with RC CH<sub>4</sub> production r<sub>I</sub> = 0.75 ± 0.20. These correlations between sniffers on-farm and RC demonstrate the potential of sniffers measurements as large-scale indicator traits for CH<sub>4</sub> emissions in dairy cattle.
DOI: 10.6084/m9.figshare.7694546.v1
title: A facile forward-genetic screen for <i>Arabidopsis</i> autophagy mutants reveals twenty-one loss-of-function mutations disrupting six <i>ATG</i> genes

description: Macroautophagy is a process through which eukaryotic cells degrade large substrates including organelles, protein aggregates, and invading pathogens. Over 40 autophagy-related (<i>ATG</i>) genes have been identified through forward-genetic screens in yeast. Although homology-based analyses have identified conserved <i>ATG</i> genes in plants, only a few <i>atg</i> mutants have emerged from forward-genetic screens in <i>Arabidopsis thaliana</i>. We developed a screen that consistently recovers <i>Arabidopsis atg</i> mutations by exploiting mutants with defective LON2/At5g47040, a protease implicated in peroxisomal quality control. <i>Arabidopsis lon2</i> mutants exhibit reduced responsiveness to the peroxisomally-metabolized auxin precursor indole-3-butyric acid (IBA), heightened degradation of several peroxisomal matrix proteins, and impaired processing of proteins harboring N-terminal peroxisomal targeting signals; these defects are ameliorated by preventing autophagy. We optimized a <i>lon2</i> suppressor screen to expedite recovery of additional <i>atg</i> mutants. After screening mutagenized <i>lon2-2</i> seedlings for restored IBA responsiveness, we evaluated stabilization and processing of peroxisomal proteins, levels of several ATG proteins, and levels of the selective autophagy receptor NBR1/At4g24690, which accumulates when autophagy is impaired. We recovered 21 alleles disrupting 6 <i>ATG</i> genes: <i>ATG2/At3g19190, ATG3/At5g61500, ATG5/At5g17290, ATG7/At5g45900, ATG16/At5g50230</i>, and <i>ATG18a/At3g62770</i>. Twenty alleles were novel, and 3 of the mutated genes lack T-DNA insertional alleles in publicly available repositories. We also demonstrate that an insertional <i>atg11</i>/<i>At4g30790</i> allele incompletely suppresses <i>lon2</i> defects. Finally, we show that NBR1 is not necessary for autophagy of <i>lon2</i> peroxisomes and that <i>NBR1</i> overexpression is not sufficient to trigger autophagy of seedling peroxisomes, indicating that <i>Arabidopsis</i> can use an NBR1-independent mechanism to target peroxisomes for autophagic degradation. <b>Abbreviations:</b> ATG: autophagy-related; ATI: ATG8-interacting protein; Col-0: Columbia-0; DSK2: dominant suppressor of KAR2; EMS: ethyl methanesulfonate; GFP: green fluorescent protein; IAA: indole-3-acetic acid; IBA: indole-3-butyric acid; ICL: isocitrate lyase; MLS: malate synthase; NBR1: Next to BRCA1 gene 1; PEX: peroxin; PMDH: peroxisomal malate dehydrogenase; PTS: peroxisomal targeting signal; thiolase: 3-ketoacyl-CoA thiolase; UBA: ubiquitin-associated; WT: wild type
DOI: 10.6084/m9.figshare.7694489
title: A bark of its own kind – the acoustics of ‘annoying’ dog barks suggests a specific attention-evoking effect for humans

description: Dog barks represent a major source of noise pollution worldwide. However, the exact reasons why dog barks annoy people and why particular people show stronger reactions to dog barks than other noises, are poorly understood. In a sound playback study, we tested Hungarian participants (<i>N</i>= 153) from three age groups and three residential areas. Each participant was tested with 12 different bark sequences, assembled from original barks, based on their pitch, inter-bark intervals and tonality. Subjects rated each sequence according to the degree of annoyance caused by the barks and also to the apparent inner state of the dog. The results showed that the residential area did not have an effect on annoyance ratings. However, compared to children and older adults, young adults found high-pitched barks to be the most annoying. This finding is consistent with earlier results of the effects of baby cries on humans. The most annoying barks showed unique acoustical structures (high pitch, low tonality), this combination was not associated with the extremities of any other emotional scales. We assume that the strong attention eliciting effect of particular barks could be one of the evolutionary reasons why barking has become the main vocalization of the dog during domestication.
DOI: 10.6084/m9.figshare.7694489.v1
title: A bark of its own kind – the acoustics of ‘annoying’ dog barks suggests a specific attention-evoking effect for humans

description: Dog barks represent a major source of noise pollution worldwide. However, the exact reasons why dog barks annoy people and why particular people show stronger reactions to dog barks than other noises, are poorly understood. In a sound playback study, we tested Hungarian participants (<i>N</i>= 153) from three age groups and three residential areas. Each participant was tested with 12 different bark sequences, assembled from original barks, based on their pitch, inter-bark intervals and tonality. Subjects rated each sequence according to the degree of annoyance caused by the barks and also to the apparent inner state of the dog. The results showed that the residential area did not have an effect on annoyance ratings. However, compared to children and older adults, young adults found high-pitched barks to be the most annoying. This finding is consistent with earlier results of the effects of baby cries on humans. The most annoying barks showed unique acoustical structures (high pitch, low tonality), this combination was not associated with the extremities of any other emotional scales. We assume that the strong attention eliciting effect of particular barks could be one of the evolutionary reasons why barking has become the main vocalization of the dog during domestication.
DOI: 10.6084/m9.figshare.7694513.v1
title: Ranking cows’ methane emissions under commercial conditions with sniffers versus respiration chambers

description: This study assessed the ranking of dairy cows using individual-level correlations for methane (CH<sub>4</sub>) emission on-farm using sniffers and in respiration chambers. In total 20 lactating dairy cows, ten Holstein and ten Jerseys were recorded using sniffers installed in milking robots for three weeks of lactation and subsequently in respiration chambers (RC) where they were each recorded on three occasions within the RC. Bivariate linear mixed models were used to determine the individual-level correlations (r<sub>I</sub>) between sniffer and RC phenotypes as proxies for genetic correlations. Despite differences in feeding and management, the predicted CH<sub>4</sub> production from sniffers correlated highly with RC CH<sub>4</sub> production r<sub>I</sub> = 0.77 ± 0.18 and CH<sub>4</sub> breath concentration correlated nearly as well with RC CH<sub>4</sub> production r<sub>I</sub> = 0.75 ± 0.20. These correlations between sniffers on-farm and RC demonstrate the potential of sniffers measurements as large-scale indicator traits for CH<sub>4</sub> emissions in dairy cattle.
DOI: 10.7284/118842
title: Radiometer data collected during research cruise AT31C using a Eppley PSP instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7694459
title: Niche conservatism promotes ecological speciation in the cycad Dioon merolae (Zamiaceae) in Mexico

description: A .zip file contains four files:<br>1) STRUCTURE format file obtained from the filtering and SNP identification method in STACKS, as described in the manuscript.<br>2) Morphological data (15 traits) of 100 individuals used in the research. <br>3) Climate data of 30 localities of Dioon merolae and 20 of other species of the Purpusii clade.<br>4) RAD-seq raw data obtained from HiSeq2500 (Illumina) of 68 samples of Dioon merolae.
DOI: 10.6084/m9.figshare.7694480
title: Evolution of hybridogenetic lineages in Cataglyphis ants - Draft genome of Cataglyphis hispanica 'his1'

description: Several species of <i>Cataglyphis</i> desert ants have evolved a peculiar breeding system called social hybridogenesis. Under this system, two divergent genetic lineages coexist within a species. Workers develop from hybrid crosses between lineages, whereas queens and males are produced by parthenogenesis and carry only the maternal genome. To gain a better understanding of the evolutionary history of social hybridogenesis in <i>Cataglyphis</i>, we studied its phylogeographic distribution in the Iberian Peninsula using both SNP nuclear markers.<br><i>C. hispanica </i>was used as an outgroup and reference for analyses. The genome of a <i>C. hispanica</i> queen was sequenced on a HiSeq 2000 (PE100; ~42x genome-wide depth). The short-read library was assembled into a draft genome using SPAdes v3.13 (Bankevich et al. 2012). BUSCO analysis (Simão et al. 2015) revealed that 79% of the single-copy orthologs specific to Hymenoptera were complete in the assembly.
DOI: 10.6084/m9.figshare.7694459.v1
title: Niche conservatism promotes ecological speciation in the cycad Dioon merolae (Zamiaceae) in Mexico

description: A .zip file contains four files:<br>1) STRUCTURE format file obtained from the filtering and SNP identification method in STACKS, as described in the manuscript.<br>2) Morphological data (15 traits) of 100 individuals used in the research. <br>3) Climate data of 30 localities of Dioon merolae and 20 of other species of the Purpusii clade.<br>4) RAD-seq raw data obtained from HiSeq2500 (Illumina) of 68 samples of Dioon merolae.
DOI: 10.6084/m9.figshare.7694480.v1
title: Evolution of hybridogenetic lineages in Cataglyphis ants - Draft genome of Cataglyphis hispanica 'his1'

description: Several species of <i>Cataglyphis</i> desert ants have evolved a peculiar breeding system called social hybridogenesis. Under this system, two divergent genetic lineages coexist within a species. Workers develop from hybrid crosses between lineages, whereas queens and males are produced by parthenogenesis and carry only the maternal genome. To gain a better understanding of the evolutionary history of social hybridogenesis in <i>Cataglyphis</i>, we studied its phylogeographic distribution in the Iberian Peninsula using both SNP nuclear markers.<br><i>C. hispanica </i>was used as an outgroup and reference for analyses. The genome of a <i>C. hispanica</i> queen was sequenced on a HiSeq 2000 (PE100; ~42x genome-wide depth). The short-read library was assembled into a draft genome using SPAdes v3.13 (Bankevich et al. 2012). BUSCO analysis (Simão et al. 2015) revealed that 79% of the single-copy orthologs specific to Hymenoptera were complete in the assembly.
DOI: 10.7284/118853
title: Multiplexed data collected during research cruise AT32 using a WHOI Calliope instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7694453
title: Raw data and R code used in meta-analysis

description: Data and code for figures and statistics reported in Midolo, G., De Frenne, P., Hölzel, N. & Wellstein, C. (2019). <i>Global patterns of intraspecific leaf trait responses to elevation</i>.<br><br>For a complete list reference of studies included in the meta-analysis, see the Supporting Information of our article.<br><br>See the "csv_file_description" file for detailed information on dataset description and the R code to analyze the data.<br><br>For any question, please contact me at: <b>gabriele.midolo@natec.unibz.it </b><br>
DOI: 10.6084/m9.figshare.7694456
title: New paroxyclaenid mammals from the early Eocene of the Paris Basin (France) shed light on the origin and evolution of these endemic European cimolestans

description: We present new species of an enigmatic family of mammals, which is endemic to Europe, the Paroxyclaenidae: <i>Merialus bruneti</i> sp. nov., <i>Fratrodon tresvauxi</i> gen. et sp. nov., <i>Paraspaniella gunnelli</i> gen. et sp. nov., and <i>Sororodon tresvauxae</i> gen. et sp. nov. The fossils described come from six localities of the Ypresian of the Paris Basin (France): Pourcy (MP7), Mutigny, Avenay, Condé-en-Brie (MP8 + 9), Grauves and Prémontré (MP10). They allow the description of three new genera and four new species belonging to the subfamilies Merialinae and Paroxyclaeninae. Two of these new species represent the earliest occurrence of each subfamily. Fossils from Mutigny, Avenay and Condé-en-Brie indicate that merialines were more abundant than paroxyclaenines during the Ypresian. Surprisingly, merialines disappeared from the fossil record at the end of the Ypresian – the youngest records are close to MP10 – while the paroxyclaenines were present in Europe until the end of the middle Eocene. Based on comparison with the data presently available for European mammals during the Ypresian, we suggest the existence of two periods of faunal turnover that must be more extensively studied in the future in order to be fully characterized: the ‘Intra-Ypresian Mammal Turnover’ and the ‘Ypresian–Lutetian Mammal Turnover’. Finally, because the oldest paroxyclaenids appear morphologically closer to cimolestids such as <i>Procerberus</i> than to pantolestans, it is suggested that similarities between paroxyclaenids and pantolestans could be due to convergence. http://zoobank.org/urn:lsid:zoobank.org:pub:8A3B21A0-6945-4CE4-975C-402736E92C51