cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rv15dv4ck
title: Data for: Body size and substrate use affect ventral, but not dorsal, brightness evolution in lizards

description: Substrate properties can affect the thermal balance of organisms, and the
 colored integument, alongside other factors, may influence heat transfer
 via differential absorption and reflection. Dark coloration may lead to
 higher heat absorption and could be advantageous when substrates are cool
 (and vice versa for bright coloration), but these effects are rarely
 investigated. Here, we examined the effect of substrate reflectance,
 specific heat capacity (cp), and body size on the dorso-ventral brightness
 using 276 samples from 12 species of cordylid lizards distributed across
 26 sites in South Africa. We predicted, and found, that bright ventral
 colors occur more frequently in low cp (i.e. drier, with little
 energy needed for temperature change) substrates, especially in larger
 body-sized individuals, possibly to better modulate heat transfer with the
 surrounding environment. By contrast, dorsal brightness was not associated
 with body size nor any substrate thermal property, suggesting selection
 pressures other than thermoregulation. Ancestral estimation and
 evolutionary rate analyses suggest that ventral brightness rapidly
 differentiated within the Cordylinae starting 25 Mya, coinciding with an
 aridification period, further hinting at a thermoregulatory role for
 ventral colors. Our study indicates that substrate properties can have a
 direct role in shaping the evolution of ventral brightness in ectotherms.
DOI: 10.5061/dryad.rn8pk0ph1
title: Long-term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest

description: It is widely accepted that phosphorus (P) limits microbial metabolic
 processes and thus soil organic carbon (SOC) decomposition in tropical
 forests. Global change factors like elevated atmospheric nitrogen (N)
 deposition can enhance P limitation, raising concerns about the fate of
 SOC. However, how elevated N deposition affects the soil priming effect
 (PE) (i.e., fresh C inputs induced changes in SOC decomposition) in
 tropical forests remains unclear. We incubated soils exposed to
 nine years of experimental N deposition in a subtropical evergreen
 broadleaved forest with two types of 13C-labeled substrates of
 contrasting bioavailability (glucose and cellulose) with and
 without P amendments. We found that N deposition decreased soil total P
 and microbial biomass P, suggesting enhanced P limitation. In P unamended
 soils, N deposition significantly inhibited the PE. In contrast, adding P
 significantly increased the PE under N deposition and by a larger extent
 for the PE of cellulose (PEcellu) than the PE of glucose (PEglu). Relative
 to adding glucose or cellulose solely, adding P with glucose alleviated
 the suppression of soil microbial biomass and C-acquiring enzymes induced
 by N deposition, whereas adding P with cellulose attenuated the
 stimulation of acid phosphatase induced by N deposition. Across
 treatments, the PEglu increased as C-acquiring enzyme activity increased,
 whereas the PEcellu increased as acid phosphatase activity decreased. This
 suggests that P limitation, enhanced by N deposition, inhibits the soil PE
 through varying mechanisms depending on substrate bioavailability; that
 is, P limitation regulates the PEglu by affecting soil microbial growth
 and investment in C acquisition, whereas regulates the PEcellu by
 affecting microbial investment in P acquisition. These findings provide
 new insights for tropical forests impacted by N loading, suggesting that
 expected changes in C quality and P limitation can affect the long-term
 regulation of the soil PE.
description: This dataset was collected by sampling soils
 exposed to 9 years of manipulative N inputs in situ in a subtropical
 forest and then incubating them in a 30-day incubation experiment. The CO2
 flux and PE were measured by NaOH trapping. Soil variables were measured
 at the end of incubation.
description: Microsoft Office
DOI: 10.5061/dryad.4xgxd25fc
title: Data and codes from: Taxon-specific responses to landscape-scale and long-term implementation of environmentally friendly rice farming

description: Rice feeds about half of the world's population. The intensification
 of rice farming has threatened biodiversity and ecosystem services, such
 as pest control. A growing body of evidence suggests that environmentally
 friendly rice farming (EFF) can be effective in biodiversity conservation.
 However, its dependence on spatial and temporal scales of EFF
 implementation and surrounding seminatural habitats has remained largely
 unknown. We evaluated the effects of three types of EFF (organic farming,
 winter flooding and Integrated Pest Management [IPM]) against conventional
 farming on plants, spiders, and waterbirds in Japan. Through systematic
 surveys of 254 rice fields across rice production areas, we monitored EFF
 implementation at field and landscape scales, considering the time since
 transition to EFF and the surrounding seminatural areas. EFF
 implementation at the field scale, such as organic farming, was found to
 have positive effects on plant richness and spider abundance, whereas the
 percent area of EFF fields within a 200-m radius positively affected
 Ardeidae abundance. However, as the percent area of surrounding
 semi-natural habitats increased, the difference in the plant richness
 between organic and other fields decreased. Prolonged implementation
 periods of IPM or winter flooding, together with a reduction of more than
 50% in synthetic fertilisers and pesticides from conventional agriculture,
 led to an increase in the spider abundance. Conversely, no clear positive
 effect of longer implementation periods of organic farming resulted in
 similar spider abundance in the three EFF types after 20 years. Synthesis
 and applications. This suggests that the benefits of environmentally
 friendly rice farming depend on their spatial and temporal scales and the
 surrounding seminatural areas. We propose that such a context dependency
 should be considered in future policy. Our findings also provide a
 starting point for future research to test the mixed biodiversity benefits
 of EFF across cropland types and around the world.
description: These files contain processed data and R-code to examine the
 effects of environmentally-friendly rice farming and species richness or
 abundance of three taxonomic groups (plants, spiders and birds) in Japan,
 using generalised linear mixed models. The raw data were collected through
 field surveys and interviews with farmers. To protect the personal
 information of farmers, longitude and latitude are not provided in this
 dataset. The included R code generates statistics and working plots.
 Details on data processing and analysis can be found in the original
 publication and accompanying Electronic Supplementary Materials.
description: The R software is required to open the files provided.
DOI: 10.5061/dryad.3r2280gmv
title: Data for: Wall fracturing versus mechanical instability as competing intrusion mechanisms of dikes: Insights from laboratory experiments

description: Igneous dike intrusion is a primary crust-forming process. Understanding
 its governing mechanism is very crucial for studies related to the
 lithosphere. We performed liquid injection experiments in the laboratory
 with two new crust analog model materials, i) ultrasound transmission gel
 (USTG) and gel wax. To conduct a properly scaled model experiment, we test
 their rheology using an Anton Paar M302e rheometer. The measured
 rheological data were presented in this present data repository. We
 identified three mechanisms from our laboratory studies: a) fracturing, b)
 interfacial instability, and c) hybrid, i.e., a combination of both. These
 three mechanisms give rise to distinct 3D geometries. To quantitatively
 analyze their geometric shapes, we performed fractal, aspect ratio, and
 skewness-kurtosis analysis. The procedure and the data collected during
 the analysis were also presented in the current data repository. 
description: For the field map, data was collected in the form of
 handwritten notes and plotted on white plain paper. Then traced using
 CorelDraw Software.  We use a high-speed camera and
 volume calculator for the volumetric flow rate calculation.
 For fractal dimension and Skewness-Kurtosis data acquisition and
 calculation, MATLAB and OriginPro were used. Rheology
 measurements are done via Anton Paar Rheometer (M302e).
description: Microsoft Word, Open source alternative: WPS Office
 Microsoft Excel, Open source alternative: WPS Office
 MATLAB Script. It could be opened in any text reader.
DOI: 10.5061/dryad.0gb5mkm61
title: Social media occurrences of the Banded Demoiselle in Great Britain

description: Social media offers an alternative, freely available and understudied
 source of biological information, useful to determine species
 distributions and with implications for conservation. To investigate the
 potential utility of this information source, UK observations of the
 Banded Demoiselle – a charismatic and easily identifiable species of
 damselfly – were collated from Flickr, Facebook, and Twitter content
 posted from 2010 onwards. Although this content was not necessarily
 intended as a biological record, when an identifiable photograph or video
 is shared along with associated date and location information, this
 provides all the data required for a species observation. This dataset
 provides key information on the Banded Demoiselle’s UK distribution that
 can complement traditional sources of biological recording and
 demonstrates the availability and applicability of social media as a
 source of ecological data.
description: Records were collected from social media platforms (Facebook,
 Twitter, and Flickr) using the search terms “Banded Demoiselle” as well as
 “<em>Calopteryx</em> <em>splendens</em>”. For
 Twitter and Facebook, this involved a manual search (completed between
 13/01/2022 and 04/04/2022), with biological records consisting of an
 identifiable photograph or video. These records included either a tagged
 location or a mention of location within the content of the post, as well
 as a date for the observation if provided (otherwise the date the content
 was shared). Records from Twitter and Facebook were geo-referenced by
 determining all the 1-km British National Grid squares covering the
 spatial extent of the location explicitly provided by the user. For each
 social media occurrence, spatial precision (estimated to the nearest
 km<sup>2</sup>) was recorded in the final dataset, identified
 as the numbr of 1-km grid squares that the location could be narrowed down
 to. For Flickr, records were collated with the Flickr application
 programming interface (API) using the
 <em>Flickr.photos.search</em>. These results were then
 manually verified to remove any misidentified observations. 
description: Microsoft Excel Spreadsheet.
DOI: 10.5061/dryad.sxksn037q
title: Data for: Variation in eye lenses of two new Late Devonian phacopid trilobites from western Junggar, NW China

description: The Suborder Phacopina, characterized by schizochroal
 eyes, is among the most common groups of trilobites in
 Devonian strata. The marine sediments of the Famennian in western Junggar,
 Xinjiang, contain abundant
 low-disparity phacopids, which have previously
 been designated to Omegops accipitrinus mobilis, Phacops
 circumspectans tuberculosus, and Omegops cornelius, based on
 small numbers of poorly preserved specimens. In this study, these
 phacopids were identified as two new species of Omegops, O.
 honggulelengensis sp. nov. and O. xiangi sp.
 nov., based on nearly 200 well-preserved specimens. The intraspecific
 variations of eye-lenses of these
 specimens were quantitatively analyzed. Based
 on differences in the total number, number of
 dorso-ventral files, and arrangement of the eye lenses, the
 absence of lenses in the middle part of the visual surface, and
 asymmetry of the number and/or arrangement of lenses in the
 two eyes, it was concluded that the reasons for
 intraspecific variation in eye lenses of Late
 Devonian Omegops from western Junggar were
 different from previously described factors, but were likely
 genetic or embryological malfunctions, or
 abnormalities caused by pathological
 conditions. Diversity of lenses in the schizochroal
 eyes shows that the number and arrangement of eye lenses
 were not stable in Phacopina. Therefore, many specimens are
 needed for quantitative study to determine the
 true characteristics of the number or arrangement of
 eye lenses when these features are used in the
 systematic taxonomy of Phacopina.
DOI: 10.5061/dryad.cz8w9gj7h
title: Comparative genomic analysis of chemosensory-related gene families in gastropods

description: Chemoreception is critical for the survival and reproduction of animals.
 Except for a reduced group of insects and spiders, the molecular identity
 of chemosensory proteins is poorly understood in invertebrates. Gastropoda
 is the extant mollusk class with the greatest species richness, including
 marine, freshwater, and terrestrial lineages, and likely, highly diverse
 chemoreception systems. Here, we performed a comprehensive comparative
 genome analysis taking advantage of the chromosome-level information of
 two Gastropoda species, one of which belongs to a lineage that underwent a
 whole genome duplication event. We identified thousands of previously
 uncharacterized chemosensory-related genes, the majority of them encoding
 G protein-coupled receptors (GPCR), mostly organized into clusters
 distributed across all chromosomes. We also detected gene families
 encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic
 receptors (IR), sensory neuron membrane proteins (SNMP), Niemann–Pick type
 C2 (NPC2) proteins, and lipocalins, although much smaller in size. Our
 phylogenetic analysis of the GPCR gene family across protostomes revealed:
 (i) large gene family expansions in Gastropoda; (ii) clades including
 members from all protostomes; and (iii) species-specific clades with a
 huge number of receptors. For the first time, we provide new and valuable
 knowledge into the evolution of the chemosensory gene families in
 invertebrates other than arthropods.
description: Please see the README document. The starting datasets were
 represented by files with the nucleotide sequence corresponding to the
 genome and proteome of three gastropod species, with their respective
 annotation files. These data are available in the server of the National
 Center for Biotechnology Information (NCBI); it was not data generated in
 our work, as we indicated in materials and methods. Then we used the
 BITACORA v.1.2.1 software to identify genes from chemosensory families,
 the output of the analysis yielded files with protein sequences identified
 by this tool. Alignments were made on these sequences with the Mafft
 v.7.453 software and phylogenetic trees were built with IQTree v.2.1.2. In
 addition, we run homemade scripts for the identification of gene clusters
 by measuring the physical distance among genes. Finally, the genetic
 distances among genes were estimated with the MEGA-CC v.11.0.11
 program.
description: Please see the README document. The sequences, alignments,
 distance matrices, and phylogenetic trees can be viewed in any text
 editor.
DOI: 10.5281/zenodo.18402815
title: Shear-Wave Splitting in Southern China: Evidence for Mantle Flow Dominated by the Hainan Plume

description: This file contains the SAC waveform data of the SKS phase for the HAVESArray, covering 10 seconds before and after the phase arrival, and is for scientific research only.
DOI: 10.5281/zenodo.18402816
title: Shear-Wave Splitting in Southern China: Evidence for Mantle Flow Dominated by the Hainan Plume

description: This file contains the SAC waveform data of the SKS phase for the HAVESArray, covering 10 seconds before and after the phase arrival, and is for scientific research only.
DOI: 10.5061/dryad.wwpzgmspz
title: A rapidly evolving cricket produces percussive vibrations: how, who, when, and why

description: Sexual signals are often transmitted through multiple modalities (e.g.,
 visual and chemical), and under selection from both intended and
 unintended receivers. A nuanced understanding of sexual signal evolution
 is important since they play a critical role in diversification. We
 recently documented percussive substrate-borne vibrations in the Pacific
 field cricket (Teleogryllus oceanicus), a species that uses airborne
 acoustic and chemical signals to attract and secure mates. The airborne
 signals of Hawaiian T. oceanicus are currently undergoing rapid evolution;
 at least five novel male morphs have arisen in the past 20 years. Nothing
 is yet known about the newly discovered percussive substrate-borne
 vibrations, so we ask ‘how’ they are produced, ‘who’ produces them (e.g.,
 population, morph), ‘when’ they produce them (e.g., whether they are
 plastic), and ‘why’ (e.g., do they play a role in mating). We show that
 the vibrations are produced exclusively by males and during courtship via
 foreleg drumming. One novel morph, purring, produces quieter airborne
 songs and is more likely to drum than the ancestral morph. However,
 drumming behavior is also contextually plastic for some males; when we
 removed the ability of males to produce airborne song, ancestral males
 became more likely to drum, whereas two novel morphs were equally likely
 to drum regardless of their ability to produce song. Opposite our
 prediction, females were less likely to mate with males who drummed. We
 discuss why that might be and describe what we can learn about complex
 signal evolution from this newly discovered behavior.
description: Between June 2018 and November
 2021, we collected ~30 adult male and ~30 adult
 female <em>Teleogryllus oceanicus</em> from each of seven
 populations (Kapa’a and Wailua on Kaua’i, La’ie and Manoa on O’ahu,
 Kalaupapa on Moloka’i, Hilo on Hawai’i, and Mo’orea in French Polynesia).
 We used airborne audio recordings to identify males as one of three
 morphs: ancestral, rattling, purring. At field stations,
 we conducted one-on-one
 courtship experiments where males could produce airborne sound and when
 they could not (silenced). We recorded whether the male drummed, producing
 substrate-borne vibrations, as well as female behaviors (spreadsheet 1).
 The second spreadsheet uses a subset of those male where we simultaneously
 recorded airborne and substrate-borne audio to calculate drumming rate
 (seconds) per airborne courtship song.
DOI: 10.5061/dryad.2z34tmprb
title: Perfluorooctanoic acid induces transcriptomic alterations in 2nd trimester human cytotrophoblasts

description: Poly- and perfluroroalkylated substances (PFAS) are a major class of
 surfactants used in industry applications and consumer products. Despite
 efforts to reduce the usage of PFAS due to their environmental
 persistence, compounds such as perfluorooctanoic acid (PFOA) are widely
 detected in human blood and tissue. While growing evidence supports that
 prenatal exposures to PFOA and other PFAS are linked to adverse pregnancy
 outcomes, the target organs and pathways remain unclear. Recent
 investigations in mouse and human cell lines suggest that PFAS may impact
 the placenta and impair trophoblast function. In this study, we
 investigated the effects of PFOA on cytotoxicity and the transcriptome in
 cultured 2nd-trimester human CTBs. We show that PFOA significantly reduces
 viability and induces cell death at 24h, in a concentration-dependent
 manner. At subcytotoxic concentrations, PFOA impacted expression of
 hundreds of genes, including several molecules (CRH, IFIT1, and TNFSF10)
 linked with lipid metabolism and innate immune response pathways.
 Furthermore, in silico analyses suggested that regulatory factors such as
 peroxisome proliferator-activated receptor (PPAR)-mediated pathways may be
 especially important in response to PFOA. In summary, this study provides
 evidence that PFOA alters primary human CTB viability and gene pathways
 that could contribute to placental dysfunction and disease.
DOI: 10.5061/dryad.k98sf7mbn
title: Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy

description: Quantifying neuron morphology and distribution at the whole brain scale is
 essential to understand the structure and diversity of cell types. It is
 exceedingly challenging to reuse recent technologies of single cell
 labeling and whole brain imaging to study human brains. We propose
 Adaptive Cell Tomography (ACTomography), a low-cost, high-throughput,
 high-efficacy tomography approach, based on adaptive targeting of
 individual cells. We established a platform to inject dyes into cortical
 neurons in surgical tissues of 18 patients with brain tumors or other
 conditions and 1 donated fresh postmortem brain. We collected 3-D images
 of 1746 cortical neurons, of which 852 neurons were reconstructed to
 quantify local dendritic morphology, and mapped to standard atlases. In
 our data, human neurons are more diverse across brain regions than by
 subject age or gender. The strong stereotypy within cohorts of brain
 regions allows generating a statistical tensor-field of neuron morphology
 to characterize anatomical modularity of a human brain.
description: Neuron reconstruction from microscopy images. See paper for
 details.