cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5068/d18d7b
title: Data from: Modularity and connectivity of nest structure scale with colony size

description: The files contained in this repository include data files and code used
 for analysis and figure creation in the article "Modularity and
 connectivity of nest structure scale with colony size". Data include
 csv files of edge-lists that are network representations of each nest,
 measures of chamber width for each nest, colony size data for each
 species, and ant length measures. These data are used in
 five sets of analyses, for which we include the R code: (1)
 Network Analysis, (2) Reference model generation and normalization,
 (3) Phylogenetically controlled analyses of network measures, (4)
 Chamber number and size measures and their phylogenetically controlled
 analyses, and (5) Phylogenetic signal for each trait. The relationships
 between files and descriptions of the variables are included in the README
 file. 
description: All data collection and data processing methods are outlined in
 detail in the article text.
DOI: 10.5061/dryad.4xgxd25b2
title: Data from: Compensatory dynamics of lotic algae break down nonlinearly with increasing nutrient enrichment

description: One important mechanism governing the temporal maintenance of biodiversity
 is asynchrony in cooccurring competitors due to fluctuating environments
 (i.e. compensatory dynamics). Temporal niche partitioning has evolved in
 response to predictable oscillations in environmental conditions so that
 species may offset competition, but we do not yet have a clear
 understanding of how novel anthropogenic stressors alter seasonal patterns
 of succession. Many primary producers are nutrient-limited, and enrichment
 may decrease the importance of environmental fluctuations that govern
 which species are effective competitors under naturally low nutrient
 regimes. Consequently, elevated nutrient concentrations may synchronize
 species responses to seasonality. By studying benthic algal assemblages
 over two years from 35 streams that spanned a wide gradient of nutrient
 enrichment, we found that compensatory dynamics characterizing seasonal
 succession under natural nutrient regimes broke down at relatively low
 levels of total phosphorus (P) enrichment (~ 25 μg L-1). With increasing P
 more species were able to coexist at any given time, and seasonal
 variation in assemblage composition was characterized by synchronous
 swings in species biovolumes. We also observed much higher instability in
 assemblage biovolumes with declines in compensatory dynamics, which
 indicates that anthropogenic alteration of nutrient regimes can affect
 community stability by changing the dominant mode of seasonal succession.
 Our findings indicate that compensatory fluctuations of stream algae are
 driven by seasonality, and provide insight about how nutrient enrichment
 alters evolved drivers of species coexistence.
description: Contains a copy of the algae data accompanying Cook and others
 (2021) organized by sampling site and event. Sampling occurred every other
 month, and spanned June 2014 to April 2016. Columns denote species names,
 an associated taxon code used for analysis, and biovolumes
 (mm<sup>3</sup> m<sup>-2</sup>).
DOI: 10.5061/dryad.qfttdz0j2
title: Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon

description: Historical DNA analysis of archival samples has added new dimensions to
 population genetic studies, enabling spatiotemporal approaches for
 reconstructing population histories and informing conservation management.
 Here we tested the efficacy of Genotyping-in-Thousands by sequencing
 (GT-seq) for collecting targeted single nucleotide polymorphism (SNP)
 genotypic data from archival scale samples, and demonstrate its
 application to a study of kokanee salmon (Oncorhynchus nerka) in Kluane
 National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe
 12-year population decline followed by a rapid rebound. We genotyped
 archival scales sampled pre-crash and contemporary fin clips collected
 post-crash, revealing high coverage (&gt;90% average genotyping across
 all individuals) and low genotyping error (&lt;0.01% within-libraries,
 0.60% among-libraries) despite the relatively poor quality of recovered
 DNA. We observed slight decreases in expected heterozygosity, allelic
 diversity, and effective population size post-crash, but none were
 significant, suggesting genetic diversity was retained despite the severe
 demographic contraction. Genotypic data also revealed the genetic
 distinctiveness of a now extirpated population just outside of KNPR,
 revealing biodiversity loss at the northern edge of the species
 distribution. More broadly, we demonstrate GT-seq as a valuable tool for
 genome-wide data collection from archival samples to address basic
 questions in ecology and evolution, and inform applied research in
 wildlife conservation and fisheries management.
description: onco_223ind_271snp.vcf: genotypic data for 23 individuals at 271
 SNPs generated via GT-seq. metadata.xlsx: individual
 metadata including sample identifiers, location, year sampled, fork
 length, weight, age and sex (if known).
DOI: 10.5061/dryad.h18931zmv
title: Genome assembly and annotations of Yoshiicerus persimilis

description: Gene duplication is an important mechanism for organism evolution and
 adaptation. Whole-genome duplication (WGD) is considered as a major driver
 of species diversification. It has been reported that ancient WGD events
 occurred during the evolution of basal hexapod; the inferred pattern based
 on gene-tree and molecular-clock analyses remains challenging. Therefore,
 the lack of chromosome-scale genome has limited the characterization of
 WGD directly upon the synteny evidence. In order to get direct
 evidence from intra-chromosome synteny, we constructed the first
 chromosome-level genome of basal hexapod (Yoshiicerus persimilis,
 Collembola). We observed only large-scale gene duplications in chromosome
 1, but not within/among other five chromosomes. These duplications were
 involved in proliferation and growth.
description: The chromosome-level genome was assembled using PacBio long reads
 and Hi-C data. Protein-coding genes (PSGs) were predicted under three
 lines of evidence including ab initio, RNA-seq and protein homology, and
 all the above evidence was integrated by Maker genome annotation pipeline.
 The repetitive sequences of the genome was constructed using
 RepeatModeler, Repbase and RepeatMasker. Non-coding RNAs, including rRNAs,
 snRNAs and miRNAs were identified by aligning the genome of Yoshiicerus
 persimilis to the Rfam database. The tRNAs were predicted using
 tRNAscan-SE. Motifs and domains in the PCGs were retrieved by performing
 InterProScan. The software eggNOG-mapper was also used for functional
 category annotation of the predicted PCGs based on the eggNOG
 database.
description: The readme file contains an explanation of each of genome
 annotation files in the dataset. Information on how the results were
 obtained could be found in the associated manuscript referenced
 above.
DOI: 10.25338/b8xp7d
title: Rapid parallel morphological and mechanical diversification of South American Pike Cichlids (Crenicichla)

description: Explosive bouts of diversification are one of the most conspicuous
 features of the tree of life. When such bursts are repeated in similar
 environments it suggests some degree of predictability in the evolutionary
 process. We assess parallel adaptive radiation of South American pike
 cichlids (Crenicichla) using phylogenomics and phylogenetic comparative
 methods. We find that species flocks in the Uruguay and Iguazú River
 basins rapidly diversified into the same set of ecomorphs that reflect
 feeding ecology. Both adaptive radiations involve expansion of functional
 morphology, resulting in unique phenotypes in terms of jaw shape, size,
 and protrusion. Yet, form and function were decoupled such that most
 ecomorphs share similar mechanical properties or the jaws (i.e., jaw
 motions during feeding). Prey mobility explained six to nine-fold
 differences in the rate of morphological evolution, but had no effect on
 the rate of mechanical evolution. We find no evidence of gene flow between
 species flocks or with surrounding coastal lineages that may explain their
 rapid diversification. When compared to cichlids of the East African Great
 Lakes and other prominent adaptive radiations, pike cichlids share many
 themes, including rapid morphological expansion, specialization along the
 benthic-to-pelagic habitat and soft-to-hard prey axes, and the evolution
 of conspicuous functional innovations. Yet, decoupled evolution of form
 and function and the absence of hybridization as a catalyzing force are
 departures from patterns observed in other adaptive radiations.
DOI: 10.5061/dryad.1g1jwstxk
title: In-depth comparative toxicogenomics of glyphosate and Roundup herbicides: Histopathology, transcriptome and epigenome signatures, and DNA damage

description: Whether or not glyphosate activates cellular mechanisms involved in
 carcinogenesis remains controversial. We tested whether
 glyphosate and three glyphosate-based commercial herbicide
 formulations activate mechanisms known to be key characteristics
 of carcinogens. The mammalian stem cell-based
 genotoxicity ToxTracker assay showed that the
 representative EU formulation Roundup MON 52276 and the UK
 formulation Roundup MON 76473, but not glyphosate and the US
 Roundup formulation MON 76207, activated oxidative stress and
 unfolded protein responses. High-throughput molecular profiling of liver
 function was performed in female Sprague-Dawley rats exposed to
 glyphosate or MON 52276 (both at 0.5, 50, 175 mg/kg bw/day glyphosate
 equivalent concentration) for 90 days. Histopathology
 and serum biochemistry analysis showed that MON 52276 but not
 glyphosate treatment increased hepatic steatosis and necrosis. MON 52276
 and glyphosate altered the expression of genes in liver reflecting TP53
 activation by DNA damage and the regulation of circadian
 rhythms. The most affected genes in liver also had their
 expression similarly altered in kidneys. Small RNA profiling in
 liver showed miR-22 and miR-17 had their levels decreased by MON
 52276, while mir-30 levels were decreased, whilst miR-10 levels were
 increased by glyphosate. DNA methylation profiling of liver
 revealed 5,727 and 4,496 differentially methylated CpG sites between the
 control and glyphosate and MON 52276 exposed groups of animals
 respectively. Direct DNA damage measurement by
 apurinic/apyrimidinic lesion formation in liver was increased with
 glyphosate exposure. Altogether, our results show that Roundup herbicide
 formulations are causing more biological changes than glyphosate alone,
 activating mechanisms involved in cellular carcinogenesis.
DOI: 10.5061/dryad.5mkkwh76z
title: Large wild herbivores slow down the rapid decline of plant diversity in a tropical forest biodiversity hotspot

description: 1. The UN declaration of the Decade of Ecosystem Restoration 2021-2030
 emphasizes the need for effective measures to restore ecosystems and
 safeguard biodiversity. Large herbivores regulate many ecosystem processes
 and functions, yet their potential as a nature-based solution to buffer
 against long-term temporal declines in biodiversity associated to global
 change and restore diversity in secondary forests remains unknown.
 2. By means of an exclusion experiment, we tested experimentally
 the buffering effects of large wild herbivores to avert against long-term
 biodiversity collapse in old-growth and secondary tropical forests in the
 Atlantic Forest of Brazil where sapling abundance and species richness
 declined circa 20% over the course of 10 years. The experiment comprised
 50 large herbivore exclosure-open control plot pairs (25 at the old-growth
 forest and 25 at the secondary forest), where 2m2 were monitored in every
 plot during a 10-year period. 3. Large herbivores were able to
 decelerate diversity declines and compositional change in the species-rich
 old-growth forest, but only decelerated compositional change in the
 secondary forest. In contrast, declines in species richness and abundance
 were unaffected by large herbivores on either forest. 4. The
 buffering effects of large herbivores were strongly non-linear and
 contingent on the initial level of diversity at the patch scale: highly
 diverse communities suffered the strongest collapse in the absence of
 large herbivores. Thus, larger buffering effects of large herbivores on
 the old growth forest are the logical consequence of large herbivores
 buffering the many high diversity plant communities found in this forest.
 Conversely, as the secondary forest held fewer high diversity patches,
 buffering effects on the secondary forest were weak. 5. Synthesis
 and applications: Our study indicates that large herbivores have moderate
 yet critical effects on slowing down community change and diversity loss
 of highly diverse plant communities, thus suggesting that the conservation
 of (and potentially trophic rewilding with) large herbivores is a
 fundamental nature-based solution for averting the global collapse of the
 strongholds of biodiversity. Its buffering effects on biodiversity loss
 operate at very small spatial scales, are likely contingent on
 successional stage, and most effective in old-growth or high diversity
 secondary forests.
DOI: 10.5061/dryad.8931zcrrq
title: Alien insect dispersal mediated by the global movement of commodities

description: Globalization and economic growth are recognized as key drivers of
 biological invasions. Alien species have become a feature of almost every
 biological community worldwide, and rates of new introductions continue to
 rise as the movement of people and goods accelerates. Insects are among
 the most numerous and problematic alien organisms, and are mainly
 introduced unintentionally with imported cargo or arriving passengers.
 However, the processes occurring prior to insect introductions remain
 poorly understood. We used a unique dataset of 1,902,392 border
 interception records from inspections at air, land and maritime ports in
 Australia, New Zealand, Europe, Japan, the United States of America and
 Canada to identify key commodities associated with insect movement through
 trade and travel. A total of 8,939 species were intercepted, and commodity
 association data were available for 1,242 species recorded between 1960
 and 2019. We used rarefaction and extrapolation methods to estimate the
 total species richness and diversity associated with different commodity
 types. Plant and wood products were the main commodities associated with
 insect movement across cargo, passenger baggage and international mail.
 Furthermore, certain species were mainly associated with specific
 commodities within these, and other broad categories. More closely related
 species tended to share similar commodity associations, but this occurred
 largely at the genus level rather than within orders or families. These
 similarities within genera can potentially inform pathway management of
 new alien species. Combining interception records across regions provides
 a unique window into the unintentional movement of insects, and provides
 valuable information on establishment risks associated with different
 commodity types and pathways.
DOI: 10.5061/dryad.7pvmcvdtn
title: Foraging networks and social tolerance in a cooperatively breeding primate (Callithrix jacchus)

description: Within-group competition over food resources can be a major cost of social
 living. In the wild, foragers are confronted with social (e.g.
 hierarchical rank) and ecological (e.g. food availability and
 distribution) challenges that affect their foraging decisions and feeding
 success. Exhibiting prosocial behaviors, such as tolerance at feeding
 sites, can benefit group members by developing affiliative social
 relationships, enhancing access to resources and maximizing fitness. We
 examined social tolerance at feeding sites in Callithrix jacchus, a
 cooperatively breeding primate species. We investigated the set of social
 (rank, age, sex) and ecological (food availability) factors that influence
 the structure and dynamics of within-group foraging association networks.
 We designed and conducted an experimental field study of four wild groups
 of common marmosets in which we controlled food distribution (concentrated
 or scattered) and productivity (high, medium, or low food rewards). Then,
 we used social network analyses to assess the number and strength of
 foraging associations among group members, their effects on individual
 food consumption, and whether recent experiences with conspecifics during
 foraging affected subsequent associations. Overall, common marmoset
 foraging association networks were cohesive, as group members jointly
 occupied feeding sites. The number and strength of associations varied
 depending on the ecological context. Associations were stronger during
 conditions in which food was concentrated at a single site. Individuals
 obtained greater access to food resources when sharing a feeding site with
 conspecifics, but once a food item was obtained, the forager moved to a
 nearby tree and consumed it away from others. Additionally, the strength
 of previous foraging associations and subsequent levels of social
 tolerance at feeding sites were positively related, a relationship
 compatible with the ability of memorizing associations over time and
 recalling the information in future decision-making. In sum, marmosets
 adjusted their partner choices and the strength of foraging associations
 in response to food availability. They exhibited increased social
 tolerance at feeding sites during conditions in which opportunities for
 contest competition were expected to be greatest. These cooperative
 breeding primates appear to mutually benefit by maintaining cohesive and
 strong affiliative relationships, and by increasing opportunities for
 coordinated behavior and offspring survival.
DOI: 10.5061/dryad.rxwdbrv98
title: Negative impact of roadside mowing on arthropod fauna and its reduction with arthropod-friendly mowing technique

description: This dataset contains data from the paper: “Steidle, J. L.M., Kimmich, T.,
 Csader, M. Betz, O. 2021. Negative impact of roadside mowing on arthropod
 fauna and its reduction with “arthropod-friendly” mowing
 technique. Journal of Applied Entomology.” The study investigates
 the impact of a conventional mowing head ("MK1200") and a
 supposedly "insects-friendly" mowing head ("Eco
 1200") during roadside mowing on the arthropod fauna. Mowing with a
 conventional mowing head caused considerable losses in arthropods, ranging
 from 29% for Heteroptera over around 50% in Araneae, Cicadina,
 Hymenoptera, and Diptera, up to 73% for holometabolous larvae, and 87% for
 Lepidoptera. These losses were fully offset for Araneae, Cicadina,
 Heteroptera, Lepidoptera, and larvae of holometabolous insects when using
 the mowing head Eco 1200. For Hymenoptera and Diptera, the losses were
 reduced by 15 and 25%, respectively. For Saltatoria and Coleoptera, we did
 not find any significant differences between all treatments. The study
 shows that mowing of roadsides with conventional mowing technology has a
 highly detrimental effect on the grassland arthropod fauna. This effect
 can be offset or at least mitigated by the use of
 "arthropod-friendly" mowing technique.
description: Plots were either not mown, or mown with the a standard mowing head "MK1200", or the mowing head "Eco 1200" (both from the company MULAG, Germany). Arthropods were sampled in the plots using biocoenometers and determinded up to the level of orders or suborders.
DOI: 10.5061/dryad.3bk3j9kks
title: Data from: Identity signaling, identity reception and the evolution of social recognition in a Neotropical frog

description: Animals recognize familiar individuals to perform a variety of important
 social behaviors. Social recognition is often mediated by communication
 between signalers who produce signals that contain identity information
 and receivers who categorize these signals based on previous experience.
 We tested two hypotheses about adaptations in signalers and receivers that
 enable the evolution of social recognition using two species of closely
 related territorial poison frogs. Male golden rocket frogs (Anomaloglossus
 beebei) recognize the advertisement calls of conspecific territory
 neighbors and display a “dear enemy effect” by responding less
 aggressively to neighbors than strangers, while male Kai rocket frogs (A.
 kaiei) do not. Our results did not support the identity signaling
 hypothesis: both species produced advertisement calls that contain similar
 amounts of identity information. Our results did support the identity
 reception hypothesis: both species exhibited habituation of aggression to
 playbacks simulating the arrival of a new neighbor, but only golden rocket
 frogs showed renewed aggression when they subsequently heard calls from a
 different male. These results suggest that an ancestral mechanism of
 plasticity in aggression common among frogs has been modified through
 natural selection to be specific to calls of individual males in golden
 rocket frogs, enabling a social recognition system.
description: See paper for methods.
description: See ReadMe files and R code.
DOI: 10.5061/dryad.b2rbnzsgc
title: Shark captures near west-central Florida by Coastal Marine Education and Research Academy

description: Identifying critical habitat for highly mobile species such as
 sharks is difficult, but
 essential for effective management and
 conservation. In regions where baseline data are lacking,
 non-traditional data sources have the potential to increase
 observational capacity for species distribution and habitat
 studies. In this study, a research and
 education organization conducted a five
 year (2013-2018) survey of shark
 populations in the coastal waters
 of west-central Florida, an area where
 a diverse shark assemblage has been observed but no
 formal population analyses have been conducted. The objectives of
 this study were to use Boosted Regression
 Tree (BRT) modeling to quantify environmental
 factors impacting the distribution
 of the shark assemblage, create species
 distribution maps from the model outputs, and identify
 spatially explicit hot spots of high
 shark abundance. A total of 1,036 sharks were
 captured, encompassing eleven species. Abundance hot spots
 for four species and for immature
 sharks (collectively) were most often located
 in areas designated as “No Internal Combustion
 Engine” zones and seagrass bottom cover,
 suggesting these environments may be fostering
 more diverse and abundant populations. The BRT models were fitted for
 immature sharks and five species where
 n&gt;100: the nurse shark (Ginglymostoma
 cirratum), blacktip shark (Carcharhinus limbatus), blacknose
 shark (C. acronotus), Atlantic sharpnose shark (Rhizoprionodon
 terraenovae), and bonnethead (Sphyrna
 tiburo). Capture data were paired
 with environmental variables: depth (m), sea surface
 temperature (ºC), surface, middle, and bottom salinity
 (psu), dissolved oxygen (mg/l), and bottom type (seagrass, artificial
 reef, or sand). Depth, temperature, and bottom type were
 most frequently identified as predictors with the
 greatest marginal effect on shark distribution, underscoring the
 importance of nearshore seagrass and barrier island habitats
 to the shark assemblage in this
 region. This approach demonstrates the
 potential contribution of unconventional science to effective management and conservation of coastal sharks.
description: Blank or missing values are denoted as "null."
 "ReadMe.csv" document contains methods of collection and data
 header descriptions. Coordinates have been rounded to the nearest tenth to
 protect locations of vulnerable or endangered species.