cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h18931znk
title: Data from: Divergent physiological acclimation responses to warming between two co-occurring salamander species and implications for terrestrial survival

description: Small differences in physiological responses are known to influence
 demographic rates such as survival. We tested for differences in the
 physiological acclimation responses of two closely-related salamander
 species that often co-occur, Ambystoma maculatum and A. opacum.
 Specifically, we measured changes in critical thermal maxima (CTmax),
 standard metabolic rates (SMRs), and respiratory surface area water loss
 (RSAWL) following exposure to three temperature treatments under
 laboratory conditions. While the magnitude of RSAWL and CTmax acclimation
 responses to warming did not differ between the study species, SMR was
 maintained across acclimation temperatures among A. maculatum, but
 declined among A. opacum acclimated to warmer temperatures. Metabolic
 compensation may facilitate maintained A. maculatum activity levels during
 warm periods following the relatively cool spring breeding season. In
 contrast, metabolic suppression may allow A. opacum to conserve energy
 when exposed to surface conditions during fall breeding and nest guarding.
 We simulated how these different SMR responses would likely alter
 post-metamorphic survival in our study species using previously collected
 data representing six weeks under relatively warm seminatural conditions.
 Our simulation indicated that, following warming and under identical study
 conditions, metabolic compensation may allow juvenile A. maculatum to
 maintain survival likelihoods, whereas metabolic depression may cause
 juvenile A. opacum to experience increased survivorship. These findings
 underscore that comparable physiological responses among ecologically
 similar, sympatric species cannot be assumed. Further, results of this
 study suggest that metabolic responses may play an important role in
 amphibian species persistence as temperatures increase due to habitat
 modification and climate change.
description: Please see the associated manuscript for full methodological
 details.
description: Available files include: R scripts
 used to: correct standard metabolic rate and
 respiratory surface area water loss data for individual body shape and
 size, and examine whether these corrected measures differed between
 species or acclimation temperature
 treatments (RSAWL_SMR_Survivors2017-2018_Jan2022.R)
 examine whether critical thermal maxima differed between species
 or following acclimation temperature treatments (CTmax.R)
 simulate juvenile ambystomatid survival probabilities given the
 results of acclimation temperature
 treatments (Simulation_Jan2022.R). 
 All necessary and previously unpublished data files to run these
 R scripts and support the findings of our study
 (CTmax-Data.csv, CTmax-Deltas.csv, 2018_Survivors_Means.csv).
 Scripts were developed and run using R version 4.1.2.
 'n/a' indicates samples for which specified data were not
 collected.
DOI: 10.5061/dryad.8cz8w9gs3
title: Data from: Palaeobiology of the early sauropodomorph Mussaurus patagonicus inferred from its long bone histology

description: We present here a detailed histological study of long bones from an
 ontogenetic series of Mussaurus patagonicus, an early sauropodomorph from
 the Early Jurassic of Argentina. Twenty long bones, including humeri,
 femora and fibulae, obtained from thirteen individuals of different body
 sizes were sampled for histological analysis. In general terms, the
 cortical bone is formed by a well vascularized fibrolamellar and parallel
 fibred bone. Except for the smaller individuals, cyclical growth marks
 (CGMs) are well recorded in all the specimens, but their number and
 relative position is highly variable. Mussaurus exhibits marked variation
 regarding relative growth rates, with some individuals growing much faster
 than others. Such variation affects the size of the adult individuals,
 which results in a poor correlation between the body size and the
 age/ontogenetic stage for this taxon. These discrepancies may be related
 to sexual dimorphism and/or developmental plasticity. Intraspecific
 variation is also recorded with regard to the growth strategies, which can
 vary from cyclical, as in other early sauropodomorphs, to continuous, as
 reported in sauropods. Sexual maturity appears to be reached between 23
 and 31 years, which is delayed in comparison to other early
 sauropodomorphs, but more compatible to derived sauropods. The attainment
 of somatic maturity appears to be reached about 14 years after the onset
 of sexual maturity. Mussaurus is a sauropodiform, phylogenetically closer
 to sauropods than most other sauropodomorphs, and therefore provides
 critical information for understanding paleobiological aspects relevant to
 the origin of sauropods and the onset of gigantism in this lineage.
DOI: 10.5061/dryad.h9w0vt4kb
title: Megachile rotundata overwintering nCounter gene expression

description: Within the United States and Canada, the primary pollinator of alfalfa is
 the alfalfa leafcutting bee (ALCB), Megachile rotundata. Our previous
 findings showed that overwintering conditions impacted gene expression
 profile in ALCB prepupae that entered diapause early in the season.
 However, ALCB are a bivoltine species, which begs the question of whether
 bees entering diapause later in the season also show this trend. To better
 understand the effects of the timing of diapause initiation, we analyzed
 mRNA copy number of genes known to be involved in diapause regulation in
 early- and late-season diapausing ALCB that were overwintered in field
 conditions or using current agricultural management conditions. We
 hypothesized that overwintering conditions for late diapausing bees also
 affects gene expression profiles. Our results showed that expression
 profiles were altered by both overwintering condition and timing of
 diapause initiation, with bees that entered diapause earlier in the season
 showing different expression patterns than those that entered diapause
 later in the season. This trend was seen in expression of members of the
 cyclin family and several targets of the insulin signaling pathway,
 including forkhead box protein O (FOXO), which is known to be important
 for diapause regulation and stress responses. But, of the genes screened,
 the proto-oncogene, Myc, was the most impacted by the timing of diapause
 initiation. Under fluctuating temperatures there was significant
 differences in Myc expression between the early and late season samples in
 all months except for November and February. This same general trend in
 Myc expression was also seen in the laboratory-maintained bees with
 significant difference in expression in all months except for November,
 February, and May. These results support previous conclusions from our
 research showing that the molecular regulation of diapause development in
 ALCB is not a simple singular cascade of gene expression but a highly
 plastic response that varies between bees depending upon their
 environmental history.
description: RNA samples were prepared for
 nCounter analysis as previously described (Cambron et al., 2021), and
 shipped on dry ice to the University of Minnesota Genomics Center
 (Minneapolis, MN) for processing with nCounter Analysis System (NanoString
 Technologies Inc.). Resulting copy numbers were normalized to the
 geometric mean of the 10 reference genes used previously (Cambron et al.,
 2021).
description: Copy number (copy num) has already been normalized to the
 reference genes (not included in dataset). Dataset shows copy number for
 individuals for a given gene. Samples are labeled
 as SeasonLocation-Month-Individual# (Example: EF-NOV-1 = early
 season/field-November-individual #1). Temperature treatment is coded
 as F:fluctuating; C:constant. Our variable ST is needed for running
 statistics on the interaction of season and temperature treatment, and is
 coded as Season X Temperature Treatment (Example: Early_F = early
 season_fluctuating).
DOI: 10.5061/dryad.73n5tb2zg
title: Sonar Estimation of Summer Chum and Pink Salmon in the Anvik River, Alaska, 2021

description: Dual-frequency identification sonar (DIDSON) was used to estimate adult
 summer chum salmon (Oncorhynchus keta) and pink salmon (O. gorbuscha)
 passage in the Anvik River from June 15 to July 26, 2021. Apportionment to
 species was determined from data collected from tower counts. A total of
 18,819 (SE 273) summer chum and 0 pink salmon were estimated to have
 passed the sonar site. A beach seine sample fishery was conducted to
 collect age, sex, and length information; however, high water prevented
 fishing for part of the season. In addition, because of low salmon
 passage, few fish were caught, and the sample fishery was discontinued
 early. Both sonar systems functioned well with minimal interruptions to
 operation. Range of ensonification was considered adequate for most fish
 that migrated upstream.
description: Sonar
DOI: 10.5061/dryad.h44j0zpn1
title: Food deprivation exposes sex-specific trade-offs between stress tolerance and lifespan in the copepod Tigriopus californicus

description: Long life is standardly assumed to be associated with high stress
 tolerance. Previous work shows that the copepod Tigriopus californicus
 breaks this rule, with longer lifespan under benign conditions found in
 males, the sex with lower stress tolerance. Here we extended this previous
 work, raising animals from the same families in food-replete conditions
 until adulthood and then transferring them to food-limited conditions
 until all animals perished. As in previous work, survivorship under
 food-replete conditions favored males. However, under food deprivation
 lifespan strongly favored females in all crosses. Compared to benign
 conditions, average lifespan under nutritional stress was reduced by 47%
 in males but only 32% in females. Further, the sex-specific mitonuclear
 effects previously found under benign conditions were erased under food
 limited conditions. Results thus demonstrate that sex-specific lifespan,
 including mitonuclear interactions, are highly dependent on nutritional
 environment.
DOI: 10.5061/dryad.np5hqbzvf
title: Feasible carbon-trade model for low-carbon density ecosystem

description: China has set a carbon-neutrality target for 2060; carbon sinks are vital
 tools to meet this target. China is leading the effort in greening the
 world through the restoration of low-carbon density ecosystems (LCDEs).
 The potential carbon sinks of LCDEs provide opportunities for carbon
 trading projects that make cash benefits accessible to the owners, thereby
 incentivizing ecosystem restoration. Unfortunately, carbon trading in
 LCDEs has, to date, been unsuccessful in China. Therefore, it is important
 to identify the barriers in the development of carbon trading projects in
 LCDEs. This study aimed at creating a feasible model for carbon trading in
 LCDEs in China. We first accounted for the carbon sink of LCDEs based on
 field sampling of 169 quadrants and 3,471 plants. Thereafter, we
 investigated the trade-off between the cost and efficiency of carbon
 projects in LCDEs. Finally, we explored the feasibility of the
 corresponding carbon sink potential by considering carbon price
 fluctuations and public–private partnership models. The main findings were
 as follows: (i) Carbon trading in LCDEs is not economically feasible at
 the current market price of carbon. In the pilot case, the LCDE carbon
 trading could only recover 41.72% of the project cost. This partially
 explains the scarcity of carbon trading for LCDEs in the current emission
 trading scheme; (ii) A benefit transfer model is essential, wherein the
 costs of ecosystem restoration are paid by the central government, and the
 benefits of carbon trade are transferred to the owners of LCDEs, providing
 sufficient incentives for the owners to participate in carbon trading.
 Policy implications. Given the scarcity of large-scale organisations and
 expertise, carbon trading in low-carbon density ecosystems (LCDEs) should
 not be treated as a purely commercial project. A public–private
 partnership network is a suitable model for engaging stakeholders to
 complete the carbon trading process in LCDEs. For the success of carbon
 trading in LCDEs, viable carbon prices and transfer of benefits from
 public investments are policy issues that need to be further explored. Our
 findings provide a policy basis for the Chinese government to mobilise
 more LCDE owners to enter the carbon market and achieve carbon-neutrality.
description: The Bureau of Forestry of
 local government provided restoration project documentation and official
 statistics on grassland restoration. Shrubs (Caragana) were planted as
 degraded grassland restoration. The area contained a total of 10,467.73 ha
 of Caragana, and shrubs were planted on 923 plots of land in Siziwang
 Banner from 2005 to 2013. Some interviews were conducted with the
 grassland owners. Some face-to-face interviews were conducted with local
 government officials about the current status of grassland, the role of
 local governments, degraded grassland restoration investments, and
 awareness of carbon trade.
description: A README file is provided to aid
 use of the dataset.
DOI: 10.5281/zenodo.18399003
title: Data set for the study "Nonclassical Nucleation and Crystallization of LiNbO3 Nanoparticles from the Aqueous Solvothermal Alkoxide Route"

description: Raw data and sample description for the NMR and HRMS experiments presented in the publication: Nonclassical Nucleation and Crystallization of LiNbO3 Nanoparticles from the Aqueous Solvothermal Alkoxide Route, Small 2023, 2306417.
DOI: 10.5281/zenodo.18399004
title: Data set for the study "Nonclassical Nucleation and Crystallization of LiNbO3 Nanoparticles from the Aqueous Solvothermal Alkoxide Route"

description: Raw data and sample description for the NMR and HRMS experiments presented in the publication: Nonclassical Nucleation and Crystallization of LiNbO3 Nanoparticles from the Aqueous Solvothermal Alkoxide Route, Small 2023, 2306417.
DOI: 10.5061/dryad.k98sf7m77
title: Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

description: Body hair is a defining mammalian characteristic, but several mammals,
 such as whales, naked mole-rats, and humans, have notably less hair than
 others. To find the genetic basis of reduced hair quantity, we used our
 evolutionary-rates-based method, RERconverge, to identify coding and
 noncoding sequences that evolve at significantly different rates in
 so-called hairless mammals compared to hairy mammals. Using RERconverge,
 we performed an unbiased, genome-wide scan over 62 mammal species using
 19,149 genes and 343,598 conserved noncoding regions to find genetic
 elements that evolve at significantly different rates in hairless mammals
 compared to hairy mammals. We show that these rate shifts resulted from
 relaxation of evolutionary constraint on hair-related sequences in
 hairless species. In addition to detecting known and potential novel
 hair-related genes, we also discovered hundreds of putative hair-related
 regulatory elements. Computational investigation revealed that genes and
 their associated noncoding regions show different evolutionary patterns
 and influence different aspects of hair growth and development. Many genes
 under accelerated evolution are associated with the structure of the hair
 shaft itself, while evolutionary rate shifts in noncoding regions also
 included the dermal papilla and matrix regions of the hair follicle that
 contribute to hair growth and cycling. Genes that were top-ranked for
 coding sequence acceleration included known hair and skin genes KRT2,
 KRT35, PKP1, and PTPRM that surprisingly showed no signals of evolutionary
 rate shifts in nearby noncoding regions. Conversely, accelerated noncoding
 regions are most strongly enriched near regulatory hair-related genes and
 microRNAs, such as mir205, ELF3, and FOXC1, that themselves do not show
 rate shifts in their protein-coding sequences. Such dichotomy highlights
 the interplay between the evolution of protein sequence and regulatory
 sequence to contribute to the emergence of a convergent phenotype.
DOI: 10.5061/dryad.ksn02v75w
title: Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

description: Informed management and conservation efforts are vital to sustainable
 recreational fishing and biodiversity conservation. Because the taxonomic
 rank of species is typically targeted in conservation and management
 strategies, success of these efforts depends on accurate species
 delimitation. The Black Basses (Micropterus) are an iconic lineage of
 freshwater fishes that include some of the world’s most popular species
 for recreational fishing and rank among the world's most invasive
 vertebrate species. Despite their popularity, previous studies to delimit
 species and lineages in Micropterus suffer from insufficient geographic
 coverage and uninformative molecular markers. Phylogenomic analyses of
 ddRAD data result in the delimitation of 19 species in Micropterus, which
 includes 14 described species, the undescribed but fairly well-known
 Altamaha Bass, Bartram’s Bass, and Choctaw Bass, and two additional
 undescribed species currently classified as Smallmouth Bass (M. dolomieu).
 We also provide a revised delimitation of species in the Largemouth Bass
 complex that necessitates a change in scientific nomenclature: Micropterus
 salmoides is retained for the Florida Bass and Micropterus nigricans is
 elevated from synonymy for the Largemouth Bass. Our findings provide a
 resolved phylogeny of all Micropterus species, insight into the role of
 introgression in the history of Micropterus diversification, and a robust
 delimitation of species that differs from current taxonomic
 classifications and the list of North American fishes maintained by the
 American Fisheries Society. The new understanding of diversity,
 distribution, and systematics of Blass Basses will serve as an important
 basis for the management and conservation of this charismatic and
 economically important clade of fishes.
DOI: 10.15468/dl.w5xafp
title: Occurrence Download

description: A dataset containing 5984900 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Royal Botanic Gardens, Kew - Herbarium Specimens"
 ]
}

 The dataset includes 5984900 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003044-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nvx0k6dtz
title: Data from: The influence of the COVID-19 pandemic on the demand for different shades of green

description: COVID-19 has heightened the dependence of urban dwellers on cultural
 ecosystem services provided by urban green spaces (UGS), specifically in
 regard to the provision of recreational opportunities, and psychological
 and physical health benefits arising from their use. As different types
 and levels of cultural ecosystem services are provided by different types
 of UGS, people may seek out different UGS to satisfy personal needs over
 various phases of COVID-19 mobility restrictions imposed by cities. We
 report on a study that took advantage of the different phases of COVID-19
 mobility restrictions to assess the demand for and perception of different
 types of UGS in Singapore. The study utilised four data sets to compare
 demand for and visitorship patterns of UGS before the pandemic
 (Pre-Circuit Breaker), the duration of the strictest mobility restrictions
 (Circuit Breaker), and after the measures were relaxed (Post-Circuit
 Breaker). We used Google Search trends as a proxy for UGS demand, Google
 mobility data for an overview of population visitorship trends, visitor
 counts for granular insights on actual visitorship trends, and qualitative
 data on perception of parks by park visitors after restrictions eased.
 Parks were categorised as manicured and less manicured UGS for analysis.
 Search interest for UGS overall fell by more than 50% from during Circuit
 Breaker but the post-Circuit Breaker levels exceeded pre-Circuit Breaker,
 with a 70.9% increase for less manicured UGS compared to 20.8% for
 manicured UGS. This corroborated with Google mobility and visitor counts,
 which showed a steep decrease in park use followed by a rapid increase in
 the same periods, and with increased visitorship in the less manicured
 UGS. The perception study also showed that more than 50% of respondents
 reported visiting parks that they have never visited before, and there was
 a greater appreciation and use of UGS after the pandemic and preference
 for less manicured and more naturalistic landscapes. The pandemic has
 heightened the demand for cultural ecosystem services provided by UGS. Our
 study showed that this demand is not uniform across different types of
 UGS, with an increase visitorship and preference for less manicured green
 spaces.
description: There are three files available: 1. ReadMe
 file with information on datasets 2. Visitor Counts of
 3 parks (.csv) 3. Visitor survey on park visitor
 patterns and perceptions (.csv)
DOI: 10.5061/dryad.rbnzs7hcp
title: Hunting suitability model: A new tool for managing wild ungulates

description: Rising numbers of wild ungulates in human-dominated landscapes of Europe
 can induce negative effects like damages to forests. Therefore, effective
 wildlife management, including harvesting through hunting is becoming
 increasingly important. However, current hunting
 practices often fail to diminish those negative effects, as many
 ungulate species retreat to areas unsuitable for hunting. This
 predator-avoidance behaviour makes it difficult to fulfill the
 demand of reducing population numbers. Thus, there is an urgent
 need for innovative and effective wildlife management
 tools to counteract this problem. Here we provide for the first time a
 hunting suitability model for wild ungulate management
 in mountainous landscapes to visualise hunting suitability
 objectively and realistically. Using red deer as a model
 species, we modelled hunting suitability with high spatial
 resolution (10 x 10 m), based on
 remote sensing information, field surveys, and expert knowledge
 of professional hunters. We analysed spatio-temporal habitat
 selection by radio-collared deer in relation to locations
 of varying hunting suitability. The suitability of
 various locations regarding hunting influenced the spatio-temporal habitat
 selection by this species, consistent with our hypothesis. Red
 deer avoided areas suitable for hunting during daylight hours in the
 hunting season, but not during the night. This
 species seems to perceive a landscape of heterogeneous
 anthropogenic predation risk, shaped by locations of various hunting
 suitability, as we modelled
 it. This confirms the empirical realism of the
 model. Concerning wild ungulate management, our hunting
 suitability model provides high-resolution predictions of
 where species like red deer will retreat when
 perceived anthropogenic predation risk increases. The model also yields
 useful insights regarding the hunting suitability of particular locations,
 which is valuable information especially for non-locals. Furthermore, the
 model can serve as planning tool to inform decisions about where
 particular hunting strategies can be performed most efficiently
 to manage wild ungulates and therefore minimize
 human-wildlife conflicts.
description: See manuscript
description: See README_hunting_suitability_model.txt