cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b77d0
title: Data from: Incompatible ages for clearwing butterflies based on alternative secondary calibrations

description: The recent publication of a time-tree for the plant family Solanaceae
 (nightshades) provides the opportunity to use independent calibrations to
 test divergence times previously inferred for the diverse Neotropical
 butterfly tribe Ithomiini. Ithomiini includes clades that are obligate
 herbivores of Solanaceae, with some genera feeding on only one genus. We
 used 8 calibrations extracted from the plant tree in a new relaxed
 molecular-clock analysis to produce an alternative temporal framework for
 the diversification of ithomiines. We compared the resulting age estimates
 to: (i) a time-tree obtained using 7 secondary calibrations from the
 Nymphalidae tree of Wahlberg et al. (2009), and (ii) Wahlberg et
 al.'s (2009) original age estimates for the same clades. We found
 that Bayesian clock estimates were rather sensitive to a variety of
 analytical parameters, including taxon sampling. Regardless of this
 sensitivity however, ithomiine divergence times calibrated with the ages
 of nightshades were always on average half the age of previous estimates.
 Younger dates for ithomiine clades appear to fit better with factors long
 suggested to have promoted diversification of the group such as the
 uplifting of the Andes, in the case of montane genera. Alternatively, if
 ithomiines are as old as previous estimates suggest, the recent ages
 inferred for the diversification of Solanaceae seem likely to be seriously
 underestimated. Our study exemplifies the difficulty of testing hypotheses
 of divergence times and of choosing between alternative dating scenarios,
 and shows that age estimates based on seemingly plausible calibrations may
 be grossly incongruent.
description: Sup_Mat_Garzonetal_syst.bioSupplemental material 1-10Supp_Mat_Garzonetal_systbio15.docx
DOI: 10.5061/dryad.8s3g3
title: Data from: Reproductive isolation with a learned trait in a structured population

description: Assortative mating displays and/or preferences can be affected by learning
 across a wide range of animal taxa, but the specifics of how this learning
 affects speciation with gene flow are not well understood. We use
 population genetic models with trait learning to investigate how the
 identity of the tutor affects the divergence of a self-referent
 phenotype-matching trait. We find that oblique learning (learning from
 unrelated individual of the previous generation) and maternal learning
 mask sexual selection and therefore do not allow the maintenance of
 divergence. In contrast, by enhancing positive frequency-dependent sexual
 selection, paternal learning can maintain more divergence than genetic
 inheritance, but leads to the loss of polymorphism more easily.
 Furthermore, paternal learning inhibits the invasion of a novel
 self-referent phenotype-matching trait, especially in a large population.
description: Mathematical
 analysesThe Mathematica notebook
 that contains all mathematical analysesM1forDryad.nbDivergence simulationThe R codes for finding the minimum divergent selection required for maintaining polymorphism or high divergence.Div_sim.rInvasion simulationThe R codes for finding the minimum divergent selection required for novel adaptation to invade.Inv_sim.r
DOI: 10.5061/dryad.1v8j2
title: Data from: Social synchronization of circadian rhythmicity in female mice depends on the number of cohabiting animals

description: Communal animals often engage in group activities that require temporal
 synchrony among its members, including synchrony on the circadian
 timescale. The principles and conditions that foster such collective
 synchronization are not understood, but existing literature hints that the
 number of interacting individuals may be a critical factor. We tested this
 by recording individual circadian body temperature rhythms of female house
 mice housed singly, in twos (pairs), or in groups of five (quintets) in
 constant darkness; determining the daily phases of the circadian peak for
 each animal; and then calculating the cycle-to-cycle phase relationship
 between cohabiting animals over time. Significant temporal coherence was
 observed in quintets: the proportion of quintets (4/7), but not pairs
 (2/8), that became synchronized was greater than could be achieved by the
 complete simulated reassortment of all individuals. We speculate that the
 social coupling of individual circadian clocks of group members may be
 adaptive under certain conditions, and we propose that optimal group sizes
 in nature may depend not only on species-specific energetics, spatial
 behaviour and natural history but also on the mathematics of synchronizing
 assemblies of weakly coupled animal oscillators.
description: Body Temperature
 filesText files containing
 the body temperature recordings from individual female laboratory mice
 housed singly, in pairs, or in groups of 5 in laboratory cages.
 Temperature is in Celsius (C = Celsius) and was recorded using iButton
 temperature dataloggers. Each line contains the date and time of the body
 temperature recording. The first number in the filename represents the
 mouse ID for that file. Singlets: SC4.1, SC10.2, SC17.4, SC35.8, SC41.10,
 SC43.10, SC54.12, SC56.13, SC61.14. Pairs: (SC2.1 with SC19.5), (SC7.2
 with SC16.4), (Sc5.1 with SC22.5), (SC27.1 with SC60.14), (SC33.8 with
 SC45.11), (SC39.9 with SC59.13), (SC44.10 with SC50.12), (SC30.7 with
 SC46.11). Quintets: (SC3.1, SC6.2, SC13.3, SC15.4, SC23.5), (SC8.2,
 SC11.3, SC14.4, SC21.5, SC25.6), (SC1.1, SC9.2, SC18.4, SC20.5, SC24.6),
 (SC26.7, SC38.9, SC42.10, SC49.11, SC52.12), (SC31.8, SC40.9, SC47.11,
 SC51.12, SC58.13), (SC34.8, SC36.9, SC53.12, SC55.13, SC62.14), (SC29.7,
 SC32.8, SC37.9, SC48.11, SC57.13)
DOI: 10.5061/dryad.ms40b
title: Data from: Mapping sclerobiosis: a new method for interpreting the distribution, biological implications, and paleoenvironmental significance of sclerobionts on biotic hosts

description: The use of sclerobiosis as a tool for paleoenvironmental and
 paleoecological research is undermined by a lack of comparable methods for
 sclerobiont data collection and analysis. We present a new method for
 mapping sclerobiont distributions across any host, and offer an example of
 how the method may be used to interpret sclerobiont data in relation to
 host orientation. This approach can also be used to assess the suitability
 of beds and fossil material for paleoenvironmental reconstruction. A
 sample of 150 encrusted dorsibiconvex atrypide brachiopods were selected
 from six beds in the Waterways Formation (latest Givetian – Early
 Frasnian; Alberta, Canada). The dorsal and ventral valves of each
 brachiopod were photographed. Sclerobiont taxa were mapped onto the
 photographs, and the maps were used to create stacked images with each of
 the 25 brachiopod specimens from each bed. Based on the life orientation
 of dorsibiconvex atrypides, three zones were designated on the host: the
 post mortem zone, (only available to sclerobionts after death and
 reorientation of the host); the shaded zone (brachial valve, excluding the
 post mortem zone); and the exposed zone (ventral valve). Randomization
 simulation results indicate that all beds likely exhibit non random
 encrustation patterns, and corroborate the hypotheses that: (1) much of
 the encrustation occurred while the hosts were alive, and (2) these beds
 and fossils have experienced little physical reworking or transport and
 would be suitable for paleoenvironmental analysis. Mapping sclerobionts
 across hosts can serve as a unifying method to increase the recognition
 and use of sclerobiosis in paleontological studies.
description: Appendix
 1Raw
 sclerobiont maps of each of the 150 brachiopod specimens included in the
 mapping study. Each image is shown to scale. The left-hand column depicts
 maps of the dorsal view, and the right-hand column depicts maps of the
 ventral view. Blank cells indicate valves that were unencrusted, and were
 therefore not mapped. The original photograph of the brachiopod has been
 removed for clarity. Sclerobionts are colour coded by taxon: Ascodictyon =
 purple, Hederella = yellow, Microconchus = red, and craniid brachiopods =
 blue.
DOI: 10.7927/5869-rz42
title: IPCC AR6 Synthesis Report SPM.7 (b) and LR Figure 4.4 (b): Potential of demand-side mitigation options by 2050

description: This panel displays the indicative potential of demand-side mitigation options for 2050. Potentials are estimated based on approximately 500 bottom-up studies representing all global regions. The baseline (white bar) is provided by the sectoral mean GHG emissions in 2050 of the two scenarios (IEA-STEPS and IP_ModAct) consistent with policies announced by national governments until 2020. The green arrow represents the demand-side emissions reductions potentials. The range in potential is shown by a line connecting dots displaying the highest and the lowest potentials reported in the literature. Food shows demand-side potential of socio-cultural factors and infrastructure use, and changes in land-use patterns enabled by change in food demand. Demand-side measures and new ways of end-use service provision can reduce global GHG emissions in end-use sectors (buildings, land transport, food) by 40–70% by 2050 compared to baseline scenarios, while some regions and socioeconomic groups require additional energy and resources. The last row shows how demandside mitigation options in other sectors can influence overall electricity demand. The dark grey bar shows the projected increase in electricity demand above the 2050 baseline due to increasing electrification in the other sectors. Based on a bottom-up assessment, this projected increase in electricity demand can be avoided through demand-side mitigation options in the domains of infrastructure use and socio-cultural factors that influence electricity usage in industry, land transport, and buildings (green arrow).
DOI: 10.5061/dryad.n0k2f
title: Data from: Joint effect of education and main lifetime occupation on late life health: a cross-sectional study of older adults in Xiamen, China

description: Background: The effects of education and occupation on health have been
 well documented individually, but little is known about their joint
 effect, especially their cumulative joint effect on late life health.
 Methods: We enrolled 14,292 participants aged 60+ years by multistage
 sampling across 173 communities in Xiamen, China, in 2013. Heath status
 was assessed by the ability to perform six basic activities of daily life.
 Education was classified in four categories: ‘Illiterate’, ‘Primary’,
 ‘Junior high school’ and ‘Senior high school and beyond’. Main lifetime
 occupation was also four categorized: ‘Employed’, ‘Farmer’, ‘Jobless’ and
 ‘Others’. Odds ratios (ORs) were estimated by random-intercept multilevel
 models regressing health status on education and main lifetime occupation
 with or without their interactions, adjusting by some covariates. Results:
 Totally, 13,880 participants had complete data, of whom 12.5% suffered
 from disability, and ‘Illiterate’ and ‘Farmer’ took up the greatest
 proportion (33.01% and 42.72%, respectively). Participants who were higher
 educated had better health status (ORs = 0.62, 0.46, and 0.44 for the
 ‘Primary’, ‘Junior high school’, and ‘Senior high school and beyond’,
 respectively, in comparison with ‘Illiterate’). Those who were long term
 jobless in early life had poorest heath (ORs = 1.88, 95% CI 1.47 to 2.40).
 Unexpectedly, for the farmers, the risk of poor health gradually increased
 in relation to higher education level (ORs = 1.26, 1.28, 1.40 and 2.24,
 respectively). For the ‘Employed’, similar ORs were obtained for the
 ‘Junior high school’ and ‘Senior high school and beyond’ educated (both
 ORs = 1.01). For the ‘Farmer’ and ‘Jobless’, participants who were
 ‘Illiterate’ and ‘Primary’ educated also showed similar ORs. Conclusions:
 Both education and main lifetime occupation were associated with late life
 health. Higher education was observed to be associated with better health,
 but such educational advantage was mediated by main lifetime occupation.
description: Survey data of 13880
 participants in Xiamen, China　data.xlsx
DOI: 10.5061/dryad.2q3r2
title: Data from: Not so colourful after all: eggshell pigments constrain avian eggshell colour space

description: Birds' eggshells are renowned for their striking colours and varied
 patterns. Although often considered exceptionally diverse, we report that
 avian eggshell coloration, sampled here across the full phylogenetic
 diversity of birds, occupies only 0.08–0.10% of the avian perceivable
 colour space. The concentrations of the two known tetrapyrrole eggshell
 pigments (protoporphyrin and biliverdin) are generally poor predictors of
 colour, both intra- and interspecifically. Here, we show that the
 constrained diversity of eggshell coloration can be accurately predicted
 by colour mixing models based on the relative contribution of both
 pigments and we demonstrate that the models' predictions can be
 improved by accounting for the reflectance of the eggshell's calcium
 carbonate matrix. The establishment of these proximate links between
 pigmentation and colour will enable future tests of hypotheses on the
 functions of perceived avian eggshell colours that depend on eggshell
 chemistry. More generally, colour mixing models are not limited to avian
 eggshell colours but apply to any natural colour. Our approach illustrates
 how modelling can aid the understanding of constraints on phenotypic
 diversity.
description: Hanley et al Constrained
 eggshell colors - 2015-1-13-Accompanying DataReflectance spectra from
 636 bird species collected from museum specimens.
DOI: 10.5061/dryad.29j8d
title: Data from: Palaeodiversity and formation counts: redundancy or bias?

description: A key question in palaeontology is whether the fossil record taken at face
 value is adequate to represent true patterns of diversity through time.
 Some methods of assessing data quality have depended on the commonly
 observed covariation of palaeodiversity and fossiliferous formation counts
 through time, based on the assumption that the count of formations
 containing fossils, to a greater or lesser extent, drives diversity; but
 what if diversity drives formations? Close study of two fossil records,
 early tetrapods (Devonian–Jurassic) and dinosaurs, shows how the
 relationship between new taxa and new fossiliferous formations varies
 through research time. Initially, each new find represents a new
 fossiliferous formation and discovery follows the ‘bonanza’ model (fossils
 drive formations). In unexplored parts of the world, new taxa are
 identified frequently in new regions/formations. Only after time, in
 well-explored continents such as Europe and North America, does collecting
 style switch to a mix of exploration for new formations and re-sampling of
 known fossiliferous formations. Data are most striking for dinosaurs,
 where the Triassic–Jurassic record largely comprises finds from Europe and
 North America, where new formation discoveries reached their half-life in
 1914. This contrasts with the Cretaceous, which is dominated by rapidly
 rising discoveries from regions outside Europe and North America and the
 formation half-life for these ‘new’ lands is 1986, showing that 50% of new
 Cretaceous dinosaur-bearing formations were identified only in the past 30
 years. The relationship between dinosaur-bearing formations and
 palaeodiversity then combines three signals in variable amounts,
 reflecting the original diversity (relative abundances of particular taxa
 in different formations), redundancy (new fossiliferous formations
 accruing because of new fossil finds) and sampling (intensity of
 exploration for new fossiliferous formations, and of search within
 already-sampled formations). For fossil vertebrates at least, formation
 counts of various kinds are poor predictors of sampling, missing, for
 example, the bonanza samples of Lagerstätten such as the Yixian Formation
 in China: thousands of specimens, dozens of species, but counted as one
 formation. These observations suggest that formation count cannot be
 regarded as an unbiased metric of sampling.
description: Appendix1Summary data for the Early tetrapods and Dinosaurs studies, together with calculations and live versions of Figures 1-10.Appendix2Species lists of Early tetrapods, by major subclade, and by time.Appendix3Species list of dinosaurs, from 1824-2011Appendix4Species lists of Early tetrapods and of Dinosaurs, sorted by geological period, by old lands vs. new lands, and in other ways.
DOI: 10.5061/dryad.vt46n
title: Data from: Modeling and mapping the probability of occurrence of invasive wild pigs across the contiguous United States

description: Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral
 hogs, are one of the most widespread and successful invasive species
 around the world. Wild pigs have been linked to extensive and costly
 agricultural damage and present a serious threat to plant and animal
 communities due to their rooting behavior and omnivorous diet. We modeled
 the current distribution of wild pigs in the United States to better
 understand the physiological and ecological factors that may determine
 their invasive potential and to guide future study and eradication
 efforts. Using national-scale wild pig occurrence data reported between
 1982 and 2012 by wildlife management professionals, we estimated the
 probability of wild pig occurrence across the United States using a
 logistic discrimination function and environmental covariates hypothesized
 to influence the distribution of the species. Our results suggest the
 distribution of wild pigs in the U.S. was most strongly limited by cold
 temperatures and availability of water, and that they were most likely to
 occur where potential home ranges had higher habitat heterogeneity,
 providing access to multiple key resources including water, forage, and
 cover. High probability of occurrence was also associated with frequent
 high temperatures, up to a high threshold. However, this pattern is driven
 by pigs' historic distribution in warm climates of the southern U.S.
 Further study of pigs' ability to persist in cold northern climates
 is needed to better understand whether low temperatures actually limit
 their distribution. Our model highlights areas at risk of invasion as
 those with habitat conditions similar to those found in pigs' current
 range that are also near current populations. This study provides a
 macro-scale approach to generalist species distribution modeling that is
 applicable to other generalist and invasive species.
description: U.S. wild pig species
 distribution model dataThis is the final
 dataset used to derive the wild pig distribution model for the contiguous
 United States presented in the accompanying publication, along with
 predictive model output values. Please see the ReadMe file for further
 details.wildpig_sdm_data.csv
DOI: 10.5061/dryad.k867f
title: Data from: Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey

description: Background: Lampreys are extant representatives of the jawless vertebrate
 lineage that diverged from jawed vertebrates around 500 million years ago.
 Lamprey genomes contain information crucial for understanding the
 evolution of gene families in vertebrates. The ATP-binding cassette (ABC)
 gene family is found from prokaryotes to eukaryotes. The recent
 availability of two lamprey draft genomes from sea lamprey Petromyzon
 marinus and Japanese lamprey Lethenteron japonicum presents an opportunity
 to infer early evolutionary events of ABC genes in vertebrates. Results:
 We conducted a genome-wide survey of the ABC gene family in two lamprey
 draft genomes. A total of 37 ABC transporters were identified and
 classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes,
 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and
 three ABCG genes. The ABCA subfamily has expanded from three genes in sea
 squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human
 and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and
 ABCG2-like genes found in sea squirts have contracted in the other species
 examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in
 sea squirts or lampreys), which coincides with the emergence of the
 gnathostome-specific adaptive immune system. All the genes in the ABCD,
 ABCE and ABCF subfamilies were conserved and had undergone limited
 duplication and loss events. In the sea lamprey transcriptomes, the ABCE
 and ABCF gene subfamilies were ubiquitously and highly expressed in all
 tissues while the members in other gene subfamilies were differentially
 expressed. Conclusions: Thirteen more lamprey ABC transporter genes were
 identified in this study compared with a previous study. By concatenating
 the same gene sequences from the two lampreys, more full length sequences
 were obtained, which significantly improved both the assignment of gene
 names and the phylogenetic trees compared with a previous analysis using
 partial sequences. The ABC gene subfamilies in chordates have undergone
 obvious expansion or contraction. The ABCA subfamily showed the highest
 gene expansion rate during chordate evolution. The evolution of ABC
 transporters in lampreys requires further evaluation because the present
 results are based on a draft genome.
description: Phytree-original-data
DOI: 10.5281/zenodo.18047693
title: VSL_BRAND1_70F_1_23C_0k_HY_single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5281/zenodo.18388995
title: VSL_BRAND1_70F_1_23C_0k_HY_single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5061/dryad.kg017
title: Data from: Photosynthetic and phenological responses of dwarf shrubs to the depth and properties of snow

description: Snow is known to have a major impact on vegetation in arctic ecosystems,
 but little is known about how snow affects plants in boreal forests, where
 the snowpack is uneven due to canopy impact. The responses of two dwarf
 shrubs, the evergreen Vaccinium vitis-idaea and the deciduous V.
 myrtillus, to snow conditions were studied in a snow manipulation
 experiment in southern Finland. The thermal insulation of the snowpack was
 expected to decrease with partial removal or compression of the snow,
 while addition of snow was expected to have the opposite effect. The
 penetration of light was manipulated by partial removal of snow or by
 formation of an artificial ice layer in the snowpack. CO2 exchange
 measurements that were carried out at the time of maximum snow depth in
 late March indicated significant photosynthetic activity in the leaves of
 V. vitis-idaea under snow. Net gain of CO2 was observed in the daytime on
 all the manipulation plots, excluding the snow addition plots, where light
 intensity was very low. The subnivean photosynthesis compensated for a
 substantial proportion (up to 80%) of the respiratory CO2 losses.
 Chlorophyll fluorescence measurements indicated reduced potential capacity
 of photosystem II in the leaves of V. vitis-idaea on those plots where
 snow cover was thin. Neither V. vitis-idaea nor V. myrtillus suffered from
 frost damage (assessed as electrolyte leakage) when thermal insulation was
 reduced by means of snow manipulations. No phenological responses were
 observed in V. vitis-idaea, but in V. myrtillus bud burst, leaf unfolding
 and flowering were advanced by 1–3 days on the addition plots. The results
 of the present study show that dwarf shrubs respond to not only the
 thickness of snow but also the physical properties of snow, both of which
 are expected to change due to climatic warming.
description: Saarinen et
 al_oikosField data collected for
 the paper 10.1111/oik.02233. For details, see
 ReadMe.txt.