cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z8w9ghxh1
title: Rapid acceleration offsets the costs of intermittent locomotion in lizards when turning

description: Intermittent locomotion is a common locomotor mode in small vertebrates.
 Pausing is thought to aid in locating a predator or prey, enhanced
 crypsis, lowering energy costs, and/or maneuvering around obstacles or
 towards a refuge. Many lizards flee predators by turning as they pass a
 potential refuge and subsequently pause, presumably to conceal themselves.
 Intermittent locomotion may be associated with turning by allowing an
 animal time to assess its surroundings and/or decreasing the likelihood of
 losing its footing before or after turning. In this study, we quantify
 locomotor performance and the use of intermittent locomotion in Florida
 Scrub Lizards (Sceloporus woodi) when navigating either a 45° or 90° turn.
 Lizards paused in 92% of all trials, and yet despite pausing, linear speed
 was not different prior to entering or when exiting the turn. This result
 suggests that turning comes at minimal cost to forward speed for lizards
 under these conditions. The angle of the turn had no effect on whether
 lizards paused, nor was there a relationship with pausing before or after
 the turn. Interestingly, the speed in the turn did not differ in trials
 with a pause before the turn vs. trials without a pause. We found that
 lizards increase peak acceleration following pauses to achieve similar
 speed, and hence explain both why, and how, intermittent locomotion is
 such a common strategy in predator escape.
description: Data were collected by recording lizards running on 45 and 90
 degree raceways while record above with high-speed video. Position data
 were digitized from lizards and a subset of trials retained to compare the
 frequency of pauses during trial and speed at various points during the
 trial. Position data were collected using DLTdv8 software, then analyzed
 in spreadsheets and using JMP analysis software. 
description: Use MS Excel or compatible spreadsheet software to open data
 file.  File
 "LizardSpeedandPause_WalkerMcBrayer.xlsx" contains for
 definitions of all variables in tab "Variable
 information". Empty cells indicate no data
 available.
DOI: 10.5061/dryad.573n5tbbt
title: Data for: The combined Hf and Nd isotope evolution of the depleted mantle requires Hadean continental formation

description: The onset and rates of continental growth are first-order indicators of
 early Earth dynamics, and whether substantial crust existed in the Hadean
 or much later has long been debated. Here we present a theoretical
 analysis of published Hf and Nd isotopic data representing the depleted
 mantle and demonstrate that continental growth must have started in the
 early Hadean. Whereas the traditional interpretation of depleted mantle
 signatures in crustal rocks assumes unrealistic instantaneous mantle
 mixing, our modeling incorporates the effect of a finite mixing time over
 which these signatures are recorded in rocks produced through mantle
 melting. This effect is shown to delay, by as much as 0.65 to 0.75 Gyr,
 the appearance of the earliest depleted mantle signatures in continental
 crust. Our results suggest that published observations of Hf, 143Nd, and
 142Nd require Hadean growth of continental crust, with a minimum of 50% of
 today’s continental volume already existing by the end of Hadean.
DOI: 10.5061/dryad.w3r2280vm
title: Revealing the drivers of parasite community assembly: using avian haemosporidians to model global dynamics of parasite species turnover

description: Why do some regions share more or fewer species than others? Community
 assembly relies on the ability of individuals to disperse, colonize, and
 thrive in new regions. Therefore, many distinct factors, such as
 geographic distance and environmental features, can determine the odds of
 a species colonizing a new environment. For parasites, host community
 composition (i.e., resources) also plays a key role in their ability to
 colonize a new environment as they rely on their hosts to complete their
 life cycle. Thus, variation in host community composition and
 environmental conditions should determine parasite turnover among regions.
 Here, we explored the global drivers of parasite turnover using avian
 malaria and malaria-like (haemosporidian) parasites. We compiled global
 databases on avian haemosporidian lineages distributions, environmental
 conditions, avian species distributions and functional traits and ran
 generalized dissimilarity models to uncover the main drivers of parasite
 turnover. We demonstrated that haemosporidian parasite turnover is mainly
 driven by geographic distance followed by host functional traits,
 environmental conditions, and host distributions. The main host functional
 traits associated with high parasite turnover were the predominance of
 resident (i.e., non-migratory) species and strong territoriality while the
 most important climatic drivers of haemosporidian turnover were mean
 temperature and temperature seasonality. Overall, we establish the
 importance of geographic distance as a key predictor of ecological
 dissimilarity and show that host resources influence parasite turnover
 more strongly than environmental conditions. We also evidenced that
 parasite turnover is most pronounced among tropical and less
 interconnected regions (i.e., regions with mostly territorial and
 non-migratory hosts). Our findings provide a robust foundation for the
 prediction of avian pathogen spread and the emergence of infectious
 diseases.
DOI: 10.25349/d93c89
title: Coccolithophores and diatoms resilient to ocean alkalinity enhancement: a glimpse of hope?

description: It is increasingly apparent that adequately mitigating anthropogenic
 climate interference will require ocean carbon dioxide removal (CDR)
 strategies. Ocean alkalinity enhancement (OAE) is an abiotic ocean CDR
 approach that aims to increase the ocean’s CO2 uptake capacity through the
 dispersal of pulverized mineral or dissolved alkali into the surface
 ocean.  However, OAE’s effect on marine biota is largely
 unexplored. Here we investigate the impacts of moderate (~700 umol kg-1)
 and high (~2700 umol kg-1) limestone-inspired alkalinity additions on two
 biogeochemically and ecologically important phytoplankton functional group
 representatives: Emiliania huxleyi (calcium carbonate producer) and
 Chaetoceros sp. (silica producer). The growth rate and elemental ratios of
 both taxa showed a neutral response to limestone-inspired alkalinization.
 While our results are encouraging, we also observed abiotic mineral
 precipitation, which removed nutrients and alkalinity from solution. Our
 findings offer the first evaluation of biogeochemical and physiological
 responses to OAE and provide evidence supporting the need for continued
 research into how OAE strategies impact marine ecosystems.
description: Microsoft Excel; R.
DOI: 10.5061/dryad.2fqz612t1
title: Data from: On the role of water table depth and urbanization on groundwater drought susceptibility

description: Propagation of meteorological drought to groundwater drought is mediated
 by a range of natural and human-induced drivers. Using long-term
 (1978–2020) in-situ groundwater level depth (GWD) time series from 2,928
 pairs of monitoring wells, this study assesses the role of two such
 drivers, viz., GWD and urbanization, on groundwater drought
 characteristics. Results show that locations with deeper GWD often
 experience less frequent but more intense groundwater droughts with longer
 average duration. In contrast, urbanization is generally associated with a
 reduction in groundwater drought duration and an increase in its
 frequency. Relative to the influence of GWD, urbanization’s imprint on
 groundwater drought characteristics is muted. These findings can aid in
 improved assessment of groundwater drought risks, and for devising more
 effective drought adaptation measures.
description: Please see the README document
 ("README.md") and the accompanying published
 article: Park, J., Malakar, P., Kumar, M.
 (2023). On the role of water table depth and urbanization on groundwater
 drought susceptibility. Geophysical Research Letters. Under
 review.
description: Please see the README document
 ("README.md") and the accompanying published
 article: Park, J., Malakar, P., Kumar, M.
 (2023). On the role of water table depth and urbanization on groundwater
 drought susceptibility. Geophysical Research Letters. Under
 review.
DOI: 10.15468/dpzg84
title: Genome Taxonomy Database r226.0

description: The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny, primarily funded by the Australian Research Council via a Laureate Fellowship (FL150100038) and Discovery Project (DP220100900), with the welcome assistance of strategic funding from The University of Queensland.

 The genomes used to construct the phylogeny are obtained from RefSeq and GenBank, and GTDB releases are indexed to RefSeq releases, starting with release 76. Importantly and increasingly, this dataset includes draft genomes of uncultured microorganisms obtained from metagenomes and single cells, ensuring improved genomic representation of the microbial world. All genomes are independently quality controlled using CheckM before inclusion in GTDB, see statistics here .
 
 The GTDB taxonomy is based on genome trees inferred using FastTree from an aligned concatenated set of 120 single copy marker proteins for Bacteria, and with IQ-TREE from a concatenated set of 53 (starting with R07-RS207) and 122 (prior to R07-RS207) marker proteins for Archaea (download page here ). Additional marker sets are also used to cross-validate tree topologies including concatenated ribosomal proteins and ribosomal RNA genes.
 
 NCBI taxonomy was initially used to decorate the genome tree via tax2tree and subsequently used as a reference source of new taxonomic opinions including new names. The 16S rRNA-based Greengenes and SILVA taxonomies were intially used to supplement the taxonomy particularly in regions of the tree with no cultured representatives, however genome assembly identifiers are now used to create placeholder names for uncultured taxa.
 
 LPSN is used as the primary nomenclatural reference for establishing naming priorities and nomenclature types. All taxonomic ranks except species are normalised using PhyloRank and the taxonomy manually curated to remove polyphyletic groups. Polyphyly and rank evenness can be visualised in PhyloRank plots . Species were originally delineated based on phylogeny and rank normalization but this was replaced with an ANI-based method (starting with R04-RS89) to enable scalable and automated assignment of genomes to species clusters. 

The GTDB taxonomy can be queried and downloaded through a number of tools at https://gtdb.ecogenomic.org/
DOI: 10.5061/dryad.jsxksn0f5
title: Data for: Higher water loss on Earth-like exoplanets in eccentric orbits

description: The climate of a terrestrial exoplanet is controlled by the type of host
 star, the orbital configuration and the characteristics of the atmosphere
 and the surface. Many rocky exoplanets have higher eccentricities than
 those in the Solar System, and about 18% of planets with masses &lt;
 10 M⊕ have ? &gt; 0.1. Underexplored are the implications of such high
 eccentricities on the atmosphere, climate, and potential habitability on
 such planets. We use WACCM6, a state-of-the-art fully-coupled Earth-system
 model, to simulate the climates of two Earth-like planets; one in a
 circular orbit (? = 0), and one in an eccentric orbit (? = 0.4). We
 quantify the effects of eccentricity on the atmospheric water abundance
 and loss given the importance of liquid water for habitability. The
 asymmetric temperature response in the eccentric orbit results in a water
 vapour mixing ratio in the stratosphere (&gt; 20 ppmv) that is
 approximately five times greater than that for circular orbit (∼ 4 ppmv).
 This leads to a ∼ 3 time increase in the atmospheric hydrogen loss rate
 and a corresponding ∼ 3 times decrease in the ocean loss timescale. Thus,
 highly-eccentric Earth-like exoplanets can still retain their oceans over
 the lifetime of the system. Using the Planetary Spectrum Generator, we
 simulate the idealised transmission spectra for both cases. We find that
 the water absorption features are stronger at all wavelengths for the ? =
 0.4 spectrum than for the circular case. Hence, highly-eccentric
 Earth-like exoplanets may be prime targets for future transmission
 spectroscopy observations to confirm, or otherwise, the presence of
 atmospheric water vapour.
description: The netCDF (.nc files) data were produced from simulations using
 the WACCM6 (CESM2.1.3) model. See https://www2.acom.ucar.edu/gcm/waccm and https://doi.org/10.1029/2019JD030943 for more information. These simulations were performed on the ARC4 HPC at the University of Leeds. The <strong><em>output variables</em></strong> from the simulations are in terms of monthly mean files (h0.files), and they are grouped in two folders for the circular and the eccentric cases. The 1-day instantaneous 'snapshots' (cam.h1 files) are used to generate synetic transit spectra using the Planetary Spectrum Generator (PSG; https://psg.gsfc.nasa.gov/) The .txt files are produced by converting the WACCM6 output (.nc files) to a binary file format (.gcm files) which can be processed through the PSG web interface. All<em> <strong>PSG related files</strong></em> are grouped into two folders for the circular and eccentric cases. To produce the figures in the manuscript, Python programming language was used.
description: Python programming language (e.g. xarray) was used to open and
 manipulate the NetCDF files.
DOI: 10.5061/dryad.cz8w9gj75
title: Functional profiling and evolutionary analysis of a marine microalgal virus pangenome

description: Phycodnaviridae are large double-stranded DNA viruses, which facilitate
 studies of host–virus interactions and co-evolution due to their
 prominence in algal infection and their role in the life cycle of algal
 blooms. However, the genomic interpretation of these viruses is hampered
 by a lack of functional information, stemming from the surprising number
 of hypothetical genes of unknown function. It is also unclear how many of
 these genes are widely shared within the clade. Using one of the most
 extensively characterized genera, Coccolithovirus, as a case study, we
 combined pangenome analysis, multiple functional annotation tools,
 AlphaFold structural modeling, and literature analysis to compare the core
 and accessory pangenome and assess support for novel functional
 predictions. We determined that the Coccolithovirus pangenome shares 30%
 of its genes with all 14 strains, making up the core. Notably, 34% of its
 genes were found in at most three strains. Core genes were enriched in
 early expression based on a transcriptomic dataset of Coccolithovirus
 EhV-201 algal infection, were more likely to be similar to host proteins
 than the non-core set, and were more likely to be involved in vital
 functions such as replication, recombination, and repair. In addition, we
 generated and collated annotations for the EhV representative EhV-86 from
 12 different annotation sources, building up information for 142
 previously hypothetical and putative membrane proteins. AlphaFold was
 further able to predict structures for 204 EhV-86 proteins with a
 modelling accuracy of good–high. These functional clues, combined with
 generated AlphaFold structures, provide a foundational framework for the
 future characterization of this model genus (and other giant viruses) and
 a further look into the evolution of the Coccolithovirus proteome.
description: AlphaFold v2.1.1 run on each EhV-86 protein (several were too
 large and not included here) using the full set of databases as outlined
 by the tool.
description: Any text-editor and protein structure visualization software
 (e.g. PyMOL).
DOI: 10.15468/dl.kgv57z
title: Occurrence Download

description: A dataset containing 1877 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Hardenbergia violacea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1877 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003462-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.b5mkkwhhc
title: Data from: Earthworm increase litter decomposition irrespective of deposited compounds

description: Earthworms modulate carbon and nitrogen cycling in terrestrial ecosystems,
 but their effect may be compromised by the deposition of pollutants from
 industrial emissions. However, studies investigating how deposited
 compounds affect the role of earthworms in carbon cycling such as litter
 decomposition are lacking, although the interaction of earthworms and
 deposited compounds are important for understanding the impact of
 pollutants on ecosystems and the potential of earthworms in
 bioremediation. We performed a 365-day in situ litterbag decomposition
 experiment in a deciduous (Quercus variabilis) and coniferous (Pinus
 massoniana) forest in southeast China. We manipulated nitrogen (N), sodium
 (Na) and polycyclic aromatic hydrocarbons (PAHs) as model compounds during
 litter decomposition with and without earthworms (Eisenia fetida).
DOI: 10.5061/dryad.z8w9ghxh2
title: Draft genome of a dung beetle, Phelotrupes auratus

description: Knowledge of population divergence history is key to understanding
 organism diversification mechanisms. The geotrupid dung beetle,
 Phelotrupes auratus, which inhabits montane forests and exhibits three
 color forms (red, green, and indigo), diverged into five local populations
 (west/red, south/green, south/indigo, south/red, and east/red) in the
 Kinki District of Honshu, Japan, based on the combined interpretation of
 genetic cluster and color-form data. Here, we estimated the demographic
 histories of these local populations using the newly assembled draft
 genome sequence of P. auratus and whole-genome resequencing data obtained
 from each local population. Using coalescent simulation analysis, we
 estimated P. auratus population divergences at ca. 3,800, 2,100, 600, and
 200 years ago, with no substantial gene flow between diverged populations,
 implying the existence of persistent barriers to gene flow. Notably, the
 last two divergence events led to three local populations with different
 color forms. The initial divergence may have been affected by climatic
 cooling around that time, and the last three divergence events may have
 been associated with the increasing impact of human activities. Both
 climatic cooling and increasing human activity may have caused habitat
 fragmentation and a reduction in the numbers of large mammals supplying
 food (dung) for P. auratus, thereby promoting the decline, segregation,
 and divergence of local populations. Our research demonstrates that
 geographic population divergence in an insect with conspicuous differences
 in traits such as body color may have occurred rapidly under the influence
 of human activity.
description: We constructed this draft genome using ONT PromethION long reads
 and Illumina HiSeq X short reads from an adult individual of
 <em>Phelotrupes auratus</em> by <em>de novo</em>
 assembly using MaSuRCA 3.4.2 (Zimin et al., 2013). The constructed draft
 genome was polished with racon 1.4.13 (Vaser et al., 2017) and Pilon 1.23
 (Walker et al., 2014), then curated using Purge Haplotigs 1.0.4 (Roach,
 Schmidt, & Borneman, 2018).
DOI: 10.5061/dryad.w0vt4b8w8
title: Comparative genome anatomy of the male and female silver arowanas provides an improved understanding of sex determination mechanisms in teleosts

description: Silver arowana, Osteoglossum bicirrhosum, is sexually monomorphic, and its
 sex determination mechanism is poorly understood, which has been a major
 hurdle in its captive breeding. To this end, we assembled two high-quality
 chromosome-level genomes for each sex of silver arowana, with chromosome
 N50 of 10.6 Mb and 10.4 Mb in female and male individuals, respectively.
 Combing re-sequencing data of 109 individuals, we identified two
 sex-specific SNPs and confirmed a ZW model of sex-determination in this
 species. Both sex-specific SNPs are located in about 26Kb upstream of
 foxl2 gene. Since foxl2 has been confirmed to be differentially expressed
 in the gonads of silver arowana, it probably plays an important role in
 sex determination via the cross-regulation with auxiliary genes
 significantly correlated to it, such as dmrt1, sox8a and cyp11a1, etc. The
 sex chromosomes are homomorphic with a potentially recent origin, as
 linkage disequilibrium analysis showed minor recombination suppression.
 Overall, we developed accurate molecular markers for sex identification of
 silver arowana in each developmental stage, subsequently improving the
 reproductive efficiency and further promoting the industrial development.
DOI: 10.5061/dryad.dncjsxm3x
title: Dynamics and recovery of forest understory biodiversity over 17 years following varying levels of retention harvesting

description: 1. Retention harvesting is advocated as an alternative to intensive timber
 harvesting, such as clear-cutting, to better maintain or facilitate
 recovery of biodiversity and other ecological values in managed forests.
 However, it is not clear how long the benefits of retention harvests
 persist. 2. We investigated responses of understory vascular plant cover,
 richness, diversity (inverse Simpson index), and composition to a gradient
 in dispersed retention (2% [clear-cut], 10%, 20%, 50% and 75% retention;
 unharvested reference [100% retention]) at 3, 6, 11, and 17 years after
 harvest, in four boreal mixed wood forest types (deciduous
 (broadleaf)-dominated, deciduous-dominated with conifer understory, mixed,
 and conifer-dominated) in western Canada. 3. Understory cover and richness
 tended to increase in the short-term (3 years), peaked at 6–11 years with
 differences following the gradient of harvesting intensity, then plateaued
 or declined in the second decade (17 years), by which time there were
 minimal or no differences among harvesting levels, including the
 reference. Responses for diversity were minimal. In contrast, composition
 varied along the gradient of harvesting intensity and showed little
 recovery towards the unharvested condition over the 17-year period.
 Generally, for plant community composition, clear-cut and lower retention
 treatments (10%, 20%) were similar to one another but differed from the
 higher retention and unharvested reference treatments. 4. Synthesis and
 applications. Retention harvests can moderate the negative impacts of
 harvesting and facilitate the recovery of biodiversity. Our results
 suggest that for the cover, richness and diversity of understory vascular
 plants, this moderating influence is weak and short-lived. However, higher
 levels of retention can temper changes in understory composition relative
 to the unharvested forest, but full recovery is likely to be slow and will
 be complicated by post-harvest regeneration dynamics.
description: # Plot-level data on understory vascular plant abundance following varying
 levels of retention harvesting Data were acquired through long-term field
 observations as part of the Ecosystem Management Emulating Natural
 Disturbance (EMEND) project
 ([http://emend.ualberta.ca](http://emend.ualberta.ca)). ## Description of
 the Data and file structure Data are provided in the sheets named
 Compartment-CoverType, Compartment-Treatments and Understory_veg_data, and
 column headings are defined in the Description sheet of the excel
 workbook. Bartels_and_Macdonald 2023-for Dryad Depository.xlsx. Updates to
 species names (minor typos and duplicates) were made in May 2024.