cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d3t53
title: Data from: The spatial segregation patterns of sharks from Western Australia

description: The extent to which sharks segregate by size and sex determines the
 population structure and the scale at which populations should be managed.
 We summarized 20 years of fisheries-dependent and independent sampling to
 define the spatial patterns of size and sexual segregation for sharks in
 Western Australia. Carcharhinus obscurus and C. plumbeus showed a
 large-scale (more than 1000 km) latitudinal gradient in size. Large
 individuals occurred predominantly in the northwest and north whereas
 smaller individuals occurred predominantly in the southwest and south.
 Mustelus antarcticus and Furgaleus macki showed strong sexual segregation
 at very large scales. Females occurred predominantly in the west and
 southwest whereas the proportion of males in catches substantially
 increased in the southeast. The populations of other shark species did not
 show sex and size segregation patterns at very large scales; most species,
 however, showed varying degrees of segregation when data were analysed at
 a smaller scale. These findings highlight the importance of matching the
 scale of observation to the scale of the phenomenon observed. As many
 shark species are highly mobile, if sampling is opportunistic and
 constrained both temporally and spatially, the observed segregation
 patterns may not be representative of those at the population level,
 leading to inaccurate scientific advice.
description: Data.for.RSOS
DOI: 10.5061/dryad.f7q88
title: Data from: Genetic structure of phenotypic robustness in the Collaborative Cross mouse diallel panel

description: Developmental stability and canalization describe the ability of
 developmental systems to minimize phenotypic variation in the face of
 stochastic micro-environmental effects, genetic variation and
 environmental influences. Canalization is the ability to minimize the
 effects of genetic or environmental effects, while developmental stability
 is the ability to minimize the effects of micro-environmental effects
 within individuals. Despite much attention, the mechanisms that underlie
 these two components of phenotypic robustness remain unknown. We
 investigated the genetic structure of phenotypic robustness in the
 Collaborative Cross (CC) mouse reference population. We analyzed the
 magnitude of fluctuating asymmetry (FA) and among-individual variation of
 cranial shape in reciprocal crosses among the eight parental strains, by
 using geometric morphometrics and a diallel analysis based on a Bayesian
 approach. Significant differences among genotypes were found for both
 measures, though they were poorly correlated at the level of individuals.
 An overall positive effect of inbreeding was found for both components of
 variation. The strain CAST/EiJ exerted a positive additive effect on FA
 and, to a lesser extent, among-individual variance. Sex and other strain
 specific effects were not significant. Neither FA nor among-individual
 variation was associated with phenotypic extremeness. Our results support
 the existence of genetic variation for both developmental stability and
 canalization. This finding is important because robustness is a key
 feature of developmental systems. Our finding that robustness is not
 related to phenotypic extremeness is consistent with theoretical work that
 suggests that its relationship to stabilizing selection is not
 straightforward.
description: CC_raw_coordinatesThis file contains the coordinates of landmarks of the skull for the parental and F1 specimens from the Collaborative Cross consortium.landmark_orderThis file contains the order and abbreviature of the skull landmarks.CC_clasifThis file contains the information on sex, age and strain for each specimen in the dataset.
DOI: 10.5061/dryad.tm32k
title: Data from: SpeciesGeoCoder: fast categorization of species occurrences for analyses of biodiversity, biogeography, ecology and evolution

description: Understanding the patterns and processes underlying the uneven
 distribution of biodiversity across space constitutes a major scientific
 challenge in systematic biology and biogeography, which largely relies on
 effectively mapping and making sense of rapidly increasing species
 occurrence data. There is thus an urgent need for making the process of
 coding species into spatial units faster, automated, transparent, and
 reproducible. Here we present SpeciesGeoCoder, an open-source software
 package written in Python and R, that allows for easy coding of species
 into user-defined operational units. These units may be of any size and be
 purely spatial (i.e., polygons) such as countries and states, conservation
 areas, biomes, islands, biodiversity hotspots, and areas of endemism, but
 may also include elevation ranges. This flexibility allows scoring species
 into complex categories, such as those encountered in topographically and
 ecologically heterogeneous landscapes. In addition, SpeciesGeoCoder can be
 used to facilitate sorting and cleaning of occurrence data obtained from
 online databases, and for testing the impact of incorrect identification
 of specimens on the spatial coding of species. The various outputs of
 SpeciesGeoCoder include quantitative biodiversity statistics, global and
 local distribution maps, and files that can be used directly in many
 phylogeny-based applications for ancestral range reconstruction,
 investigations of biome evolution, and other comparative methods. Our
 simulations indicate that even datasets containing hundreds of millions of
 records can be analyzed in relatively short time using a standard
 computer. We exemplify the use of SpeciesGeoCoder by inferring the
 historical dispersal of birds across the Isthmus of Panama, showing that
 lowland species crossed the Isthmus about twice as frequently as montane
 species with a marked increase in the number of dispersals during the last
 10 million years.
description: Supplemental figures
 1-4Topel-et-al_SM.docxSupplemental table 1Table_S1.xlsSpeciesGeoCoderGithub repository for the code presented in this paper. The repository also contains example data for running SpeciesGeoCoder and a wiki with additional information about the program.
DOI: 10.5061/dryad.sq135
title: Data from: Isodars unveil asymmetric effects on habitat use caused by competition between two endangered species

description: In order for competing species to coexist, segregation on some ecological
 niche component is required and is often mediated by differential habitat
 use. When unequal competitors are involved, the dominant species tends to
 displace the subordinate one to its less preferred habitat. Here, we use
 habitat isodars, an approach which reflects evolutionary stable strategies
 of habitat selection, to evaluate whether interspecific competition
 between two competing species with distinct habitat preferences, the
 little bustard Tetrax tetrax and the great bustard Otis tarda, modulates
 their habitat use. Field data on these endangered species demonstrate that
 unequal competitors can coexist without completely segregating on their
 preferred habitats. The negatively sloped isodar of the subordinate little
 bustard unveils its competition with the dominant great bustard.
 Interference from great bustards in secondary cereal habitats reinforces
 use of preferred natural habitat by little bustards. Studies of
 density-dependent habitat selection by a single-species can thus aid in
 identifying the effects of competition on community composition, and guide
 the conservation of at-risk species. Isodars, in particular, represent a
 promising method to gain clear knowledge on interspecific competition for
 species in which experimental manipulations are not feasible.
description: Little and great bustard
 observations in central SpainTarjueloetal2016_Oikos.rar
DOI: 10.5061/dryad.h3tc2
title: Data from: Multi-locus analyses reveal four giraffe species instead of one

description: Traditionally, one giraffe species and up to eleven subspecies have been
 recognized [ 1 ]; however, nine subspecies are commonly accepted [ 2 ].
 Even after a century of research, the distinctness of each giraffe
 subspecies remains unclear, and the genetic variation across their
 distribution range has been incompletely explored. Recent genetic studies
 on mtDNA have shown reciprocal monophyly of the matrilines among seven of
 the nine assumed subspecies [ 3, 4 ]. Moreover, until now, genetic
 analyses have not been applied to biparentally inherited sequence data and
 did not include data from all nine giraffe subspecies. We sampled natural
 giraffe populations from across their range in Africa, and for the first
 time individuals from the nominate subspecies, the Nubian giraffe, Giraffa
 camelopardalis camelopardalis Linnaeus 1758 [ 5 ], were included in a
 genetic analysis. Coalescence-based multi-locus and population genetic
 analyses identify at least four separate and monophyletic clades, which
 should be recognized as four distinct giraffe species under the genetic
 isolation criterion. Analyses of 190 individuals from maternal and
 biparental markers support these findings and further suggest subsuming
 Rothschild’s giraffe into the Nubian giraffe, as well as Thornicroft’s
 giraffe into the Masai giraffe [ 6 ]. A giraffe survey genome produced
 valuable data from microsatellites, mobile genetic elements, and accurate
 divergence time estimates. Our findings provide the most inclusive
 analysis of giraffe relationships to date and show that their genetic
 complexity has been underestimated, highlighting the need for greater
 conservation efforts for the world’s tallest mammal.
description: This file contains
 additional figures, table and information that could not be included in
 the main paper or supplementary information due to space
 limitationsThis file contains
 additional figures, table and information that could not be included in
 the main paper or supplementary information due to space limitations. List
 of content: Figure 1. A ML tree from seven concatenated nuclear loci
 Figure 2. Details of the genome assembly Figure 3. BEAST Divergence time
 estimates among sampled giraffe subspecies Table 1: ID, subspecies and
 locations of all 141 own samples used in this study Table 2:
 Microsatellite loci in the giraffe genome Table 3: Percentages of mobile
 DNA elements in the giraffe genomeFennessy.dryad
 information.docx
DOI: 10.5061/dryad.7df44
title: Data from: ‘Out of tune’: consequences of inbreeding on bird song

description: The expression of bird song is expected to signal male quality to females.
 ‘Quality’ is determined by genetic and environmental factors, but,
 surprisingly, there is very limited evidence if and how genetic aspects of
 male quality are reflected in song. Here, we manipulated the genetic
 make-up of canaries (Serinus canaria) via inbreeding, and studied its
 effects upon song output, complexity, phonetics and, for the first time,
 song learning. To this end, we created weight-matched inbred and outbred
 pairs of male fledglings, which were subsequently exposed to the same
 tutor male during song learning. Inbreeding strongly affected syllable
 phonetics, but there were little or no effects on other song features.
 Nonetheless, females discriminated among inbred and outbred males, as they
 produced heavier clutches when mated with an outbred male. Our study
 highlights the importance of song phonetics, which has hitherto often been
 overlooked.
description: Inbreeding effects on
 bird songIn this datafile, all
 syllables sang in 240 (s) of continuous song are noted for 9 outbred
 birds, 9 inbred birds, and 9 tutor birds. The duration, amplitude,
 frequency modulation (FM), mean frequency, and entropy of these syllables
 are noted. Inbred and outbred birds were reared together in presence of a
 tutor bird (tutor-tutee groups), and, thus, song learning, and song
 expression could be compared between inbred and outbred
 birds.SONG-RAISSADEBOER.csvFemale investment in inbred and outbred malesThe clutch investment of outbred females mated with an inbred male, or an outbred male, is noted in this file. It is also noted how many eggs females laid, and the weight of each egg.FEMALE-INVESTMENT-RAISSADEBOER.csvThe song bout length of inbred and outbred malesThe song duration of each song for 9 inbred birds, 9 outbred birds, and 9 tutor birds is noted in this file.SONGBOUTLENGTH-RAISSADEBOER.csv
DOI: 10.5061/dryad.j34hk
title: Data from: Regeneration processes on coarse woody debris in mixed forests: do tree germinants and seedlings have species-specific responses when grown on coarse woody debris?

description: Tree regeneration on coarse woody debris (CWD) is considered to be one the
 most ecologically valuable aspects of CWD in forest systems. However, most
 studies have focused solely on uncovering the differences in establishment
 and growth on CWD (regarded as a homogeneous substrate) in comparison with
 the forest floor. Our study concentrates on the underlying mechanisms of
 germinant and seedling colonization patterns and demographic responses
 relative to various properties of CWD. We analysed the effects of CWD
 properties (decay class, form, species and diameter) on: (i) germinant and
 seedling annual counts; (ii) annual germinant and seedling survival; and
 (iii) seedling growth and height. Our study comprised three species
 (beech, fir and spruce) over 7-year span in two old-growth stands in the
 Western Carpathians, and employed generalized linear models and mixed
 models to test for differences between species. CWD properties affected
 regeneration at the germination stage. There were some demographic
 differences between species relative to CWD properties. Decay class had
 the most pronounced effect on beech, not only on its establishment but
 also survival and growth. Beech and spruce established and survived in
 higher densities on beech CWD, while their height growth was enhanced on
 conifer-derived CWD, particularly on spruce CWD. Stumps enhanced
 establishment of all species and survival of conifer seedlings. Synthesis.
 Our study shows that CWD properties do influence seedling establishment,
 growth, height distribution and survival. Moreover, there may be
 trade-offs between seedling growth and survival among tree species growing
 on different species of CWD. This highlights the need to include CWD
 heterogeneity as a factor that can affect the role of CWD in regeneration
 in forest ecosystems.
description: Numbers of germinants on
 CWDGerminants_counts.csvNumbers of seedlings on CWDSeedlings_counts.csvBeech germinants survival on CWDsurvival_germ_beech.csvFir germinants survival on CWDsurvival_germ_fir.csvSpruce germinants survival on CWDsurvival_germ_spruce.csvBeech seedling survival on CWDsurvival_seedl_beech.csvFir seedlings survival on CWDsurvival_germ_fir.csvSpruce seedlings survival on CWDsurvival_seedl_spruce.csvBeech seedlings height growth on CWDgrowth_seedl_beech.csvFir seedlings height growth on CWDgrowth_seedl_fir.csvSpruce seedlings height growth on CWDgrowth_seedl_spruce.csv
DOI: 10.15468/dl.eavs7g
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Imperata cylindrica"
 ]
}

 The dataset includes 198 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001468-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.802q5
title: Data from: A parallel population genomic and hydrodynamic approach to fishery management of highly-dispersive marine invertebrates: the case of the Fijian black-lip pearl oyster Pinctada margaritifera

description: Fishery management and conservation of marine species increasingly relies
 on genetic data to delineate biologically relevant stock boundaries.
 Unfortunately for high gene flow species which may display low, but
 statistically significant population structure, there is no clear
 consensus on the level of differentiation required to resolve distinct
 stocks. The use of fine-scale neutral and adaptive variation, considered
 together with environmental data can offer additional insights to this
 problem. Genome-wide genetic data (4,123 SNPs), together with an
 independent hydrodynamic particle dispersal model were used to inform farm
 and fishery management in the Fijian black-lip pearl oyster Pinctada
 margaritifera, where comprehensive fishery management is lacking, and the
 sustainability of exploitation uncertain. Weak fine-scale patterns of
 population structure were detected, indicative of broad-scale panmixia
 among wild oysters, while a hatchery-sourced farmed population exhibited a
 higher degree of genetic divergence (Fst = 0.0850–0.102). This
 hatchery-produced population had also experienced a bottleneck (NeLD =
 5.1; 95% C.I. = [5.1–5.3]); compared to infinite NeLD estimates for all
 wild oysters. Simulation of larval transport pathways confirmed the
 existence of broad-scale mixture by surface ocean currents, correlating
 well with fine-scale patterns of population structuring. Fst outlier tests
 failed to detect large numbers of loci supportive of selection, with 2–5
 directional outlier SNPs identified (average Fst = 0.116). The lack of
 biologically significant population genetic structure, absence of evidence
 for local adaptation and larval dispersal simulation, all indicate the
 existence of a single genetic stock of P. margaritifera in the Fiji
 Islands. This approach using independent genomic and oceanographic tools
 has allowed fundamental insights into stock structure in this species,
 with transferability to other highly-dispersive marine taxa for their
 conservation and management.
description: Genotype file (4123
 SNPs)Genotypic data at 4,123
 SNPs for 427 individuals of P. margaritifera from the Fiji
 IslandsGenotype_file_4123_SNPs.xlsx
DOI: 10.5061/dryad.bb095
title: Data from: Long-term nitrous oxide fluxes in annual and perennial agricultural and unmanaged ecosystems in the upper Midwest USA

description: Differences in soil nitrous oxide (N2O) fluxes among ecosystems are often
 difficult to evaluate and predict due to high spatial and temporal
 variabilities and few direct experimental comparisons. For 20 years, we
 measured N2O fluxes in 11 ecosystems in southwest Michigan USA: four
 annual grain crops (corn–soybean–wheat rotations) managed with
 conventional, no-till, reduced input, or biologically based/organic
 inputs; three perennial crops (alfalfa, poplar, and conifers); and four
 unmanaged ecosystems of different successional age including mature
 forest. Average N2O emissions were higher from annual grain and N-fixing
 cropping systems than from nonleguminous perennial cropping systems and
 were low across unmanaged ecosystems. Among annual cropping systems
 full-rotation fluxes were indistinguishable from one another but rotation
 phase mattered. For example, those systems with cover crops and reduced
 fertilizer N emitted more N2O during the corn and soybean phases, but
 during the wheat phase fluxes were ~40% lower. Likewise, no-till did not
 differ from conventional tillage over the entire rotation but reduced
 emissions ~20% in the wheat phase and increased emissions 30–80% in the
 corn and soybean phases. Greenhouse gas intensity for the annual crops
 (flux per unit yield) was lowest for soybeans produced under conventional
 management, while for the 11 other crop × management combinations
 intensities were similar to one another. Among the fertilized systems,
 emissions ranged from 0.30 to 1.33 kg N2O-N ha−1 yr−1 and were best
 predicted by IPCC Tier 1 and ΔEF emission factor approaches. Annual
 cumulative fluxes from perennial systems were best explained by soil
 inline image pools (r2 = 0.72) but not so for annual crops, where
 management differences overrode simple correlations. Daily soil N2O
 emissions were poorly predicted by any measured variables. Overall,
 long-term measurements reveal lower fluxes in nonlegume perennial
 vegetation and, for conservatively fertilized annual crops, the overriding
 influence of rotation phase on annual fluxes.
description: Soil N2O emissions and
 other environmental variables for KBS LTERThe data files contains
 basic data used in the publicationDataset for Gelfand et al
 2016.xls
DOI: 10.15468/dl.dwbc2y
title: Occurrence Download

description: A dataset containing 1782 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Laurus novocanariensis"
 ]
}

 The dataset includes 1782 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001461-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5jk4d
title: Data from: Adding biotic complexity alters the metabolic benefits of mutualism

description: Mutualism is ubiquitous in nature and plays an integral role in most
 communities. To predict the eco-evolutionary dynamics of mutualism it is
 critical to extend classic pair-wise analysis to include additional
 species. We investigated the effect of adding a third species to a
 pair-wise mutualism in a spatially structured environment. We tested the
 hypotheses that selection for costly excretions in a focal population (i)
 decreases when an exploiter is added (ii) increases when a third mutualist
 is added relative to the pair-wise scenario. We assayed the selection
 acting on Salmonella enterica when it exchanges methionine for carbon in
 an obligate mutualism with an auxotrophic Escherichia coli. A third
 bacterium, Methylobacterium extorquens, was then added and acted either as
 an exploiter of the carbon or third obligate mutualist depending on the
 nitrogen source. In the tripartite mutualism M. extorquens provided
 nitrogen to the other species. Contrary to our expectations, adding an
 exploiter increased selection for methionine excretion in S. enterica.
 Conversely, selection for cooperation was lower in the tripartite
 mutualism relative to the pair-wise system. Genome-scale metabolic models
 helped identify the mechanisms underlying these changes in selection. Our
 results highlight the utility of connecting metabolic mechanisms and
 eco-evolutionary dynamics.
description: AM1_KOMetabolic model of
 Methylobacterium extorquens mutantEC_iJO_KOMetabolic model of E. coli mutantSal_cheatMetabolic model of non-cooperative S. entericaSal_mutualistMetabolic model of cooperative S. enterica mutantSal_mutualist_adjKMMetabolic model of cooperative S. enterica with adjusted Km for uptake of NH4LayoutsLayout files. Layouts with the same number have the same arrangement of E. coli and Salmonella. For each arrangement there is a layout for each of the treatments.