cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1794
title: Data from: Bone-eating Osedax females and their 'harems' of dwarf males are recruited from a common larval pool

description: Extreme male dwarfism occurs in Osedax (Annelida: Siboglinidae), marine
 worms with sessile females that bore into submerged bones. Osedax are
 hypothesized to use environmental sex-determination (ESD), in which
 undifferentiated larvae that settle on bones develop as females, and
 subsequent larvae that settle on females transform into dwarf males. This
 study addresses several hypotheses regarding possible recruitment sources
 for the males: (1) common larval pool — males and females are sampled from
 a common pool of larvae; (2) neighborhood — males are supplied by a
 limited number of neighboring females; and (3) arrhenotoky — males are
 primarily the sons of host females. Osedax rubiplumus were sampled from
 submerged whalebones located at 1820 and 2893 m depths in Monterey Bay,
 California. Immature females typically did not host males, but mature
 females maintained male "harems" that grew exponentially in the
 number of males as female size increased. Allozyme analysis of the females
 revealed binomial proportions of nuclear genotypes, an indication of
 random sexual mating. Analysis of mitochondrial DNA sequences from the
 male harems and their host females allowed us to reject the arrhenotoky
 and neighborhood hypotheses for male recruitment. No significant
 partitioning of mitochondrial diversity existed between the male and
 female sexes, or between subsamples of worms collected at different depths
 or during different years (2002–2007). Mitochondrial sequence diversity
 was very high in these worms, suggesting that as many as 106 females
 contributed to a common larval pool from which the two sexes were randomly
 drawn.
description: osemales.TXTThese data were collected in the Monterey Bay, CA, extracted and sequenced. The file is a nexus file created by MacClade and edited for submission to GenBank.
DOI: 10.5061/dryad.8445
title: Data from: The assembly of ecological communities inferred from taxonomic and functional composition

description: Among-site variation in metacommunities (beta diversity) is typically
 correlated with the distance separating the sites (spatial lag). This
 distance decay in similarity pattern has been linked to both niche-based
 and dispersal-based community assembly hypotheses. Here we show that beta
 diversity patterns in community composition, when supplemented with
 functional-trait information, can be used to diagnose assembly processes.
 First, using simulated data, we show how the relationship between distance
 decay patterns in taxonomic and functional measures of community
 composition can be used to predict the influence of a given trait on
 community assembly. We then use the patterns generated by the simulation
 as a template to show that the sorting of benthic macroinvertebrate
 metacommunities in headwater streams is likely influenced by different
 sets of functional traits at regional and local scales. We suggest that
 functional-trait databases and spatially referenced taxonomic surveys can
 be used to predict the spatial scales at which different aspects of
 interspecific functional variation are involved in niche-based community
 assembly while accounting for the influence of dispersal-based community
 assembly processes.
description: Online Appendix
 CContents: Table C1 –
 Site data for 24 headwater streams in the southern Blue Ridge. Table C2 –
 Observed benthic macroinvertebrate densities. Table C3 – Trait scores for
 North American aquatic insects. Table C4 – Trait
 descriptions.
DOI: 10.5061/dryad.04k5q
title: Data from: Major histocompatibility complex-linked social signalling affects female fertility

description: Genes of the major histocompatibility complex (MHC) have been shown to
 influence social signalling and mate preferences in many species,
 including humans. First observations suggest that MHC signalling may also
 affect female fertility. To test this hypothesis, we exposed 191 female
 horses (Equus caballus) to either a MHC-similar or a MHC-dissimilar
 stimulus male around the time of ovulation and conception. A
 within-subject experimental design controlled for non-MHC linked male
 characteristics, and instrumental insemination with semen of other males
 (N=106) controlled for potential confounding effects of semen or embryo
 characteristics. We found that females were more likely to become pregnant
 if exposed to a MHC-dissimilar than to a MHC-similar male, while overall
 genetic distance to the stimulus males (based on microsatellite markers on
 20 chromosomes) had no effect. Our results demonstrate that early
 pregnancy failures can be due to maternal life-history decisions (cryptic
 female choice) influenced by MHC-linked social signalling.
description: Burger et al. µsat
 markersMicrosatellite data of
 mares and stimulus stallionsBurger et al. MHC and r
 versus pregnancyMHC types, pregnant or
 not, pairwise relatedness r, pairwise sharing of MHC antigens, semen
 cryopreserved or not, Mare age and breed
DOI: 10.5061/dryad.663fb
title: Data from: Persistence of long-distance, insect-mediated pollen movement for a tropical canopy tree species in remnant forest patches in an urban landscape

description: As deforestation and urbanization continue at rapid rates in tropical
 regions, urban forest patches are essential repositories of biodiversity.
 However, almost nothing is known about gene flow of forest-dependent tree
 species in urban landscapes. In this study, we investigated gene flow in
 the insect-pollinated, wind-dispersed tropical tree Koompassia malaccensis
 in and among three remnant forest patches in the urbanized landscape of
 Singapore. We genotyped the vast majority of adults (N=179) and a large
 number of recruits (N=2103) with 8 highly polymorphic microsatellite
 markers. Spatial genetic structure of the recruit and adult cohorts was
 significant, showing routine gene dispersal distances of ~100–400 m.
 Parentage analysis showed that 97% of recruits were within 100 m of their
 mother tree, and a high frequency of relatively short-distance pollen
 dispersal (median ~143–187 m). Despite routine seed and pollen dispersal
 distances of within a few hundred meters, interpatch gene flow occurred
 between all patches and was dominated by pollen movement: parentage
 analysis showed 76 pollen versus 2 seed interpatch dispersal events, and
 the seedling neighborhood model estimated ~1–6% seed immigration and
 ~21–46% pollen immigration rates, depending on patch. In addition, the
 smallest patch (containing five adult K. malaccensis trees) was entirely
 surrounded by &gt;2.5 km of ‘impervious’ substrate, yet had the
 highest proportional pollen and seed immigration estimates of any patch.
 Hence, contrary to our hypothesis, insect-mediated gene flow persisted
 across an urban landscape, and several of our results also parallel key
 findings from insect-pollinated canopy trees sampled in mixed
 agricultural–forest landscapes.
description: microsatellite markers,
 Koompassia malaccensis in SingaporeMicrosatellite data (8
 loci) for 179 adults and 2,013 recruits of the canopy tree Koompassia
 malaccensis from three primary forest patches within
 Singapore.dryad data submission
 Koompassia malaccensis .txt
DOI: 10.5061/dryad.hp6tb
title: Data from: Contrasting genetic responses to population fragmentation in a coevolving fig and fig wasp across a mainland-island archipelago

description: Interacting species of pollinator–host systems, especially the obligate
 ones, are sensitive to habitat fragmentation, due to the nature of mutual
 dependence. Comparative studies of genetic structure can provide insights
 into how habitat fragmentation contributes to patterns of genetic
 divergence among populations of the interacting species. In this study, we
 used microsatellites to analyse genetic variation in Chinese populations
 of a typical mutualistic system – Ficus pumila and its obligate pollinator
 Wiebesia sp. 1 – in a naturally fragmented landscape. The plants and wasps
 showed discordant patterns of genetic variation and geographical
 divergence. There was no significant positive relationship in genetic
 diversity between the two species. Significant isolation-by-distance (IBD)
 patterns occurred across the populations of F. pumila and Wiebesia sp. 1
 as whole, and IBD also occurred among island populations of the wasps, but
 not the plants. However, there was no significant positive relationship in
 genetic differentiation between them. The pollinator populations had
 significantly lower genetic variation in small habitat patches than in
 larger patches, and three island pollinator populations showed evidence of
 a recent bottleneck event. No effects of patch size or genetic bottlenecks
 were evident in the plant populations. Collectively, the results indicate
 that, in more fragmented habitats, the pollinators, but not the plants,
 have experienced reduced genetic variation. The contrasting patterns have
 multiple potential causes, including differences in longevity and hence
 number of generations experiencing fragmentation; different dispersal
 patterns, with the host's genes dispersed as seeds as well as a
 result of pollen dispersal via the pollinator; asymmetrical responses to
 fluctuations in partner populations; and co-existence of a rare second
 pollinating wasp on some islands. These results indicate that strongly
 interdependent species may respond in markedly different ways to habitat
 fragmentation.
description: data file of Ficus
 pumila and Wiebesia sp.sdata file of Ficus pumila and
 Wiebesia sp.1.xlsx
DOI: 10.5061/dryad.98s363k3
title: Data from: Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey

description: Most species with lengthy migrations display some degree of natal homing;
 some (e.g., migratory birds and anadromous salmonids) show spectacular
 feats of homing. However, studies of the sea lamprey (Petromyzon marinus)
 indicate that this anadromous species locates spawning habitat based on
 pheromonal cues from larvae rather than through philopatry. Previous
 genetic studies in the anadromous Pacific lamprey (Entosphenus
 tridentatus) have both supported and rejected the hypothesis of natal
 homing. To resolve this, we used nine microsatellite loci to examine
 population structure in 965 Pacific lamprey from 20 locations from central
 British Columbia to southern California, and supplemented this analysis
 with mitochondrial DNA restriction fragment length polymorphism analysis
 on a subset of 530 lamprey. Microsatellite analysis revealed: 1)
 relatively low but often statistically significant genetic differentiation
 among locations (97% pairwise FST values were less than 0.04 but 73.7%
 were significant); and 2) weak but significant isolation-by-distance (r2 =
 0.0565, P = 0.0450) but no geographic clustering of samples. The few
 moderate FST values involved comparisons with sites that were
 geographically distant or far upstream. The mtDNA analysis—although
 providing less resolution among sites (only 4.7% FST values were
 significant)—was broadly consistent with the microsatellite results: 1)
 the southernmost site and some sites tributary to the Salish Sea were
 genetically distinct; and 2) southern sites showed higher haplotype and
 private haplotype richness. These results are inconsistent with
 philopatry, suggesting that anadromous lampreys are unusual among species
 with long migrations, but suggest that limited dispersal at sea precludes
 panmixia in this species.
description: Microsatellite allele
 sizes of Pacific lamprey from 20 locations along the west coast of North
 AmericaMicrosatellite allele
 sizes determined using Genemapper, formatted for
 Genepop.Genepop.txtList of haplotypes and composite haplotypes for Pacific lamprey collected from 20 locations along the west coast of North AmericaRFLP haplotypes determined by gel electrophoresisRFLP results.txt
DOI: 10.5061/dryad.5jf43
title: Data from: Forest productivity mitigates human disturbance effects on late-seral prey exposed to apparent competitors and predators

description: Primary production can determine the outcome of management actions on
 ecosystem properties, thereby defining sustainable management. Yet human
 agencies commonly overlook spatio-temporal variations in productivity by
 recommending fixed resource extraction thresholds. We studied the
 influence of forest productivity on habitat disturbance levels that boreal
 caribou – a threatened, late-seral ungulate under top-down control –
 should be able to withstand. Based on 10 years of boreal caribou
 monitoring, we found that adult survival and recruitment to populations
 decreased with landscape disturbance, but increased with forest
 productivity. This benefit of productivity reflected the net outcome of an
 increase in resources for apparent competitors and predators of caribou,
 and a more rapid return to the safety of mature conifer forests. We
 estimated 3-fold differences in forest harvesting levels that caribou
 populations could withstand due to variations in forest productivity. The
 adjustment of ecosystem provisioning services to local forest productivity
 should provide strong conservation and socio-economic advantages.
description: Dataset_FortinetalThe datasets analysed during the study
DOI: 10.5061/dryad.9fp38
title: Data from: Plant water potential improves prediction of empirical stomatal models

description: Climate change is expected to lead to increases in drought frequency and
 severity, with deleterious effects on many ecosystems. Stomatal responses
 to changing environmental conditions form the backbone of all ecosystem
 models, but are based on empirical relationships and are not well-tested
 during drought conditions. Here, we use a dataset of 34 woody plant
 species spanning global forest biomes to examine the effect of leaf water
 potential on stomatal conductance and test the predictive accuracy of
 three major stomatal models and a recently proposed model. We find that
 current leaf-level empirical models have consistent biases of
 over-prediction of stomatal conductance during dry conditions,
 particularly at low soil water potentials. Furthermore, the recently
 proposed stomatal conductance model yields increases in predictive
 capability compared to current models, and with particular improvement
 during drought conditions. Our results reveal that including stomatal
 sensitivity to declining water potential and consequent impairment of
 plant water transport will improve predictions during drought conditions
 and show that many biomes contain a diversity of plant stomatal strategies
 that range from risky to conservative stomatal regulation during water
 stress. Such improvements in stomatal simulation are greatly needed to
 help unravel and predict the response of ecosystems to future climate
 extremes.
description: AllData_PLoSONE_SI_2017_v1
DOI: 10.5061/dryad.s5k6k
title: Data from: Strong dispersal in a parasitoid wasp overwhelms habitat fragmentation and host population dynamics

description: The population dynamics of a parasite depend on species traits, host
 dynamics, and the environment. Those dynamics are reflected in the genetic
 structure of the population. Habitat fragmentation has a greater impact on
 parasites than on their hosts because resource distribution is
 increasingly fragmented for species at higher trophic levels. This could
 lead to either more or less genetic structure than the host, depending on
 the relative dispersal rates of species. We examined the spatial genetic
 structure of the parasitoid wasp Hyposoter horticola, and how it was
 influenced by dispersal, host population dynamics, and habitat
 fragmentation. The host, the Glanville fritillary butterfly, lives as a
 metapopulation in a fragmented landscape in the Åland islands, Finland. We
 collected wasps throughout the 50 by 70 km archipelago and determined the
 genetic diversity, spatial population structure, and genetic
 differentiation using 14 neutral DNA microsatellite loci. We compared
 genetic structure of the wasp with that of the host butterfly using
 published genetic data collected over the shared landscape. Using
 maternity assignment, we also identified full-siblings among the sampled
 parasitoids to estimate the dispersal range of individual females. We
 found that, because the parasitoid is dispersive, it has low genetic
 structure, is not very sensitive to habitat fragmentation, and has less
 spatial genetic structure than its butterfly host. The wasp is sensitive
 to regional rather than local host dynamics, and there is a geographic
 mosaic landscape for antagonistic coevolution of host resistance and
 parasite virulence.
description: genotype
 dataHyposoter horticola DNA
 microsatellite genotype dataHyposoter horticola DNA
 microsatellite genotype data.xlsxhabitat patches
 geographic coordinateshabitat patches
 geographic coordinates
DOI: 10.5061/dryad.dd8h5
title: Data from: Comparing entire colour patterns as birds see them

description: Colour patterns and their visual backgrounds consist of a mosaic of
 patches that vary in colour, brightness, size, shape and position. Most
 studies of crypsis, aposematism, sexual selection, or other forms of
 signalling concentrate on one or two patch classes (colours), either
 ignoring the rest of the colour pattern, or analysing the patches
 separately. We summarize methods of comparing colour patterns making use
 of known properties of bird eyes. The methods are easily modifiable for
 other animal visual systems. We present a new statistical method to
 compare entire colour patterns rather than comparing multiple pairs of
 patches. Unlike previous methods, the new method detects differences in
 the relationships among the colours, not just differences in colours. We
 present tests of the method's ability to detect a variety of kinds of
 differences between natural colour patterns and provide suggestions for
 analysis.
description: TetrahedralCalculationsThis zip file contains MATLAB .m files to do calculations in the tetrahedron (directory TetrahedralCalculations), do the permutation tests (directory (LMP5), read an OceanOptics spectral file, convert spetra to bird eye data, and data on bird eyes and ambient light.E&Mfiles.zip
DOI: 10.5061/dryad.3702g
title: Data from: Corridors restore animal-mediated pollination in fragmented tropical forest landscapes

description: Tropical biodiversity and associated ecosystem functions have become
 heavily eroded through habitat loss. Animal-mediated pollination is
 required in &gt;94% of higher tropical plant species and 75% of the
 world´s leading food crops, but it remains unclear if corridors avert
 deforestation-driven pollination breakdown in fragmented tropical
 landscapes. Here, we used manipulative resource experiments and field
 observations to show that corridors functionally connect neotropical
 forest fragments for forest-associated hummingbirds and increase pollen
 transfer. Further, corridors boosted forest-associated pollinator
 availability in fragments by 14.3 times compared to unconnected
 equivalents, increasing overall pollination success. Plants in patches
 without corridors showed pollination rates equal to bagged control
 flowers, indicating pollination failure in isolated fragments. This
 indicates, for the first time, that corridors benefit tropical forest
 ecosystems beyond boosting local species richness, by functionally
 connecting mutualistic network partners. We conclude that small-scale
 adjustments to landscape configuration safeguard native pollinators and
 associated pollination services in tropical forest landscapes.
description: Heliconia_PollinationThe file describes the number of pollinated Heliconia tortuosa styles as a function of the number of corridors connecting the forest fragment.Phaguy_OccupThe file describes the number of detected Green Hermits P. Guy in small forest fragments as a function of the number of corridors connecting the forest fragment.Amatza_OccupThe file describes the number of detected Amazilia tzacatl hummingbirds in small forest fragments as a function of the number of corridors connecting the forest fragment.TitrationThe file describes the number of observed hummingbirds at artificial feeders, with and without corridors. Feeders at distance "0" and "1" are at the forest edge, distance "2" corresponds to 10 meters distance to the edge, "3" to 20 meters distance, etc. up to "6" for 50 meters distance.PowdertransferThe file describes the number of fluorescent dye particles transferred between experimental feeders by hummingbirds, either along a corridor ("c"), through forest ("f") or through pasture ("p").
DOI: 10.5061/dryad.v36v0
title: Data from: Predicting biotic interactions and their variability in a changing environment

description: Global environmental change is altering the patterns of biodiversity
 worldwide. Observation and theory suggest that species' distributions
 and abundances depend on a suite of processes, notably abiotic filtering
 and biotic interactions, both of which are constrained by species'
 phylogenetic history. Models predicting species distribution have
 historically mostly considered abiotic filtering and are only starting to
 integrate biotic interaction. However, using information on present
 interactions to forecast the future of biodiversity supposes that biotic
 interactions will not change when species are confronted with new
 environments. Using bacterial microcosms, we illustrate how biotic
 interactions can vary along an environmental gradient and how this
 variability can depend on the phylogenetic distance between interacting
 species.
description: Results of monoculture
 experimentMeasurements of OD and
 fluorescence intensity in the monoculture experiment for 12 bacterial
 strains. Column names represent: Raw data Number, Microplate Row,
 Microplate Column, Content (Blank/Treatment ID), Raw Optical Density (OD),
 Corrected optical density (OD), Raw fluorescence intensity, Corrected
 fluorescence intensity, Time, Strain, Replicate, Salinity
 levelmonoculture_exp.csvResults of polyculture experimentMeasurements of OD and fluorescence intensity in the polyculture experiment. Column names represent: Raw data Number, Microplate Row, Microplate Column, Content (Blank/Treatment ID), Raw Optical Density (OD), Corrected optical density (OD), Raw fluorescence intensity, Corrected fluorescence intensity, Time, Strain, Replicate, Salinity levelpolyculture_exp.csv