cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n2v20
title: Data from: Interspecific Y chromosome variation is sufficient to rescue hybrid male sterility and is influenced by the grandparental origin of the chromosomes

description: Y chromosomes display population variation within and between species.
 Co-evolution within populations is expected to produce adaptive
 interactions between Y chromosomes and the rest of the genome. One
 consequence is that Y chromosomes from disparate populations could disrupt
 harmonious interactions between co-evolved genetic elements and result in
 reduced male fertility, sterility or inviability. Here we address the
 contribution of ‘heterospecific Y chromosomes’ to fertility in hybrid
 males carrying a homozygous region of Drosophila mauritiana introgressed
 in the Drosophila simulans background. In order to detect Y
 chromosome–autosome interactions, which may go unnoticed in a
 single-species background of autosomes, we constructed hybrid genotypes
 involving three sister species: Drosophila simulans, D. mauritiana, and D.
 sechellia. These engineered strains varied due to: (i) species origin of
 the Y chromosome (D. simulans or D. sechellia); (ii) location of the
 introgressed D. mauritiana segment on the D. simulans third chromosome,
 and (iii) grandparental genomic background (three genotypes of D.
 simulans). We find complex interactions between the species origin of the
 Y chromosome, the identity of the D. mauritiana segment and the
 grandparental genetic background donating the chromosomes. Unexpectedly,
 the interaction of the Y chromosome and one segment of D. mauritiana
 drastically reduced fertility in the presence of Ysim, whereas the
 fertility is partially rescued by the Y chromosome of D. sechellia when it
 descends from a specific grandparental genotype. The restoration of
 fertility occurs in spite of an autosomal and X-linked genome that is
 mostly of D. simulans origin. These results illustrate the multifactorial
 basis of genetic interactions involving the Y chromosome. Our study
 supports the hypothesis that the Y chromosome can contribute significantly
 to the evolution of reproductive isolation and highlights the conditional
 manifestation of infertility in specific genotypic combinations.
description: RAW DATA final
 experimentExcel table with progeny
 numbers from males of each combination of ancestral background, homozygote
 introgression and Y chromosome origin. These were the raw data used in the
 statistical comparisons.
DOI: 10.5061/dryad.617vp
title: Data from: Heritable variation in heat shock gene expression: a potential mechanism for adaptation to thermal stress in embryos of sea turtles

description: The capacity of species to respond adaptively to warming temperatures will
 be key to their survival in the Anthropocene. The embryos of egg-laying
 species such as sea turtles have limited behavioural means for avoiding
 high nest temperatures, and responses at the physiological level may be
 critical to coping with predicted global temperature increases. Using the
 loggerhead sea turtle (Caretta caretta) as a model, we used quantitative
 PCR to characterise variation in the expression response of heat shock
 genes (hsp60, hsp70, and hsp90; molecular chaperones involved in cellular
 stress response) to an acute non-lethal heat shock. We show significant
 variation in gene expression at the clutch and population levels for some,
 but not all hsp genes. Using pedigree information, we estimated
 heritabilities of the expression response of hsp genes to heat shock and
 demonstrated both maternal and additive genetic effects. This is the first
 evidence that the heat shock response is heritable in sea turtles and
 operates at the embryonic stage in any reptile. The presence of heritable
 variation in the expression of key thermotolerance genes is necessary for
 sea turtles to adapt at a molecular level to warming incubation
 environments.
description: Tedeschi et
 al_RSPB-2015-2320_NEW dataset for DRYADRaw Cq data for all gene
 expression analysis performed
DOI: 10.5061/dryad.hs26b
title: Data from: Natural epigenetic variation contributes to heritable flowering divergence in a widespread asexual dandelion lineage

description: Epigenetic variation has been proposed to contribute to the success of
 asexual plants, either as a contributor to phenotypic plasticity or by
 enabling transient adaptation via selection on transgenerationally stable,
 but reversible, epialleles. While recent studies in experimental plant
 populations have shown the potential for epigenetic mechanisms to
 contribute to adaptive phenotypes, it remains unknown whether heritable
 variation in ecologically relevant traits is at least partially
 epigenetically determined in natural populations. Here, we tested the
 hypothesis that DNA methylation variation contributes to heritable
 differences in flowering time within a single widespread apomictic clonal
 lineage of the common dandelion (Taraxacum officinale s. lat.). Apomictic
 clone members of the same apomictic lineage collected from different field
 sites showed heritable differences in flowering time, which was correlated
 with inherited differences in methylation-sensitive AFLP marker profiles.
 Differences in flowering between apomictic clone members were
 significantly reduced after in vivo demethylation using the DNA
 methyltransferase inhibitor zebularine. This synchronization of flowering
 times suggests that flowering time divergence within an apomictic lineage
 was mediated by differences in DNA methylation. While the underlying basis
 of the methylation polymorphism at functional flowering time-affecting
 loci remains to be demonstrated, our study shows that epigenetic variation
 contributes to heritable phenotypic divergence in ecologically relevant
 traits in natural plant populations. This result also suggests that
 epigenetic mechanisms can facilitate adaptive divergence within
 genetically uniform asexual lineages.
description: Flowering time,
 microsatellite and MS-AFLP data from apomictic dandelionApomictic clone members
 from common dandelion microspecies Taraxacum officinale 'Alatum'
 screened under common greenhouse environments for variation in
 microsatellites, methylation-sensitive AFLPs and flowering
 time.data_wilschut_et_al.xlsx
DOI: 10.5061/dryad.6hn20
title: Data from: Possible glimpses into early speciation: the effect of ovarian fluid on sperm velocity accords with post-copulatory isolation between two guppy populations

description: Identifying mechanisms of reproductive isolation is key to understanding
 speciation. Among the putative mechanisms underlying reproductive
 isolation, sperm-female interactions (postmating-prezygotic barriers) are
 arguably the hardest to identify, not least because these are likely to
 operate at the cellular or molecular level. Yet sperm-female interactions
 offer great potential to prevent the transfer of genetic information
 between different populations at the initial stages of speciation. Here we
 provide a preliminary test for the presence of a putative
 postmating-prezygotic barrier operating between three populations of
 Trinidadian guppies (Poecilia reticulata), an internally fertilizing fish
 that inhabits streams with different levels of connectivity across
 Trinidad. We experimentally evaluate the effect of female ovarian fluid on
 sperm velocity (a predictor of competitive fertilization success)
 according to whether males and females were from the same (native) or
 different (foreign) populations. Our results reveal the potential for
 ovarian fluid to act as a postmating-prezygotic barrier between two
 populations from different drainages, but also that the strength of this
 barrier is different among populations. This result may explain the
 previous finding that, in some populations, sperm from native males have
 precedence over foreign sperm, which could eventually lead to reproductive
 isolation between these populations.
description: Dataset_Devigili et
 al_JEB_2017Dataset used for the
 analysis on guppy sperm velocity.
DOI: 10.5061/dryad.rv524
title: Data from: Genetic and ecotypic differentiation in a Californian plant polyploid complex (Grindelia, Asteraceae)

description: Studies of ecotypic differentiation in the California Floristic Province
 have contributed greatly to plant evolutionary biology since the
 pioneering work of Clausen, Keck, and Hiesey. The extent of gene flow and
 genetic differentiation across interfertile ecotypes that span major
 habitats in the California Floristic Province is understudied, however,
 and is important for understanding the prospects for local adaptation to
 evolve or persist in the face of potential gene flow across populations in
 different ecological settings. We used microsatellite data to examine
 local differentiation in one of these lineages, the Pacific Coast
 polyploid complex of the plant genus Grindelia (Asteraceae). We examined
 439 individuals in 10 different populations. The plants grouped broadly
 into a coastal and an inland set of populations. The coastal group
 contained plants from salt marshes and coastal bluffs, as well as a
 population growing in a serpentine grassland close to the coast, while the
 inland group contained grassland plants. No evidence for hybridization was
 found at the single location where adjacent populations of the two groups
 were sampled. In addition to differentiation along ecotypic lines, there
 was also a strong signal of local differentiation, with the plants
 grouping strongly by population. The strength of local differentiation is
 consistent with the extensive morphological variation observed across
 populations and the history of taxonomic confusion in the group. The
 Pacific Clade of Grindelia and other young Californian plant groups
 warrant additional analysis of evolutionary divergence along the steep
 coast-to-inland climatic gradient, which has been associated with local
 adaptation and ecotype formation since the classic studies of Clausen,
 Keck, and Hiesey.
description: Grindelia_allele_frequenciesThis is a tab-delimited text file with the information on which alleles were present in each individual. In total, there are data from six microsatellite loci (columns) and 439 individuals (rows). Loci and individuals are identified in a header row or column, respectively. Data were gathered from wild-collected leaf material and scored using PeakScanner v. 1.0.
DOI: 10.5061/dryad.r5gg0
title: Data from: Modeling the perception of audiovisual distance: Bayesian causal inference and other models

description: Studies of audiovisual perception of distance are rare. Here, visual and
 auditory cue interactions in distance are tested against several
 multisensory models, including a modified causal inference model. In this
 causal inference model predictions of estimate distributions are included.
 In our study, the audiovisual perception of distance was overall better
 explained by Bayesian causal inference than by other traditional models,
 such as sensory dominance and mandatory integration, and no interaction.
 Causal inference resolved with probability matching yielded the best fit
 to the data. Finally, we propose that sensory weights can also be
 estimated from causal inference. The analysis of the sensory weights
 allows us to obtain windows within which there is an interaction between
 the audiovisual stimuli. We find that the visual stimulus always
 contributes by more than 80% to the perception of visual distance. The
 visual stimulus also contributes by more than 50% to the perception of
 auditory distance, but only within a mobile window of interaction, which
 ranges from 1 to 4 m.
description: Mendonça et al Plos One
 2016Data from experiment on
 audiovisual distance perception. Data from 6 subjects, identified by
 letters, and 6 sessions, numbered. Each row is a trial. 1st column: where
 in distance V stimulus was; 2nd column: where in distance A stimulus was;
 3rd column: where is distance subject perceived the V stimulus; 4th
 column: where in distance subject perceived A stimulus. Dryad_Mendonça
 Plos2016.zip
DOI: 10.5061/dryad.7kv86
title: Data from: Species divergence in offspring begging and parental provisioning is linked to nutritional dependency

description: In animal species in which parents provide food to their dependent young,
 offspring often display conspicuous begging signals. These solicitation
 behaviors are important components of parent–offspring communication, but
 it is currently unclear how they and the parental response covary with
 offspring dependency on parental food provisioning across species. Burying
 beetles (Nicrophorus) are well known for providing elaborate biparental
 care, including provisioning of begging larvae. By using a multispecies
 approach, we show that larval begging intensity, as well as the time
 parents spend provisioning, differ greatly between individuals of the 3
 species: N. orbicollis, N. pustulatus, and N. vespilloides. Our results
 demonstrate that the most dependent offspring of N. orbicollis invest the
 most time in begging, whereas the most independent offspring of N.
 pustulatus invest the least amount of time in begging. Thus, we suggest
 that begging intensity differs due to intrinsic differences in nutritional
 need between the species rather than because of an arbitrary divergence in
 begging behavior. We further show that in all 3 species, females spend
 significantly more time provisioning than males, although there is
 considerable divergence between species in the extent to which females and
 males contribute to the provisioning of larvae. We discuss the potential
 selective factors leading to this diversification of offspring begging and
 parental provisioning in relation to the distinct variation in offspring
 dependence between the 3 species.
description: Begging_FeedingBegging and feeding rate of the three burying beetle species Nicrophorus orbicollis, N. pustulatus, and N. vespilloidesCapodeanu-Nägler et al. 2017 Data.xlsx
DOI: 10.5061/dryad.f66db
title: Data from: Root foraging performance and life-history traits

description: Plants use their roots to forage for nutrients in heterogeneous soil
 environments, but different plant species vastly differ in the intensity
 of foraging they perform. This diversity suggests the existence of
 constraints on foraging at the species level. We therefore examined the
 relationships between the intensity of root foraging and plant body traits
 across species in order to estimate the degree of coordination between
 plant body traits and root foraging as a form of plant behavior. We
 cultivated 37 perennial herbaceous Central European species from open
 terrestrial habitats in pots with three different spatial gradients of
 nutrient availability (steep, shallow and no gradient). We assessed the
 intensity of foraging as differences in root placement inside pots with
 and without a spatial gradient of resource supply. For the same set of
 species, we retrieved data about body traits from available databases:
 maximum height at maturity, mean area of leaf, specific leaf area, shoot
 lifespan, ability to self-propagate clonally, maximal lateral spread (in
 clonal plants only), realized vegetative growth in cultivation and
 realized seed regeneration in cultivation. Clonal plants and plants with
 extensive vegetative growth showed considerably weaker foraging than their
 non-clonal or slow-growing counterparts. There was no phylogenetic signal
 in the amount of expressed root foraging intensity. Since clonal plants
 foraged less than non-clonals and foraging intensity did not seem to be
 correlated with species phylogeny, we hypothesize that clonal growth
 itself (i.e. the ability to develop at least partly self-sustaining
 ramets) may be an answer to soil heterogeneity. Whereas unitary plants use
 roots as organs specialized for both resource acquisition and transport to
 overcome spatial heterogeneity in resource supply, clonal plants separate
 these two functions. Becoming a clonal plant allows higher specialization
 at the organ level, since a typical clonal plant can be viewed as a
 network of self-sustainable harvesting units connected together with
 specialized high-throughput connection organs. This may be an effective
 alternative for coping with spatial heterogeneity in resource
 availability.
description: root biomass per pot
 halfRoot foraging data for
 37 plant species. The experiment was run in two years. Each row
 corresponds to a pot. In each pot, there was either no spatial gradient of
 nutrients, or shallow gradient or steep gradient (column
 "contrast"). Dry belowground biomass is reported for each half
 of the pot (root biomass content in the nutrients-poor half: column
 "lowconc_half_roots[g]"; root biomass content in the
 nutrients-rich half: column "highconc_half_roots[g]"); for pots
 with no gradient, identity of halves was chosen at random. Aboveground dry
 biomass and sum of the belowground halves are reported,
 too.root_foraging_per_pot_data.csv
DOI: 10.5061/dryad.hv7369k
title: Data from: Questioning assumptions of trophic behavior in a broadly ranging marine predator guild

description: We evaluated whether existing assumptions regarding the trophic ecology of
 a poorly-studied predator guild, northwest (NW) Atlantic skates (family:
 Rajidae), were supported across broad geographic scales. Four hypotheses
 were tested using carbon (δ13C) and nitrogen (δ15N) stable isotope values
 as metrics of foraging behavior: 1) species exhibit ontogenetic shifts in
 habitat and thus display a shift in 13C with differential use of the
 continental shelf; 2) species exhibit ontogenetic prey shifts (i.e., from
 smaller to larger prey items) and become enriched in 15N; 3) individuals
 acquire energy from spatially confined local resource pools and exhibit
 limited displacement; and 4) species exhibit similarly sized and highly
 overlapping trophic niches. We found someweak evidence for ontogenetic
 shifts in habitat-use (δ13C) for thorny and little skate and diet (δ15N)
 for thorny and winter skate and hypothesize that individuals exhibit
 gradual trophic niche transition, especially in δ15N space, rather than a
 clear and distinct shift in diet throughout ontogeny. Spatial isoscapes
 generated for little, thorny, and winter skate, highlighted distinct
 spatial patterns in isotopic composition across the coastal shelf. For
 little and thorny skate, patterns mimicked the expected spatial
 variability in isotopic composition of phytoplankton/POM, suggesting
 limited displacement and utilization of spatially confined resource pools.
 Winter skate, however, exhibited a much narrower range of δ13C and δ15N,
 suggesting individuals may pool resources from a more confined latitudinal
 range. Although high total trophic niche overlap was observed between some
 species (e.g., little and thorny skate), sympatric species (e.g., little
 and winter skate) exhibited potential trophic niche separation. These
 findings offer new insight into the trophic dynamics of a poorly studied,
 vulnerable group of predators, and highlight a need to re-examine
 assumptions pertaining to aspects of their ecology.
description: Shipley_ECOG_DryadMeta data used in publication
DOI: 10.5061/dryad.1s834
title: Data from: A multi-scale analysis of gene flow for the New England cottontail, an imperiled habitat specialist in a fragmented landscape

description: Landscape features of anthropogenic or natural origin can influence
 organisms’ dispersal patterns and the connectivity of populations.
 Understanding these relationships is of broad interest in ecology and
 evolutionary biology and provides key insights for habitat conservation
 planning at the landscape scale. This knowledge is germane to restoration
 efforts for the New England cottontail (Sylvilagus transitionalis), an
 early-successional habitat specialist of conservation concern. We
 evaluated local population structure and measures of genetic diversity of
 a geographically isolated population of cottontails in the northeastern
 United States. We also conducted a multi-scale landscape genetic analysis,
 in which we assessed genetic discontinuities relative to the landscape and
 developed several resistance models to test hypotheses about landscape
 features that promote or inhibit cottontail dispersal within and across
 the local populations. Bayesian clustering identified four genetically
 distinct populations, with very little migration among them, and
 additional substructure within one of those populations. These populations
 had private alleles, low genetic diversity, critically low effective
 population sizes (3.2 -36.7), and evidence of recent genetic bottlenecks.
 Major highways and a river were found to limit cottontail dispersal and to
 separate populations. The habitat along roadsides, railroad beds and
 utility corridors, on the other hand, was found to facilitate cottontail
 movement among patches. The relative importance of dispersal barriers and
 facilitators on gene flow varied among populations in relation to
 landscape composition, demonstrating the complexity and context dependency
 of factors influencing gene flow and highlighting the importance of
 replication and scale in landscape genetic studies. Our findings provide
 information for the design of restoration landscapes for the New England
 cottontail and also highlight the dual influence of roads, as both
 barriers and facilitators of dispersal for an early-successional habitat
 specialist in a fragmented landscape.
description: Microsatellite genotypes
 and locations of New England cottontails in Maine and New
 HampshireMicrosatellite genotypes
 for 11 loci, including a Y chromosome marker, are provided in Excel
 spreadsheet format. These genotypes are from individual New England
 cottontails identified from fecal pellet samples collected during field
 surveys. Location data, in the form of lat/long geographic coordinates,
 are provided for each sample collected. Column headings and other metadata
 are found in the spreadsheet.Fenderson2014_EcolEvol_Cottontail_Dataset.xlsx
DOI: 10.5061/dryad.609
title: Data from: Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides

description: The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial
 DNA sequences to test conflicting vicariant and dispersal biogeographic
 hypotheses regarding the southern hemisphere range of this freshwater
 group. Although phylogenetic resolution of cytochrome b and 16S rRNA
 sequences is largely limited to more recent divergences, our data indicate
 that the radiation can be interpreted as a number of relatively recent
 dispersal events superimposed on an ancient gondwanan radiation. Genetic
 relationships contradict the findings of recent morphological analyses of
 galaxioid fishes. In particular, a number of hypotheses regarding
 phylogenetic placement of the enigmatic Lepidogalaxias are examined. While
 most workers consider Lepidogalaxias to be an unusual scaled member of the
 southern hemisphere galaxioids, it has also been suggested that this
 species is related to the northern hemisphere esocoids. Our data strongly
 suggest that this species is not a galaxiid; the alternative hypothesised
 esocoid relationship cannot be rejected. The species-rich genus Galaxias
 is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is
 reassessed in the light of phylogenetic relationships. Juvenile
 saltwater-tolerance is phylogenetically distributed throughout the
 Galaxiinae and the loss of this migratory phase may be a major cause of
 speciation.
description: Waters et al Data
 SetWaters.nexus