cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853966.v1
title: Intrageneric evolutionary timing and hidden genetic diversity of <i>Paramecium</i> lineages (Ciliophora: Oligohymenophorea)

description: Members of the genus <i>Paramecium</i> (Ciliophora, Oligohymenophorea) are widespread ciliates able to colonize many fresh, brackish and marine water environments around the globe. Despite they have been historically used in a variety of research fields, ranging from genomics to ecology, their evolutionary origin and genetic structure remains elusive for most valid species. There are currently 19 valid species distributed in 5 subgenera, which can have restricted to cosmopolitan distribution patterns. However, their true biodiversity and biographical distribution are blurred by evidences of cryptic species within most of these valid species. Here, we inferred a 18S rDNA-based time-calibrated tree to determine the evolutionary origin of extant <i>Paramecium</i> lineages and intra-genus phylogenetic relationships. Next, we used two common computational species delimitation algorithms (PTP and mPTP) to analyze a population-level (cytochrome oxidase subunit I [COI]) phylogeny to predict the existence of independent evolutionary unities (IEUs) within valid <i>Paramecium</i> morphospecies. Our data suggest that, some cosmopolitan <i>Paramecium</i> may have emerged prior to the Cretaceous period (before the complete separation of the continents), thus, explaining their wide distribution pattern. We found that the diversity of cryptic species may be higher than previous though and that most of the valid <i>Paramecium</i> species should be, in fact considered as complexes of species, composed each by IEUs that can co-occur within restricted or wide geographical areas. Moreover, our data indicate that these species delimitation algorithms (PTP and mPTP) may be of great assistance to uncover the diversity of cryptic species within <i>Paramecium</i> (or any other microeukaryote) by indicating potential candidates for more in detail future studies of taxonomists through integrative taxonomy frameworks.
DOI: 10.6084/m9.figshare.12853942
title: Phylogenomic analyses reveal a rare new genus of wasp (Hymenoptera, Ichneumonidae, Cryptinae) from the Brazilian Atlantic Forest

description: Within the ichneumonid wasp tribe Cryptini (Ichneumonidae, Cryptinae), <i>Acrosnemus</i> gen. nov. and its single species <i>A</i>. <i>occultus</i> sp. nov. are proposed, described, and illustrated. The phylogenetic placement of the new genus is tested using data from genomic ultraconserved elements in a matrix with 126 other species of Cryptini and five outgroup taxa. Phylogenetic analyses indicate the new genus is related to <i>Melanocryptus</i> Cameron, from which it can be distinguished by the presence of a conspicuous anterolateral tooth on the first metasomal tergite; tip of ventral valve of ovipositor with a dorsal lobe that partly encloses dorsal valve; posterior transverse carina represented only by two distinct sublateral crests; and female antenna with a distinct white band. The new genus presents a mosaic of morphological traits from various cryptine lineages, highlighting the ubiquitous morphological homoplasy among cryptines. The single species is recorded only from one Atlantic Forest fragment in south-eastern Brazil. Sampling history suggests it is naturally rare. http://www.zoobank.org:pub:F2519AD0-9150-4207-9F17-74E72DDC4C6
DOI: 10.6084/m9.figshare.12853942.v1
title: Phylogenomic analyses reveal a rare new genus of wasp (Hymenoptera, Ichneumonidae, Cryptinae) from the Brazilian Atlantic Forest

description: Within the ichneumonid wasp tribe Cryptini (Ichneumonidae, Cryptinae), <i>Acrosnemus</i> gen. nov. and its single species <i>A</i>. <i>occultus</i> sp. nov. are proposed, described, and illustrated. The phylogenetic placement of the new genus is tested using data from genomic ultraconserved elements in a matrix with 126 other species of Cryptini and five outgroup taxa. Phylogenetic analyses indicate the new genus is related to <i>Melanocryptus</i> Cameron, from which it can be distinguished by the presence of a conspicuous anterolateral tooth on the first metasomal tergite; tip of ventral valve of ovipositor with a dorsal lobe that partly encloses dorsal valve; posterior transverse carina represented only by two distinct sublateral crests; and female antenna with a distinct white band. The new genus presents a mosaic of morphological traits from various cryptine lineages, highlighting the ubiquitous morphological homoplasy among cryptines. The single species is recorded only from one Atlantic Forest fragment in south-eastern Brazil. Sampling history suggests it is naturally rare. http://www.zoobank.org:pub:F2519AD0-9150-4207-9F17-74E72DDC4C6
DOI: 10.6084/m9.figshare.12853936
title: Phylogenetic position of a bizarre lizard <i>Harpesaurus</i> implies the co-evolution between arboreality, locomotion, and reproductive mode in Draconinae (Squamata: Agamidae)

description: Viviparous reproduction has evolved independently more than 100 times in the evolutionary history of Squamata (lizards and snakes). Adaptation to cold climates is the dominant hypothesis explaining shifts to viviparity, but viviparous species are also present in the tropical lowlands, implying the presence of other factors that may also promote the evolution of viviparity. For example, the tropical Asian/Oceanian subfamily, Draconinae, includes two viviparous genera (<i>Cophotis</i> and <i>Harpesaurus</i>). However, one of them, <i>Harpesaurus</i>, is extremely rare, making it difficult to study aspects of their ecology or evolution. We managed to collect a <i>H</i>. <i>borneensis</i>, and this provided an opportunity to address the evolution of viviparity in draconine lizards. Based on a new molecular phylogenetic hypothesis, including all viviparous groups in Draconinae, we infer that viviparity has evolved twice within the subfamily. Ancestral state reconstruction analyses indicated that shifts to viviparity were preceded by the evolution of arboreality and slow-moving locomotion. Our analysis strongly suggests evolutionary correlations between habitats, locomotion, and reproductive modes. Taken together, these results suggest that the use of arboreal habitats and slow locomotion facilitated the evolution of viviparity in these tropical/subtropical lizards. Arboreal, slow-moving species are considered to rely more on crypsis in predator avoidance rather than fleeing. Therefore, we propose that such species are relatively insusceptible to the concomitant cost of viviparity: reduced locomotive ability and increased risk of predation during pregnancy. We also describe and discuss the unique behaviours of <i>H</i>. <i>borneensis</i>.
DOI: 10.6084/m9.figshare.12853936.v1
title: Phylogenetic position of a bizarre lizard <i>Harpesaurus</i> implies the co-evolution between arboreality, locomotion, and reproductive mode in Draconinae (Squamata: Agamidae)

description: Viviparous reproduction has evolved independently more than 100 times in the evolutionary history of Squamata (lizards and snakes). Adaptation to cold climates is the dominant hypothesis explaining shifts to viviparity, but viviparous species are also present in the tropical lowlands, implying the presence of other factors that may also promote the evolution of viviparity. For example, the tropical Asian/Oceanian subfamily, Draconinae, includes two viviparous genera (<i>Cophotis</i> and <i>Harpesaurus</i>). However, one of them, <i>Harpesaurus</i>, is extremely rare, making it difficult to study aspects of their ecology or evolution. We managed to collect a <i>H</i>. <i>borneensis</i>, and this provided an opportunity to address the evolution of viviparity in draconine lizards. Based on a new molecular phylogenetic hypothesis, including all viviparous groups in Draconinae, we infer that viviparity has evolved twice within the subfamily. Ancestral state reconstruction analyses indicated that shifts to viviparity were preceded by the evolution of arboreality and slow-moving locomotion. Our analysis strongly suggests evolutionary correlations between habitats, locomotion, and reproductive modes. Taken together, these results suggest that the use of arboreal habitats and slow locomotion facilitated the evolution of viviparity in these tropical/subtropical lizards. Arboreal, slow-moving species are considered to rely more on crypsis in predator avoidance rather than fleeing. Therefore, we propose that such species are relatively insusceptible to the concomitant cost of viviparity: reduced locomotive ability and increased risk of predation during pregnancy. We also describe and discuss the unique behaviours of <i>H</i>. <i>borneensis</i>.
DOI: 10.6084/m9.figshare.12853963
title: Testing the monophyly of the ground-dweller spider genus <i>Harpactea</i> Bristowe, 1939 (Araneae, Dysderidae) with the description of three new species

description: The genus <i>Harpactea</i> Bristowe, 1939 (Araneae, Dysderidae) is one of the most diverse and abundant components of the Mediterranean ground-dwelling spider fauna. However, the taxonomic boundaries of the genus are unclear and its monophyly has been questioned, yet never tested, in a quantitative framework. The only taxonomic revisions in the genus trace back to the 1960s–1990s, and most subsequent work has consisted of single species descriptions. Part of the confusion surrounding the genus and species groups delimitations have to do with the lack of a standardized nomenclature for diagnostic structures based on explicit homology statements. Here we use the description of new species of <i>Harpactea</i> to propose a set of homologies in the male and female genitalia and a standardized nomenclature for those structures. We formally describe three new <i>Harpactea</i> species: <i>H. salvatorei</i> sp. nov., from a cave in the north-eastern Italian Alps, and <i>H. damini</i> sp. nov. and <i>H. mateparlovi</i> sp. nov. from different caves on the Biokovo Mountain and surroundings in Croatia. All the new taxa belong to the <i>lepida</i> species group. In addition, we use a multilocus target gene approach to provide the first hypothesis on the internal phylogenetic structure of the genus <i>Harpactea</i> and the subfamily Harpacteinae, which includes representatives of all currently accepted species groups in the genus and genera in the subfamily. Our results support the close affinities of the species here described but reject the monophyly of both <i>Harpactea</i> and some of the species groups proposed in the literature. http://zoobank.org/NomenclaturalActs/bd2739c9-c1f0-451f-88cc-06c784987a62 http://zoobank.org/NomenclaturalActs/ffb50b2e-ac7b-49a8-aa0d-408143c8a990 http://zoobank.org/NomenclaturalActs/184c58fe-6501-4cc2-ba50-cca4fcff8289
DOI: 10.6084/m9.figshare.12853963.v1
title: Testing the monophyly of the ground-dweller spider genus <i>Harpactea</i> Bristowe, 1939 (Araneae, Dysderidae) with the description of three new species

description: The genus <i>Harpactea</i> Bristowe, 1939 (Araneae, Dysderidae) is one of the most diverse and abundant components of the Mediterranean ground-dwelling spider fauna. However, the taxonomic boundaries of the genus are unclear and its monophyly has been questioned, yet never tested, in a quantitative framework. The only taxonomic revisions in the genus trace back to the 1960s–1990s, and most subsequent work has consisted of single species descriptions. Part of the confusion surrounding the genus and species groups delimitations have to do with the lack of a standardized nomenclature for diagnostic structures based on explicit homology statements. Here we use the description of new species of <i>Harpactea</i> to propose a set of homologies in the male and female genitalia and a standardized nomenclature for those structures. We formally describe three new <i>Harpactea</i> species: <i>H. salvatorei</i> sp. nov., from a cave in the north-eastern Italian Alps, and <i>H. damini</i> sp. nov. and <i>H. mateparlovi</i> sp. nov. from different caves on the Biokovo Mountain and surroundings in Croatia. All the new taxa belong to the <i>lepida</i> species group. In addition, we use a multilocus target gene approach to provide the first hypothesis on the internal phylogenetic structure of the genus <i>Harpactea</i> and the subfamily Harpacteinae, which includes representatives of all currently accepted species groups in the genus and genera in the subfamily. Our results support the close affinities of the species here described but reject the monophyly of both <i>Harpactea</i> and some of the species groups proposed in the literature. http://zoobank.org/NomenclaturalActs/bd2739c9-c1f0-451f-88cc-06c784987a62 http://zoobank.org/NomenclaturalActs/ffb50b2e-ac7b-49a8-aa0d-408143c8a990 http://zoobank.org/NomenclaturalActs/184c58fe-6501-4cc2-ba50-cca4fcff8289
DOI: 10.6084/m9.figshare.4774780
title: Duration and Onset data

description: This contains the data sets used for the optimization of stimulus duration and onset. .mat files are matlab tables used to create figure 2. <br>
DOI: 10.6084/m9.figshare.4774780.v1
title: Duration and Onset data

description: This contains the data sets used for the optimization of stimulus duration and onset. .mat files are matlab tables used to create figure 2. <br>
DOI: 10.6084/m9.figshare.4774777
title: 10 steps to integrate CIViCdb with other public data in Wikidata

description: Precision medicine has shifted our understanding of the etiology and treatment of cancer from a focus on anatomical to molecular features. The genetic fingerprint of a patient can be deterministic in both the onset and treatment of the disease. However the etiological network of a specific disease consists of very diverse factors from genetic to environmental. With such diverse knowledge comes a diverse data infrastructure. Data is scattered across data silos and different data formats/structures. This poses a serious bottleneck when interpreting data in a clinical and/or research setting. CIViC (http://www.civicdb.org) is an open-access, community-based, highly-curated cancer variant database. It is a platform where data on cancer genomic alterations from different data sources are curated and interpreted for clinical application. These interpretations with their evidence are captured and stored as structured data in the public domain. In order to reach an even broader audience an effort was made to include CIViC's data into Wikidata. Wikidata contains and feeds structured data into Wikipedia and to other Wikimedia projects. It has all the traits of Wikipedia (open-access, editable, community-driven) and is accessible to both humans and machines. Although Wikidata has a Wikipedia narrative, its application is not limited to it. The open APIs allow broader application. Adding public domain datasets to Wikidata benefits audiences in both directions. In this case, Wikidata gains additional content from a highly-curated resource, while CIViC gains exposure to a wider audience, the ability to link to other data types and domains (e.g. drugs) and the benefits of Wikidata’s being a hub on the Semantic Web, allowing complex queries to be performed. We report the process involved in linking CIViC to Wikidata. This led to eight new Wikidata relations and a model to capture provenance. The resulting statements are built upon common standards coming from ontologies and other resources. The success of the data integration is proof that different data models can work together without any loss of information and we invite other resources to follow.
DOI: 10.6084/m9.figshare.4774762
title: Amplitude vs Frequency Data

description: The master data tables for amplitude and frequency comparison. The scripts for calculating the stats.The .mat files are matlab files containing the data used to generate figure 3.
DOI: 10.6084/m9.figshare.4774759
title: Brace part files

description: Parts for the brace used to mobilize the bird. Files include .STL files for 3D printers as well as the files for the CAD software FreeCAD.
DOI: 10.6084/m9.figshare.4774759.v1
title: Brace part files

description: Parts for the brace used to mobilize the bird. Files include .STL files for 3D printers as well as the files for the CAD software FreeCAD.
DOI: 10.6084/m9.figshare.4774753
title: DNA matrix for "Phylogenetic reassessment of tribe Anemoneae (Ranunculaceae): non-monophyly of Anemone s.l. revealed by plastid datasets"

description: This DNA matrix is the paper entitled "Phylogenetic reassessment of tribe Anemoneae (Ranunculaceae): non-monophyly of Anemone s.l. revealed by plastid datasets", which will be published in PLoS One. This dataset includes seven DNA markers, nrITS, atpB-rbcL, matK, psbA-trnQ, rbcL, rpoB-trnC and rps16.
DOI: 10.6084/m9.figshare.4774678
title: Greenhouse Common Garden Experiment: Nodes

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the number of nodes per plant data was collected. Time 1 through Time 10 are the number of nodes per plant at that time point. The time that elapsed between time points is roughly every two weeks..
DOI: 10.6084/m9.figshare.4774681
title: Greenhouse Common Garden Experiment Leaves

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the number of leaves per plant data was collected. Time 1 through Time 10 are the number of leaves per plant at that time point. The time that elapsed between time points is roughly every two weeks.
DOI: 10.6084/m9.figshare.4774675
title: Greenhouse common garden experiment: Height

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the height per plant data was collected. Time 1 through Time 10 are the heights per plant at that time point. The time that elapsed between time points is roughly every two weeks.
DOI: 10.6084/m9.figshare.4774678.v1
title: Greenhouse Common Garden Experiment: Nodes

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the number of nodes per plant data was collected. Time 1 through Time 10 are the number of nodes per plant at that time point. The time that elapsed between time points is roughly every two weeks..
DOI: 10.6084/m9.figshare.4774654
title: Functional Lacandona

description: Data used for replicate analyzes
DOI: 10.6084/m9.figshare.4774681.v1
title: Greenhouse Common Garden Experiment Leaves

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the number of leaves per plant data was collected. Time 1 through Time 10 are the number of leaves per plant at that time point. The time that elapsed between time points is roughly every two weeks.
DOI: 10.6084/m9.figshare.4774675.v1
title: Greenhouse common garden experiment: Height

description: Plant number indicates the plant identification number during the experiment on plant species Achyranthes japonica. Soil Source identifies which population location the soil was sourced from for the experiment. Soil sources used in this experiment include: Warfield, Kentucky; Henderson, Kentucky; and Chestnut Hills Nature Preserve, Illinois. Seed source identifies which population the seeds were collected and sourced. Seeds were sourced from locations Chestnut Hills, Illinois; Limekiln Springs, Illinois; Cypress Creek, Illinois; Louisville, Kentucky; and Warfield, Kentucky. Rep identifies which Repetition the plant received during experiment which also indicated what experimental block the plants were grown on. Time 1 through Time 10 indicated sampling points where the height per plant data was collected. Time 1 through Time 10 are the heights per plant at that time point. The time that elapsed between time points is roughly every two weeks.
DOI: 10.6084/m9.figshare.4774654.v1
title: lcd_env.csv

description: Data used for replicate analyzes
DOI: 10.6084/m9.figshare.4774654.v3
title: Functional Lacandona

description: Data used for replicate analyzes
DOI: 10.6084/m9.figshare.4774654.v2
title: Functional Lacandona

description: Data used for replicate analyzes
DOI: 10.6084/m9.figshare.4772362
title: folder_12

description: honeybee accelerometer recordings FLAC
DOI: 10.6084/m9.figshare.4772362.v1
title: folder_12

description: honeybee accelerometer recordings FLAC