cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k66j68h
title: Data from: Spatio-temporal scaling of biodiversity in acoustic tropical bird communities

description: Automated analysis of acoustic communities is a rapidly emerging approach
 for the characterization and monitoring of biodiversity. To evaluate its
 utility, we should verify that such “bioacoustics” can accurately detect
 ecological signal in spatiotemporal acoustic data. Targeting the
 Biological Dynamics of Forest Fragments Project sites in Brazil, we ask:
 What is the relative contribution of the spatial, temporal and habitat
 dimension to variation in bird acoustic communities in a previously
 fragmented tropical rainforest? Does the functional diversity of bird
 communities scale similarly to space and time as does species diversity,
 when both are recorded by bioacoustics means? Overall, is the imprint of
 landscape fragmentation 30 years ago still audible in the present‐day
 soundscape? We sampled forty‐four sites in secondary forest and 107 sites
 in old‐growth forest, resulting in 11,000 hours of audio recordings. We
 detected 60 bird species with satisfactory precision and recovered a
 linear log‐log relation between sampling time and species diversity. Sites
 in primary forest host more species than sites in secondary forest, but
 the difference decreased with sampling time, as the slope was slightly
 higher in secondary than primary forests. Functional diversity, as exposed
 by vocalizing birds, accumulates faster than does species diversity. The
 similarity among local communities decreases with distance in both time
 and space, but stability in time is remarkably high: two acoustic samples
 from the same site one year (or more) apart prove more similar than two
 samples taken at the same time but from sites situated just a few hundred
 meters apart. These findings suggest that habitat modification can be
 heard as a long‐lasting imprint on the soundscape of regenerating habitats
 and identify Soundscape–Area and Soundscape–Time Relations as a promising
 tool for biodiversity research, applied biomonitoring and restoration
 ecology.
description: all_data_0.9
DOI: 10.5061/dryad.1kt2n9v
title: Data from: Experimental evidence for the role of sexual selection in the evolution of cuticular hydrocarbons in the dung beetle, Onthophagus taurus

description: A role for sexual selection in the evolution of insect cuticular
 hydrocarbons (CHCs) is suggested by observations of selection acting on
 male CHCs during female mate choice. However, evidence that CHCs evolve in
 response to sexual selection is generally lacking, and there is a need to
 extend our understanding beyond well-studied taxa. Experimental evolution
 offers a powerful approach to investigate the effect of sexual selection
 on the evolution of insect CHCs. We conducted such an experiment using the
 dung beetle, Onthophagus taurus. After six, 12 and 21 generations of
 experimental evolution, we measured the CHCs of beetles from three
 populations subject to sexual selection and three populations within which
 sexual selection had been removed via enforced monogamy. We found that the
 male CHC profile responded to the experimental removal of sexual
 selection. Conversely, the CHC profile of females responded to the
 presence of sexual selection but not to its removal. These results show
 that sexual selection can be an important mechanism affecting the
 evolution of insect CHCs, and that male and female CHCs can evolve
 independently.
description: Sexual selection and
 evolution of CHCs_Data
DOI: 10.5061/dryad.63v6b83
title: Data from: Imaging and manipulating pituitary function in the awake mouse

description: Extensive efforts have been made to explore how the activities of multiple
 brain cells combine to alter physiology through imaging and cell-specific
 manipulation in different animal models. However, the temporal regulation
 of peripheral organs by the neuroendocrine factors released by the brain
 is poorly understood. We have established a suite of adaptable
 methodologies to interrogate in vivo the relationship of hypothalamic
 regulation with the secretory output of the pituitary gland, which has
 complex functional networks of multiple cell types intermingled with the
 vasculature. These allow imaging and optogenetic manipulation of cell
 activities in the pituitary gland in awake mouse models, in which both
 neuronal regulatory activity and hormonal output are preserved. This
 methodology is now readily applicable for longitudinal studies of
 short-lived events (e.g. calcium signals controlling hormone exocytosis)
 and slowly-evolving processes such as tissue remodelling in health and
 disease over a period of days to weeks.
description: Supplementary
 information_Hoa et al_EndocrinologySupplementary
 information. 6 sup figuresVideo
 1Video 1. Head-fixed in
 vivo imaging of pituitary blood flow (see Figure 1F, right panel). 100
 frames/sec.Video
 2Video 2. Head-fixed in
 vivo imaging of pituitary cells expressing GCAMP6s (see Figure 4G). 10
 frames/sec.Video
 3
DOI: 10.5061/dryad.1v26h11
title: Data from: The role of bite force in the evolution of head shape and head shape dimorphism in Anolis lizards

description: 1. Patterns of convergent evolution in head shape, combined with
 performance measures, provide ideal opportunities to understand the
 processes driving its evolution. Anole lizards represent an excellent
 subject to test this, as recurrent habitat specialists or ecomorphs
 evolved independently across different islands. 2. We show that phenotypic
 similarity corresponds to both phylogenetic similarity and similarity in
 habitat, indicating that there is convergent evolution in head shape among
 ecomorphs. Moreover, we show that the evolution of tall, wide heads
 correlates with the evolution of higher bite forces, driving head shape
 variation among and within ecomorphs. 3. In addition, the processes
 affecting head shape variation can differ between sexes, leading to sexual
 head shape dimorphism. These processes might, however, still depend on the
 habitat. Consequently, there could also be convergent evolution in head
 shape dimorphism among ecomorphs. 4. We found no evidence for convergent
 evolution in sexual head shape dimorphism. Moreover, the sexual head shape
 dimorphism correlates poorly with bite force, suggesting that intersexual
 head shape differences are related to other functions. Different processes
 are thus driving the evolution of head shape and head shape dimorphism.
description: Mean head size and bite
 force_AnolisMean ± S.D. of each
 log-transformed size variable and bite force per sex per species, as well
 as the ecomorph and the amount of specimens (N) used per species. Used
 abbreviations: CG = crown-giant, GB = Grass-bush, TC = Trunk-crown, TG =
 Trunk-ground, Tr = Trunk, Tw = Twig; SVL = snout-vent-length, HW = Head
 width, HH = Head height, HL = Head length, LJL = Lower jaw Length, QL =
 Quadrate length, CL = Coronoid length, BF = Bite force.Table
 means.xlsxMean head shape and bite
 force_AnolisMean ± S.D. of each
 shape variable and size-corrected bite force per sex per species, as well
 as the ecomorph and the amount of specimens (N) used per species. Used
 abbreviations: CG = crown-giant, GB = Grass-bush, TC = Trunk-crown, TG =
 Trunk-ground, Tr = Trunk, Tw = Twig; HW = Head width, HH = Head height, HL
 = Head length, LJL = Lower jaw Length, QL = Quadrate length, CL = Coronoid
 length, sBF = size-corrected Bite force. Shape variables are calculated as
 the residuals of a linear regression against
 snout-vent-length.Table size corrected
 means.xlsxDimorphism
 degrees_AnolisOverview of the
 dimorphism degrees of each head shape variable and size-corrected bite
 force in 26 Anolis species (CG = crown-giant, GB = Grass-bush, TC =
 Trunk-crown, TG = Trunk-ground, Tr = Trunk, Tw = Twig) Dimorphism degrees
 are calculated as
 log(Mean_measurement_male)-log(Mean_measurement_female)Table dimorphism
 degrees.xlsx
DOI: 10.5061/dryad.10rp4mn
title: Data from: Kin but less than kind: within-group male relatedness does not increase female fitness in seed beetles

description: Theory maintains within-group male relatedness can mediate sexual conflict
 by reducing male-male competition and collateral harm to females. We
 tested whether male relatedness can lessen female harm in the seed beetle
 Callosobruchus maculatus. Male relatedness did not influence female
 lifetime reproductive success or individual fitness across two different
 ecologically relevant scenarios of mating competition. However, male
 relatedness marginally improved female survival. Because male relatedness
 improved female survival in late life when C. maculatus females are no
 longer producing offspring, our results do not provide support for the
 role of within-group male relateness in mediating sexual conflict. The
 fact that male relatedness improves the post-reproductive part of female
 life cycle strongly suggests that the effect is non-adaptive. We discuss
 adaptive and non-adaptive mechanisms that could result in reduced female
 harm in this and previous studies and suggest that cognitive error is a
 likely explanation.
description: Data on female lifespan
 and total reproductionData on female lifespan
 (number of days) as well as total number of eclosed young produced over
 her lifetime.Berg_lifespan_totrep_data.csvFemale age-specific (daily) reproductionTotal number of eclosed young produced per day by a female during her lifetime.Berg_agespecific_reproduction.csv
DOI: 10.5061/dryad.9tf3hr5
title: Data from: Body shape is related to attempt rate and passage success of brook trout at in-stream barriers

description: 1. The ability to move between habitats has important implications for
 fitness in many species. In-stream barriers such as culverts can impede
 movements of riverine fishes and thus reduce connectivity between
 habitats. The ability of fish to overcome barriers is related to the
 features of the environment and the barrier itself, but also to
 physiological, morphological, and behavioural traits of the fish. Among
 these, body shape varies among and within species and influences swimming
 ability, a key component of passage performance through culverts. 2. We
 conducted an experimental study on wild brook trout (Salvelinus
 fontinalis) to assess the effects of individual body shape on attempt rate
 and passage success through culverts on six streams. 3. A more streamlined
 body shape was associated with an increased motivation to enter and ascend
 the culverts, and, to a lesser extent, with the probability of successful
 passage once an attempt was staged. Motivation and successful passage were
 also influenced by the density of conspecifics below the culvert, time of
 day, fish body size, and water velocity. 4. Policy implications While fish
 body shape is expected to influence swimming performance, our research
 shows the most important effect of body shape to be on an individual’s
 motivation to stage passage attempts at culverts. This study points to an
 important connection between behaviour and morphological traits that
 influence passage success and suggests that in-stream barriers may be an
 important agent of selection on behavior and morphology in wild fish
 populations.
description: Goerigetal_BodyShapeCulvertPassageThis data package allows reproducing all analysis and figures included in the article. The package comprises R scripts and .csv files.
DOI: 10.5061/dryad.sd7cd06
title: Data from: Unsupervised machine learning reveals mimicry complexes in bumble bees occur along a perceptual continuum

description: Müllerian mimicry theory states that frequency dependent selection should
 favour geographic convergence of harmful species onto a shared colour
 pattern. As such, mimetic patterns are commonly circumscribed into
 discrete mimicry complexes each containing a predominant phenotype.
 Outside a few examples in butterflies, the location of transition zones
 between mimicry complexes and the factors driving mimicry zones has rarely
 been examined. To infer the patterns and processes of Müllerian mimicry,
 we integrate large-scale data on the geographic distribution of colour
 patterns of social bumble bees across the contiguous United States and use
 these to quantify colour pattern mimicry using an innovative, unsupervised
 machine learning approach based on computer vision. Our data suggest that
 bumble bees exhibit geographically clustered, but sometimes imperfect
 colour patterns and that mimicry patterns gradually transition spatially,
 rather than exhibit discrete boundaries. Additionally, examination of
 colour pattern transition zones of three comimicking, polymorphic species,
 where active selection is driving phenotype frequencies, revealed their
 transition zones to differ in location within a broad region of poor
 mimicry. Potential factors influencing mimicry transition zone dynamics
 are discussed.
description: Bumble_bee_colour_mimicry_dataThis repository contains datafiles and scripts used in “Unsupervised machine learning reveals mimicry complexes in bumble bees occur along a perceptual continuum.” Specifically, we provide scripts, species colour diagrams, and data files used to infer the extent of mimetic fidelity and the properties of mimicry transition zones in bumble bees across the contiguous United States.
DOI: 10.5061/dryad.4p6n481
title: Data from: Performance of gene expression analyses using de novo assembled transcripts in polyploid species

description: Motivation: Quality of gene expression analyses using de novo assembled
 transcripts in species that experienced recent polyploidization remains
 unexplored. Results: Differential gene expression (DGE) analyses using
 putative genes inferred by Trinity, Corset and Grouper performed slightly
 differently across five plant species that experienced various poly-ploidy
 histories. In species that lack recent polyploidy events that occurred in
 the past several millions of years, DGE analyses using de novo assembled
 transcriptomes identified 54–82% of the differen-tially expressed genes
 recovered by mapping reads to the reference genes. However, in species
 that experienced more recent polyploidy events, the percentage decreased
 to 21–65%. Gene co-expression network analyses using de novo assemblies
 vs. mapping to the reference genes recov-ered the same module that
 significantly correlated with treatment in one species that lacks recent
 polyploidization.
description: 1.4_Trinity_assemblies.tarDe novo transcriptome assemblies from five species1.6_reference_base_coverage.tarThe sequencing depth files generated by Samtools. The files were used to calculate the total number of reference bases, the number and proportion of expressed reference bases2.2_2.3_getting_Corset_Grouper_cluster_information.tar.gzFiles used to generate Corset and Grouper clusters5_evaluate_dge.tar.gzfiles that used for evaluating the DGE analyses for wheat. RNA seq data were from Li et al. (2019)6_gene_coexpression_WGCNA.tar.gz3.2_evaluating_clustering.tarClusters and files used to evaluate quality of clustersReadme
DOI: 10.5061/dryad.tb3243s
title: Data from: The Life Aquatic: an association between habitat type and skin thickness in snakes

description: An aquatic animal faces challenges not encountered by its terrestrial
 counterparts, promoting adaptive responses in multiple traits. For
 example, a thicker dermis might protect snakes when they are pushed
 against sharp objects by water currents, and might enable a snake to shed
 fouling organisms attached to its skin. We thus predicted that marine
 snakes should have thicker skin than terrestrial species; and that smaller
 sea snakes should have relatively thicker skin (because absolute, not
 relative, thickness determines vulnerability to fouling). Measurements of
 192 snakes of 44 species supported those predictions. Many (but not all)
 sea snakes have skins 50% thicker than those of terrestrial and amphibious
 snake species, representing multiple independent evolutionary origins of
 thicker skin (in acrochordids, and Laticauda sea kraits, and both main
 clades of hydrophiine sea snakes). Marine snakes showed different
 allometries of skin thickness than did their terrestrial counterparts;
 larger snakes had thicker skin within and among species of amphibious and
 terrestrial snakes, but larger aquatic snake species had thinner skin than
 did smaller taxa. Interspecific variation in skin thickness was primarily
 due to increased collagen in the deep dermis, a physical barrier
 well-suited to protecting against physical injury and to resisting
 penetration by epibionts.
description: Skin
 thicknessskin thickness 6 March
 2019.xlsx
DOI: 10.5061/dryad.kb89vs7
title: Data from: Timing manipulations reveal the lack of a causal link across timing of annual-cycle stages in a long-distance migrant

description: Organisms need to time their annual-cycle stages, like breeding and
 migration, to occur at the right time of the year. Climate change has
 shifted the timing of annual-cycle stages at different rates, thereby
 tightening or lifting time constraints of these annual-cycle stages, a
 rarely studied consequence of climate change. The degree to which these
 constraints are affected by climate change depends on whether consecutive
 stages are causally linked (I) or whether the timing of each stage is
 independent of other stages (II). Under (I), a change in timing in one
 stage has knock-on timing effects on subsequent stages, whereas under (II)
 a shift in the timing of one stage affects the degree of overlap with
 previous and subsequent stages. For testing this we combined field
 manipulations, captivity measurements and geolocation data. We advanced
 and delayed hatching dates in pied flycatchers (Ficedula hypoleuca) and
 measured how the timing of subsequent stages (male moult and migration)
 were affected. There was no causal effect of manipulated hatching dates on
 the onset of moult and departure to Africa. Thus, advancing hatching dates
 reduced the male moult-breeding overlap with no effect on the
 moult-migration interval. Interestingly, the wintering location of delayed
 males was more westwards, suggesting that delaying the termination of
 breeding carries-over to winter location. Because we found no causal
 linkage of the timing of annual-cycle stages, climate change can shift
 these stages at different rates, with the risk that the time available for
 some become so short that this will have major fitness consequences.
description: Tomotani_etal_2019Experimental data collected in the field and partly in captivity. The Excel file contains 5 sheets with all data used in the manuscript and an additional sheet with explanations for each column. It contains the data used to analyse: a) timing of egg-laying, hatching and moult; b) prolactin, arrival, departure and wintering longitude; c) adult condition; d) the number of visits to the nest; e) chick condition.
DOI: 10.5061/dryad.17q550q
title: Data from: Spatial variation in bird pollination and its mitigating effects on the genetic diversity of pollen pools accepted by Camellia japonica trees within a population at a landscape level

description: Bird pollination can vary spatially in response to spatial fluctuations in
 flowering even within plant populations. In this study, we examined the
 hypothesis that the spatial variation in bird pollination may induce
 mitigating effects which maintains or increases genetic diversity of
 pollen pools at local sites with low flowering densities. To test this
 hypothesis, we analyzed the landscape-level genetic effects within a
 population of Camellia japonica on the pollen pools accepted by
 individuals in two reproductive years by using genotypes at eight
 microsatellite loci of 1323 seeds from 19 seed parents. Regression
 analyses using the quadratic models of correlated paternity between pollen
 pools against spatial distances between the seed-parent pairs revealed not
 only local pollination but also some amount of long-distance pollen
 dispersal. The genetic diversity of pollen pools accepted by seed parents
 tended to be negatively related to the densities of flowering individuals
 near the seed parents during winter (when the effective pollination of C.
 japonica is mediated mostly by Zosterops japonica). We show that the low
 density of flowering individuals may induce the expansion of the foraging
 areas of Z. japonica and consequently increase the genetic diversity of
 pollen pools. This spatial variation in bird pollination may induce the
 mitigating effects on the C. japonica population. The comparisons between
 the two study years indicate that the overall pattern of bird pollination
 and the genetic effects described here, including the mitigating effects,
 may be stable over time.
description: Camellia_japonica_Data
DOI: 10.5061/dryad.0bv02ss
title: Data from: Spatio-temporal variation of biotic and abiotic stress agents determines seedling survival in assisted oak regeneration

description: 1. Mediterranean oak woodlands are currently undergoing considerable
 anthropogenic changes that globally threaten their long-term persistence.
 Restoration efforts via assisted regeneration depend on species traits and
 type of stress. However, how different sources of stress vary across space
 (microsites) and time (intra and inter-annual variation) for co-occurring
 oak species remains largely unknown. 2. We examined spatio-temporal
 variation of biotic (herbivory, seed predation) and abiotic (drought)
 stress agents to evaluate seedling survival across different regeneration
 microsites, and considering two climatically contrasting years. We used
 two co-occurring species of contrasting ecology and leaf traits in
 California oak woodlands: the deciduous Quercus lobata and the evergreen
 Q. agrifolia. 3. Most oak seedlings (98.8%) suffered from some type of
 stress. For both species, summer drought was the main cause of mortality,
 followed by rodent damage, ungulate browsing and insect damage. Rodents
 represented the predominant biotic stress, as all rodent-affected
 seedlings eventually died. Interactions among stress factors were nuanced:
 insect and ungulate-browsing stresses were greater during dry year,
 whereas rodent damage was similar in dry and average years.
 Intra-annually, rodent damage was the main stress agent in early spring,
 whereas water stress and ungulate-browsing were greater in late
 spring-early fall. Plant species traits were also determinant: overall,
 the evergreen species had greater survival probability than the deciduous
 one. 4. Across microsites, water stress showed higher occurrence in open
 grassland habitats, while rodent damage was prevalent under palatable
 shrubs and ungulate browsing under conspecific trees. Shrub and tree cover
 reduced damage attributed to water stress but increased rodent and
 ungulate damage, respectively. Interestingly, lower water stress but
 higher rodent damage was found further inside the shrub cover. 5.
 Synthesis and applications. Intra and inter-annual variation are critical
 determinants of stress type and intensity on oak recruitment. Spatial
 variation (microsite identity) is also informative to manipulate stress
 agent impact. We conclude that assisted regeneration should consider not
 only the predominance and lethality of each stress type and microsite, but
 also the interactions thereof and thus manipulate protective microsites
 accordingly.
description: Plantation in Santa Cruz
 Mountains, Northern, CaliforniaEach row is a plant. For
 each plant is defined the species, microsite, protection, position,
 survival and stress agents.Plantation_Dryad.xlsx