cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9730712.v1
title: Press release_RSBL-2019-0182_R2.odt from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

description: Understanding biological diversity is crucial for ecological and evolutionary studies. Even though a great part of animal diversity has already been documented, both morphological surveys and metabarcoding analyses have previously shown that some animal groups, such as Platyhelminthes, may harbour hidden diversity. To better understand the molecular diversity of Platyhelminthes, one of the most diverse and biomedically important animal phyla, we here combined data from six marine and two freshwater metabarcoding expeditions that cover a broad variety of aquatic habitats and analysed the data by phylogenetic placement. Our results show that a great part of the hidden diversity is located in early-branching clades such as Catenulida and Macrostomorpha, as well as in late-diverging clades such as Proseriata and Rhabdocoela. We also report the first freshwater record of Gnosonesimida, a group previously thought to be exclusively marine. Finally, we identified two putative novel freshwater platyhelminth clades that branch between well-defined orders of the phylum. Thus, our analyses of several environmental datasets confirm that a large part of the diversity of Platyhelminthes remains undiscovered, point to groups with more potential novel species and identify freshwater environments as potential reservoirs for novel species of flatworms.
DOI: 10.6084/m9.figshare.9730715
title: Placement files and comparison from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: The two jplace files contain the results of EPA and pplacer. The .txt file is the comparison of these files conducted by the software genesis.
DOI: 10.6084/m9.figshare.9730724.v2
title: Best-hit placement tree from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: It is the tree of the figure 1C and 2A. It shows the position with the highest likelihood-weight score of the short queries in the reference tree.
DOI: 10.6084/m9.figshare.9730718
title: PaPaRa alignment of short reads from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: Short reads aligned to the reference sequences. This is the file that was used by EPA and pplacer to produce the jplace files.
DOI: 10.6084/m9.figshare.9730724.v1
title: Maximum-likelihood tree with new clades from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

description: It is the tree of figure 2B.The tree was inferred in RAxML under the GTR+GAMMA substitution model from the combination of 22 OTUs with interesting placements and 455 reference sequences. Nodal support indicates 1,000 ML rapid bootstrap replicates.
DOI: 10.6084/m9.figshare.9730721
title: Best-hit placement tree from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: It is the tree of the figure 1C and 2A. It shows the position with the highest likelihood-weight score of the short queries in the reference tree.
DOI: 10.6084/m9.figshare.9730715.v2
title: Placement files and comparison from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: The two jplace files contain the results of EPA and pplacer. The .txt file is the comparison of these files conducted by the software genesis.
DOI: 10.6084/m9.figshare.9730718.v2
title: PaPaRa alignment of short reads from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: Short reads aligned to the reference sequences. This is the file that was used by EPA and pplacer to produce the jplace files.
DOI: 10.6084/m9.figshare.9730715.v1
title: PaPaRa alignment of short reads from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

description: Short reads aligned to the reference sequences. This is the file that was used by EPA and pplacer to produce the jplace files.
DOI: 10.6084/m9.figshare.9730721.v2
title: Best-hit placement tree from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades.

description: It is the tree of the figure 1C and 2A. It shows the position with the highest likelihood-weight score of the short queries in the reference tree.
DOI: 10.6084/m9.figshare.9730718.v1
title: Reference tree alignment from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

description: This is the alignment used to produce the reference tree.
DOI: 10.6084/m9.figshare.9730721.v1
title: Best-hit placement tree from A global metabarcoding analysis expands molecular diversity of Platyhelminthes and reveals novel early-branching clades

description: It is the tree of the figure 1C and 2A. It shows the position with the highest likelihood-weight score of the short queries in the reference tree.
DOI: 10.6084/m9.figshare.9730763
title: R script from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: All R scripts used in the statistical analysis
DOI: 10.6084/m9.figshare.9730772
title: Data on female age-specific reproduction from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: Raw data on female age-specific reproduction (number of eclosed offspring produced per day)
DOI: 10.6084/m9.figshare.9730763.v2
title: R script from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: All R scripts used in the statistical analysis
DOI: 10.6084/m9.figshare.9730766
title: Data on total offspring production and lifespan from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: Raw data on female lifetime reproductive success (total number of eclosed offspring) and lifespan (measured in days) for both blocks of the experiment
DOI: 10.6084/m9.figshare.9730763.v1
title: R script from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles

description: All R scripts used in the statistical analysis
DOI: 10.6084/m9.figshare.9730772.v2
title: Data on female age-specific reproduction from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: Raw data on female age-specific reproduction (number of eclosed offspring produced per day)
DOI: 10.6084/m9.figshare.9730766.v2
title: Data on total offspring production and lifespan from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles.

description: Raw data on female lifetime reproductive success (total number of eclosed offspring) and lifespan (measured in days) for both blocks of the experiment
DOI: 10.6084/m9.figshare.9730772.v1
title: Data on female age-specific reproduction from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles

description: Raw data on female age-specific reproduction (number of eclosed offspring produced per day)
DOI: 10.6084/m9.figshare.9730766.v1
title: Data on total offspring production and lifespan from Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles

description: Raw data on female lifetime reproductive success (total number of eclosed offspring) and lifespan (measured in days) for both blocks of the experiment
DOI: 10.6084/m9.figshare.9730847
title: Flow cytometry data and taxonomic information for sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments.

description: For each individual sorted cell the flow cytometric information alongside the OTUs and taxonomy assignements of both 18S rRNA genes and plastid and mitochondrial 16S rRNA genes are given.
DOI: 10.6084/m9.figshare.9730847.v2
title: Flow cytometry data and taxonomic information for sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments.

description: For each individual sorted cell the flow cytometric information alongside the OTUs and taxonomy assignements of both 18S rRNA genes and plastid and mitochondrial 16S rRNA genes are given.
DOI: 10.6084/m9.figshare.9730847.v1
title: Flow cytometry data and taxonomic information for sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

description: For each individual sorted cell the flow cytometric information alongside the OTUs and taxonomy assignements of both 18S rRNA genes and plastid and mitochondrial 16S rRNA genes are given.
DOI: 10.6084/m9.figshare.9730856
title: Sequences retrieved from sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments.

description: Fasta file with 18S rRNA and 16S rRNA sequences representative for the OTUs (clustered at 99%) retrieved from the single cell sorts.
DOI: 10.6084/m9.figshare.9730856.v2
title: Sequences retrieved from sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments.

description: Fasta file with 18S rRNA and 16S rRNA sequences representative for the OTUs (clustered at 99%) retrieved from the single cell sorts.
DOI: 10.6084/m9.figshare.9730856.v1
title: Sequences retrieved from sorted cells from The need to account for cell biology in characterizing predatory mixotrophs in aquatic environments

description: Fasta file with 18S rRNA and 16S rRNA sequences representative for the OTUs (clustered at 99%) retrieved from the single cell sorts.
DOI: 10.6084/m9.figshare.9756647
title: Supplemental Behavioral Sequence Data from The cleaner shrimp <i>Lysmata amboinensis</i> adjusts its behaviour towards predatory versus non-predatory clients.

description: Raw behavioral data from in situ observations in the two-column format used in data analyses and described in Methods.
DOI: 10.6084/m9.figshare.9756647.v2
title: Supplemental Behavioral Sequence Data from The cleaner shrimp <i>Lysmata amboinensis</i> adjusts its behaviour towards predatory versus non-predatory clients.

description: Raw behavioral data from in situ observations in the two-column format used in data analyses and described in Methods.
DOI: 10.6084/m9.figshare.9756647.v1
title: Supplemental Behavioral Sequence Data from The cleaner shrimp <i>Lysmata amboinensis</i> adjusts its behaviour towards predatory versus non-predatory clients

description: Raw behavioral data from in situ observations in the two-column format used in data analyses and described in Methods.
DOI: 10.6084/m9.figshare.9763073
title: Appendix I from Phylogenetic and kinematic constraints on avian flight signals.

description: Many birds vocalize in flight. Because wingbeat and respiratory cycles are often linked in flying vertebrates, birds in these cases must satisfy the respiratory demands of vocal production within the physiological limits imposed by flight. Using acoustic triangulation and high-speed video, we found that avian vocal production in flight exhibits a largely phasic and kinematic relationship with the power stroke. However, the sample of species showed considerable flexibility, especially those from lineages known for vocal plasticity (songbirds, parrots and hummingbirds), prompting a broader phylogenetic analysis. We thus collected data from 150 species across 12 avian orders and examined the links between wingbeat period, flight call duration and body mass. Overall, shorter wingbeat periods, controlling for ancestry and body mass, were correlated with shorter flight call durations. However, species from vocal learner lineages produced flight signals that, on average, exceeded multiple phases of their wingbeat cycle, while vocal non-learners had signal periods that were, on average, closer to the duration of their power stroke. These results raise an interesting question: is partial emancipation from respiratory constraints a necessary step in the evolution of vocal learning or an epiphenomenon? Our current study cannot provide the answer, but it does suggest several avenues for future research.
DOI: 10.6084/m9.figshare.9763073.v2
title: Appendix I from Phylogenetic and kinematic constraints on avian flight signals.

description: Many birds vocalize in flight. Because wingbeat and respiratory cycles are often linked in flying vertebrates, birds in these cases must satisfy the respiratory demands of vocal production within the physiological limits imposed by flight. Using acoustic triangulation and high-speed video, we found that avian vocal production in flight exhibits a largely phasic and kinematic relationship with the power stroke. However, the sample of species showed considerable flexibility, especially those from lineages known for vocal plasticity (songbirds, parrots and hummingbirds), prompting a broader phylogenetic analysis. We thus collected data from 150 species across 12 avian orders and examined the links between wingbeat period, flight call duration and body mass. Overall, shorter wingbeat periods, controlling for ancestry and body mass, were correlated with shorter flight call durations. However, species from vocal learner lineages produced flight signals that, on average, exceeded multiple phases of their wingbeat cycle, while vocal non-learners had signal periods that were, on average, closer to the duration of their power stroke. These results raise an interesting question: is partial emancipation from respiratory constraints a necessary step in the evolution of vocal learning or an epiphenomenon? Our current study cannot provide the answer, but it does suggest several avenues for future research.
DOI: 10.6084/m9.figshare.9763079
title: ESM Fig I from Phylogenetic and kinematic constraints on avian flight signals.

description: Sample phylogeny taken from 100 phylogenetic trees (Jetz et al. 2012, Nature) used in a Bayesian phylogenetic analysis of ½ wingbeat period, vocal signal period and body mass in 150 bird species. Species from vocal learner lineages are shown in red font; non-vocal learner lineages are shown in black font. Names of clades are given to the right with red lines for vocal learners, red-hashed lines for groups with and without vocal learning; black lines signify lineages without vocal learning. Bird images are scaled to size.
DOI: 10.6084/m9.figshare.9763073.v1
title: Appendix II from Phylogenetic and kinematic constraints on avian flight signals

description: Many birds vocalize in flight. Since wingbeat and respiratory cycles are often linked in flying vertebrates, birds in these cases must satisfy the respiratory demands of vocal production within the physiological limits imposed by flight. Using acoustic triangulation and high-speed video, we found that avian vocal production in flight exhibits a largely phasic and kinematic relationship with the power stroke. However, the sample of species showed considerable flexibility, especially those from lineages known for vocal plasticity (songbirds, parrots and hummingbirds), prompting a broader phylogenetic analysis. We thus collected data from 150 species across 12 avian orders and examined the links between wingbeat period, flight call duration and body mass. Overall, shorter wingbeat periods, controlling for ancestry and body mass, were correlated with shorter flight call durations. However, species from vocal learner lineages produced flight signals that, on average, exceeded multiple phases of their wingbeat cycle, while vocal non-learners had signal periods that were, on average, closer to the duration of their power stroke. These results raise an interesting question: is partial emancipation from respiratory constraints a necessary step in the evolution of vocal learning or an epiphenomenon? Our current study cannot provide the answer, but it does suggest several avenues for future research.
DOI: 10.6084/m9.figshare.9763079.v2
title: ESM Fig I from Phylogenetic and kinematic constraints on avian flight signals.

description: Sample phylogeny taken from 100 phylogenetic trees (Jetz et al. 2012, Nature) used in a Bayesian phylogenetic analysis of ½ wingbeat period, vocal signal period and body mass in 150 bird species. Species from vocal learner lineages are shown in red font; non-vocal learner lineages are shown in black font. Names of clades are given to the right with red lines for vocal learners, red-hashed lines for groups with and without vocal learning; black lines signify lineages without vocal learning. Bird images are scaled to size.
DOI: 10.6084/m9.figshare.9763079.v1
title: Appendix I from Phylogenetic and kinematic constraints on avian flight signals

description: ESM Fig I Sample phylogeny taken from 100 phylogenetic trees (Jetz et al. 2012, Nature) used in a Bayesian phylogenetic analysis of ½ wingbeat period, vocal signal period and body mass in 150 bird species. Species from vocal learner lineages are shown in red font; non-vocal learner lineages are shown in black font. Names of clades are given to the right with red lines for vocal learners, red-hashed lines for groups with and without vocal learning; black lines signify lineages without vocal learning. Bird images are scaled to size.
DOI: 10.6084/m9.figshare.9777896
title: Supplemental File 2 from Placental genotype affects early postpartum maternal behaviour.

description: Project Code
DOI: 10.6084/m9.figshare.9777899
title: Imprinting Project Behavior Data from Placental genotype affects early postpartum maternal behaviour.

description: Excel file containing raw data for each test
DOI: 10.6084/m9.figshare.9777896.v2
title: Supplemental File 2 from Placental genotype affects early postpartum maternal behaviour.

description: Project Code
DOI: 10.6084/m9.figshare.9777899.v2
title: Imprinting Project Behavior Data from Placental genotype affects early postpartum maternal behaviour.

description: Excel file containing raw data for each test
DOI: 10.6084/m9.figshare.9777896.v1
title: Supplemental File 2 from Placental genotype affects early postpartum maternal behaviour

description: Project Code
DOI: 10.6084/m9.figshare.9777899.v1
title: Imprinting Project Behavior Data from Placental genotype affects early postpartum maternal behaviour

description: Excel file containing raw data for each test
DOI: 10.6084/m9.figshare.9779243
title: Table S2 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

description: Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant <i>Mimiviridae</i>, incorporating the <i>Cafeteria roenbergensis</i> virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (<i>e</i>-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.
DOI: 10.6084/m9.figshare.9779243.v2
title: Table S2 from Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.

description: Giant viruses have remarkable genomic repertoires—blurring the line with cellular life—and act as top–down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four ‘PacV’ partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant <i>Mimiviridae</i>, incorporating the <i>Cafeteria roenbergensis</i> virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (<i>e</i>-value −5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the Ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence–absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs.This article is part of the discussion meeting issue ‘Single cell ecology’.