cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.03mn0
title: Data from: Conserved G-matrices of morphological and life-history traits among continental and island blue tit populations

description: The genetic variance–covariance matrix (G-matrix) summarizes the genetic
 architecture of multiple traits. It has a central role in the
 understanding of phenotypic divergence and the quantification of the
 evolutionary potential of populations. Laboratory experiments have shown
 that G-matrices can vary rapidly under divergent selective pressures.
 However, because of the demanding nature of G-matrix estimation and
 comparison in wild populations, the extent of its spatial variability
 remains largely unknown. In this study, we investigate spatial variation
 in G-matrices for morphological and life-history traits using long-term
 data sets from one continental and three island populations of blue tit
 (Cyanistes caeruleus) that have experienced contrasting population history
 and selective environment. We found no evidence for differences in
 G-matrices among populations. Interestingly, the phenotypic
 variance–covariance matrices (P) were divergent across populations,
 suggesting that using P as a substitute for G may be inadequate. These
 analyses also provide the first evidence in wild populations for additive
 genetic variation in the incubation period (that is, the period between
 last egg laid and hatching) in all four populations. Altogether, our
 results suggest that G-matrices may be stable across populations
 inhabiting contrasted environments, therefore challenging the results of
 previous simulation studies and laboratory experiments.
description: Data
 MorphologyThis file corresponds to
 the morphological data. All the variables required to perform the
 morphological animal models are contained in this
 table.Data.Morphology.csvData.LHTThis file corresponds to the life-history trait data. All the variables required to perform the life-history animal models are contained in this table.Pedigree MorphologyThis table contains the pedigree for the individuals used in the morphological animal models.Pedigree.Morphology.csvPedigree LHTThis table contains the pedigree for the individuals used in the life history animal models.Pedigree.LHT.csv
DOI: 10.5061/dryad.sd813
title: Data from: Heterozygosity and survival in blue tits (Cyanistes caeruleus): contrasting effects of presumably functional and neutral loci

description: The relationship between genetic diversity and fitness has important
 implications in evolutionary and conservation biology. This relationship
 has been widely investigated at the individual level in studies of
 heterozygosity-fitness correlations (HFC). General effects due to
 inbreeding and/or local effects at single loci have been used as
 explanations of HFC, but the debate about the causes of HFC in open,
 natural populations is still ongoing. Study designs that control for
 variation in the inbreeding level of the individuals, and knowledge on the
 function and location of the markers used to measure heterozygosity, are
 fundamental to understand the causes of HFC. Here we investigated
 correlations between individual heterozygosity and estimates of survival
 at different life-history stages in an open population of blue tits
 (Cyanistes caeruleus). For survival at the embryo, nestling and fledgling
 stage we used a full-sibling approach, i.e. we controlled for the level of
 inbreeding. We genotyped 1496 individuals with 79 microsatellites
 distributed across 25 chromosomes in another passerine and classified
 either as potentially functional (58 loci) or neutral (21 loci). We found
 different effects of standardized multilocus heterozygosity (SH):
 SHfunctional had a negative effect on the probability of hatching and
 local recruitment of females, whereas SHneutral had a positive effect on
 adult survival. The negative effects of functional loci are better
 explained by local effects, whereas the positive effects of neutral
 markers could reflect inbreeding effects in the population. Our results
 highlight the importance of considering the characteristics of the markers
 used in HFC studies and confirm the mixed effects of heterozygosity in
 different contexts (e.g. sex and life-history stage).
description: Single-locus
 heterozygosity of all individualsHeterozygosity (0 =
 homozygous and 1 = heterozygous) for all individuals and loci. Loci names
 see Olano-Marin et al. 2011, table 1.Olano_etal_hetero.txtEarly survival dataSurvival until hatching (hatched), survival until fledging (fledged) and survival until first breeding season (recruited) are listed for each chick. Year of birth (season), fledging mass at day 14, clutch size and z-transformed laying date are added when used in the analyses.Olano_etal_early_surv.txtYearling survival dataSurvival until next breeding seasons (survival) are listed for all yearlings. Year of first breeding season (season), sex (1 = male, 2 = female) and recruitment status (1 = local recruit, 0 = immigrant) are added.Olano_etal_yearling_surv.txt
DOI: 10.5061/dryad.s612m
title: Data from: Evidence for strategic cooperation in humans

description: Humans may cooperate strategically, cooperating at higher levels than
 expected from their short-term interests, to try and stimulate others to
 cooperate. To test this hypothesis, we experimentally manipulated the
 extent an individual's behaviour is known to others, and hence
 whether or not strategic cooperation is possible. In contrast with many
 previous studies, we avoided confounding factors by preventing individuals
 from learning during the game about either pay-offs or about how other
 individuals behave. We found clear evidence for strategic cooperators—just
 telling some individuals that their groupmates would be informed about
 their behaviour led to them tripling their initial level of cooperation,
 from 17 to 50%. We also found that many individuals play as if they do not
 understand the game, and their presence obscures the detection of
 strategic cooperation. Identifying such players allowed us to detect and
 study strategic motives for cooperation in novel, more powerful, ways.
description: Strategic_Coop_ms_dataData file used for all analyses within manuscript and ESM. Variables are annotated. Data overlaps with data used in two other studies (Burton-Chellew et al 2016, Conditional cooperation and confusion in public goods games, PNAS; and Burton-Chellew et al 2017, Social learning and the demise of costly cooperation in humans, PRSB).ms_Strategic_Coop_analyses_output_main_doc_POSTREVIEWA printout of the analyses conducted in SPSS for the results in the main document. Analyses were conducted via the GUI, but the log records the equivalent syntax.ms_Strategic_Coop_analyses_output_ESM_POSTREVIEWThe printout from the analyses conducted in SPSS for the ESM.
DOI: 10.5061/dryad.mb204
title: Data from: Adoption of alternative migratory tactics: a view from the ultimate mechanism and threshold trait changes in a salmonid fish

description: Partial migration, in which a portion of the population migrates while the
 rest of the population remains as residents, is a common form of
 migration. Alternative migratory tactics (AMTs) of partial migration are
 often determined by polygenic threshold traits. However, the ultimate
 mechanisms that drive inter-population variations in threshold traits are
 not well understood. We present a simple schematic model to explain how
 the threshold trait changes with fitness consequences under opposing
 natural and artificial selection forces. We conducted a field test to
 evaluate the effects of migration difficulty (as a natural selective
 force) and selective captive breeding (as an artificial selective force)
 on threshold traits of a partially migratory fish. Male masu salmon
 (Oncorhynchus masou) in the Shari River system have AMTs divided into
 three population categories of hatchery, wild/above the waterfall, and
 wild/below the waterfall (control). The wild/above the waterfall salmon
 live in a high-migration-cost situation, and the threshold trait changed
 in a direction that promoted residency. In hatchery salmon, which are
 produced by migrant-selective captive breeding, the threshold trait
 changed in a direction that promoted migration. In contrast, Dolly Varden
 charr (Salvelinus malma) displayed only resident tactics, and the
 threshold trait did not differ between the populations above and below the
 waterfall, indicating that environment did not explain the variation in
 the threshold trait. Our results support the model and suggest that
 opposing natural and artificial selection forces drive variations in the
 threshold traits and migratory patterns in the studied species. Our
 conceptual framework for the ultimate mechanism may help to better
 understand adoption of AMTs and production of diverse intraspecific traits
 in migratory animals.
description: Measurement data of masu
 salmon (Oncorhynchus masou) and Dolly Varden charr (Salvelinus
 malma)Measurement data of masu
 salmon (Oncorhynchus masou) and Dolly Varden charr (Salvelinus malma). The
 salmon and charr were collected at the 13 tributaries of the Shari River
 system in the eastern part of Hokkaido Island, Japan.data_file.xls
DOI: 10.5061/dryad.f1kc3
title: Data from: Evidence for enemy release and increased seed production and size for two invasive Australian acacias

description: Invasive plants are hypothesized to have higher fitness in introduced
 areas due to their release from pathogens and herbivores and the
 relocation of resources to reproduction. However, few studies have tested
 this hypothesis in native and introduced regions. A biogeographical
 approach is fundamental to understanding the mechanisms involved in plant
 invasions and to detect rapid evolutionary changes in the introduced area.
 Reproduction was assessed in native and introduced ranges of two invasive
 Australian woody legumes, Acacia dealbata and A. longifolia. Seed
 production, pre-dispersal seed predation, seed and elaiosome size and
 seedling size were assessed in 7–10 populations from both ranges, taking
 into account the effect of differences in climate. There was a
 significantly higher percentage of fully developed seeds per pod, a lower
 proportion of aborted seeds and the absence of pre-dispersal predation in
 the introduced range for both Acacia species. Acacia longifolia produced
 more seeds per pod in the invaded range, whereas A. dealbata produced more
 seeds per tree in the invaded range. Seeds were bigger in the invaded
 range for both species, and elaiosome: seed ratio was smaller for A.
 longifolia in the invaded range. Seedlings were also larger in the invaded
 range, suggesting that the increase in seed size results into greater
 offspring growth. There were no differences in the climatic conditions of
 sites occupied by A. longifolia in both regions. Minimum temperature was
 higher in Portuguese A. dealbata populations, but this difference did not
 explain the increase in seed production and seed size in the introduced
 range. It did have, however, a positive effect on the number of pods per
 tree. Synthesis. Acacia dealbata and A. longifolia escape pre-dispersal
 predation in the introduced range and display a higher production of fully
 developed seeds per fruit and bigger seeds. These differences may explain
 the invasion of both species because they result in an increased seedling
 growth and the production of abundant soil seedbanks in the introduced
 area.
description: JEcol-2015-0799.R1Acacia dealbata: seed weight, elaiossome weight, seedlings weight, number of seeds per pod (aborted, preyed, fully developed) for Portugal and Australia; 7 populations in each country; Acacia longifolia: seed weight, elaiossome weight, seedlings weight number of seeds per pod (aborted, preyed, fully developed) for Portugal and Australia; 10 populations in each country.
DOI: 10.5061/dryad.5df61
title: Data from: A framework for developing ecosystem-specific nutrient criteria: integrating biological thresholds with predictive modeling

description: We present a novel ecosystem-specific framework for developing nutrient
 criteria from biological thresholds and predictive modeling (BTPM) and an
 application of this framework to lakes in Michigan, U.S. The four main
 components for the BTPM framework are: (1) to predict each ecosystem s
 expected nutrient concentration in the absence of human effects using a
 predictive model, (2) to identify important biological thresholds along a
 nutrient gradient (i.e., biological [BIO] benchmarks), (3) to determine
 each ecosystem s current nutrient concentration, and (4) to use the above
 information to derive a nutrient criterion for each ecosystem using the
 BTPM algorithm. The BTPM framework is extremely flexible in that it can be
 applied to any aquatic ecosystem type or nutrient and the four components
 can be implemented in a variety of ways. Our BTPM framework has two
 additional features: it recognizes that prior to human disturbance,
 ecosystems varied in their natural nutrient concentrations, and it
 incorporates risk into the decision-making process. In the simplest
 scheme, a nutrient criterion is set at a BIO benchmark greater than the
 expected nutrient concentration. However, to protect ecosystems more
 conservatively, a criterion is set at current lake nutrient concentrations
 if current is less than the BIO benchmark. In our application of the BTPM
 framework, we developed total phosphorus (TP) criteria for a diverse set
 of 374 lakes in MI. The expected lake TP concentrations in the absence of
 human effects ranged from 3 µg L-1 to 24 µg L-1, suggesting that a single
 criterion approach would not be appropriate.We found two predominant
 benchmarks in the biological data along the TP gradient, one for
 zooplankton metrics at 8 µg L-1, and one for phytoplankton metrics at 18
 µg L-1. We present the sequence of analyses and decisions that could be
 used to apply this approach in a management context using Michigan lakes
 as an example.
description: Soranno-MI-NUTR-CRITERIA-2008
DOI: 10.5061/dryad.2vg05
title: Data from: A recombination suppressor contributes to ecological speciation in Ostrinia moths

description: Despite unparalleled access to species’ genomes in our post-genomic age,
 we often lack adequate biological explanations for a major hallmark of the
 speciation process—genetic divergence. In the presence of gene flow,
 chromosomal rearrangements such as inversions are thought to promote
 divergence and facilitate speciation by suppressing recombination. Using a
 combination of genetic crosses, phenotyping of a trait underlying
 ecological isolation, and population genetic analysis of wild populations,
 we set out to determine whether evidence supports a role for recombination
 suppressors during speciation between the Z and E strains of European corn
 borer moth (Ostrinia nubilalis). Our results are consistent with the
 presence of an inversion that has contributed to accumulation of
 ecologically adaptive alleles and genetic differentiation across roughly
 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest
 that chromosomal divergence may involve two separate phases—one driving
 its transient origin through local adaptation and one determining its
 stable persistence through differential introgression. As the evolutionary
 rate of rearrangements in lepidopteran genomes appears to be one of the
 fastest among eukaryotes, structural mutations may have had a
 disproportionate role during adaptive divergence and speciation in
 Ostrinia and in other moths and butterflies.
description: Figure2Dat1Genotype data for between strain pedigree.Figure2Dat2Genotype data for within strain pedigreeFigure3DatGenotype and phenotype data for between strain pedigree.2071Aligned sequence data for locus BGIBMGA002071.2076Aligned sequence file for locus BGIBMGA0020762032Aligned sequence data for locus BGIBMGA0020322104Aligned sequence data for locus BGIBMGA0021042005Aligned sequence data for locus BGIBMGA002005622Aligned sequence data for locus BGIBMGA000622643Aligned sequence data for locus BGIBMGA000643647Aligned sequence data for locus BGIBMGA000647563Aligned sequence data for locus BGIBMGA000563559Aligned sequence data for locus BGIBMGA000559680Aligned sequence data for locus BGIBMGA000680683Aligned sequence data for locus BGIBMGA000683My537Aligned sequence data for locus BGIBMGA000537532Aligned sequence data for locus BGIBMGA000532524shortAligned sequence data for locus BGIBMGA000524710Aligned sequence data for locus BGIBMGA0007101368Aligned sequence data for locus BGIBMGA0004949691Aligned sequence data for locus BGIBMGA00048013318Aligned sequence data for locus BGIBMGA01331813333Aligned sequence data for locus BGIBMGA0133338010Aligned sequence data for locus BGIBMGA01229512292Aligned sequence data for locus BGIBMGA01229213832Aligned sequence data for locus BGIBMGA0122492623Aligned sequence data for locus BGIBMGA012238
DOI: 10.5061/dryad.5q114
title: Data from: Patch dynamics and temporal dispersal partly shape annual plant communities in ephemeral habitat patches

description: Most organisms in ephemeral habitat patches have resting stages which form
 a local species pool in response to temporal variations in the patch’s
 availability and suitability. Temporal dispersal from the local species
 pool may, therefore, be an important process shaping the community
 assembly, particularly soon after patch creation, and possibly interacting
 with environmental filtering. As the temporal variation of the
 environmental conditions has a major effect on the composition of the
 local species pool, we investigated how well contemporary conditions (both
 patch availability and patch suitability) and temporal dispersal
 (approximated by environmental temporal variation and temporal distance)
 explain the changes in community composition in a given locality through
 successive ephemeral habitat cycles. We used arable weeds in annual crops
 as models. We calculated temporal weed community dissimilarity indices
 between weed communities surveyed in cropping seasons at intervals of two
 to eight years within a given field. The weeds were surveyed twice each
 cropping season to account for any changes in the relative contributions
 of temporal dispersal and contemporary conditions during the season. Patch
 availability explained most of the temporal weed dissimilarity, suggesting
 that patch dynamics have the greatest effect on weed community assembly.
 Temporal distance and temporal variation of the environmental conditions
 had more effect at the start of the cropping season than later, while
 patch suitability had more effect in the middle of the season. These
 results suggest that temporal dispersal drives the weed community assembly
 when ephemeral habitat patches are created. These assemblies are further
 shaped by environmental filtering. This is consistent with a temporal
 source-sink dynamic mechanism where the seed bank acts as the main weed
 source. However, a large part of temporal weed dissimilarity remains
 unexplained, suggesting that other ecological processes such as spatial
 dispersal and founder effect may also shape the weed community.
description: Temporal Beta-Diversity
 in weed communitiesThis data file provides
 two beta-diversity indices, namely Jaccard and Bray-Curtis, computed from
 successive weed communities growing in 493 arable fields distributed over
 the whole French national territory. Temporal environmental distances,
 environmental heterogeneity and temporal distance are also furnished.
 Weeds were surveyed in two kind of plots, without herbicide application
 (control, "c") and with herbicide application (sprayed,
 "s"). Each year, weeds were surveyed twice, at the begining (n1)
 and at the middle (n2) of the cropping season.Data_Patch_Dynamics.xlsx
DOI: 10.5061/dryad.ks824
title: Data from: Evolution of iris colour in relation to cavity nesting and parental care in passerine birds

description: Strong selection pressures are known to act on animal coloration. Although
 many animals vary in eye colour, virtually no research has investigated
 the functional significance of these colour traits. Passeriformes have a
 range of iris colours, making them an ideal system to investigate how and
 why iris colour has evolved. Using phylogenetic comparative methods, we
 tested the hypothesis that conspicuous iris colour in passerine birds
 evolved in response to (a) coordination of offspring care and (b) cavity
 nesting, two traits thought to be involved in intra-specific gaze
 sensitivity. We found that iris colour and cooperative offspring care by
 two or more individuals evolved independently, suggesting that bright eyes
 are not important for coordinating parental care through eye gaze.
 Furthermore, we found that evolution between iris colour and nesting
 behaviour did occur in a dependent manner, but contrary to predictions,
 transitions to coloured eyes were not more frequent in cavity nesters than
 non-cavity nesters. Instead, our results indicate that selection away from
 having bright eyes was much stronger in non-cavity nesters than cavity
 nesters, perhaps because conspicuous eye coloration in species not
 concealed within a cavity would be more visible to predators.
description: Trait
 Matricestrait categorisation for
 iris colour, nesting and parental care. Presence =1, absence =
 0.TraitMatrices.xlsxIris colour phylogenetic treePhylogenetic tree used for iris colour evolutionIrisTree.nexNesting phylogenetic treePhylogenetic tree used for nesting evolutionNestingTree.nexIris colour and nesting behaviour treePhylogenetic tree used for correlated evolution between iris colour and nesting behaviourIrisandNestingTree.nexIris colour and parental care treePhylogenetic tree used for correlated evolution between iris colour and parental careIrisandParentalCareTree.nex
DOI: 10.5061/dryad.30064
title: Data from: Molecular systematics of the Philippine forest skinks (Squamata: Scincidae: Sphenomorphus): testing morphological hypotheses of interspecific relationships

description: Skinks of the genus Sphenomorphus are the most diverse clade of squamates
 in the Philippine Archipelago. Morphological examination of these species
 has defined six phenotypic groups that are commonly used in
 characterizations of taxonomic hypotheses. We used a molecular phylogeny
 based on four mitochondrial and two nuclear genes to assess the
 group's biogeographical history in the archipelago and examine the
 phylogenetic validity of the currently recognized Philippine species
 groups. We re-examined traditional characters used to define species
 groups and used multivariate statistics to quantitatively evaluate group
 structure in morphometric space. Clustering analyses of phenotypic
 similarity indicate that some (but not all) members of previously defined
 species groups are phenotypically most similar to other members of the
 same group. However, when species group membership was mapped on our
 partitioned Bayesian phylogenetic hypothesis, only one species group
 corresponds to a clade; all other species group arrangements are strongly
 rejected by our phylogeny. Our results demonstrate that (1) previously
 recognized species group relationships were misled by phenotypic
 convergence; (2) Sphenomorphus is widely paraphyletic; and (3) multiple
 lineages have independently invaded the Philippines. Based on this new
 perspective on the phylogenetic relationships of Philippine Sphenomorphus,
 we revise the archipelago's diverse assemblage of species at the
 generic level, and resurrect and/or expand four previously recognized
 genera, and describe two new genera to accommodate the diversity of
 Philippine skinks of the Sphenomorphus group.
description: Table4_morphMorphological data used in Pricipal Components Analysis and UPGMAsphenomorphus group ZJLSphilippines.nex