cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r12cq4r
title: Data from: Biogeographic and anthropogenic correlates of Aleutian Islands plant diversity: a machine-learning approach

description: This is the first comprehensive analysis of vascular plant diversity
 patterns in the Aleutian Islands to identify and quantify the impact of
 Aleutian Island distance dispersal barriers, geographical, ecological and
 anthropogenic factors. Data from public Open Access databases, printed
 floristic accounts, and from collections made by the primary author were
 used to develop an Aleutian floristic database. The most common plant
 distribution pattern was ‘an eastern origin community’, though it compared
 similarly to the ‘Western’ and ‘Widespread’ distribution pattern. We
 established an ecological plant community composition class for each
 island, based on clustering species assemblage dissimilarity measurements
 (Jaccard Index), and a measurement of phylogenetic dissimilarity
 (UniFrac). We modelled these composition classes and species richness
 values in non-parametric algorithmic models and concepts (data cloning
 using machine learning, stochastic boosting- TreeNet,) based on classic
 and Aleutians-specific island biogeography hypotheses. Plant species
 richness is strongly associated with the equilibrium model variables of
 area and island isolation, as well as distance to the Alaska Peninsula,
 and island total stream length. Species composition is strongly associated
 with the landmass groups during the last glacial maximum, maximum island
 elevation, island isolation and island area. Phylogenetic composition is
 associated with island area, distance from the islands to the Chukotka
 Peninsula, maximum island elevation, island geologic age, and island
 isolation. This study extends the equilibrium theory of island
 biogeography by including additional drivers of diversity during the
 Anthropocene, such as the landmass during the LGM, as well as factors that
 may be related to anthropogenic extinction rate.
description: Plant species of the
 AleutiansA matrix of plant
 species vs. species characteristics (taxonomy, island occurrence,
 phenotype). See README.txt for metadata.Garroutte_et_al_Flora_of_Aleutians.tsv
DOI: 10.5061/dryad.r0874
title: Data from: Sex-specific shifts in morphology and colour pattern polymorphism during range expansion of an invasive lizard

description: Aim: Human-assisted range expansion of animals to new environments can
 lead to phenotypic shifts over ecological timescales.We investigated
 whether phenotypic changes are sex-specific using an invasive lizard
 (Lampropholis delicata). Location: Pacific region (Hawaiian Islands, Lord
 Howe Island, New Zealand, eastern Australia) Methods: Using our knowledge
 of theintroduction history of L. delicata, we examined museum specimens of
 individuals collected across the native and introduced range to determine
 whether shifts in morphologyor colour pattern polymorphism had occurred
 during its range expansion, and if so, whether they differed between the
 sexes. Results: Sexual dimorphism in both size and shape was documented
 within the native range of the delicate skink. However, during range
 expansion, phenotypic shifts were observed in shape, but not size. In two
 of the three invasive populations, these phenotypic shifts were
 sex-specific. In the Hawaiian Islands, changes in shape were driven by
 males, whereas in New Zealand it was due to shifts in females.Similarly,
 changes in the frequency of a colour pattern polymorphism, a mid-lateral
 stripe shown to have sex-specific impacts on fitness (positive in females,
 negative in males), occurred following colonisation of the Hawaiian
 Islands and Lord Howe Island. In Hawaii, the incidence of the polymorphism
 increased over time in females, and decreased in males. Main conclusions:
 Phenotypic shifts during the range expansion of invasive species may be
 sex-specific, and are potentially related to the degree of realised niche
 shift that has occurred between the source and introduced range.
description: morphological_data_Ldelicata_JBI13075"morphological_data_Ldelicata_JBI13075.csv" contains the morphological measurements recorded from 1,188 L. delicata specimens across the native range in eastern Australia, and in the invasive ranges in New Zealand, Lord Howe Island, and the Hawaiian Islands. All specimens are identified by the ID code from the respective museums, with the year of collection, the sex of each specimen, and the respective range of distribution. See paper for more details on clade numbers and abbreviations for the morphological data.
DOI: 10.5061/dryad.6ff85
title: Data from: A new tuberculated Pristimantis (Anura, Terrarana, Strabomantidae) from the Venezuelan Andes, redescription of Pristimantis pleurostriatus, and variation within Pristimantis vanadisae

description: A new tuberculated Pristimantis is described from the eastern versant of
 the Venezuelan Andes. The new species is found in cloud forest at around
 1600 masl on the eastern side of the Cordillera de Mérida. It is
 distinguished from other similar tuberculated species by its round,
 ill-defined canthus rostralis, ill-defined canthal stripe, and absence of
 pale spots on the groin and posterior surface of thighs. Pristimantis
 pleurostriatus is a poorly known species found in cloud forest on the
 western slopes of the Venezuelan Andes. We redescribe the species based on
 topotypic specimens. Pristimantis vanadisae is a polychomatic species
 varying dramatically in pattern; four chromotypes are described. Molecular
 data are presented which distinguish among tuberculated and other species
 of Pristimantis in the Cordillera de Merida. Molecular data also support
 placement of Mucubatrachus and Paramophrynella in Pristimantis.
description: P_conservatio_alignmentAlignment of 12S and 16S sequences with ambiguous regions deleted, used to generate tree depicted in Figure 9.
DOI: 10.5061/dryad.mh6kq
title: Data from: Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

description: Historical factors, current population size, population connectivity and
 selective processes at linked loci contribute to shaping contemporary
 patterns of neutral genetic diversity. It is now widely acknowledged that
 nuclear and mitochondrial markers react differently to current demography
 as well as to past history, so the use of both types of markers is often
 advocated to gain insight on both historical and contemporary processes.
 We used 12 microsatellite loci genotyped in 13 populations of a mountain
 lizard (Iberolacerta bonnali) to test if the historical scenario favoured
 by a previous mitochondrial study was also supported by nuclear markers
 and thereby evaluated the consequences of post-glacial range movements on
 nuclear diversity. Congruent signals of recent history were revealed by
 nuclear and mitochondrial markers using an Approximate Bayesian
 Computation approach but contemporary patterns of mtDNA and nuclear DNA
 diversity were radically different. Although dispersal in this species is
 probably highly restricted at all spatial scales, colonisation abilities
 have been historically good, suggesting capability for reestablishment of
 locally extinct populations except in fully disconnected habitats.
description: bonnali_diyabc_inputinput file for running ABC analysis with DIYABC v2bonnali_genepop_inputinput files based on 12 microsatellites for running Genepopdata_bonnaligeographic coordinates of Iberolacerta bonnali locations sampled in FranceMatriceDistanceCretesgeographic distances between I. bonnali populations following the suitable habitats throughout the mountainsmatriceLn(distances)ln ( direct geographic distances) between I bonnali populations
DOI: 10.15468/dl.tq4eyv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Leptoglossis albiflora",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000941-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.j101c
title: Data from: Understanding admixture patterns in supplemented populations: a case study combining molecular analyses and temporally explicit simulations in Atlantic salmon

description: Genetic admixture between wild and introduced populations is a rising
 concern for the management of endangered species. Here we use a dual
 approach based on molecular analyses of samples collected before and after
 hatchery fish introduction in combination with a simulation study to get
 insight into the mechanisms of admixture in wild populations. Using 17
 microsatellites we genotyped pre- and post-stocking samples from four
 Atlantic salmon populations supplemented with non-native fish to estimate
 genetic admixture. We also used individual-based temporally explicit
 simulations based on realistic demographic and stocking data to predict
 the extent of admixture. We found a low admixture by hatchery stocks
 within pre-stocking samples but moderate to high values in post-stocking
 samples (from 12 % to 60 %). The simulation scenarios best fitting the
 real data suggested a 10 to 25 times lower survival of stocked fish
 relative to wild individuals. Simulations also suggested relatively high
 dispersal rates of stocked and wild fish, which may explain some high
 levels of admixture in weakly stocked populations and the persistence of
 indigenous genotypes in heavily stocked populations. This study overall
 demonstrates that combining genetic analyses with simulations can
 significantly improve the understanding of admixture mechanisms in wild
 populations.
description: dataGenotypes of the
 individuals, ordered by rivers and cohorts.
DOI: 10.5061/dryad.t1tk4
title: Data from: Variation in thermal stress response in two populations of the brown seaweed, Fucus distichus, from the Arctic and subarctic intertidal

description: It is unclear whether intertidal organisms are ‘preadapted’ to cope with
 the increase of temperature and temperature variability or if they are
 currently at their thermal tolerance limits. To address the dichotomy, we
 focused on an important ecosystem engineer of the Arctic intertidal rocky
 shores, the seaweed Fucus distichus and investigated thermal stress
 responses of two populations from different temperature regimes (Svalbard
 and Kirkenes, Norway). Thermal stress responses at 20°C, 24°C and 28°C
 were assessed by measuring photosynthetic performance and expression of
 heat shock protein (HSP) genes (shsp, hsp90 and hsp70). We detected
 population-specific responses between the two populations of F. distichus,
 as the Svalbard population revealed a smaller decrease in photosynthesis
 performance but a greater activation of molecular defence mechanisms
 (indicated by a wider repertoire of HSP genes and their stronger
 upregulation) compared with the Kirkenes population. Although the
 temperatures used in our study exceed temperatures encountered by F.
 distichus at the study sites, we believe response to these temperatures
 may serve as a proxy for the species’ potential to respond to
 climate-related stresses.
description: Stress measurements in
 F.distichusThe file contains two
 tables with (1) photosynthetic performance (PI_abs and Fv/Fm) and (2) gene
 expression (3 hsp genes) of F. distichus individuals from two populations
 (Svalbard and Kirkenes) during thermal stress experiments. Experiments
 were performed at 20˚C, 24˚C and 28˚C with measurements taken at 0 min
 (control), 15 min of stress, 60 min of stress and 24 hours of
 recovery.2015-08-Fd_DATA.xls
DOI: 10.5061/dryad.1790
title: Data from: Directional cultural change by modification and replacement of memes

description: Evolutionary approaches to culture remain contentious. A source of
 contention is that cultural mutation may be substantial and, if it drives
 cultural change, then current evolutionary models are not adequate. But we
 lack studies quantifying the contribution of mutations to directional
 cultural change. We estimated the contribution of one type of cultural
 mutations – modification of memes - to directional cultural change using
 an amenable study system: learned birdsongs in a species that recently
 entered an urban habitat. Many songbirds have higher minimum song
 frequency in cities, to alleviate masking by low-frequency noise. We
 estimated that the input of meme modifications in an urban songbird
 population explains about half the extent of the population divergence in
 song frequency. This contribution of cultural mutations is large, but
 insufficient to explain the entire population divergence. The remaining
 divergence is due to selection of memes or creation of new memes. We
 conclude that the input of cultural mutations can be quantitatively
 important, unlike in genetic evolution, and that it operates together with
 other mechanisms of cultural evolution. For this and other traits where
 the input of cultural mutations might be important, quantitative studies
 of cultural mutation are necessary to calibrate realistic models of
 cultural evolution.
description: Measurements of
 dark-eyed junco songsMeasurements of minimum
 song frequency and others, averaged for each bird and song type. From
 field recordings.CardosoAtwell-dataset.xls
DOI: 10.5061/dryad.mm317th7
title: Data from: Gene flow and pathogen transmission among bobcats (Lynx rufus) in a fragmented urban landscape

description: Urbanization can result in the fragmentation of once contiguous natural
 landscapes into a patchy habitat interspersed within a growing urban
 matrix. Animals living in fragmented landscapes often have reduced
 movement among habitat patches due to avoidance of intervening human
 development, which potentially leads to both reduced gene flow and
 pathogen transmission between patches. Mammalian carnivores with large
 home ranges, such as bobcats (Lynx rufus), may be particularly sensitive
 to habitat fragmentation. We performed genetic analyses on bobcats and
 their directly transmitted viral pathogen, feline immunodeficiency virus
 (FIV), to investigate the effects of urbanization on bobcat movement. We
 predicted that urban development, including major freeways, would limit
 bobcat movement and result in genetically structured host and pathogen
 populations. We analyzed molecular markers from 106 bobcats and 19 FIV
 isolates from seropositive animals in urban southern California. Our
 findings indicate that reduced gene flow between two primary habitat
 patches has resulted in genetically distinct bobcat subpopulations
 separated by urban development including a major highway. However, the
 distribution of genetic diversity among FIV isolates determined through
 phylogenic analyses indicates that pathogen genotypes are less spatially
 structured – exhibiting a more even distribution between habitat
 fragments. We conclude that the types of movement and contact sufficient
 for disease transmission occur with enough frequency to preclude
 structuring among the viral population, but that the bobcat population is
 structured due to low levels of effective bobcat migration resulting in
 gene flow. We illustrate the utility in using multiple molecular markers
 that differentially detect movement and gene flow between subpopulations
 when assessing connectivity.
description: Accessible data
 spreadsheetMicrosatellite fragment
 lengths for 106 bobcats and GenBank accession numbers for two feline
 immunodeficiency virus gene fragments from 19 infected
 individuals.
DOI: 10.5061/dryad.8011
title: Data from: Colour, design, and reward: phenotypic integration of fleshy fruit displays

description: The functional or structural linkage among traits (phenotypic integration;
 PI) within complex structures can constrain the evolutionary response of
 individual traits. To analyse whether frugivores with distinct sensory
 ecology have shaped the patterns of fruit diversification differently, we
 compared PI values of fleshy fruits that are consumed by birds and
 mammals. We used phylogenetic comparative analyses of PI among 13
 morphological, nutritional and visual fruit traits from 111 Mediterranean
 plant species. Results showed that morphological traits had higher PI
 values than nutritional and colour traits. Visual and nutritional traits
 show positive phylogenetic covariance, while negative covariation occurs
 between fruits size and nutrients. Importantly, fruits consumed by birds
 were relatively more integrated than fruits consumed partly or solely by
 mammals. Hence we show that major groups of mutualistic frugivores can
 shape the covariance among some fruit traits differently and thereby
 influence fruit diversification.
description: Table_S1_Valido
 etal_Fruit_Integration_DataSetDataset of fruit
 variables (morphology, pulp nutrient, and colour) (see also Appendix S1
 for literature sources).
DOI: 10.5061/dryad.b29k1
title: Data from: Appearance of an early closure of the Isthmus of Panama is the product of biased inclusion of data in the metaanalysis

description: In their PNAS article “Biological evidence supports an early and complex
 emergence of the Isthmus of Panama,” Bacon et al. (1 -
 http://dx.doi.org/10.1073/pnas.1423853112) use data from molecular
 comparisons of terrestrial and marine organisms taken from the literature
 to estimate dates of rate shifts in migration. One of their conclusions is
 that “events separating marine organisms in the Atlantic and Pacific
 oceans [occurred] at ca. 23 and 7 Ma” (1). The authors base this
 conclusion on two kinds of molecular dating: (i) 31 dates from phylogenies
 with evolutionary rates calibrated from fossils at one or more nodes, and
 (ii) 52 dates from mitochondrial divergence between sister species on
 either side of the Isthmus taken from the review by Lessios (2) (note:
 complete data are available from the Dryad Digital Repository at
 http://dx.doi.org/10.5061/dryad.6m653). For the latter, divergence was
 converted to time by assuming a mitochondrial DNA divergence rate of 2%
 per million years. Unfortunately, Bacon et al.’s metaanalysis of
 separations of marine organisms contains unexplained omissions of data and
 mistakes.
description: Complete transisthmian
 date valuesThe spreadsheet contains
 all data from publications cited in Bacon et al. 2015, showing data that
 were omitted, data that were corrected, and data that were correct, as
 well as summary statistics.Datasheet
 v.3.xls
DOI: 10.5061/dryad.c6j8p
title: Data from: Seasonal food scarcity prompts long-distance foraging by a wild social bee

description: Foraging is an essential process for mobile animals and its optimization
 serves as a foundational theory in ecology and evolution; however, drivers
 of foraging are rarely investigated across landscapes and seasons. Using a
 common bumble bee species from the Western US (Bombus vosnesenskii), we
 ask if seasonal decreases in food resources prompt changes in foraging
 behavior and space use. We employ a unique integration of population
 genetic tools and spatially-explicit foraging models to estimate foraging
 distances and rates of patch visitation for wild bumble bee colonies
 across three study regions and two seasons. By mapping the locations of
 669 wild-caught individual foragers, we find substantial variation in
 colony-level foraging distances, often exhibiting a 60-fold difference
 within a study region. Our analysis of visitation rates indicates that
 foragers display a preference for high-cover destination patches and
 forage significantly further for these patches, but only in the summer,
 when landscape-level resources are low. Overall, these results indicate
 that an increasing proportion of long-distance foraging bouts take place
 in the summer. As pollinators, the foraging dynamics of wild bees are of
 urgent concern given the potential impacts of global change on their
 movement and services. The behavioral shift towards long-distance foraging
 with seasonal declines in food resources suggests a novel
 phenologically-directed approach to landscape-level pollinator
 conservation and increased evaluation of late-season floral resources.
description: Locations of foraging
 bumblebees along transectscolony_id = unique
 colony identifier; bee_id = unique bee identifier; transect = transect
 slash region name; sampling_point = the site along the transect where the
 bee was collected; season = season (early or late); day = days since Jan
 1st 2012 when collection took place.bee_locations.csvLocations of sampling points along transectstransect = transect slash region name; sampling_point = point along transect; easting_utm_zone10 = easting in m, location of point; northing_utm_zone10 = northing in m, location of point; season = sampling season (early or late); landscape_floral_density = average floral density in landscape (floral cover/m^2); patch_floral_density = average floral density in sampling point (floral cover/m^2)transect_locations.csvMicrosatellite genotypesbee_id = unique bee identifier; a/b = genotype at microsat locus, 0 indicates missing data.bee_genotypes.csv
DOI: 10.5061/dryad.2016
title: Data from: Are blue eggs a sexually selected signal of female collared flycatchers? A cross-fostering experiment

description: Impressive variation in egg colouration among birds has puzzled
 evolutionary biologists for a long time. The most frequently studied
 selective forces moulding egg colouration – predation and brood parasitism
 – have either received little empirical support or may play a role in only
 a minority of species. A novel hypothesis has suggested that egg colour
 may be significantly influenced by sexual selection. Females may deposit a
 blue-green pigment biliverdin into eggshells instead of using it for
 themselves as a powerful antioxidant. By this handicap females may signal
 their quality to males which are then hypothesized to increase their
 paternal effort. We experimentally tested the hypothesis in the collared
 flycatcher (Ficedula albicollis), a species laying blue-green eggs. We
 cross-fostered clutches between nests to disentangle effects of
 female/territory quality and egg colour on paternal effort and nestling
 quality. The results supported two assumptions of sexual signalling
 through egg colour hypothesis: blue pigment seems to be a limited resource
 for females and female quality is positively correlated with intensity of
 blue-green colour. However, we did not find support for the main
 prediction of the hypothesis as male parental effort parameters (feeding
 frequencies to nestlings and intensity of nest defence) were unrelated to
 egg colour. We discuss possible reasons for the discrepancy between our
 results and previous correlative analyses that supported the hypothesis
 that blue egg colour may be a postmating sexually selected signal in
 females.
description: datasetindividual_eggs