cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8703q25
title: Data from: Spatial-temporal variability and related factors of soil organic carbon in Henan province

description: Spatial variability and influence factors are important to evaluate soil
 organic carbon(SOC) and the carbon pool in large areas. In the present
 study, sampling was conducted from May to November 2011 in Henan province,
 a typical agricultural region of central China, to study the effects of
 soil properties and anthropogenic factors on SOC variability in cropland.
 Physicochemical properties of soil samples were analyzed, which were
 collected at 280 sites from the surface layer (at a depth of 0–20 cm), and
 related data about the sampling sites were also collected from the Second
 State Soil Survey of China (SSSSC), conducted in 1981. The main results
 were as follows: 1) Increasing trends in soil organic carbon density
 (SOCD) and soil organic carbon pool (SOCP) were obvious from 1981 to 2011,
 and we conclude that cropland presents great carbon sequestration
 potential for the future. Carbon pool ability varied with soil properties:
 the order of fixed carbon amount in different soil types was found to be
 Inceptisols &gt; Luvisols &gt; Semi-hydromorphic soil &gt;
 Anthrosols, and the average SOCP increased significantly from 1981 to
 2011. 2) Soil bulk density, pH and returning straw are the key influence
 factors for SOCD in the past 30 years. 3) Although random factors
 (returning straw) only explain 29.1% of SOCD variability, the factor
 should be paid more attention, because application of returning strawwas
 the most dominant anthropogenic factors, which can be used to improve
 cropland productivity and carbon sink capacity within a short period if
 they are properly managed in the future.
description: Data of Soil Organic
 Carbon in Henan ProvinceData.xlsx
DOI: 10.5061/dryad.j909k
title: Data from: Male care and life history traits in mammals

description: Male care has energetic and opportunity costs, and is more likely to
 evolve when males gain greater certainty of paternity or when future
 mating opportunities are scarce. However, little is known about the
 substantial benefits that males may provide to females and offspring.
 Using phylogenetic comparative methods and a sample of over 500 mammalian
 species, we show that mammals in which males carry the offspring have
 shorter lactation periods, which leads to more frequent breeding events.
 Provisioning the female is associated with larger litters and shorter
 lactation. Offspring of species with male care have similar weaning mass
 to those without despite being supported by a shorter lactation period,
 implying that they grow faster. We propose that males provide an energetic
 contribution during the most expensive time of female reproduction,
 lactation, and that different male care behaviours increase female
 fecundity, which in turn helps males offset the costs of caring.
description: West & Capellini
 NComm Male care datasetThe data file contains
 data on the presence/absence of male parental care behaviours, allocare,
 social monogamy, life history traits, and citation counts in mammalian
 species, at the global scale. Here we provide basic details of the
 variables included in the data file. The full description of the data and
 data collection protocols for all behavioural and life history traits can
 be found in the Methods section of the Nature Communications paper. The
 total sample size of species in this dataset is 529 mammals, although not
 all species have data for all variables.LH paper
 dataset.xlsx
DOI: 10.5061/dryad.903vs08
title: Data from: The unrealized potential of herbaria in global change biology

description: Plant and fungal specimens in herbaria are becoming primary resources for
 investigating how plant phenology and geographic distributions shift with
 climate change, greatly expanding inferences across spatial, temporal, and
 phylogenetic dimensions. However, these specimens contain a wealth of
 additional data—including nutrients, defensive compounds, herbivore
 damage, disease lesions, and signatures of physiological processes—that
 capture ecological and evolutionary responses to the Anthropocene but
 which are less frequently utilized. Here, we outline the diversity of
 herbarium data, global change topics to which they have been applied, and
 new hypotheses they could inform. We find that herbarium data have been
 used extensively to study impacts of climate change and invasive species,
 but that such data are less commonly used to address other drivers of
 biodiversity loss, including habitat conversion, pollution, and
 overexploitation. In addition, we note that fungal specimens are
 under-explored relative to vascular plants. To facilitate broader
 application of plant and fungal specimens in global change research, we
 consider the limitations of these data and modern sampling and statistical
 tools that may be applied to surmount challenges they present. Using a
 case study of insect herbivory, we illustrate how novel herbarium data may
 be employed to test hypotheses for which few data exist. With the goal of
 positioning herbaria as hubs for global change research, we suggest future
 research directions and curation priorities.
description: Dryad_Meineke_EcolMon2018
DOI: 10.5061/dryad.913t0
title: Data from: Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes

description: Environmental gradients have been shown to disrupt gene flow in marine
 species, yet their influence in structuring populations at depth remains
 poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis)
 are demersal species co-occurring in the Benguela Current system, where
 decades of intense fishing resulted in severely depleted stocks in the
 past. Previous studies identified conflicting mtDNA genetic substructuring
 patterns and thus contrasting evolutionary trajectories for both species.
 Using 10 microsatellite loci, the control region of mtDNA and employing a
 seascape genetics approach, we investigated genetic connectivity and the
 impact of prolonged exploitation in the two species, which are
 characterized by different patterns of fishing pressure. Three consecutive
 years were sampled covering the entire distribution (N = 2100 fishes).
 Despite large estimated population sizes, both species exhibited low
 levels of contemporary genetic diversity (0.581 &lt; HE &lt;
 0.692), implying that fishing has had a significant impact on their
 genetic composition and evolutionary trajectories. Further, for M.
 paradoxus, significant temporal, but not spatial, divergence points to the
 presence of genetic chaotic patchiness. In contrast, M. capensis exhibited
 a clear latitudinal cline in genetic differentiation between Namibia and
 South Africa (FST = 0.063, P &lt; 0.05), with low (0.2% per
 generation) estimates of contemporary gene flow. Seascape analyses reveal
 an association with bathymetry and upwelling events, suggesting that
 adaptation to local environmental conditions may drive genetic
 differentiation in M. capensis. Importantly, our results highlight the
 need for temporal sampling in disentangling the complex factors that
 impact population divergence in marine fishes.
description: Microsatellite dataset
 for Merluccius capensisTable containing all M.
 capensis individuals genotyped for nine microsatellite loci, for the three
 years sampledMcapensis.txtMicrosatellite dataset for Merluccius paradoxusTable containing all M. paradoxus individuals genotyped for nine microsatellite markers, for the three sampled yearsMparadoxus.txt
DOI: 10.5061/dryad.c8c58
title: Data from: Phenotypic selection favors missing trait combinations in coexisting annual plants

description: Trade-offs among traits are important for maintaining biodiversity, but
 the role of natural selection in their construction is not often known. It
 is possible that trade-offs reflect fundamental constraints, negative
 correlational selection, or directional selection operating on costly,
 redundant traits. In a Sonoran Desert community of winter annual plants,
 we have identified a trade-off between relative growth rate and water-use
 efficiency among species, such that species with high relative growth rate
 have low water-use efficiency and vice versa. We measured selection on
 water-use efficiency, relative growth rate, and underlying traits within
 populations of four species at two study sites with different average
 climates. Phenotypic trait correlations within species did not match the
 among-species trade-off. In fact, for two species with high water-use
 efficiency, individuals with high relative growth rate also had high
 water-use efficiency. All populations experienced positive directional
 selection for water-use efficiency and relative growth rate. Selection
 tended to be stronger on water-use efficiency at the warmer and drier
 site, and selection on relative growth rate tended to be stronger at the
 cooler and wetter site. Our results indicate that directional natural
 selection favors a phenotype not observed among species in the community,
 suggesting that the among-species trade-off could be due to pervasive
 genetic constraints, perhaps acting in concert with processes of community
 assembly.
description: Standardized Trait
 DataKimballetalData.xlsx
DOI: 10.5061/dryad.kt57q
title: Data from: Environmental and scale-dependent evolutionary trends in the body size of crustaceans

description: The ecological and physiological significance of body size is well
 recognized. However, key macroevolutionary questions regarding the
 dependency of body size trends on the taxonomic scale of analysis and the
 role of environment in controlling long-term evolution of body size are
 largely unknown. Here, we evaluate these issues for decapod crustaceans, a
 group that diversified in the Mesozoic. A compilation of body size data
 for 792 brachyuran crab and lobster species reveals that their maximum,
 mean and median body size increased, but no increase in minimum size was
 observed. This increase is not expressed within lineages, but is rather a
 product of the appearance and/or diversification of new clades of larger,
 primarily burrowing to shelter-seeking decapods. This argues against
 directional selective pressures within lineages. Rather, the trend is a
 macroevolutionary consequence of species sorting: preferential origination
 of new decapod clades with intrinsically larger body sizes. Furthermore,
 body size evolution appears to have been habitat-controlled. In the
 Cretaceous, reef-associated crabs became markedly smaller than those in
 other habitats, a pattern that persists today. The long-term increase in
 body size of crabs and lobsters, coupled with their increased diversity
 and abundance, suggests that their ecological impact may have increased
 over evolutionary time.
description: DatabaseDatabase with Mesozoic decapod crustacean occurrences, body sizes, and sedimentary environments. For any questions please contact .
DOI: 10.5061/dryad.h4s73s5c
title: Data from: Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data

description: BACKGROUND: Introgression likely plays a significant role in evolution,
 but understanding the extent and consequences of this process requires a
 clear identification of species boundaries in each focal group. The
 delimitation of species, however, is a contentious endeavor. This is true
 not only because of the inadequacy of current tools to identify species
 lineages, but also because of the inherent ambiguity between natural
 populations and species paradigms. The result has been a debate about the
 supremacy of various species concepts and criteria. Here, we utilized
 multiple separate sources of molecular data, mtDNA, nuclear sequences, and
 microsatellites, to delimit species under a polytypic species concept
 (PTSC) and estimate the frequency and genomic extent of introgression in a
 Neotropical genus of cichlid fishes (Cichla). We compared our inferences
 of species boundaries and introgression under this paradigm to those when
 species are identified under a diagnostic species concept (DSC). RESULTS:
 We find that, based on extensive molecular data and an inclusive species
 concept, 8 separate biological entities should be recognized rather than
 the 15 described species of Cichla. Under the PTSC, fewer individuals are
 expected to exhibit hybrid ancestry than under the DSC (~2% vs. ~12%), but
 more of the species exhibit introgression from at least one other species
 (75% vs. 60%). Under either species concept, the phylogenetic breadth of
 introgression in this group is notable, with both sister species and
 species from different major mtDNA clades exhibiting introgression.
 CONCLUSIONS: Introgression was observed to be a widespread phenomenon for
 delimited species in this group. While several instances of introgressive
 hybridization were observed in anthropogenically altered habitats, most
 were found in undisturbed natural habitats, suggesting that introgression
 is a natural but ephemeral part of the evolution of many tropical species.
 Nevertheless, even transient introgression may facilitate an increase in
 genetic diversity or transfer of adaptive mutations that have important
 consequences in the evolution of tropical biodiversity.
description: Cichla_microsatellite_datasee Readme file
DOI: 10.5061/dryad.53924
title: Data from: Cooperative breeding influences the number and type of vocalizations in avian lineages

description: Although communicative complexity is often predicted to correlate with
 social complexity in animal societies, few studies have employed
 large-scale comparative analyses to test whether socially complex species
 have more complex systems of communication. I tested this social
 complexity hypothesis in birds (Class: Aves) using the large amount of
 natural history information that describes both vocal repertoire and
 social system in these species. To do so, I marshalled data from primary
 and secondary records of avian vocal repertoires (n = 253), and for each
 of the species in the dataset I recorded the reported repertoire size and
 associated species information. Using phylogenetic comparative methods, I
 found that cooperative breeding was a strong and repeatable predictor of
 vocal repertoire size, while other social variables, e.g. group size and
 group stability, had little or no influence on repertoire size.
 Importantly, repertoire sizes expanded concurrently with the evolution of
 cooperative breeding, suggesting a direct link between these two traits.
 Cooperatively breeding species devoted significantly more of their
 repertoire to contact calls and alarm calls. Overall, these results
 therefore lend support to the hypothesis that social complexity via
 behavioural coordination leads to increases in vocal complexity.
description: Social and Vocal
 DatabaseSocVocFull04_14_17.csvRepertoiresListedRepertoires.xlsxInter-observer reliabilityMatchedRepertoireSizes.csv
DOI: 10.5061/dryad.1411n
title: Data from: Geographic signatures in species turnover: decoupling colonization and extinction across a latitudinal gradient

description: High latitude communities have low species richness and are rapidly
 warming with climate change. Thus, temporal changes in community
 composition are expected to be greatest at high latitudes. However, at the
 same time traits such as body size can also change with latitude,
 potentially offsetting or increasing changes to community composition over
 time. We tested how zooplankton communities (copepods and cladocerans)
 have changed over a 25-75 year time span by assessing colonization and
 extinction rates from lakes across an 1800 km latitudinal gradient, and
 further tested whether species traits predict rates of community change
 over time. Lake-level dissimilarity, measured with Sorenson distance,
 decreased at higher latitudes. This decrease was due to higher
 colonization rates of cladocerans in lower latitude lakes and consistent
 extinction rates across the latitudinal gradient. At the species level,
 colonization increased with regional occupancy, and tended to be higher
 for smaller bodied, locally abundant, species. Local extinction rates were
 negatively correlated with local abundance and regional occupancy, but
 were not influenced by body size. None of these species-specific
 characteristics changed predictably with latitude. Contrary to our
 expectations, low-latitude zooplankton communities changed more rapidly
 than high-latitude communities by becoming more species rich, not by
 losing species that were historically present. Moreover, colonization and
 extinction trends suggest that lakes have become increasingly dominated by
 species with smaller body sizes and that are already common locally and
 regionally. Together, these findings indicate that rates of species
 turnover in freshwater lakes across a latitudinal gradient are not
 predicted by rates of temperature change, but that turnover is nonetheless
 resulting in trait-shifts that favour small, generalist species.
description: Lake location,
 zooplankton species abundance and body size dataThis file contains the
 raw data used in all analyses. Within the file is the zooplankton species
 composition from 2011 (relative abundance) and historical samples
 (relative abundance and presence/absence). In addition, body length data
 (micrometers) for a subset of the lakes is present. Finally, geographic
 coordinates for each lake (latitude/longitude) are in the data
 file.data
 for Dryad.xlsx
DOI: 10.5061/dryad.6s0h6
title: Data from: Reciprocal specialization in multihost malaria parasite communities of birds: a temperate-tropical comparison

description: How specialization of consumers with respect to resources varies with
 respect to latitude is poorly understood. Coexistence of many species in
 the tropics might be possible only if specialization also increases.
 Alternatively, lower average abundance of more diverse biotic resources in
 the tropics might force consumers to become more generalized foragers. We
 examine levels of reciprocal specialization in an antagonistic
 system—avian malaria—to determine whether the number of host species used
 and/or parasite lineages harbored differ between a temperate and a
 tropical assemblage. We evaluate the results of network analysis, which
 can incorporate both bird and parasite perspectives on specialization in
 one quantitative index, in comparison to null models. Specialization was
 significantly greater in both sample sites than predicted from null
 models. We found evidence for lower per-host species parasite diversity in
 temperate compared to tropical birds. However, specialization did not
 differ between the tropical and temperate sites from the parasite
 perspective. We supplemented the network analysis with estimates of
 specialization that incorporate phylogenetic relationships of associates
 and found no differences between sites. Thus, our analyses indicate that
 specialization within an antagonistic host-parasite (resource-consumer)
 system varies little between tropical and temperate localities.
description: Interaction Matrices and
 species-level specialization valuesInteraction matrices of
 birds and malaria parasites in the two study sites. Also provided are
 sample sizes (N), the number of associates (degree), species-level
 specialization (d’), and phylogenetic species-level specialization (wMPD).
 We placed “TI” in front of each lineage number from Tiputini to
 distinguish these from “OZ” lineages and an “H” or a “P” in front of each
 lineage name to distinguish between Haemoproteus and Plasmodium. An “L” is
 placed after lineage names consisting of more than one
 haplotype.InteractionMatrices.csvGenBank ID numbersGenBank IDs of associate bird species and parasite lineages used in the phylogenetic specificity indices.GenBankIDs.csvBird RAG-1 alignmentBird RAG-1 alignment file. Outgroup species begin with "out" and are followed by their GenBank ID.Bird_RAG1.fastaParasite cytb alignmentParasite cytb alignment file. Outgroup species begin with "O" and are followed by their GenBank ID.Parasite_cytb.fasta
DOI: 10.5061/dryad.4d02r
title: Data from: Tolerance to deer herbivory and resistance to insect herbivores in the common evening primrose (Oenothera biennis)

description: The evolution of plant defence in response to herbivory will depend on the
 fitness effects of damage, availability of genetic variation, and
 potential ecological and genetic constraints on defence. Here we examine
 the potential for evolution of tolerance to deer herbivory in Oenothera
 biennis while simultaneously considering resistance to natural insect
 herbivores. We examined: i) the effects of deer damage on fitness; ii) the
 presence of genetic variation in tolerance and resistance; iii) selection
 on tolerance; iv) genetic correlations with resistance that could
 constrain evolution of tolerance; and v) plant traits that might predict
 defence. In a field experiment, we simulated deer damage occurring early
 and late in the season, recorded arthropod abundances, flowering
 phenology, and measured growth rate and lifetime reproduction. Our study
 showed that deer herbivory has a negative effect on fitness, with effects
 being more pronounced for late-season damage. Selection acted to increase
 tolerance to deer damage, yet there was low and non-significant genetic
 variation in this trait. In contrast, there was substantial genetic
 variation in resistance to insect herbivores. Resistance was genetically
 uncorrelated with tolerance, whereas positive genetic correlations in
 resistance to insect herbivores suggest there exists diffuse selection on
 resistance traits. In addition, growth rate and flowering time did not
 predict variation in tolerance, but flowering phenology was genetically
 correlated with resistance. Our results suggest that deer damage has the
 potential to exert selection because browsing reduces plant fitness, but
 limited standing genetic variation in tolerance is expected to constrain
 adaptive evolution in O. biennis.
description: Data_tolerance to deer
 herbivory and resistance to insectsData on which analyses
 were based on. See the "readme" document for column
 descriptions.Puentes and Johnson -tolerance
 and resistance_data.xlsx