cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.c394c12
title: Data from: Divergence in sex peptide-mediated female post-mating responses in Drosophila melanogaster

description: Transfer and receipt of seminal fluid proteins crucially affect
 reproductive processes in animals. Evolution in these male ejaculatory
 proteins is explained with post-mating sexual selection, but we lack a
 good understanding of the evolution of female post-mating responses to
 these proteins. Some of these proteins are expected to mediate sexually
 antagonistic coevolution generating the expectation that females evolve
 resistance. One candidate in Drosophila melanogaster is the sex peptide
 (SP) which confers cost of mating in females. Here, we compared female
 SP-induced post-mating responses across three D. melanogaster wild type
 populations after mating with SP-lacking versus control males including
 fitness measures. Surprisingly, we did not find any evidence for
 SP-mediated fitness costs in any of the populations. However, female
 lifetime reproductive success and lifespan were differently affected by SP
 receipt indicating that female post-mating responses diverged among
 populations. Injection of synthetic SP into virgin females further
 supports these findings and suggests that females from different
 populations require different amounts of SP to effectively initiate
 post-mating responses. Molecular analyses of the sex peptide receptor
 suggest that genetic differences might explain the observed phenotypical
 divergence. We discuss the evolutionary processes that might have caused
 this divergence in female post-mating responses.
description: Rawdata_phenotypic_responsesDNA sequences SP and SPR exon 6Sequences SP and SPR.zip
DOI: 10.5061/dryad.cc2kq
title: Data from: Cultural traditions across a migratory network shape the genetic structure of southern right whales around Australia and New Zealand

description: Fidelity to migratory destinations is an important driver of connectivity
 in marine and avian species. Here we assess the role of maternally
 directed learning of migratory habitats, or migratory culture, on the
 population structure of the endangered Australian and New Zealand southern
 right whale. Using DNA profiles, comprising mitochondrial DNA (mtDNA)
 haplotypes (500 bp), microsatellite genotypes (17 loci) and sex from 128
 individually-identified whales, we find significant differentiation among
 winter calving grounds based on both mtDNA haplotype (FST = 0.048,
 ΦST = 0.109, p &lt; 0.01) and microsatellite allele frequencies
 (FST = 0.008, p &lt; 0.01), consistent with long-term fidelity to
 calving areas. However, most genetic comparisons of calving grounds and
 migratory corridors were not significant, supporting the idea that whales
 from different calving grounds mix in migratory corridors. Furthermore, we
 find a significant relationship between δ13C stable isotope profiles of 66
 Australian southern right whales, a proxy for feeding ground location, and
 both mtDNA haplotypes and kinship inferred from microsatellite-based
 estimators of relatedness. This indicates migratory culture may influence
 genetic structure on feeding grounds. This fidelity to migratory
 destinations is likely to influence population recovery, as long-term
 estimates of historical abundance derived from estimates of genetic
 diversity indicate the South Pacific calving grounds remain at &lt;10%
 of pre-whaling abundance.
description: Australian right whale
 microsatellite and stable isotope dataThis file contains the
 sampling location and state, mtDNA haplotype, sex, stable isotope and
 multi-locus microsatellite genotype data for Australian southern right
 whale samples used in the study.SREP16182_SRWdata_Archive.xlsxComparing_stable_isotope&genetic_similarity_filesDryad Archive for SREP16182: SI_SRW_data.zip. This zip file contains: 1 - Files of estimates of pairwise relatedness generated from microsatellite loci in SREP16182_SRWdata_Archive in the program COANCESTRY, using the kinship estimators of Lynch & Ritland 1999 (Lynch&Ritland_relatedness.txt) and Ritland 1996 (Ritland_relatedness.txt). 2 – Files of sample stable isotope values for both d13C (Sample_dC.txt) and d15N (Sample_dN.txt), as well as pairwise similarities of d13C calculated using Euclidean distance in program GENODIVE (dC_euclidean_correct_names.gdv). 3 – A file that includes d13C, d15N, mtDNA, sampling location and sex ID data for the samples used in the GLM work (SI_data_Aus_SRWtxt.txt) 4 – R code for (1) running the comparison of similarities between d13C and microsatellite-based kinship estimators and (2) running GLMs on d13C data, with mtDNA, sex and sampling state as potential explanatory factors. R code is annotated so it can be easily run if the files are placed in the appropriate files and required packages are downloaded.SI_SRW_data.zip
DOI: 10.5061/dryad.d362v
title: Data from: Mapping extinction debt highlights conservation opportunities for birds and mammals in the South American Chaco

description: 1. Habitat loss is the primary cause of local extinctions. Yet, there is
 considerable uncertainty regarding how fast species respond to habitat
 loss, and how time-delayed responses vary in space. 2. We focused on the
 Argentine Dry Chaco (ca. 32 million ha), a global deforestation hotspot,
 and tested for time-delayed response of bird and mammal communities to
 landscape transformation. We quantified the magnitude of extinction debt
 by modelling contemporary species richness as a function of either
 contemporary or past (2000 and 1985) landscape patterns. We then used
 these models to map communities’ extinction debt. 3. We found strong
 evidence for an extinction debt: landscape structure from 2000 explained
 contemporary species richness of birds and mammals better than
 contemporary and 1985 landscapes. This suggests time-delayed responses
 between 10 and 25 years. Extinction debt was especially strong for forest
 specialists. 4. Projecting our models across the Chaco highlighted areas
 where future local extinctions due to unpaid extinction debt are likely.
 Areas recently converted to agriculture had highest extinction debt,
 regardless of the post-conversion land use. Few local extinctions were
 predicted in areas with remaining larger forest patches. 5. Synthesis and
 applications. The evidence for an unpaid extinction debt in the Argentine
 Dry Chaco provides a substantial window of opportunity for averting local
 biodiversity losses. However this window may close rapidly if conservation
 activities such as habitat restoration are not implemented swiftly. Our
 extinction debt maps highlights areas where such conservation activities
 should be implemented.
description: Semper-Pascual_et_al_DataSemperPascual_et_al_Data.rar
DOI: 10.5061/dryad.j536j
title: Data from: Social and ecological drivers of reproductive seasonality in geladas

description: Many non-seasonally breeding mammals demonstrate some degree of synchrony
 in births, which is generally associated with ecological factors that
 mediate fecundity. However, disruptive social events, such as alpha male
 replacements, also have the potential to affect the timing of female
 reproduction. Here, we examined reproductive seasonality in a wild
 population of geladas (Theropithecus gelada) living at high altitudes in
 an afro-alpine ecosystem in Ethiopia. Using 9 years of demographic data
 (2006-2014) we determined that, while females gave birth year-round, a
 seasonal peak in births coincided with peak green grass availability
 (their staple food source). This post-rainy season “ecological peak” in
 births meant that estimated conceptions for these births occurred when
 temperatures were at their highest and mean female fecal glucocorticoid
 concentrations were at their lowest. In addition to this ecological birth
 peak, we also found a separate birth peak that occurred only for females
 in groups that had experienced a recent replacement of the dominant male
 (i.e., a takeover). Because new dominant males cause abortions in pregnant
 females and kill the infants of lactating females, takeovers effectively
 “reset” the reproductive cycles of females in the group. This “social
 birth peak” was distinct from the ecological peak and was associated with
 higher rates of cycling and conceptions overall and higher glucocorticoid
 levels immediately following a takeover as compared to females that did
 not experience a takeover. These data demonstrate that social factors (in
 this case, male takeovers) can contribute to population-level reproductive
 seasonality above and beyond group-level reproductive synchrony.
description: seasonality_in_geladas_dataseasonality in geladas analysisCode for all analyses.
DOI: 10.5061/dryad.731j7
title: Data from: Constraints of cold and shade on the phenology of spring ephemeral herb species

description: Spring ephemeral herb species in temperate deciduous forests are active
 above-ground only briefly each year. This study tested experimentally how
 two countervailing constraints – cold and darkness – influence the
 phenology of six spring herb species. Dormancy of underground structures,
 maintained by cold temperatures in a growth chamber, was broken at six
 25-day intervals from January or February to June in two consecutive
 years. Upon emergence, survival and flowering were measured on cohorts
 grown outdoors. Shade cloth was added at the time of normal canopy
 closure. Cardamine concatenata, Dicentra cucullaria, Erythronium albidum
 and Trillium recurvatum had no or low 2-year survival in the two or three
 earliest cohorts and no or low survival in the latest cohort, relative to
 their natural cohort. Allium canadense and Claytonia virginica had
 survival in all cohorts. Flowering never occurred in the first two or
 three cohorts for three species and never occurred or declined in later
 cohorts in all species. Despite widely differing emergence dates,
 senescence was completed within a 40-day period soon after shade was
 imposed for all cohorts for all species. Consequently, leaf life span
 became shorter as date of emergence was delayed among cohorts. In general,
 the brief growth period of spring herb species is an adaptation to avoid
 winter cold and late-spring canopy shade. These constraints are
 species-specific and differ for survival and flowering for some species.
 Claytonia virginica is the most tolerant among the species to a wider
 range of conditions. Synthesis. Knowing that cold and shade constrain a
 plant's non-dormant period is important because of the significant
 role plant phenology plays in responses to climate change.
description: Raw data survival,
 flower, senescence for each cohortFile Description One
 Excel File with four sheets: 1. Survival and flower raw data for each
 cohort in each species: Initial number 1997, Number survive through 1998,
 Number flower in 1997 or 1998. 2. Proportion survive flower for each
 cohort in each species: Proportion of initial number that survive to 1998,
 Proportion flower in 1997 or 1998. 3. Senescence raw data for each
 individual in each species in 1997 (also Allium for 1998): (Julian
 calendar) date begin senescence, Date end senescence, Number of days of
 senescence, Date from cold room to greenhouse, Date outside, Leaf lifespan
 calculated as: LifespanSen2 = (Date begin senescence – date to
 greenhouse), LifespanEnd2 = (Date end senescence – date to greenhouse),
 LifespanSen1 = (Date begin senescence – date to outside), LifespanEnd1 =
 (Date end senescence – date to outside). 4. Senescence descriptive
 statistics for each cohort for each species: Mean, Standard Deviation,
 Standard Error, N for: Date begin senescence, Date end senescence, Number
 of days of senescence LifespanSen1, LifespanEnd1, LifespanSen2,
 LifespanEnd2.
DOI: 10.5061/dryad.9j1cp
title: Data from: Individual learning performance and exploratory activity are linked to colony foraging success in a mass-recruiting ant

description: Learning plays an important role in the life of many animals. In social
 insects, colony foraging success depends on the combined actions of many
 individuals and learning contributes to individual foraging success. In
 many ants, for example, route learning helps foragers to navigate between
 the nest and a food source. Here, we studied if the foraging success of a
 colony depends on the route-learning performance of its individuals. We
 used a doubly bifurcating T-maze to assess the route-learning performance
 of ants from 12 Lasius niger colonies. We also measured the propensity of
 workers to deposit trail pheromone and to explore the surrounding of their
 nest. We then tested colony foraging performance in a complex maze, set up
 either as a poor environment (one food source at the end of one tip), or a
 rich environment (a food source at the end of each tip). We found that
 individual learning performance was linked to colony foraging success in
 the rich, but not the poor environment. The propensity of individual ants
 to lay pheromone correlated negatively with their learning performance and
 only predicted colony foraging success in colonies with poor learning
 abilities in a rich environment. The strongest predictor of colony
 foraging success was exploratory activity, which differed consistently
 between colonies. Our results suggest that the importance of individual
 learning for colony foraging success depends on the environment and that
 explorative activity is an important factor for colony foraging success.
description: Pasquier_Grüter_Raw_DataThe file contains the raw data from the study
DOI: 10.5061/dryad.92p3p
title: Data from: Twentieth-century changes in the genetic composition of Swedish field pea metapopulations

description: Landrace crops are formed by local adaptation, genetic drift and gene flow
 through seed exchange. In reverse, the study of genetic structure between
 landrace populations can reveal the effects of these forces over time. We
 present here the analysis of genetic diversity in 40 Swedish field pea
 (Pisum sativum L.) populations, either available as historical seed
 samples from the late nineteenth century or as extant gene bank accessions
 assembled in the late twentieth century. The historical material shows
 constant high levels of within-population diversity, whereas the extant
 accessions show varying, and overall lower, levels of within-population
 diversity. Structure and principal component analysis cluster most
 accessions, both extant and historical, in groups after geographical
 origin. County-wise analyses of the accessions show that the genetic
 diversity of the historical accessions is largely overlapping. In
 contrast, most extant accessions show signs of genetic drift. They harbor
 a subset of the alleles found in the historical accessions and are more
 differentiated from each other. These results reflect how, historically
 present metapopulations have been preserved during the twentieth century,
 although as genetically isolated populations.
description: LeinoetalPisumMicrosatellite data from genotypings of eight individuals each of in total 40 extant and historical accessions. Microsatellite markers are from Loridon et al 2005.
DOI: 10.5061/dryad.p2f4b
title: Data from: Do wild ungulates experience higher stress with humans than with large carnivores?

description: Predation is a major selective pressure for prey; however, the stress
 response to predation risk and the relative importance of natural versus
 anthropogenic stress factors in wild populations of animals have rarely
 been studied. We investigated the level of fecal glucocorticoid
 metabolites (FGMs) in 6 populations of red deer and roe deer exposed to
 potentially different levels of stress, resulting from both natural
 (predator presence, forest cover, undergrowth, ungulate density, and
 temperature) and anthropogenic (hunting harvest, percentage of build-up
 areas, and road density) factors. We found the highest and most variable
 FGM concentrations in both ungulates in areas without large carnivores,
 and the lowest and least variable FGM levels in areas with wolf and lynx.
 Anthropogenic factors (hunting harvest, roads, and built-up area)
 positively correlated with the gradient of FGM levels in both species.
 Both the mean and the variance of the FGM concentrations measured within
 populations of both red deer and roe deer were affected positively by
 variation in hunting harvest and negatively by the minimum temperature.
 The variance in the roe deer FGM was also positively influenced by the
 percentage of built-up areas. The results indicate that stress in wild
 ungulate populations is lower and less variable in areas utilized by large
 carnivores than in carnivore-free areas where human-related factors
 predominate. This may be explained by evolutionary adaptations of prey
 animals constantly exposed to the risk of natural predation and their
 inability of adapting to the risk from humans probably due to its high
 intensity and erratic occurrence.
description: FGM and environmental
 data, red deerFull database of fecal
 glucucocorticoid metabolites (FGM) concentration in pellets of red deer
 (Cervus elaphus) collected in 6 areas in Poland along with environmental
 data (see text for details on sources of data).data_red_deer.csvFGM and environmental data, roe deerFull database of fecal glucucocorticoid metabolites (FGM) concentration in pellets of roe deer (Capreolus capreolus) collected in 6 areas in Poland along with environmental data (see text for details on sources of data).data_roe_deer.csv
DOI: 10.5061/dryad.sc35630
title: Data from: Context-dependent interactions between pathogens and a mutualist affect pathogen fitness and mutualist benefits to hosts

description: Plants and animals host many microbial symbionts, including both pathogens
 and mutualists. However, most experimental studies include only one
 symbiont, and few examine interactions of more than two microbes with
 their host. Here, we examined whether coinfection with two pathogens
 causes a synergistic reduction in the benefits that hosts receive from a
 microbial mutualist. We also measured the effects of a microbial mutualist
 on the within and between host competition between coinfecting pathogens.
 We manipulated the presence of Clover yellow vein virus (ClYVV), Bean
 common mosaic virus (BCMV), rhizobia bacteria, and nitrogen fertilizer in
 common beans (Phaseolus vulgaris). We found asymmetric, context-dependent
 interactions among the three microbial symbionts and their host.
 Coinfection with both viruses led to greater than additive negative
 effects on the amount of nitrogen that plants received from rhizobia.
 Rhizobia colonization decreased immune signaling in singly infected
 plants, but not in coinfected plants. Compared to single ClYVV infections,
 ClYVV reached higher concentrations within hosts coinfected with BCMV, but
 only in the presence of rhizobia. Coinfection increased BCMV vertical
 transmission rates for plants without supplemental nitrogen, but overall
 vertical transmission opportunities were not affected due to reduced seed
 production. Examining interactions between multiple microbes sharing a
 host can reveal important insights about nutrient cycling, disease
 severity, and pathogen epidemiology.
description: MarchettoPowerRhizobiaCoinfectionData.csvThese data accompany the paper, “Context-dependent interactions between pathogens and a mutualist affect pathogen fitness and mutualist benefits to hosts” by Katherine Marchetto and Alison Power published in Ecology.
DOI: 10.5061/dryad.sh487
title: Data from: Heterozygosity-behaviour correlations in nine-spined stickleback (Pungitius pungitius) populations: contrasting effects at random and functional loci

description: The study of heterozygosity-fitness correlations has a long history in the
 fields of ecology and evolutionary biology but remains controversial.
 Recently, it has been shown that the location of markers i.e. their
 genomic position with respect to their distance from functional loci can
 be an important factor to be considered in addition to marker number and
 variability. In this study, we investigated the correlation between
 individual heterozygosity and behaviour (aggression, boldness and feeding
 activity) in nine-spined stickleback individuals originating from four
 populations in two contrasting environments. Offspring of full-sib
 families raised in a common garden setting were assessed for behaviour and
 genotyped using 84 microsatellite markers that were either located within
 or near behaviourally or physiologically important genes (termed
 ‘functional’) or were randomly selected. No associations were detected
 with any behavioural trait in any population or over all populations when
 genetic variability was measured using all markers combined. However, when
 the markers were separated into three functional categories, several
 significant associations were observed both with functional markers and
 random markers in one of the four populations. Contrasting correlations
 with behaviour were observed when using physiological gene (negative) and
 random (positive) markers. Upon dividing the physiological gene markers
 into further subcategories based on their specific physiological
 functions, a strong relationship between the heterozygosity of markers
 linked to osmoregulation-related genes and behaviour was revealed in the
 brackish water population. Our results indicate that both local
 (physiological) and general (neutral) effects are important in shaping
 behaviour and that heterozygosity-behaviour correlations are population
 dependent.
description: Laine_etal_2012_HBC-DATAStandardised heterozygosity values calculated from different marker groups and principal components from behavioural measurements. More details in ReadMe file.Laine_etal_2012_behaviourThe behavioural measurements of the nine-spined sticklebacks for the principal component analyses. Time_of_orient: time spent with orientation towards the stimulus fish; Number_of_attacks:number of attacks towards the stimulus fish; Time_to_feed:time until first feeding attempt in normal environment; Risk_taking: time until first feeding attempt in a disturbed environment; Time_to_headout:time until the fish's head was out from refuge; Time_to_bodyout:time until the whole fish was out from refugeLaine_etal_2012_microsatsThe microsatellite alleles as fragment lengths. F1,2,3,4,5: Mother of that family; M1,2,3,4,5: Father of that family