cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.db6s4
title: Data from: Linking vital rates of landbirds on a tropical island to rainfall and vegetation greenness

description: Remote tropical oceanic islands are of high conservation priority, and
 they are exemplified by range-restricted species with small global
 populations. Spatial and temporal patterns in rainfall and plant
 productivity may be important in driving dynamics of these species. Yet,
 little is known about environmental influences on population dynamics for
 most islands and species. Here we leveraged avian capture-recapture,
 rainfall, and remote-sensed habitat data (enhanced vegetation index [EVI])
 to assess relationships between rainfall, vegetation greenness, and
 demographic rates (productivity, adult apparent survival) of three native
 bird species on Saipan, Northern Mariana Islands: rufous fantail
 (Rhipidura rufifrons), bridled white-eye (Zosterops conspicillatus), and
 golden white-eye (Cleptornis marchei). Rainfall was positively related to
 vegetation greenness at all but the highest rainfall levels. Temporal
 variation in greenness affected the productivity of each bird species in
 unique ways. Predicted productivity of rufous fantail was highest when dry
 and wet season greenness values were high relative to site-specific 5-year
 seasonal mean values (i.e., relative greenness); while the white-eye
 species had highest predicted productivity when relative greenness
 contrasted between wet and dry seasons. Survival of rufous fantail and
 bridled white eye was positively related to relative dry-season greenness
 and negatively related to relative wet-season greenness. Bridled white-eye
 survival also showed evidence of a positive response to overall greenness.
 Our results highlight the potentially important role of rainfall regimes
 in affecting population dynamics of species on oceanic tropical islands.
 Understanding linkages between rainfall, vegetation, and animal population
 dynamics will be critical for developing effective conservation strategies
 in this and other regions where the seasonal timing, extent, and
 variability of rainfall is expected to change in the coming decades.
description: Saipan bird, rainfall,
 and EVI data and analysis code7 data files and 3 R
 workspaces (for survival analyses) are included to reproduce results
 reported in the paper. Individual files and R code are included in the
 README.pdf file.SaraccoPONEdata.zip
DOI: 10.5061/dryad.n5p7g
title: Data from: A role of OCRL in clathrin-coated pit fission and uncoating revealed by studies of Lowe syndrome cells

description: Mutations in the inositol 5-phosphatase OCRL cause Lowe syndrome and
 Dent's disease. Although OCRL, a direct clathrin interactor, is
 recruited to late-stage clathrin-coated pits, clinical manifestations have
 been primarily attributed to intracellular sorting defects. Here we show
 that OCRL loss in Lowe syndrome patient fibroblasts impacts
 clathrin-mediated endocytosis and results in an endocytic defect. These
 cells exhibit an accumulation of clathrin-coated vesicles and an increase
 in U-shaped clathrin-coated pits, which may result from sequestration of
 coat components on uncoated vesicles. Endocytic vesicles that fail to lose
 their coat nucleate the majority of the numerous actin comets present in
 patient cells. SNX9, an adaptor that couples late-stage endocytic coated
 pits to actin polymerization and which we found to bind OCRL directly,
 remains associated with such vesicles. These results indicate that OCRL
 acts as an uncoating factor and that defects in clathrin-mediated
 endocytosis likely contribute to pathology in patients with OCRL
 mutations.
description: OCRL interactors
 identified by label-free quantitative proteomics from cell lines
 expressing GFP-OCRL near endogenous levelsproteinGroups_OCRL1x_vs_GFP.xlsxOCRL interactors identified by label-free quantitative proteomics in immunoprecipitates from cell lines expressing GFP-OCRL at 5X endogenous levelsproteinGroups_OCRL5x_vs_GFP.xlsx
DOI: 10.5061/dryad.gv0n8
title: Data from: High temperatures reveal cryptic genetic variation in a polymorphic female sperm storage organ

description: Variation in female reproductive morphology may play a decisive role in
 reproductive isolation by affecting the relative fertilization success of
 alternative male phenotypes. Yet, knowledge of how environmental variation
 may influence the development of the female reproductive tract and thus
 alter the arena of post-copulatory sexual selection is limited. Yellow
 dung fly females possess either three or four sperm storage compartments,
 a polymorphism with documented influence on sperm precedence. We performed
 a quantitative genetics study including 12 populations reared at three
 developmental temperatures complemented by extensive field data to show
 that warm developmental temperatures increase the frequency of females
 with four compartments, revealing striking hidden genetic variation for
 the polymorphism. Systematic genetic differentiation in growth rate and
 spermathecal number along latitude, and phenotypic covariance between the
 traits across temperature treatments suggest that the genetic architecture
 underlying the polymorphism is shaped by selection on metabolic rate. Our
 findings illustrate how temperature can modulate the preconditions for
 sexual selection by differentially exposing novel variation in
 reproductive morphology. This implies that environmental change may
 substantially alter the dynamics of sexual selection. We further discuss
 how temperature-dependent developmental plasticity may have contributed to
 observed rapid evolutionary transitions in spermathecal morphology.
description: SPdataARCNatural populations sampled along a latitudinal cline within Europe. Collected in 2007 and 2009. Data from common garden experiments in 2008 & 2009 on: tibia length (body size), development time, growth rate, and Spermathecal number (3 or 4). Common garden included 3 developmental temperatures: 12, 18 or 24C. Data only on females.
DOI: 10.5061/dryad.8kt67
title: Data from: Experimental manipulation of brood size affects several levels of phenotypic variance in offspring and parent pied flycatchers

description: Parental provisioning of offspring should reflect selection on life
 history aspects of parenting and on foraging behavior. Life history and
 foraging theory generally make predictions about mean behavior, but some
 circumstances might favor changes in the variance of parent and offspring
 behaviors. We analyzed data on free-living pied flycatchers (Ficedula
 hypoleuca) experiencing a brood size manipulation. We used double
 hierarchical generalized linear models to investigate patterns in means
 and variances of provisioning, brood begging, and parental mass. As
 predicted by life history theory, parents with enlarged broods of
 intensely begging nestlings fed at higher rates and delivered more food
 per unit of time. They also delivered food at a more consistent rate. This
 contradicts the prediction from variance-sensitive foraging theory that
 parents facing higher brood demand should choose more variable foraging
 options. Indirect evidence suggests that reduced variance in trip time
 arose from shifts in parental time budgets. Exploratory analyses revealed
 patterns in residual variance of both nestling begging and parental mass
 changes, with enlarged broods begging less consistently and female body
 mass changes being more variable after longer foraging trips. We show that
 parent pied flycatchers simultaneously adjust means and variances in
 multiple aspects of their provisioning effort to changes in brood demand
 and that these responses might be linked with nestling begging and changes
 in parental body mass. Our study highlights both the importance of
 adopting sophisticated statistical approaches and the potential
 intersection of two bodies of theory that may affect strategic adjustments
 of individuals engaged in central place provisioning.
description: Pied Flycatcher Data for
 BEAS paperContains the variables
 and cases used in all analyses described in associated
 paper.PF
 Data BES.csv
DOI: 10.5061/dryad.576hg
title: Data from: Widespread hybridization within mound-building wood ants in Southern Finland results in cytonuclear mismatches and potential for sex-specific hybrid breakdown

description: Hybridization and gene flow between diverging lineages is increasingly
 recognized as a common evolutionary process and its consequences can vary
 from hybrid breakdown to adaptive introgression. We have previously found
 a population of wood ant hybrids between Formica aquilonia and F.
 polyctena that shows antagonistic effects of hybridization: females with
 introgressed alleles show hybrid vigour, whereas males with the same
 alleles show hybrid breakdown. Here we investigate whether hybridization
 is a general phenomenon in this species pair, and analyze 647 worker
 samples from 16 localities in Finland using microsatellite markers and a
 1200 bp mitochondrial sequence. Our results show that 27 sampled nests
 contained parental-like gene pools (six putative F. polyctena and 21
 putative F. aquilonia) and all remaining nests (69), from nine localities,
 contained hybrids of varying degrees. Patterns of genetic variation
 suggest these hybrids arise from several hybridization events or, instead,
 have backcrossed to the parental gene pools to varying extents. In
 contrast to expectations, the mitochondrial haplotypes of the parental
 species were not randomly distributed among the hybrids. Instead, nests
 that were closer to parental-like F. aquilonia for nuclear markers
 preferentially had F. polyctena's mitochondria and vice versa. This
 systematic pattern suggests there may be underlying selection favoring
 cytonuclear mismatch and hybridization. We also found a new hybrid
 locality with strong genetic differences between the sexes similar to
 those predicted under antagonistic selection on male and female hybrids.
 Further studies are needed to determine the selective forces that act on
 male and female genomes in these newly discovered hybrids.
description: Microsatellite_genotype_dataThis data file contains all the microsatellite genotype data. Samples are coded by their ID, nest number and locality. File contains three sheets. The first sheet contains worker genotypes used in Structure and PCoA analyses. The second sheet contains male and female (worker) genotypes from locality Tvärminne Road. The second sheet contains male, female (young queens) and female worker genotypes from locality Halsholmen. Diploid males are indicated. All other males are haploid, but their genotypes are coded as diploid (e.g. allele 198 in a male is coded 198/198).Genotype_data_to_dryad.xlsxMitochondrial_sequencesThis data file contains all the mitochondrial sequences used in the study Beresford et al. in a fasta format.mt_sequences_to_dryad.fasta
DOI: 10.5061/dryad.gg39253p
title: Data from: Fast molecular evolution associated with high active metabolic rates in poison frogs

description: Molecular evolution is simultaneously paced by mutation rate, genetic
 drift, and natural selection. Life history traits also affect the speed of
 accumulation of nucleotide changes. For instance, small body size, rapid
 generation time, production of reactive oxygen species, and high resting
 metabolic rate (RMR) are suggested to be associated with faster rates of
 molecular evolution. However, phylogenetic correlation analyses failed to
 support a relationship between RMR and molecular evolution in ectotherms.
 In addition, resting metabolic rate might underestimate the metabolic
 budget (e.g., digestion, reproduction or escaping predation). An
 alternative is to test other metabolic rates, such as active metabolic
 rate (AMR), and their association with molecular evolution. Here, I
 present comparative analyses of the associations between life history
 traits (i.e., AMR, RMR, body mass, and fecundity) with rates of molecular
 evolution of nuclear and mitochondrial loci from a large ectotherm clade,
 the poison frogs. My results support a strong positive association between
 mass-specific AMR and rates of molecular evolution for both mitochondrial
 and nuclear loci. In addition, I found weaker and genome specific
 covariates such as mass and fecundity for mitochondrial and nuclear loci,
 respectively. No direct association was found between mass-specific RMR
 and rates of molecular evolution. Therefore, a multifactorial model that
 includes AMR might explain the rates of molecular evolution in ectothermic
 lineages.
description: Santos_MBE_12and16SSantos_MBE_ND1ND2Cytb2_No_A_juaniSantos_MBE_nucleargenesSantos_MBE_tRNAsVLMSantos_supermatrix_chrono_treeSantos_supermatrix_ML_tree
DOI: 10.5061/dryad.k8g2672
title: Data from: Land-use change interacts with climate to determine elevational species redistribution

description: Climate change is driving global species redistribution with profound
 social and economic impacts. However, species movement is largely
 constrained by habitat availability and connectivity, of which the
 interaction effects with climate change remain largely unknown. Here we
 examine published data on 2798 elevational range shifts from 43 study
 sites to assess the confounding effect of land-use change on
 climate-driven species redistribution. We show that baseline forest cover
 and recent forest cover change are critical predictors in determining the
 magnitude of elevational range shifts. Forest loss positively interacts
 with baseline temperature conditions, such that forest loss in warmer
 regions tends to accelerate species’ upslope movement. Consequently, not
 only climate but also habitat loss stressors and, importantly, their
 synergistic effects matter in forecasting species elevational
 redistribution, especially in the tropics where both stressors will
 increase the risk of net lowland biotic attrition.
description: Shift_site_43Shift data used for site-level (aggregated) analysis (n =43)Supplementary Data 1.xlsxShift_species_2798Data used for species-level (disaggregated) analysis (n = 2798)Supplementary Data 2.xlsx
DOI: 10.5061/dryad.4187519
title: Data from: Proactive avoidance behaviour and pace-of-life syndrome in Atlantic salmon

description: Individuals in a fish population differ in key life history traits such as
 growth rate and body size. This raises the question of whether such traits
 cluster along a fast-slow growth continuum according to a pace-of-life
 syndrome (POLS). Fish species like salmonids may develop a bimodal size
 distribution, providing an opportunity to study the relationships between
 individual growth and behavioural responsiveness. Here we test whether
 proactive characteristics (bold behaviour coupled with low post-stress
 cortisol production) are related to fast growth and developmental rate in
 Atlantic salmon, Salmo salar. Boldness was tested in a highly controlled
 two-tank hypoxia test were oxygen levels were gradually decreased in one
 of the tanks. All fish became inactive close to the bottom at 70% oxygen
 saturation. At oxygen saturation level of 40% a fraction of the fish
 actively sought out to avoid hypoxia. A proactive stress coping style was
 verified by lower cortisol response to a standardized stressor. Two
 distinct clusters of bimodal growth trajectories were identified, with
 fast growth and early smoltification in 80% of the total population. There
 was a higher frequency of proactive then reactive individuals in this
 fast-developing fraction of fish. The smolts were associated with higher
 post-stress plasma cortisol than parr, and the proactive smolts leaving
 hypoxia had significant lower post-stress cortisol than the stayers. The
 study demonstrated a link between a proactive coping and fast growth and
 developmental ratio, and suggests that selection for domestic production
 traits promotes this trait cluster.
description: Data from Damsgård et
 al
DOI: 10.5061/dryad.f65bn
title: Data from: Are ant supercolonies crucibles of a new major transition in evolution?

description: The biological hierarchy of genes, cells, organisms and societies is a
 fundamental reality in the living world. This hierarchy of entities did
 not arise ex nihilo at the origin of life, but rather has been serially
 generated by a succession of critical events known as ‘evolutionary
 transitions in individuality’ (ETIs). Given the sequential nature of ETIs,
 it is natural to look for candidates to form the next hierarchical tier.
 We analyse claims that these candidates are found among ‘supercolonies’,
 ant populations in which discrete nests cooperate as part of a wider
 collective, in ways redolent of cells in a multicellular organism.
 Examining earlier empirical work and new data within the recently proposed
 ‘Darwinian space’ framework, we offer a novel analysis of the evolutionary
 status of supercolonies and show how certain key conditions might be
 satisfied in any future process transforming these collaborative networks
 into true Darwinian individuals.
description: Formica aquilonia -
 MorphometricsLandmark assignation
 data from tps morphometry suite.Formica fennica -
 MorphometricsLandmark assignation
 data from tps morphometry suite.Formica pratensis -
 MorphometricsLandmark assignation
 data from tps morphometry suite.Formica pressilabris -
 MorphometricsLandmark assignation
 data from tps morphometry suite.Formica truncorum
 (non-supercolonial) - MorphometricsLandmark assignation
 data from tps morphometry suite.Formica truncorum
 (supercolonial) - MorphometricsLandmark assignation
 data from tps morphometry suite.All species - Foraging
 ResultsProtein/carbohydrate
 foraging experimentF. aquilonia -
 Aggression ResultsAggression
 bioassay.F. fennica - Aggression
 ResultsAggression
 bioassay.F. pratensis -
 Aggression ResultsAggression
 bioassay.F. pressilabris -
 Aggression ResultsAggression
 bioassay.F. truncorum
 (non-supercolonial) - Aggression ResultsAggression
 bioassay.F. truncorum
 (supercolonial) - Aggression ResultsAggression
 bioassay.
DOI: 10.5061/dryad.3dk40
title: Data from: Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus)

description: Double digest restriction site-associated DNA sequencing (ddRADseq) and
 target capture sequencing methods are used to explore population and
 phylogenetic questions in non-model organisms. ddRADseq offers a simple
 and reliable protocol for population genomic studies, however it can
 result in a large amount of missing data due to allelic dropout. Target
 capture sequencing offers an opportunity to increase sequencing coverage
 with little missing data and consistent orthologous loci across samples,
 although this approach has generally been applied to conserved markers for
 deeper evolutionary questions. Here, we combine both methods to generate
 high quality sequencing data for population genomic studies of all marine
 lobster species from the genus Jasus. We designed probes based on ddRADseq
 libraries of two lobster species (Jasus edwardsii and Sagmariasus
 verreauxi) and evaluated the captured sequencing data in five other Jasus
 species. We validated 4,465 polymorphic loci amongst these species using a
 cost effective sequencing protocol, of which 1,730 were recovered from all
 species, and 4,026 were present in at least three species. The method was
 also successfully applied to DNA samples obtained from museum specimens.
 This data will be further used to assess spatial-temporal genetic
 variation in Jasus species found in the Southern Hemisphere.
description: Probes sequences in
 fasta file formatMYcroarray custom
 baitset designed for target enriched sequencing in Jasus
 spp.probes_sequences.fasta
DOI: 10.5061/dryad.b0v7h
title: Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific

description: The role of speciation processes in shaping current biodiversity patterns
 represents a major scientific question for ecologists and biogeographers.
 Hence, numerous methods have been developed to determine the geography of
 speciation based on co-occurrence between sister-species. Most of these
 methods rely on the correlation between divergence time and several
 metrics based on the geographic ranges of sister-taxa (i.e. overlap,
 asymmetry). The relationship between divergence time and these metrics has
 scarcely been examined in a spatial context beyond regression curves.
 Mapping this relationship across spatial grids, however, may unravel how
 speciation processes have shaped current biodiversity patterns through
 space and time. This can be particularly relevant for coral reef fishes of
 the Indo-Pacific since the origin of the exceptional concentration of
 biodiversity in the Indo-Australian Archipelago (IAA) has been actively
 debated, with several alternative hypotheses involving species
 diversification and dispersal. We reconstructed the phylogenetic
 relationships between three species-rich families of coral reef fish
 (Chaetodontidae, Labridae, Pomacentridae) and calculated co-occurrence
 metrics between closely related lineages of those families. We
 demonstrated that repeated biogeographic processes can be identified in
 present-day species distribution by projecting co-occurrence metrics
 between related lineages in a geographical context. Our study also
 evidence that sister-species do not co-occur randomly across the
 Indo-Pacific, but tend to overlap their range within the IAA. We
 identified the imprint of two important biogeographic processes that
 caused this pattern in 48% of the sister-taxa considered: speciation
 events within the IAA and repeated divergence between the Indian and
 Pacific Ocean, with subsequent secondary contact in the IAA.
description: Chronogram of the
 Chaetodontidae familyThis file contains the
 consensus chronogram of the Chaetodontidae family in the nexus
 formattree_chae_cons.nexChronogram of the Labridae familyThis file contains the consensus chronogram of the Labridae family in the nexus format.tree_lab_cons.nexChronogram of the Pomacentridae familiyThis file contains the consensus chronogram of the Pomacentridae family in the nexus format.tree_poma_cons.nex