cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ff7mq
title: Data from: Mouse fitness measures reveal incomplete functional redundancy of Hox paralogous group 1 proteins

description: Here we assess the fitness consequences of the replacement of the Hoxa1
 coding region with its paralog Hoxb1 in mice (Mus musculus) residing in
 semi-natural enclosures. Previously, this Hoxa1B1 swap was reported as
 resulting in no discernible embryonic or physiological phenotype (i.e.,
 functionally redundant), despite the 51% amino acid sequence differences
 between these two Hox proteins. Within heterozygous breeding cages no
 differences in litter size nor deviations from Mendelian genotypic
 expectations were observed in the outbred progeny; however, within
 semi-natural population enclosures mice homozygous for the Hoxa1B1 swap
 were out-reproduced by controls resulting in the mutant allele being only
 87.5% as frequent as the control in offspring born within enclosures.
 Specifically, Hoxa1B1 founders produced only 77.9% as many offspring
 relative to controls, as measured by homozygous pups, and a 22.1%
 deficiency of heterozygous offspring was also observed. These data suggest
 that Hoxa1 and Hoxb1 have diverged in function through either sub- or
 neo-functionalization and that the HoxA1 and HoxB1 proteins are not
 mutually interchangeable when expressed from the Hoxa1 locus. The fitness
 assays conducted under naturalistic conditions in this study have provided
 an ultimate-level assessment of the postulated equivalence of competing
 alleles. Characterization of these differences has provided greater
 understanding of the forces shaping the maintenance and diversifications
 of Hox genes as well as other paralogous genes. This fitness assay
 approach can be applied to any genetic manipulation and often provides the
 most sensitive way to detect functional differences.
description: Offspring genotypes from
 Hoxa1B1 and Control lineage heterozygous breeding cages.File includes counts of
 offspring genotypes with three genotypes per breeding cage provided. Each
 line of data being a single genotype.Breeding_cage_genotypes.csvOffspring genotypes from three populations in semi-natural OPA enclosures.Three genotypes are reported per sampling with each line of data being a genotype.OPA_genotypes.csvTerritorial occupation from three populations in semi-natural OPA enclosures.Paired counts of territories held by Hoxa1B1 and control male founders. “Territories held” is the number of individual territories held at a given time by a treatment. “Total territories occupied” represents the number of territories (maximum of six) held collectively by both treatments at a given sampling period.OPA_Territories.csv
DOI: 10.15468/dl.stjjvf
title: Occurrence Download

description: A dataset containing 666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lysinema pentapetalum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 666 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001349-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bw6j9e
title: Occurrence Download

description: A dataset containing 381248 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Odonata, Lepidoptera, Orthoptera)",
 "DatasetKey is NABU|naturgucker",
 "Country is Germany",
 "Geometry POLYGON((\n 8.9 47.2,\n 13.9 47.2,\n 13.9 50.6,\n 8.9 50.6,\n 8.9 47.2\n ))",
 "HasCoordinate is true",
 "Year is greater than or equal to 1960",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 381248 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001338-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.tt12g
title: Data from: Study on expression modes and cleavage role of miR156b/c/d and its target gene Vv-SPL9 during the whole growth stage of grapevine

description: miR156 regulates the expression of its target SPL (PROMOTER BINDING-LIKE)
 genes during flower and fruit development, diverse developmental stage
 transitions, especially from vegetative to reproductive growth phases, by
 cleaving the target mRNA SPL of one plant-specific transcription factor.
 However, systematic reports on grapevine have yet to be presented. Here,
 the precise sequence of miR156 (vvi-miR156b/c/d) in grapevine “Takatsuma”
 was cloned with a previously cloned grapevine SPL (Vv-SPL9). Expression
 profiles in 18 grapevine tissues were identified through stem-loop RT-PCR.
 The interaction mode between vvi-miR156b/c/d and Vv-SPL9 was further
 validated by detecting the cleavage site and cleavage products of 3′- and
 5′-ends via an integrated approach of 5′-RLM-RACE (RNA ligase-mediated
 5′-rapid amplification of cDNA ends), 3′-PPM-RACE (poly(A)
 polymerase-mediated 3′-rapid amplification of cDNA ends), and qRT-PCR
 (real time reverse transcriptase-polymerase chain reaction). The variation
 in their cleavage roles in the whole growth stage of grapevine was also
 systematically investigated. Results showed that vvi-miR156b/c/d exhibited
 typical temporal–spatial-specific expression levels. The expression levels
 were higher in vegetative organs, such as leaf, than in reproductive
 organs, such as tendrils, flowers, and berries. A significant variation
 was observed during vegetative-to-reproductive transition. The expression
 patterns of Vv-SPL9 showed the opposite trends with those of vvi-miR156b.
 We confirmed that the cleavage site was at the 10th site of
 vvi-miR156b/c/d complementary to Vv-SPL9 in “Takatsuma” grapevine. We also
 identified the temporal–spatial variation of the cleavage products. This
 variation can indicate the regulatory function of miR156 on SPL in
 grapevines. Our findings provide further insights into the functions of
 vvi-miR156b/c/d and its target Vv-SPL9, and also help enrich our knowledge
 of small RNA-mediated regulation in grapevine.
description: List of miR156b,c,d
 sequences cloned by miR-RACEThis file contained the
 three sequences of mature miR156b,c,d cloned by miR-RACE, these three
 seqeunces were same, and their size is 20 bp.List of miR156b,c,d
 sequences.docx
DOI: 10.5061/dryad.7s8h6
title: Data from: Phylogeny of Cecropieae (Urticaceae) and the evolution of an ant-plant mutualism

description: Ant-plant mutualisms are abundant in the tropics and are popular models
 for ecological study, but investigating the origin and evolution of such
 systems requires a phylogenetic framework. A common ant-plant mutualism in
 the Neotropics involves the genus Cecropia, a group of fast-growing
 pioneer trees that are important in forest regeneration. Relationships
 between genera in the tribe Cecropieae (Urticaceae), including Cecropia,
 Coussapoa, Musanga, Myrianthus, and Pourouma, are unknown and are
 necessary to investigate the evolutionary history of the Cecropia-ant
 mutualism. Bayesian phylogenetic analyses of the NADH dehydrogenase (ndhF)
 chloroplast gene region, the 26S region of nuclear ribosomal DNA, and an
 exon-primed intron-crossing DNA region support the position of
 non-myrmecophytic African Musanga within a paraphyletic Cecropia.
 Neotropical Pourouma and Coussapoa are supported as sister taxa with
 African Myrianthus as their closest relative. Although it remains
 uncertain whether myrmecophytism was the ancestral condition of the
 Cecropia clade, a close relationship between non-myrmecophytic Cecropia
 sciadophylla and Musanga suggests that the loss of ant associations did
 not accompany African colonization.
description: CecropieaeMorphologyDescription of morphological characters used in phylogenetic reconstruction of Cecropieae tribe (Urticaceae)Cecropieae morphological matrixMatrix used for tree analysis of Cecropieae based on characters outlined in Cecropieae morphology.Cecropieae_morphOnly_2.nex
DOI: 10.5061/dryad.hv248
title: Data from: Thermoregulation as an alternate function of the sexually dimorphic fiddler crab claw

description: Fiddler crabs are highly sexually-dimorphic. Males possess one small
 (minor) feeding claw and one greatly enlarged (major) claw; females
 possess two small claws. The major claw is used to attract mates and for
 burrow defense but is costly for the male to possess. We tested the
 hypothesis that the major claw also functions as a thermoregulatory
 structure, a function that would allow males to spend a greater amount of
 time on the surface, foraging and attracting potential mates. Fiddler
 crabs, Uca panacea, were exposed to a source of radiant heat and body
 temperatures were monitored. Four groups of crabs were tested: intact
 males, males with the minor claw removed, males with the major claw
 removed, and females. Males without the major claw increased in body
 temperature more rapidly and reached higher temperatures than males with
 the major claw intact, but were similar to females. These results support
 the hypothesized thermoregulatory function of the major claw. The major
 claw may function as a heat sink, transferring heat away from the body and
 dissipating it into the air. Enhanced thermoregulatory ability provided by
 the major claw may partially ameliorate the energetic costs of possessing
 such a large claw.
description: dataSee readme file for more
 information.
DOI: 10.5061/dryad.14nn1
title: Data from: A metabolic and body-size scaling framework for parasite within-host abundance, biomass, and energy flux

description: Energetics may provide a useful currency for studying the ecology of
 parasite assemblages within individual hosts. Parasite assemblages may
 also provide powerful models to study general principles of ecological
 energetics. Yet there has been little ecological research on parasite-host
 energetics, probably due to methodological difficulties. However, the
 scaling relationships of individual metabolic rate with body or cell-size
 and temperature may permit us to tackle the energetics of parasite
 assemblages in hosts. This paper offers the foundations and initial
 testing of a metabolic theory of ecology (MTE) framework for parasites in
 hosts. I first provide equations to estimate energetic flux through
 observed parasite assemblages. I then develop metabolic-scaling theory for
 parasite abundance, energetics, and biomass in individual hosts. In
 contrast to previous efforts, the theory factors in both host and parasite
 metabolic scaling, how parasites use host space, and whether energy or
 space dictates carrying capacity. Empirical tests indicate that host
 energetic flux can set parasite carrying capacity, which decreases as
 predicted considering the scaling of host and parasite metabolic rates.
 The theory and results also highlight that the phenomenon of “energetic
 equivalence” is not an assumption of MTE, but a possible outcome
 contingent on how species partition resources. Hence, applying MTE to
 parasites can lend mechanistic, quantitative, predictive insight into the
 nature of parasitism and can inform general ecological theory.
description: DataHechingerFig2Data underlying Fig 2 in the manuscript. See ReadMe file for metadata.DataHechingerFig3Data underlying Fig 3 of manuscript. For metadata, see ReadMe file associated with DataHechingerFig2.txt.
DOI: 10.5061/dryad.bc0qk
title: Data from: Marine subsidies change short-term foraging activity and habitat utilization of terrestrial lizards

description: Resource pulses are brief periods of unusually high resource abundance.
 While population and community responses to resource pulses have been
 relatively well-studied, how individual consumers respond to resource
 pulses has received less attention. Local consumers are the first to
 respond to a resource pulse, and the form and timing of individual
 responses may influence how the effects of the pulse are transmitted
 throughout the community. Previous studies in Bahamian food webs have
 shown that detritivores associated with pulses of seaweed wrack provide an
 alternative prey source for lizards. When seaweed is abundant, lizards
 (Anolis sagrei) shift to consuming more marine-derived prey and increase
 in density, which has important consequences for other components of the
 food web. We hypothesized that the diet shift requires individuals to
 alter their habitat use and foraging activity, and that such responses may
 happen very rapidly. In this study, we investigated the immediate
 responses of lizards to an experimental seaweed pulse. We added seaweed to
 5 treatment plots for comparison with 5 control plots. Immediately after
 seaweed addition, lizards decreased average perch height and increased
 movement rate, but these effects persisted for only two days. To explore
 the short-term nature of the response, we used our field data to
 parametrize heuristic Markov chain models of perch height as a function of
 foraging state. These models suggest a “Synchronized-satiation
 Hypothesis,” whereby lizards respond synchronously and feed quickly to
 satiation in the presence of subsidy (causing an initial decrease in
 average perch height) and then return to the relative safety of higher
 perches. We suggest that the immediate responses of individual consumers
 to resource-pulse events can provide insight into the mechanisms by which
 these consumers ultimately influence community-level processes.
description: Lizard habitat use and
 foraging activity scored from video observations.Each row of the data set
 represents a single video observation bout of a lizard (n = 87). The data
 set captures lizard habitat use and foraging activity in treatment and
 control plots before and after the addition of a seaweed
 subsidy.masterlog
 2017-10-24.csv
DOI: 10.5061/dryad.hk81qh1
title: Data from: Torpor reduces predation risk by compensating for the energetic cost of antipredator foraging behaviours

description: Foraging activity is needed for energy intake but increases the risk of
 predation, and antipredator behavioural responses, such as reduced
 activity, generally reduce energy intake. Hence, mortality and indirect
 effects of predation risk are dependent on the energy requirements of
 prey. Torpor, a controlled reduction in resting metabolism and body
 temperature, is a common energy-saving mechanism of small mammals that
 enhances their resistance to starvation. Here we test the hypothesis that
 torpor could also reduce predation risk by compensating for the energetic
 cost of antipredator behaviours. We measured the foraging behaviour and
 body temperature of house mice in response to manipulation of perceived
 predation risk by adjusting levels of ground cover and starvation risk by
 24-h food withdrawal every third day. We found that a voluntary reduction
 in daily food intake in response to lower cover (high predation risk) was
 matched by the extent of a daily reduction in body temperature. Our study
 provides the first experimental evidence of a close link between
 energy-saving torpor responses to starvation risk and behavioural
 responses to perceived predation risk. By reducing the risk of starvation,
 torpor can facilitate stronger antipredator behaviours. These results
 highlight the interplay between capacity for reducing metabolic energy
 expenditure, optimal decisions about foraging behaviour, and the
 life-history ecology of prey.
description: Turbill.Stojanovski_dataData from experiment testing for effects of manipulation of perceived predation risk on foraging effort and regulation of body temperature by house mice.
DOI: 10.5061/dryad.d27vt
title: Data from: Den site selection, pack composition, and reproductive success in endangered African wild dogs

description: Habitat quality is often assumed to be directly related to increased
 consumer density, but such assumptions cannot be made without supporting
 demographic data that indicate improved fitness. Habitat selection might
 be especially important for denning species, where vulnerable offspring
 are confined to a single location for extended periods, but the effect of
 den choice on the reproductive success of denning species is poorly
 understood. By combining airborne high-resolution Light Detection and
 Ranging (LiDAR) measurements with data on pack composition, we
 investigated den site selection by endangered African wild dogs in
 Hluhluwe-iMfolozi Park, South Africa, examining whether habitat selection
 based on ecological factors resulted in increased litter sizes and thus
 reproductive success compared with social factors known to be important.
 Although there was selection for den sites in areas of increased terrain
 ruggedness and vegetation density, only vegetation density was associated
 with larger litter sizes and translated into increased reproductive
 success. Moreover, pack size was only influential when a minimum
 vegetation density around den sites was achieved, indicating that although
 social variables have a powerful effect on reproductive success, they are
 mediated by ecological factors defining habitat quality. Our results
 demonstrate the importance of distinguishing between density- and
 fitness-based indicators of habitat quality, and how this can affect
 management actions, particularly for endangered species conservation.
description: Wild dog den sites and
 random sitesCSV file containing the
 ecological attributes associated with each den and random site. Ecological
 data were derived from airborne LiDAR measurements.Dens are coded as 1 and
 random sites as 0 under the column "site". Dens are further
 distinguished as being either first (1) or secondary (2) den sites under
 the column "YearID".dens_random_sites.csvCharacteristics of the environment around den and random sitesCSV file containing ecological data in a 250 m radius around den and random sites. Data were derived from airborne LiDAR measurements and interpolated over the environment area (250 m radius). The data therefore represent averaged values around each den and random site. Dens are coded as 1 and random sites as 0 under the column "site". Dens are further distinguished as being either first (1) or secondary (2) den sites under the column "YearID".den_environment_250m.csvEcological and social (pack attributes) data associated with each wild dog den siteCSV file containing the ecological and social (pack) attributes associated with each wild dog den site. Ecological data were derived from airborne LiDAR measurements.pack_litter_size.csv
DOI: 10.5061/dryad.5gn79
title: Data from: The role of species pools in determining species diversity in spatially heterogeneous communities

description: 1. The 'habitat-specific species pool hypothesis' proposes that
 differences between habitats in the sizes of their species pools are the
 main drivers of diversity responses to habitat heterogeneity. Empirical
 tests of this hypothesis are not trivial since species might be missing
 from ecologically suitable habitats due to limited dispersal, while others
 may occur in unsuitable habitats by means of source-sink dynamics and mass
 effect. 2. We tested the habitat-specific species pool hypothesis in a
 local, environmentally heterogeneous community of annual plants using a
 novel 'ecological selection' experiment. Mixtures of seeds
 representing the whole community were sown in each habitat, and the
 emerging species were exposed to six generations of selection by
 environmental filtering and competition while being blocked from
 dispersal. A comparison of the total number of species that were able to
 survive in each habitat (i.e., to pass the selection test) with data on
 species richness in the natural community allowed us to test the degree to
 which observed differences in species richness between habitats could be
 explained by differences in the sizes of the respective species pools. 3.
 Results supported the species pool hypothesis, showing that differences in
 the sizes of the habitat-specific species pools were important in
 determining diversity responses to habitat heterogeneity. Moreover,
 species richness showed a unimodal response to local-scale gradients in
 habitat productivity, and this response could be attributed to underlying
 differences in species-pool sizes. Both results were robust to properties
 of the data and the method of analysis. 4. Synthesis. Our results provide
 a strong experimental evidence that differences in the sizes of
 habitat-specific species pools might be important in shaping the diversity
 of local communities. Future theoretical and empirical studies in
 community ecology should explore the potential sources and implications of
 such differences.
description: Ron et al. 2017 JE
 dataplot level, habitat
 level and regional level species diversity for plots of four different
 soil depths
DOI: 10.5061/dryad.948kq
title: Data from: A father effect explains sex-ratio bias

description: Sex ratio allocation has important fitness consequences, and theory
 predicts that parents should adjust offspring sex ratio in cases where the
 fitness returns of producing male and female offspring vary. The ability
 of fathers to bias offspring sex ratios has traditionally been dismissed
 given the expectation of an equal proportion of X- and
 Y-chromosome-bearing sperm (CBS) in ejaculates due to segregation of sex
 chromosomes at meiosis. This expectation has been recently refuted. Here
 we used Peromyscus leucopus to demonstrate that sex ratio is explained by
 an exclusive effect of the father, and suggest a likely mechanism by which
 male-driven sex-ratio bias is attained. We identified a male sperm
 morphological marker that is associated with the mechanism leading to sex
 ratio bias; differences among males in the sperm nucleus area (a proxy for
 the sex chromosome that the sperm contains) explain 22% variation in
 litter sex ratio. We further show the role played by the sperm nucleus
 area as a mediator in the relationship between individual genetic
 variation and sex-ratio bias. Fathers with high levels of genetic
 variation had ejaculates with a higher proportion of sperm with small
 nuclei area. This, in turn, led to siring a higher proportion of sons (25%
 increase in sons per 0.1 decrease in the inbreeding coefficient). Our
 results reveal a plausible mechanism underlying unexplored male-driven
 sex-ratio biases. We also discuss why this pattern of paternal bias can be
 adaptive. This research puts to rest the idea that father contribution to
 sex ratio variation should be disregarded in vertebrates, and will
 stimulate research on evolutionary constraints to sex ratios—for example,
 whether fathers and mothers have divergent, coinciding, or neutral sex
 allocation interests. Finally, these results offer a potential explanation
 for those intriguing cases in which there are sex ratio biases, such as in
 humans.
description: Data-Malo et al
 2017Data for the main
 analysis of the paper entitled "A father effect explains sex-ratio
 bias", relating the effects of sperm nucleus area and sperm nucleus
 length on offspring sex ratio (figure 1), the effects of the coefficient
 of inbreeding on offspring sex ratio weighing each data point for the
 total number of offspring (figure 2), and the effects of the coefficient
 of inbreeding on sperm nucleus area and sperm nucleus length (figure
 3).