cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rjdfn2z89
title: Genomic architecture of a genetically assimilated seasonal color pattern

description: Developmental plasticity allows genomes to encode multiple distinct
 phenotypes that can be differentially manifested in response to
 environmental cues. Alternative plastic phenotypes can be selected through
 a process called genetic assimilation; although the mechanisms are still
 poorly understood. We assimilated a seasonal wing color phenotype in a
 naturally plastic population of butterflies, and characterized three
 responsible genes. Combined with endocrine assays, and chromatin
 accessibility and conformation analyses, we found that the transition of
 wing coloration from an environmentally determined trait to a
 predominantly genetic trait occurred through selection for regulatory
 alleles of downstream wing patterning genes. This mode of genetic
 evolution is likely favored by selection because it allows tissue- and
 trait-specific tuning of reaction norms without affecting core cue
 detection or transduction mechanisms.
description: Data and code supporting article aaz3017: Genomic architecture of
 a genetically assimilated seasonal color pattern
DOI: 10.5061/dryad.1vhhmgqr1
title: Data from: Kin recognition in guppies uses self-referencing on olfactory cues

description: Kin recognition plays an important role in social behavior and evolution,
 but the proximate mechanisms by which individuals recognize kin remain
 poorly understood. In many species, individuals form a “kin template” that
 they compare against conspecifics’ phenotypes to assess phenotypic
 similarity–and by association, relatedness. Individuals may form a kin
 template through self-inspection (i.e. self-referencing) and/or by
 observing their rearing associates (i.e. family-referencing). However,
 despite much interest, few empirical studies have successfully
 disentangled self- and family-referencing. Here, we employ a novel set of
 breeding crosses using the Trinidadian guppy (Poecilia reticulata) to
 disentangle referencing systems by manipulating exposure to kin from
 conception onwards. We show that guppies discriminate among their full-
 and maternal half-siblings, which can only be explained by
 self-referencing. Additional behavioral experiments revealed no evidence
 that guppies incorporate the phenotypes of their broodmates or mother into
 the kin template. Finally, by manipulating the format of our behavioral
 tests, we show that olfactory communication is both necessary and
 sufficient for kin discrimination. These results provide robust evidence
 that individuals recognize kin by comparing the olfactory phenotypes of
 conspecifics against their own. This study resolves key questions about
 the proximate mechanisms underpinning kin recognition, with implications
 for the ontogeny and evolution of social behavior.
DOI: 10.5068/d1vw96
title: Transmission of West Nile and five other temperate mosquito-borne viruses peaks at temperatures between 23-26ºC

description: The temperature-dependence of many important mosquito-borne diseases has
 never been quantified. These relationships are critical for understanding
 current distributions and predicting future shifts from climate change. We
 used trait-based models to characterize temperature-dependent transmission
 of 10 vector–pathogen pairs of mosquitoes (Culex pipiens, Cx.
 quinquefascsiatus, Cx. tarsalis, and others) and viruses (West Nile,
 Eastern and Western Equine Encephalitis, St. Louis Encephalitis, Sindbis,
 and Rift Valley Fever viruses), most with substantial transmission in
 temperate regions. Transmission is optimized at intermediate temperatures
 (23–26ºC) and often has wider thermal breadths (due to cooler lower
 thermal limits) compared to pathogens with predominately tropical
 distributions (in previous studies). The incidence of human West Nile
 virus cases across US counties responded unimodally to average summer
 temperature and peaked at 24ºC, matching model-predicted optima (24–25ºC).
 Climate warming will likely shift transmission of these diseases,
 increasing it in cooler locations while decreasing it in warmer locations.
description: Mosquito and virus trait data were digitized from previously
 published papers (see eLife publication for full citations).
 Encephalitis case data were obtained from the CDC website.
DOI: 10.5061/dryad.cfxpnvx3q
title: Adjacency matrices and nodal attributes for prestige and homophily predict network structure for social learning of medicinal plant knowledge

description: Human subsistence societies have thrived in environmental extremes while
 maintaining biodiversity through social learning of ecological knowledge,
 such as techniques to prepare food and medicine from local resources.
 However, there is limited understanding of which processes shape social
 learning patterns and configuration in ecological knowledge networks, or
 how these processes apply to resource management and biological
 conservation. In this study, we test the hypothesis that the prestige
 (rarity or exclusivity) of knowledge shapes social learning networks. In
 addition, we test whether people tend to select who to learn from based on
 prestige (knowledge or reputation), and homophily (e.g., people of the
 same age or gender). We used interviews to assess five types of medicinal
 plant knowledge and how 303 people share this knowledge across four
 villages in Solomon Islands. We developed exponential random graph models
 (ERGMs) to test whether hypothesized patterns of knowledge sharing based
 on prestige and homophily are more common in the observed network than in
 randomly simulated networks of the same size. We found that prestige
 predicts five hypothesized network configurations and all three
 hypothesized learning patterns, while homophily predicts one of three
 hypothesized network configurations and five of the seven hypothesized
 learning patterns. These results compare the strength of different
 prestige and homophily effects on social learning and show how cultural
 practices such as intermarriage can affect certain aspects of prestige and
 homophily. By advancing our understanding of how prestige and homophily
 affect ecological knowledge networks, we identify which social learning
 patterns have the largest effects on biocultural conservation of
 ecological knowledge.
description: These files contain the adjacency matrices and nodal attributes
 used for explonential random graph models (ERGMs) used in M.O. Bond and
 O.G. Gaoue. 2020. Prestige and Homophily Predict Network Structure for
 Social Learning of Medicinal Plant Knowledge. PLOS ONE (in
 press).
DOI: 10.5061/dryad.r7sqv9s9d
title: Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution

description: The reissner lamprey Lethenteron reissneri belonging to Cyclostomata,
 serves as a bridge between invertebrates and jawed vertebrates, and is
 considered the most direct ancestor of vertebrates. However, the
 genetic mechanisms underlying the adaptive evolution of lampreys remain
 unclear. Here, we supplied the genome data and annotation data of
 Lethenteron reissneri. Total 5 files were uploaded, including the
 assembled genome of Lethenteron reissneri, the gene annotation
 file in gff format, the gene function annotation file, the LIP gene
 sequences of 50 species used in the article, and the readme
 file. This study not only provides the first chromosome-level
 reference genome in Cyclostomata, but also indicates the unique biology
 and adaptive evolution of lampreys.
description: A male reissner lamprey (L. reissneri) was collected from the
 Taizi River, Fushun City, Liaoning Province, China for genome and
 transcriptome sequencing. To obtain sufficient high-quality DNA and avoid
 programmed genome rearrangement (PGR) in somatic cells, the fresh testis
 tissue of the reissner lamprey was ground into a powder in liquid nitrogen
 to extract the DNA using a Blood & Cell Culture DNA Mini
 kit (Qiagen, Hilden, Germany). it was then prepared for PacBio (Menlo
 Park, CA, USA), Illumina HiSeq X-ten (libraries with short insert sizes of
 350 bp for 2 x 150 bp paired-end sequencing) (San Diego, CA, USA), and
 Hi-C sequencing.  To fully understand the genome size
 and other characteristics of the reissner lamprey genome, we performed
 genome survey analysis using the ~113.60-Gb short-insert-size clean reads
 produced by the Illumina platform. The results indicated that the reissner
 lamprey genome was ~1.15 Gb and had a high ratio of heterozygosity and
 repetitive sequences, suggesting that the genome is complex. To acquire a
 high-quality genome assembly, ~102.19 Gb (~96.13-fold coverage of the
 estimated genome size) PacBio long reads (reads number: 9,738,768; N50:
 ~17 Kb) were produced and used for genome assembly using FALCON software
 (v0.7). To further improve the quality and accuracy of the assembled
 genome, we corrected the genome using QUIVER with default parameters. We
 obtained a ~1.06-Gb genome assembly with the contig N50 of ~2.07 Mb. The
 assembled genome size was close to the k-mer estimated genome size (~1.15
 Gb), which covered ~92.17% of the evaluated genome. To obtain the
 chromosome-level assembly, 176.14 Gb Hi-C reads were produced for
 chromosome construction using 3D <i>de novo</i> assembly
 software. A total of 72 chromosomes were anchored, with a mounting rate of
 up to 90.29%, and with a scaffold N50 of 13.23 Mb, indicating successful
 acquisition of the chromosome-level reference genome of reissner lamprey.
 The annotation step and other method were performaed using the method
 described in this article. The raw genome sequencing data and RNA-seq data
 were deposited in the National Center for Biotechnology Information
 database with the accession number PRJNA558325.
DOI: 10.25338/b8cg94
title: Thermal tolerance and routine oxygen consumption of convict cichlid, Archocentrus nigrofasciatus, acclimated to constant temperatures (20 °C and 30 °C) and a daily temperature cycle (20 °C → 30 °C)

description: Organismal temperature tolerance and metabolic responses are correlated to
 recent thermal history, but responses to thermal variability are less
 frequently assessed. There is great interest in whether organisms that
 experience greater thermal variability can gain metabolic or tolerance
 advantages through phenotypic plasticity. We compared thermal tolerance
 and routine aerobic metabolism of Convict cichlid acclimated for 2 weeks
 to constant 20°C, constant 30°C, or a daily cycle of 20→30°C (1.7°C/hr).
 Acute routine mass-specific oxygen consumption (Ṁo 2 ) and Critical
 Thermal Maxima/Minima (CTMax/CTMin) were compared between groups, with
 cycle acclimated fish sampled from the daily minimum (20°C, 0900 hrs) and
 maximum (30°C, 1600 hrs). Cycle-acclimated fish demonstrated statistically
 similar CTMax at the daily minimum and maximum (39.0°C, 38.6°C) but
 distinct CTMin values, with CTMin 2.4°C higher for fish sampled from the
 daily 30°C maximum (14.8°C) compared to the daily 20°C minimum (12.4°C).
 Measured acutely at 30°C, Ṁo 2 decreased with increasing acclimation
 temperature; 20°C acclimated fish had an 85% higher average Ṁo 2 than 30°C
 acclimated fish. Similarly, acute Ṁo 2 at 20°C was 139% higher in 20°C
 acclimated fish compared to 30°C acclimated fish. Chronic Ṁo 2 was
 measured in separate fish continually across the 20→30°C daily cycle for
 all 3 acclimation groups. Chronic Ṁo 2 responses were very similar between
 groups between average individual hourly values, as temperatures increased
 or decreased (1.7°C/hr). Acute Ṁo 2 and thermal tolerance responses
 highlight “classic” trends, but dynamic, chronic trials suggest
 acclimation history has little effect on the relative change in oxygen
 consumption during a thermal cycle. Our results strongly suggest that the
 minimum and maximum temperatures experienced more strongly influence fish
 physiology, rather than the thermal cycle itself. This research highlights
 the importance of collecting data in both cycling and static (constant)
 thermal conditions, and further research should seek to understand whether
 ectotherm metabolism does respond uniquely to fluctuating temperatures.
DOI: 10.5061/dryad.37pvmcvhh
title: Synthesis and in vitro anticancer activities of substituted N-(4’-Nitrophenyl)-L-prolinamides

description: Prolinamides are present in secondary metabolites and have wide-ranging
 biological properties as well as antimicrobial and cytotoxic activities.
 N-(4’-substituted phenyl)-L-prolinamides 4a–4w were synthesised in two
 steps, starting from the condensation of p-fluoronitrobenzene 1a–1b with
 L-proline 2a–2b, under aqueous–alcoholic basic conditions to afford
 N-aryl-L-prolines 3a–3c, which underwent amidation via a two-stage,
 one-pot reaction involving SOCl2 and amines, to furnish L-prolinamides in
 20–80% yield. The cytotoxicities of 4a–4w against four human carcinoma
 cell lines (SGC7901, HCT-116, HepG2 and A549) were evaluated by MTT assay;
 with good tumour inhibitory activities (79.50 ± 1.24%–50.04 ± 1.45%)
 against HepG2. 4a exhibited the best antitumour activity against A549 with
 % cell inhibition of 95.41 ± 0.67% at 100 µM. Likewise, 4s (70.13 ± 3.41%)
 and 4u (83.36 ± 1.70%) displayed stronger antineoplastic potencies against
 A549 than the standard, 5-fluorouracil (64.29 ± 2.09%) whereas 4a (93.33 ±
 1.36%) and 4u (81.29 ± 2.32%) outperformed the reference (81.20 ± 0.08%)
 against HCT-116. SGC7901 showed lower % cell viabilities with 4u (8.02 ±
 1.54%) and 4w (27.27 ± 2.38%). These results underscore the
 antiproliferative efficacies of L-prolinamides whilst exposing 4a and 4u
 as promising broad-spectrum anticancer agents. SAR studies are discussed.
DOI: 10.5061/dryad.dr7sqv9wk
title: Data from: Evaluation of the severity of major depression using a voice index for emotional arousal

description: We first developed an arousal level voice index (ALVI) to measure arousal
 levels using the Interactive Emotional Dyadic Motion Capture database.
 Then, we calculated ALVI from the voices of depressed patients from two
 hospitals H1 and H2 and compared them with the severity of
 depression as measured by the Hamilton Rating Scale for Depression
 (HAM-D). Depending on the HAM-D score, the datasets were classified into a
 no depression (HAM-D&lt;8) and a depression group (HAM-D≥8) for each
 hospital. A comparison of the mean ALVI between the groups was performed
 using the Wilcoxon rank-sum test.
DOI: 10.5061/dryad.wh70rxwkp
title: Data from: Incomplete convergence of gliding-mammal skeletons

description: Ecology and biomechanics play central roles in the generation of
 phenotypic diversity. When unrelated taxa invade a similar ecological
 niche, biomechanical demands can drive convergent morphological
 transformations. Thus, identifying and examining convergence helps to
 elucidate the key catalysts of phenotypic change. Gliding mammals are
 often presented as a classic case of convergent evolution because they
 independently evolved in numerous clades, each possessing patagia (‘wing’
 membranes) that generate lift during gliding. We use phylogenetic
 comparative methods to test whether the skeletal morphologies of the six
 clades of extant gliding mammals demonstrate convergence. Our results
 indicate that glider skeletons are convergent, with glider groups
 consistently evolving proportionally longer, more gracile limbs than
 arborealists, likely to increase patagial surface area. Nonetheless, we
 interpret gliders to represent incomplete convergence because (i)
 evolutionary model-fitting analyses do not indicate strong selective
 pressures for glider trait optima, (ii) the three marsupial glider groups
 diverge rather than converge, and (iii) the gliding groups remain
 separated in morphospace (rather than converging on a single morphotype),
 which is reflected by an unexpectedly high level of morphological
 disparity. That glider skeletons are morphologically diverse is further
 demonstrated by fossil gliders from the Mesozoic Era, which possess unique
 skeletal characteristics that are absent in extant gliders. Glider
 morphologies may be strongly influenced by factors such as body size and
 attachment location of patagia on the forelimb, which can vary among
 clades. Thus, convergence in gliders appears to be driven by a simple
 lengthening of the limbs, whereas additional skeletal traits reflect
 nuances of the gliding apparatus that are distinct among
 different evolutionary lineages. Our unexpected results add to growing
 evidence that incomplete convergence is prevalent in vertebrate clades,
 even among classic cases of convergence, and they highlight the importance
 of examining form-function relationships in light of phylogeny,
 biomechanics, and the fossil record.
DOI: 10.5061/dryad.wpzgmsbk1
title: No-analogue associations in the fossil record of southern conifers reveal conservatism in precipitation, but not temperature axes

description: Aim: Southern conifers have evolved under different evolutionary pressures
 to northern lineages, but in both regions these plants have undergone
 extensive extinction and range alteration over the Cenozoic (the last 66
 million years). It is not possible to directly observe the ecology of
 fossils, but indirect evidence of changes in bioclimatic envelopes can be
 derived from no-analogue assemblages – groups of co-occurring fossils that
 have climatically incongruous living relatives. We identify and examine
 the specific pairs of no-analogue fossils within assemblages to
 disentangle the effects of climatic factors on past conifer extinctions,
 and suggest which of these factors are likely to threaten southern conifer
 biodiversity in the future. Location: Southern Hemisphere Time period:
 Cenozoic Major taxa studied: Conifers Methods: We use a recently developed
 method, ‘hyperoverlap’, to identify no-analogue pairs of southern
 conifers. We characterise each pair in terms of temperature and
 precipitation, and evaluate temporal patterns in no-analogue pairs. These
 analyses represent a novel approach to studying both no-analogue fossils,
 and past changes in bioclimatic envelopes. Results: We identified 240
 no-analogue pairs in the Cenozoic record of southern conifers. Most
 (75.4%) observations of no-analogue pairs are likely to result from a
 change in the thermal (rather than hydrological) distribution between the
 fossil taxa and their extant counterparts, regardless of region or
 assemblage age. Thus, the fossil record shows some thermal lability, but
 strong hydrological stability in the tolerances of these plants. This
 implies that most southern conifers have inhabited wet climates through
 the Cenozoic, which is consistent with physiological evidence suggesting
 strong conservatism in drought tolerance. Main conclusions: Southern
 conifers have successfully adapted to a wide range of temperatures, but
 future changes in rainfall are likely to pose the greatest threat to these
 plants, either directly or indirectly (e.g., through increased incidence
 of fire in mesic areas).
description: This dataset was collected from the Global Biodiversity
 Information Facility (GBIF; https://www.gbif.org/) and curated to exclude
 fossil, cultivated or suspected erroneous records. We extracted five
 environmental variables that are linked to physiological stresses in
 plants (Table 1) from WorldClim V2 at a resolution of 30 seconds
 (approximately 1km2). Precipitation variables were fourth-root transformed
 to an approximately normal distribution to account for the non-linear
 physiological responses to precipitation. The environmental variables were
 then normalised to the global means and standard deviations to ensure that
 axes were comparable. See README file for more details. 
description: Missing values denoted by empty cells or NA values. See README
 file for explanations of each variable.
DOI: 10.5061/dryad.2jm63xsmq
title: Data from: Variation and conservation implications of the effectiveness of anti-bear interventions

description: Human-bear conflicts triggered by nuisance behaviour in public places and
 damage to livestock, crops, beehives and trees are among the main threats
 to bear populations globally. The effectiveness of interventions used to
 minimize bear-caused damage is insufficiently known and comparative
 reviews are lacking. We conducted a meta-analysis of 77 cases from 48
 publications and used the relative risk of damage to compare the
 effectiveness of non-invasive interventions, invasive management
 (translocations) and lethal control (shooting) against bears. We show that
 the most effective interventions are electric fences (95% confidence
 interval = 79.2-100% reduction in damage), calving control (100%) and
 livestock replacement (99.8%), but the latter two approaches were applied
 in only one case each and need more testing. Deterrents varied widely in
 their effectiveness (13.7-79.5%) and we recommend applying these during
 the peak periods of damage infliction. We found shooting (-34.2 to 100%)
 to have a short-term positive effect with its effectiveness decreasing
 significantly and linearly over time. We did not find relationships
 between bear density and intervention effectiveness, possibly due to
 differences in spatial scales at which they were measured (large scales
 for densities and local fine scales for effectiveness). We appeal for more
 effectiveness studies and their scientific publishing in regard to
 under-represented conflict species and regions.
DOI: 10.5061/dryad.x95x69pg6
title: Offspring sex-ratios are stable across the life-course in Drosophila simulans

description: Within populations, adult sex ratios influence population growth and
 extinction risk, mating behaviors and parental care. Additionally, sex
 ratio adjustment can have pronounced effects on individual fitness.
 Accordingly, it is important that we understand how often, and why,
 offspring sex ratios deviate from parity. In Drosophila melanogaster,
 females appear to improve their fitness by producing fewer sons when
 paired with older males. However, facultative sex ratio adjustment in D.
 melanogaster is controversial, and our understanding of how sex ratio skew
 affects fitness is hampered by pronounced sexual conflict in this species.
 Additionally, it is unclear if maternal age or quality interact with
 paternal age to influence offspring sex ratios. Here, we test whether
 offspring sex ratios vary as a function of maternal quality, and maternal
 and paternal age in Drosophila simulans, a sister species of D.
 melanogaster that lacks overt sexual conflict. We find that offspring sex
 ratios are slightly male biased overall, but constant across the female
 life-course, and independent of female quality, or paternal age. To really
 understand if, how and when females skew offspring sex ratios, we need
 studies linking offspring sex ratios to male and female phenotypes that
 are predicted to shift optimal investment in sons and daughters.
description: The raw data are attached and data collection methods are
 described in the manuscript. Please feel free to get in touch if any
 questions.
description: Each sheet in the file attached has a key that should be
 sufficient for users to interpret the data. If not, please do get in
 touch. Ruth Archer – rutharcher0@gmail.com