cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mk301
title: Data from: Homogenous population genetic structure of the non-native raccoon dog (Nyctereutes procyonoides) in Europe as a result of rapid population expansion

description: The extent of gene flow during the range expansion of non-native species
 influences the amount of genetic diversity retained in expanding
 populations. Here, we analyse the population genetic structure of the
 raccoon dog (Nyctereutes procyonoides) in north-eastern and central
 Europe. This invasive species is of management concern because it is
 highly susceptible to fox rabies and an important secondary host of the
 virus. We hypothesized that the large number of introduced animals and the
 species’ dispersal capabilities led to high population connectivity and
 maintenance of genetic diversity throughout the invaded range. We
 genotyped 332 tissue samples from seven European countries using 16
 microsatellite loci. Different algorithms identified three genetic
 clusters corresponding to Finland, Denmark and a large ‘central’
 population that reached from introduction areas in western Russia to
 northern Germany. Cluster assignments provided evidence of long-distance
 dispersal. The results of an Approximate Bayesian Computation analysis
 supported a scenario of equal effective population sizes among different
 pre-defined populations in the large central cluster. Our results are in
 line with strong gene flow and secondary admixture between neighbouring
 demes leading to reduced genetic structuring, probably a result of its
 fairly rapid population expansion after introduction. The results
 presented here are remarkable in the sense that we identified a homogenous
 genetic cluster inhabiting an area stretching over more than 1500km. They
 are also relevant for disease management, as in the event of a significant
 rabies outbreak, there is a great risk of a rapid virus spread among
 raccoon dog populations.
description: genetic_dataFile with individual ID, population, geographical coordinates, microsatellite genotypes at 16 loci
DOI: 10.5061/dryad.pb730
title: Data from: Time for recovery of riparian plants in restored northern Swedish streams: a chronosequence study

description: A lack of ecological responses in stream restoration projects has been
 prevalent throughout recent literature with many studies reporting
 insufficient time for recovery. We assessed the relative importance of
 time, site variables, and landscape setting for understanding how plant
 species richness and understory productivity recover over time in riparian
 zones of northern Swedish streams. We used a space-for-time substitution
 consisting of 13 stream reaches restored 5–25 years ago, as well as five
 unrestored channelized reference reaches. We inventoried the riparian zone
 for all vascular plant species along 60-m study reaches and quantified
 cover and biomass in plots. We found that while species richness increased
 with time, understory biomass decreased. Forbs made up the majority of the
 species added, while the biomass of graminoids decreased the most over
 time, suggesting that the reduced dominance of graminoids favored less
 productive forbs. Species richness and density patterns could be
 attributed to dispersal limitation, with anemochorous species being more
 associated with time after restoration than hydrochorous, zoochorous, or
 vegetatively reproducing species. Using multiple linear regression, we
 found that time along with riparian slope and riparian buffer width (e.g.,
 distance to logging activities) explained the most variability in species
 richness, but that variability in total understory biomass was explained
 primarily by time. The plant community composition of restored reaches
 differed from that of channelized references, but the difference did not
 increase over time. Rather, different time categories had different
 successional trajectories that seemed to converge on a unique climax
 community for that time period. Given our results, timelines for achieving
 species richness objectives should be extended to 25 years or longer if
 recovery is defined as a saturation of the accumulation of species over
 time. Other recommendations include making riparian slopes as gentle as
 possible given the landscape context and expanding riparian buffer width
 for restoration to have as much impact as possible.
description: Riparian plant
 diversity, biomass, species occurence, and environmental
 variablesAll data for plant
 diversity, biomass, species occurrence, and environmental variables used
 in Hasselquist et al.Hasselquist - riparian plants -
 enviro vars, spp rich, biomass.xlsx
DOI: 10.6084/m9.figshare.31154015
title: Additional file 1 of Comparative metabolomic analysis in roots of natural and cultivated Astragalus membranaceus in Mongolia

description: Supplementary Material 1: Supplementary Table (1) List of differentially accumulated metabolites in n-Am and c-Am roots. Supplementary Table (2) Metabolic pathways associated with enriched metabolites in n-Am and c-Am roots. Supplementary Table (3) Metabolic pathways associated with differentially accumulated metabolites in n-Am and c-Am roots.
DOI: 10.6084/m9.figshare.31154015.v1
title: Additional file 1 of Comparative metabolomic analysis in roots of natural and cultivated Astragalus membranaceus in Mongolia

description: Supplementary Material 1: Supplementary Table (1) List of differentially accumulated metabolites in n-Am and c-Am roots. Supplementary Table (2) Metabolic pathways associated with enriched metabolites in n-Am and c-Am roots. Supplementary Table (3) Metabolic pathways associated with differentially accumulated metabolites in n-Am and c-Am roots.
DOI: 10.5061/dryad.12np0
title: Data from: Consequences of sibling rivalry vary across life in a passerine bird

description: Many studies have assessed the costs of sibling rivalry in systems where
 offspring always have competitors, but conclusions about sibling rivalry
 in these species are restricted to interpreting the cost of changes in the
 relative level of competition and are often complicated by the expression
 of potentially costly rivalry related traits. Additionally, the majority
 of studies focus on early-life sibling rivalry, but the costs of
 competition can also affect later-life performance. We test a suite of
 hypothesized immediate (early-life body mass, telomere length, and
 survival) and delayed (adult reproductive potential and lifespan) costs of
 sibling rivalry for offspring of differing competitive ability in
 Seychelles warblers, where most offspring are raised singly and hence
 competitor success can be compared to a competition-free scenario.
 Compared to those raised alone, all competing nestlings had lower body
 mass and weaker competitors experienced reduced survival. However, the
 stronger competitors appeared to have longer adult breeding tenures and
 lifespan than those raised alone. We propose that comparisons with
 competition-free groups, as well as detailed fitness measures across
 entire lifetimes, are needed to understand the evolution of sibling
 rivalry and thus individual reproductive strategy in wild systems.
description: Data for all analysis of
 sibling rivalry across lifeEach tab contains the
 data used for one analysis.Dryad all data
 upload.xlsx
DOI: 10.5061/dryad.0tn0s
title: Data from: Purifying selection maintains dosage-sensitive genes during degeneration of the threespine stickleback Y chromosome

description: Sex chromosomes are subject to unique evolutionary forces that cause
 suppression of recombination, leading to sequence degeneration and the
 formation of heteromorphic chromosome pairs (i.e., XY or ZW). Although
 progress has been made in characterizing the outcomes of these
 evolutionary processes on vertebrate sex chromosomes, it is still unclear
 how recombination suppression and sequence divergence typically occur and
 how gene dosage imbalances are resolved in the heterogametic sex. The
 threespine stickleback fish (Gasterosteus aculeatus) is a powerful model
 system to explore vertebrate sex chromosome evolution, as it possesses an
 XY sex chromosome pair at relatively early stages of differentiation.
 Using a combination of whole-genome and transcriptome sequencing, we
 characterized sequence evolution and gene expression across the sex
 chromosomes. We uncovered two distinct evolutionary strata that correspond
 with known structural rearrangements on the Y chromosome. In the oldest
 stratum, only a handful of genes remain, and these genes are under strong
 purifying selection. By comparing sex-linked gene expression with
 expression of autosomal orthologs in an outgroup, we show that dosage
 compensation has not evolved in threespine sticklebacks through
 upregulation of the X chromosome in males. Instead, in the oldest stratum,
 the genes that still possess a Y chromosome allele are enriched for genes
 predicted to be dosage sensitive in mammals and yeast. Our results suggest
 that dosage imbalances may have been avoided at haploinsufficient genes by
 retaining function of the Y chromosome allele through strong purifying
 selection.
description: pamlDivergenceThis program calls the X and Y chromosome alleles for every SNP and indel, finds the longest open reading frame, constructs the sequence alignments, and calls PAML to calculate dN, dS, and dN/dS for every transcript.XYDifferentialExpressionThis program computes the normalized X:Y RNA expression ratios for each transcript.
DOI: 10.5061/dryad.p208f1t
title: Data from: Flexible parents: joint effects of handicapping and brood size manipulation on female parental care in Nicrophorus vespilloides

description: Parental care is highly variable, reflecting that parents make flexible
 decisions in response to variation in the cost of care to themselves and
 the benefit to their offspring. Much of the evidence that parents respond
 to such variation derives from handicapping and brood size manipulations,
 the separate effects of which are well understood. However, little is
 known about their joint effects. Here we fill this gap by conducting a
 joint handicapping and brood size manipulation in the burying beetle
 Nicrophorus vespilloides. We handicapped half of the females by attaching
 a lead weight to their pronotum, leaving the remaining females as
 controls. We also manipulated brood size by providing each female with 5,
 20 or 40 larvae. In contrast to what we predicted, handicapped females
 spent more time provisioning food than controls. We also found that
 handicapped females spent more time consuming carrion. Furthermore,
 handicapped females spent a similar amount of time consuming carrion
 regardless of brood size, while controls spent more time consuming carrion
 as brood increased. Females spent more time provisioning food towards
 larger broods, and females were more likely to engage in carrion
 consumption when caring for larger brood. We conclude that females respond
 to both handicapping and brood size manipulations, but these responses are
 largely independent of each other. Overall, our results suggest that
 handicapping might lead to a higher investment into current reproduction,
 and that it might be associated with compensatory responses that negate
 the detrimental impact of higher cost of care in handicapped parents.
description: Life-history and
 behavioural traits dataThe file contains data
 on the mass (g) of mice used for rearing experimental broods, egg-laying
 date and weighting date, female treatment (C=Control, W=Weighted), body
 mass (g) of females before/after handling and (for weighted females only)
 weighting, at day 1 after egg-hatching and at larval dispersal (before and
 after handling and washing dirt around the lead weight), brood mass (g) at
 different larval stages, mass (g) of the lead weights, offspring survival
 rate until dispersal and eclosion, date and time each 30-min observation
 has been performed, frequency (number of scans out of 30 scans) each
 behaviour has been recorded, and the total number of larvae
 begging.Data_Ratz_and_Smiseth_2018_Flexible_parental_care.csv
DOI: 10.5061/dryad.95486
title: Data from: Current spring warming as a driver of selection on reproductive timing in a wild passerine

description: 1. Evolutionary adaptation as a response to climate change is expected for
 fitness-related traits affected by climate and exhibiting genetic
 variance. Although the relationship between warmer spring temperature and
 earlier timing of reproduction is well documented, quantifications and
 predictions of the impact of global warming on natural selection acting on
 phenology in wild populations remain rare. If global warming affects
 fitness in a similar way across individuals within a population, or if
 fitness consequences are independent of phenotypic variation in
 key-adaptive traits, then no evolutionary response is expected for these
 traits. 2. Here we quantified the selection pressures acting on laying
 date during a 24-year monitoring of blue tits in southern Mediterranean
 France, a hot spot of climate warming. We explored the temporal
 fluctuation in annual selection gradients and we determined its
 temperature-related drivers. 3. We first investigated the month-specific
 warming since 1970 in our study site and tested its influence on selection
 pressures using a model averaging approach. Then, we quantified the
 selection strength associated with temperature anomalies experienced by
 the blue tit population. 4. We found that natural selection acting on
 laying date significantly fluctuated both in magnitude and in sign across
 years. After identifying a significant warming in spring and summer, we
 showed that warmer daily maximum temperatures in April were significantly
 associated with stronger selection pressures for reproductive timing. Our
 results indicated an increase in the strength of selection by 46% for
 every +1°C anomaly. 5. Our results confirm the general assumption that
 recent climate change translates into strong selection favouring earlier
 breeders in passerine birds. Our findings also suggest that differences in
 fitness among individuals varying in their breeding phenology increase
 with climate warming. Such climate driven influence on the strength of
 directional selection acting on laying date could favour an adaptive
 response in this trait, since it is heritable.
description: Tits_Females_datasetPhenotypic data on titsClimatic_dataClimatic data, South France (Monthly temperature 1970-2015)
DOI: 10.5061/dryad.75s6t
title: Data from: Individual shifts toward safety explain age-related foraging distribution in a gregarious shorebird

description: Although age-related spatial segregation is ubiquitous, the underlying
 mechanisms are poorly understood. Here, we aim to elucidate the processes
 behind a previously established age-related foraging distribution of red
 knots (Calidris canutus canutus) in their main wintering area in West
 Africa (Banc d’Arguin, Mauritania). Based on 10 years of observations of
 1232 uniquely color-ringed individuals of 1 to 18+ years old, we examined
 whether the observed age-related foraging distribution resulted from 1)
 spatial differences in mortality or 2) age-related shifts in habitat use.
 Using multistate capture–recapture modeling, we showed that with age
 foraging red knots moved away from the shoreline, that is, to areas with
 fewer surprise attacks by raptors. Considering uncertainties in the
 subjective gradient in predation danger with increasing distance from
 shore (as assessed from correlations between vigilance and distance from
 shore in foraging birds), we applied 2 different danger zone boundaries,
 at 40 m and 500 m from shore. Between years, red knots had a much higher
 chance to move from the dangerous nearshore area to the “safe” area beyond
 (71–78% and 26% for 40-m and 500-m danger zone boundary, respectively),
 than vice versa (4% and 14%). For neither danger zone boundary value did
 we find differences in annual mortality for individuals using either
 dangerous or safe zone, so the move away from the shore with age is
 attributed to individual careers rather than differential mortality. We
 argue that longitudinal studies like ours will reveal that ontogenetic
 shifts in habitat use are more common than so far acknowledged.
description: text
 filesData are provided for:
 Fig. 2 panels a (avgHUdfs10.txt) and b (vigilance_largescale.txt):
 vigilance as a function of distance from shore; Fig. 3: Number of
 individuals that were observed in nearshore dangerous and offshore safe
 habitat, shown for the 40 m (ch.knots.40m.txt ) and 500 m
 (ch.knots.500m.txt) danger zone boundaries; for the Multi-state
 mark-recapture analyses with use of the RMark package, including fig.
 4(cr.knots.May2015.txt)for
 Dryad.7z
DOI: 10.5061/dryad.31tc3s8
title: Data from: Gene flow does not prevent personality and morphological differentiation between two blue tit populations

description: Understanding the causes and consequences of population phenotypic
 divergence is a central goal in ecology and evolution. Phenotypic
 divergence among populations can result from genetic divergence,
 phenotypic plasticity or a combination of the two. However, few studies
 have deciphered these mechanisms for populations geographically close and
 connected by gene flow, especially in the case of personality traits. In
 this study, we used a common garden experiment to explore the genetic
 basis of the phenotypic divergence observed between two blue tit
 (Cyanistes caeruleus) populations inhabiting contrasting habitats
 separated by 25 km, for two personality traits (exploration speed and
 handling aggression), one physiological trait (heart rate during
 restraint) and two morphological traits (tarsus length and body mass).
 Blue tit nestlings were removed from their population and raised in a
 common garden for up to five years. We then compared adult phenotypes
 between the two populations, as well as trait-specific Qst and Fst . Our
 results revealed differences between populations similar to those found in
 the wild, suggesting a genetic divergence for all traits. Qst - Fst
 comparisons revealed that the traits divergences likely result from
 dissimilar selection patterns rather than from genetic drift. Our study is
 one of the first to report a Qst - Fst comparison for personality traits
 and adds to the growing body of evidence that population genetic
 divergence is possible at a small scale for a variety of traits including
 behavioural traits.
description: Data
 filesArchive.zip
DOI: 10.5061/dryad.082v2
title: Data from: Experimental evidence for phonemic contrasts in a nonhuman vocal system

description: The ability to generate new meaning by rearranging combinations of
 meaningless sounds is a fundamental component of language. Although animal
 vocalizations often comprise combinations of meaningless acoustic
 elements, evidence that rearranging such combinations generates
 functionally distinct meaning is lacking. Here, we provide evidence for
 this basic ability in calls of the chestnut-crowned babbler (Pomatostomus
 ruficeps), a highly cooperative bird of the Australian arid zone. Using
 acoustic analyses, natural observations, and a series of controlled
 playback experiments, we demonstrate that this species uses the same
 acoustic elements (A and B) in different arrangements (AB or BAB) to
 create two functionally distinct vocalizations. Specifically, the addition
 or omission of a contextually meaningless acoustic element at a single
 position generates a phoneme-like contrast that is sufficient to
 distinguish the meaning between the two calls. Our results indicate that
 the capacity to rearrange meaningless sounds in order to create new
 signals occurs outside of humans. We suggest that phonemic contrasts
 represent a rudimentary form of phoneme structure and a potential early
 step towards the generative phonemic system of human language.
description: Engesser et al.
 DryadFiles include data and
 values used to generate figures
DOI: 10.5281/zenodo.18383096
title: Mineralogical, oxygen isotope, geochemical data

description: Mineralogical, oxygen isotope, geochemical data
DOI: 10.5281/zenodo.18383097
title: Mineralogical, oxygen isotope, geochemical data

description: Mineralogical, oxygen isotope, geochemical data
DOI: 10.5061/dryad.3m680
title: Data from: Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa

description: Protists, the most diverse eukaryotes, are largely considered to be
 free-living bacterivores, but vast numbers of taxa are known to parasitize
 plants or animals. High-throughput sequencing (HTS) approaches now
 commonly replace cultivation-based approaches in studying soil protists,
 but insights into common biases associated with this method are limited to
 aquatic taxa and samples. We created a mock community of common
 free-living soil protists (amoebae, flagellates, ciliates), extracted DNA
 and amplified it in the presence of metazoan DNA using 454 HTS. We aimed
 at evaluating whether HTS quantitatively reveals true relative abundances
 of soil protists and at investigating whether the expected protist
 community structure is altered by the co-amplification of
 metazoan-associated protist taxa. Indeed, HTS revealed fundamentally
 different protist communities from those expected. Ciliate sequences were
 highly over-represented, while those of most amoebae and flagellates were
 under-represented or totally absent. These results underpin the biases
 introduced by HTS that prevent reliable quantitative estimations of
 free-living protist communities. Furthermore, we detected a wide range of
 nonadded protist taxa probably introduced along with metazoan DNA, which
 altered the protist community structure. Among those, 20 taxa most closely
 resembled parasitic, often pathogenic taxa. Therewith, we provide the
 first HTS data in support of classical observational studies that showed
 that potential protist parasites are hosted by soil metazoa. Taken
 together, profound differences in amplification success between protist
 taxa and an inevitable co-extraction of protist taxa parasitizing soil
 metazoa obscure the true diversity of free-living soil protist
 communities.
description: OTU representative
 sequencesRepresentative sequences
 for all OTUs for the forward (Euk20F) and Reverse (Euk302r) sequencing
 directionsOTUtableall.faBioinformatic scriptsFull scripts for bioinformatic pipeline as applied for sequence data analysis for Geisen et al. 2015 Mol. EcologyScripts_Ecofinders_faunalbarcoding_run1_Protozoa.docxAmoebozoa alignmentAllignment of 18S sequences (NEXUS-file), as used for phylogenetic analysis on Amoebazoa, as presented in Fig.3 of Geisen et al. 2015, Mol Ecology. Allignment includes OTUs recovered in this study, as well as sequences associated with those OTUs (downloaded from NCBI).