cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5874k
title: Data from: Geographic variation in morphology of Dark-eyed Juncos and implications for population divergence

description: Geographic variation in morphology that develops among closely related
 populations can help drive genetic divergence, and eventually speciation,
 when those morphological traits are the basis for social interactions that
 influence reproduction. The North American Dark-eyed junco (Junco
 hyemalis) complex is an interesting case in speciation. The numerous
 subspecies have distinct breeding ranges and unique plumage coloration,
 but based on the presence of hybrid populations and recent genetic data,
 can be considered to belong to a single species. Research within various
 populations of juncos has shown first, that wing length and the amount of
 white on the tail feathers (“tail white”) influence an individual’s
 dominance status and mating success, and second, that these traits can
 undergo rapid evolution when social and environmental conditions change.
 Here, I used museum specimens to examine tail white and body size, as
 measured by wing and tail length, of males and females within and among 13
 geographically distinct Dark-eyed Junco subspecies. I documented
 geographic variation of mean values for each of these morphological
 traits, as well as patterns of trait co-variation and the degree of sexual
 dimorphism. I discuss these results in relation to what they may indicate
 about the generation and maintenance of divergence among the subspecies.
description: E_Ferree_JuncosPre1950Measurements of junco museum specimens collected prior to 1950. Data were entered into excel.E_Ferree_Sexual DimorphismPre1950Summary of measurements taken on junco museum specimens, used to calculate sexual dimorphism. Data were entered into excel.
DOI: 10.5061/dryad.jc8cp
title: Data from: Of niche differentiation, dispersal ability and historical legacies: what drives woody community assembly in recent Mediterranean forests?

description: Community assembly rules have been extensively studied, but its
 association with regional environmental variation and land use history
 remains largely unexplored. Land use history might be especially important
 in Mediterranean forests, considering their historical deforestation and
 recent afforestation. Using forest inventories and historical (1956) and
 recent (2000) land cover maps, we explored the following hypotheses: 1)
 woody species assembly is driven by environmental factors, but also by
 historical landscape attributes; 2) recent forests exhibit lower woody
 species richness than pre-existing due to the existence of colonization
 credits; 3) these credits are modulated by species’ life-forms and
 dispersal mechanisms. We examined the association of forest historical
 type (pre-existing versus recent) with total species richness and that of
 diverse life-forms and dispersal groups, also considering the effects of
 current environment and past landscape factors. When accounting for these
 effects, no significant differences in woody species richness were found
 between forest historical types except for vertebrate-dispersed species.
 Species richness of this group was affected by the interaction of forest
 historical type with distance to coast and rainfall: vertebrate-dispersed
 species richness increased with rainfall and distance to the coast in
 recent forests, while it was higher in dryer sites in pre-existing
 forests. In addition, forest historical types showed differences in woody
 species composition associated to diverse environmental and past landscape
 factors. In view of these results we can conclude that: 1) community
 assembly in terms of species richness is fast enough to exhaust most
 colonization credit in recent Mediterranean forests except for
 vertebrate-dispersed species; 2) for these species, colonization credit is
 affected by the interplay of forest history and a set of proxies of niche
 and landscape constraints of species dispersal and establishment; 3) woody
 species assemblage is mostly shaped by the species’ ecological niches in
 these forests.
description: Raw data species
 richness, environment, forest historyRawdata_dryad_002534.xlsx
DOI: 10.5061/dryad.5nm5g
title: Data from: Re-visiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

description: Although the phylogeography of European mammals has been extensively
 investigated since the 1990s, many studies were limited in terms of
 sampling distribution, the number of molecular markers used and the
 analytical techniques employed, frequently leading to incomplete
 postglacial recolonisation scenarios. The broad-scale genetic structure of
 the European badger (Meles meles) is of interest as it may result from
 historic restriction to glacial refugia and/or recent anthropogenic
 impact. However, previous studies were based mostly on samples from
 western Europe, making it difficult to draw robust conclusions about the
 location of refugia, patterns of postglacial expansion and recent
 demography. In the present study, continent-wide sampling and analyses
 with multiple markers provided evidence for two glacial refugia (Iberia
 and southeast Europe) that contributed to the genetic variation observed
 in badgers in Europe today. Approximate Bayesian computation provided
 support for a colonisation of Scandinavia from both Iberian and
 southeastern refugia. In the whole of Europe, we observed a decline in
 genetic diversity with increasing latitude, suggesting that the reduced
 diversity in the peripheral populations resulted from a postglacial
 expansion processes. Although MSVAR v.1.3 also provided evidence for
 recent genetic bottlenecks in some of these peripheral populations, the
 simulations performed to estimate the method’s power to correctly infer
 the past demography of our empirical populations suggested that the timing
 and severity of bottlenecks could not be established with certainty. We
 urge caution against trying to relate demographic declines inferred using
 MSVAR with particular historic or climatological events.
description: dryad_uploadMicrosatellite raw data & geographic coordinates
DOI: 10.5061/dryad.r122k
title: Data from: Phylogenetic ANOVA: the Expression Variance and Evolution model for quantitative trait evolution

description: A number of methods have been developed for modeling the evolution of a
 quantitative trait on a phylogeny. These methods have received renewed
 interest in the context of genome-wide studies of gene expression, in
 which the expression levels of many genes can be modeled as quantitative
 traits. We here develop a new method for joint analyses of quantitative
 traits within- and between species, the Expression Variance and Evolution
 (EVE) model. The model parameterizes the ratio of population to
 evolutionary expression variance, facilitating a wide variety of analyses,
 including a test for lineage-specific shifts in expression level, and a
 phylogenetic ANOVA that can detect genes with increased or decreased
 ratios of expression divergence to diversity, analogous to the famous
 Hudson Kreitman Aguadé (HKA) test used to detect selection at the DNA
 level. We use simulations to explore the properties of these tests under a
 variety of circumstances and show that the phylogenetic ANOVA is more
 accurate than the standard ANOVA (no accounting for phylogeny) sometimes
 used in transcriptomics. We then apply the EVE model to a mammalian
 phylogeny of 15 species typed for expression levels in liver tissue. We
 identify genes with high expression divergence between species as
 candidates for expression level adaptation, and genes with high expression
 diversity within species as candidates for expression level conservation
 and/or plasticity. Using the test for lineage-specific expression shifts,
 we identify several candidate genes for expression level adaptation on the
 catarrhine and human lineages, including genes putatively related to
 dietary changes in humans. We compare these results to those reported
 previously using a model which ignores expression variance within species,
 uncovering important differences in performance. We demonstrate the
 necessity for a phylogenetic model in comparative expression studies and
 show the utility of the EVE model to detect expression divergence,
 diversity, and branch-specific shifts.
description: EVE software
 releaseEVE_release_v0.zip
DOI: 10.5061/dryad.863c0
title: Data from: Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot

description: 1. Plant elemental properties are fundamentally important for physiology
 and biogeochemical cycling in ecosystems. No study has examined foliar
 elements and their interaction with soil and climate conditions at large
 geographic scales in Karst areas of China, a biodiversity hotspot in the
 world. Yet such information is important for understanding the functional
 diversity of nutrient strategies and the physiological adaptations of
 plants to climatic and edaphic heterogeneity. 2. We assessed the influence
 of phylogeny, soil type and the climate on leaf element concentrations in
 a clade of taxonomically diverse Karst plants from the subfamily
 Didymocarpoideae under an explicit phylogenetic framework. We measured
 leaf concentrations of seven elements and evaluated soil properties for
 422 populations of 177 Didymocarpoideae species. The phylogenetic signals
 present in the leaf element concentrations and in soil and climatic
 variables were quantified at both the subfamily (Didymocarpoideae) and
 genus (Primulina) levels. The correlations between leaf elements and soil
 and climate conditions were analyzed at these two phylogenetic scales. 3.
 The Didymocarpoideae subfamily is generally characterized by higher Ca and
 Mg contents relative to other plants in China. Across the subfamily, a
 strong phylogenetic signal is detected for all of the leaf elements
 analyzed as well as for most soil and climate variables, whereas the genus
 Primulina exhibits no significant phylogenetic signal in leaf elements or
 in most soil variables. 4. We detected an influence of both soil and
 climatic conditions on leaf element concentrations. However, the patterns
 of the relationships between leaf elements and soil and climate variables
 vary at the subfamily and genus levels. The phylogeny has a stronger
 effect than soil and climatic factors on leaf element concentrations at
 the subfamily level, while the leaf element contents within the genus
 Primulina are mostly influenced by environmental conditions. We conclude
 that the influences of taxonomy, soil and climate on leaf element
 concentrations are dependent on the phylogenetic scale of analysis.
description: didymocarpoideae_dataTrait data of 56 species of the Didymocarpoideae subfamilydidymocarpoideae_treePhylogenetic tree for 56 Didymocarpoideae speciesprimulina_dataTrait data of 100 species of the Primulina genusprimulina_treePhylogenetic tree for 100 Primulina speciesR scriptR script for measuring pylogenetic signal in the Primulina genusR scriptR script for measuring pylogenetic signal in the Didymocarpoideae subfamilyR scriptR script for PGLS regressions for the Didymocarpoideae subfamily
DOI: 10.5061/dryad.v95q1
title: Data from: Phylogeographic patterns of the desert poplar in northwest China shaped by both geology and climatic oscillations

description: Background: The effects of historical geology and climatic events on the
 evolution of plants around the Qinghai-Tibetan Plateau region have been at
 the center of debate for years. To identify the influence of the uplift of
 the Tianshan Mountains and/or climatic oscillations on the evolution of
 plants in arid northwest China, we investigated the phylogeography of the
 Euphrates poplar (Populus euphratica) using chloroplast DNA (cpDNA)
 sequences and nuclear microsatellites, and estimated its historical
 distribution using Ecological Niche Modeling (ENM). Results: We found that
 the Euphrates poplar differed from another desert poplar, P. pruinosa, in
 both nuclear and chloroplast DNA. The low clonal diversity in both
 populations reflected the low regeneration rate by seed/seedlings in many
 locations. Both cpDNA and nuclear markers demonstrated a clear divergence
 between the Euphrates poplar populations from northern and southern
 Xinjiang regions. The divergence time was estimated to be early
 Pleistocene based on cpDNA, and late Pleistocene using an Approximate
 Bayesian Computation analysis based on microsatellites. Estimated gene
 flow was low between these two regions, and the limited gene flow occurred
 mainly via dispersal from eastern regions. ENM analysis supported a wider
 distribution of the Euphrates poplar at 3 Ma, but a more constricted
 distribution during both the glacial period and the interglacial period.
 Conclusions: These results indicate that the deformation of the Tianshan
 Mountains has impeded gene flow of the Euphrates poplar populations from
 northern and southern Xinjiang, and the distribution constriction due to
 climatic oscillations further accelerated the divergence of populations
 from these regions. To protect the desert poplars, more effort is needed
 to encourage seed germination and seedling establishment, and to conserve
 endemic gene resources in the northern Xinjiang region.
description: Populus euphratica SSR
 dataPopulus pruinosa SSR
 dataPopulus euphratica
 multilocus genotypesPopulus pruinosa
 multilocus genotypesPopulation
 information
DOI: 10.5061/dryad.dh1sd
title: Data from: Highway widening and underpass effects on vertebrate road mortality

description: Road widening (a.k.a. road dualling) and the presence of mitigation
 structures may have opposing effects on the number of animal-vehicle
 collisions. Their influence in tropical areas is poorly quantified, and we
 know little about how modifications of road structure affect fauna
 roadkill and mitigation. We evaluated how road widening and proximity to a
 wildlife underpass affect roadkill of medium and large mammals, using
 roadkill records from before and after the widening of 150 km of road with
 new and old wildlife underpasses. Roadkilled species were divided into
 three groups based on mobility and sensitivity to human disturbance. Four
 out of 16 species exhibited significantly higher roadkill after widening.
 Roadkill near underpasses was generally higher than by chance, despite our
 expectation of reduction of roadkills. This result indicates that we must
 adopt more effective mitigation measures, such as appropriate fencing
 combined with underpasses.
description: Mammals roadkills for
 the year 2006Rodkills2006.xlsxMammals roadkills for the year 2007Roadkills2007.xlsxMammals roadkills for the year 2008Roadkills2008.xlsMammals roadkills for the year 2009roadkills2009.xlsx
DOI: 10.5061/dryad.ps6k0
title: Data from: Effects of forest certification on the ecological condition of Mediterranean streams

description: 1. Forest certification, a proxy for sustainable forest management, covers
 more than 10% of the world's forests. Under forest certification,
 forest managers and landowners must comply with environmental, economic
 and social management standards aiming to promote forest conservation.
 Despite an increasing area of certified forests, there is a dearth of data
 on how forest certification is affecting the conservation of forest
 ecosystems and associated habitats. 2. Here we assess the effects of
 Forest Stewardship Council (FSC) certification, one of the largest
 certification schemes in the world, on the ecological condition of streams
 crossing Mediterranean evergreen oak woodlands. 3. We used the Stream
 Visual Assessment Protocol (SVAP) to compare the ecological condition of
 streams located in areas with three and five years of certification, in
 non-certified areas and in least-disturbed streams. 4. Forest
 certification positively affected the ecological condition of the surveyed
 streams but its effects were only measurable after five years of
 certification. Streams with five years of certification had more
 continuous, dense and diverse riparian vegetation when compared to streams
 located in non-certified areas. Moreover, the condition of streams located
 in areas with five years of forest certification was similar to the
 condition of least- disturbed streams. 5. Synthesis and applications.
 Forest certification promotes the ecological condition of streams
 occurring within Mediterranean evergreen oak woodlands. This mainly
 happens because in areas under forest certification managers and
 landowners have to comply with management practices that require them to
 remove or reduce the main causes for stream degradation, allowing riparian
 habitats to recover. Within landscapes with large and increasing areas
 under forest certification, such as the Mediterranean cork oak woodlands,
 the positive effects of certification on the ecological condition of
 streams may spread across the hydrographic network in the medium to long
 term.
description: Dataset stored in R
 workspace for "Effects of forest certification on the ecological
 condition of Mediterranean streams"This is an R workspace
 containing the dataset used in "Effects of forest certification on
 the ecological condition of Mediterranean streams"Dataset.RDataR code required for reproducing the analysis presented in "Effects of forest certification on the ecological condition of Mediterranean streams"R code required for reproducing the analysis presented in "Effects of forest certification on the ecological condition of Mediterranean streams"Rcode_for_analysis.R
DOI: 10.5061/dryad.330c1
title: Data from: The role of neuropeptide F in a transition to parental care

description: The genetics of complex social behaviour can be dissected by examining the
 genetic influences of component pathways, which can be predicted based on
 expected evolutionary precursors. Here, we examine how gene expression in
 a pathway that influences the motivation to eat is altered during parental
 care that involves direct feeding of larvae. We examine the expression of
 neuropeptide F, and its receptor, in the burying beetle Nicrophorus
 vespilloides, which feeds pre-digested carrion to its begging larvae. We
 found that the npf receptor was greatly reduced during active care. Our
 research provides evidence that feeding behaviour was a likely target
 during the evolution of parental care in N. vespilloides. Moreover,
 dissecting complex behaviours into ethologically distinct sub-behaviours
 is a productive way to begin to target the genetic mechanisms involved in
 the evolution of complex behaviours.
description: NPF_paper_raw_data_Dryad_Biol_LettersThe raw cycle threshold (CT) values and associated identifiers of biological replicate and treatment for the analyses preformed in the linked paper.
DOI: 10.5061/dryad.s4t7m
title: Data from: Selection for alternative male reproductive tactics alters intralocus sexual conflict

description: Intralocus sexual conflict (IASC) arises when fitness optima for a shared
 trait differ between the sexes; such conflict may help maintain genetic
 variation within populations. Sex-limited expression of sexually
 antagonistic traits may help resolve the conflict, but the extent of this
 resolution remains a subject of debate. In species with alternative male
 reproductive tactics, unresolved conflict should manifest more in a more
 sexually dimorphic male phenotype. We tested this prediction in the bulb
 mite (Rhizoglyphus robini), a species in which aggressive fighters coexist
 with benign scramblers. To do this, we established replicated lines in
 which we increased the proportion of each of the alternative male morphs
 using artificial selection. After approximately 40 generations, the
 proportion of fighters and scramblers stabilized at &gt;0.9 in
 fighter- and scrambler-selected lines, respectively. We then measured
 several female fitness components. As predicted by IASC theory, female
 fecundity and longevity was lower in lines selected for fighters and
 higher in lines selected for scramblers. This finding indicates that
 sexually selected phenotypes are associated with an ontogenetic conflict
 that is not easily resolved. Furthermore, we suggest that IASC may be an
 important mechanism contributing to the maintenance of genetic variation
 in the expression of alternative reproductive tactics.
description: Plesnar_Bielak_etal_evolution_data
DOI: 10.5061/dryad.c6f5b
title: Data from: The importance of social dimension and maturation stage for the probabilistic maturation reaction norm in Poecilia reticulata

description: Maturation is an important event in an organism's life history, with
 important implications on dynamics of both wild and captive populations.
 The probabilistic maturation reaction norm (PMRN) has emerged as an
 important method to describe variation in maturation in wild fish. Because
 most PMRNs are based on age and size only, it is important to understand
 limitations of these variables in explaining maturation. We experimentally
 assessed (i) the sensitivity of age- and size-based PMRNs to unaccounted
 sources of plasticity, (ii) the role of social environment on maturation
 and (iii) the significance of estimating PMRNs early and late in the
 maturation process (initiation and completion of maturation,
 respectively). We reared male guppies (Poecilia reticulata) under
 laboratory conditions, subjected to two food levels and three different
 social cues. We found that growth and social environment affected the
 maturation in a way that could not be accounted for by their effect on age
 and size. PMRNs estimated for the initiation stage were less plastic
 (growth differences and social cues influenced the PMRN shape only little)
 than those for completion. The initiation of maturation is probably closer
 to the maturation ‘decision’ and allows determining factors influencing
 maturation decision most accurately.
description: GuppyMaturation_DiazPauli_HeinoAge, length and height of male guppies measured at two weeks intervals. Initiation and completion refers at two maturation stages, and food and social refer to treatments (see manuscript). In the few instances when measurements were not taken at exactly two weeks intervals (but one or two days difference), “length_real” refers to the actual measurement and “length” refers to estimated value by interpolatation.
DOI: 10.5061/dryad.d48n3
title: Data from: Primer development for the plastid region ycf1 in Annonaceae and other magnoliids

description: PREMISE OF THE STUDY: Primers were developed for a portion of the ycf1
 plastid gene in magnoliid taxa to investigate the utility of ycf1 in
 phylogenetic analyses. METHODS AND RESULTS: Twenty-six species across six
 families within the magnoliid group (Canellales, Piperales, Laurales, and
 Magnoliales) were sampled to examine the ability to amplify ycf1.
 Additionally, 29 accessions of Asimina and Deeringothamnus (Annonaceae)
 were sequenced to assess levels of variation in ycf1 compared to matK and
 trnL-F. CONCLUSIONS: Results indicate that ycf1 is easily amplifi ed and
 sequenced. In Annonaceae, ycf1 provides more informative phylogenetic
 characters than commonly used markers such as matK and trnL-F .
description: Annonaceae
 matKNexus matrix of matK
 sequences of various AnnonaceaeAnnonaceae
 trnLFNexus matrix of trnL-F
 sequences of various Annonaceae.Annonaceae
 ycf1Nexus file of ycf1
 sequences of various Annonaceae.