cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sf7m0ck5
title: Data from: The assembly and importance of a novel ecosystem: the ant community of coffee farms in Puerto Rico

description: Agricultural ecosystems are, by their very nature novel, and, by
 definition, the more general biodiversity associated with them must
 likewise constitute a novel community. Here we examine the community of
 arboreally foraging ants in the coffee agroecosystem of Puerto
 Rico.  We surveyed 20 coffee plants in 25 farms three times in a
 period of one year. We also conducted a more spatially explicit sampling
 in two of the farms and conducted a species interaction study between the
 two most abundant species, Wasmannia auropunctata and Solenopsis invicta
 in the laboratory. We find that the majority of the most common species
 are well-known invasive ants and that there is a highly variable pattern
 of dominance that varies considerably over the main coffee producing
 region of Puerto Rico, suggesting an unusual modality of community
 structure. The distribution pattern of the two most common species, W.
 auropunctata and S. invicta, suggests strong competitive exclusion.
 However, they also have opposite relationships with the percent of shade
 cover, with W. auropunctata showing a positive relationship with shade,
 while S. invicta has a negative relationship. The spatial distribution of
 these two dominant species in the two more intensively studied farms
 suggests that young colonies of S. invicta can displace W. auropunctata.
 Laboratory experiments confirm this. These results suggest the existence
 of a spatially explicit  intransitive loop that includes these
 two species and is mediated by a phorid fly parasitoid that attack the
 larger workers of S. invicta. In addition to the elaboration of the nature
 and extent of this novel ant community, we speculate on the possibilities
 of its active inclusion as part of a biological control system dealing
 with several coffee pests, including one of the ants itself, W.
 auropunctata.
description: Field collected in coffee farms in Puerto Rico
description: Data are self explanitory in an excel workbook.
DOI: 10.5061/dryad.gf1vhhmmn
title: Bottom-up synthesis of multi-metal micro/nano motors

description: In the past two decades, micro/nano motors have experienced rapid
 development, especially in environment remediation, biomedical field, and
 cargo delivery. In this article, we synthesize a micro-nano motor composed
 of a variety of materials through the bottom-up method (template
 electrodeposition), and we use different functional layers and catalytic
 layers in the synthesis process. With this method, we test the motion
 effects of different materials in solution. In order to better analyze the
 influence of different factors on the motor movement effect, we mainly
 selected three factors to analyse from different aspects, respectively,
 hydrogen peroxide concentration, surfactant type, surfactant
 concentration. According to these statistical data, the movement
 efficiency and diversity of micromotors in different environments will be
 achieved.
DOI: 10.5061/dryad.mw6m905v6
title: Taxonomy based on limited genomic markers may underestimates species diversity of rockhopper penguins and threaten their conservation

description: Delimiting recently diverged species is challenging. During speciation,
 genetic differentiation may be distributed unevenly across the genome, as
 different genomic regions can be subject to different selective pressures
 and evolutionary histories. Reliance on limited numbers of genetic markers
 that may be underpowered can make species delimitation even more
 challenging, potentially resulting in taxonomic inconsistencies.
 Rockhopper penguins of the genus Eudyptes comprise three
 broadly recognized taxa: northern (E. moseleyi), southern (E. chrysocome),
 and eastern rockhopper (E. filholi). Their taxonomic status has been
 controversial for decades, with researchers disagreeing about
 whether E. chrysocome and E. filholiare
 distinct species or conspecific. Our goal is to evaluate genome-wide
 patterns of divergence to evaluate genetic differentiation and species
 delimitation in rockhopper penguins, and to assess which
 mechanisms may underlie previous discordance among nuclear versus
 mitochondrial analyses. We generated reduced-representation
 genomic libraries using Double Digest Restriction-site Associated DNA
 (ddRAD) sequencing to evaluate genetic differentiation, contemporary
 migration rates and admixture among colonies of rockhopper
 penguins. The extent of genetic differentiation among the three
 taxa was consistently higher than population-level genetic differentiation
 found within these and other penguin species. There was no evidence of
 admixture among the three taxa, suggesting the absence of ongoing gene
 flow among them. Species delimitation analyses based on molecular data,
 along with other lines of evidence, provide strong support for the
 taxonomic distinction of three species of rockhopper
 penguins. Our results provide strong support for the existence of
 three distinct species of rockhopper penguins. The recognition of this
 taxonomic diversity is crucial for the management and conservation of this
 widely distributed species group. This study illustrates that widespread
 dispersive seabird lineages lacking obvious morphological differences may
 nevertheless have complex evolutionary histories and comprise cryptic
 species diversity.
DOI: 10.5061/dryad.05qfttf19
title: Non-continuous reproductive phenology of animal-dispersed species in young forest restoration plantings

description: Tree species that produce resources for fauna are recommended for forest
 restoration plantings to attract pollinators and seed dispersers; however,
 information regarding the flowering and fruiting of these species during
 early growth stages is scarce. We evaluated the reproductive phenology of
 animal-dispersed tree species widely used in Atlantic Forest restoration.
 We marked 16 animal-dispersed tree species in 3- to 8-year-old forest
 restoration plantings in Itu-São Paulo, southeast Brazil. We noted the age
 of the first reproductive event, flowering and fruiting seasonality,
 percentage of trees that reached reproductive stages, and intensity of
 bud, flower, and fruit production for each species. Flowering and fruiting
 are seasonal for most species; only two, Cecropia pachystachya and Ficus
 guaranitica, exhibited continuous flowering and fruiting throughout the
 year; we also identified Schinus terebinthifolia and Dendropanax cuneatus
 fruiting in the dry season during resource scarcity. Therefore, we
 recommend all as framework species, that is, species that are
 animal-dispersed with early flowering and fruiting potential, for forest
 restoration. Further, we recommend identifying and planting similar
 animal-dispersed tree species that produce fruits constantly or in the dry
 season to maximize fauna resource availability throughout the year in
 tropical forest restoration plantings.
description: We marked between six and 22 randomly selected individual trees
 per species per age of plantation. The six plantations are distributed
 along the Forest Experiment Center, and they were 3- (planted in 2013), 4-
 (2012), 5- (2011), 6- (2010), 7- (2009), and 8-years old (2008). Trees
 marked totaled 750 individuals of 16 animal-dispersed species. We observed
 the reproductive phenology of all marked trees monthly over two years,
 from September 2015 to August 2017. During this time, we observed the
 presence/absence of buds, flowers, and unripe and ripe fruits, and we
 classified these variables using the Fournier semi-quantitative scale
 (Fournier, 1974). The Fournier scale visually estimates reproductive
 phenophases using a score of 0 to 4, where 0 denotes absence of a
 phenophase, and 1, 2, 3, and -4 represent 1-25, 26-50, 51-75, and 76-100%
 of maximum phenophase intensity, respectively.
DOI: 10.5061/dryad.d7wm37pzx
title: Nest survival, female survival, and average covariates used in modeling, along with metadata

description: Females must balance physiological and behavioral demands of producing
 offspring with associated expenditures, such as resource acquisition and
 predator avoidance. Nest success is an important parameter underlying
 avian population dynamics. Galliforms are particularly susceptible to low
 nest success due to exposure of ground nests to multiple predator guilds,
 lengthy incubation periods, and substantive reliance on crypsis for
 survival. Hence, it is plausible that nesting individuals prioritize
 productivity and survival differently, resulting in a gradient of
 reproductive strategies. Fine-scale movement patterns during incubation
 are not well documented in ground-nesting birds, and the influence of
 reproductive movements on survival is largely unknown. Using GPS data
 collected from female wild turkeys (n = 278) across the southeastern
 United States, we evaluated the influence of incubation recess behaviors
 on tradeoffs between nest and female survival. We quantified daily recess
 behaviors including recess duration, recess frequency, total distance
 traveled, and incubation range size for each nest attempt as well as
 covariates for nest concealment, nest attempt, and nest age. Of 374 nests,
 91 (24%) hatched and 39 (14%) females were depredated during incubation.
 Average nest survival during the incubation period was 0.19, whereas
 average female survival was 0.78. On average, females took 1.6 daily
 unique recesses (SD = 1.2), spent 2.1 hrs off the nest each day (SD =
 1.8), and traveled 357.6 m during recesses (SD = 396.6). Average nest
 concealment was 92.5 cm (SD = 47). We found that females who took longer
 recess bouts had higher individual survival, but had increased nest loss.
 Females who recessed more frequently had lower individual survival. Our
 findings suggest behavioral decisions made during incubation represent
 life-history tradeoffs between predation risk and reproductive success on
 an unpredictable landscape.
DOI: 10.5061/dryad.2z34tmpjv
title: Hybrid incompatibilities and transgressive gene expression between two closely related subspecies of Drosophila

description: Genome-wide assays of expression between species and their hybrids have
 identified genes that become either over or under-expressed relative to
 the parental species (i.e. transgressive). Transgressive expression in
 hybrids is of interest because it highlights possible changes in gene
 regulation directly linked to hybrid dysfunction. Previous studies in
 Drosophila that used long-diverged species pairs with complete or nearly
 complete isolation (i.e. full sterility and partial inviability of
 hybrids) and high-levels of genome misregulation have found correlations
 between expression and coding sequence divergence. The work highlighted
 the possible effects of directional selection driving sequence divergence
 and transgressive expression. Whether the same is true for taxa at early
 stages of divergence that have only achieved partial isolation remains
 untested. Here, we reanalyze previously published genome expression data
 and available genome sequence reads from a pair of partially isolated
 subspecies of Drosophila to compare expression and sequence divergence. We
 find a significant correlation in rates of expression and sequence
 evolution, but no support for directional selection driving transgressive
 expression in hybrids. We find that most transgressive genes in hybrids
 show no differential expression between parental subspecies and used SNP
 data to explore the role of stabilizing selection through compensatory
 mutations. We also examine possible misregulation through cascade effects
 that could be driven by interacting gene networks or co-option of
 off-target cis-regulatory elements.
DOI: 10.5061/dryad.d51c5b018
title: Fitness consequences of biochemical adaptation in Drosophila melanogaster populations under simultaneous selection for faster pre-adult development and extended life-span

description: In holometabolous insect like Drosophila melanogaster, critical size is an
 important time point during larval life, for irreversible commitment to
 metamorphosis. Here, we studied the impact of restricted growth duration
 in terms of selection for faster pre-adult development in Drosophila
 melanogaster populations which resulted in the evolution of reduced
 critical size on adult life history traits. Selection for faster pre-adult
 development resulted in biochemical adaptation in larval physiology with
 no compromise in major biomolecules at critical size time point. 
 The flies from the selected populations seem to not only commit to
 metamorphosis on the attainment of critical size but also seem to
 channelize resources to reproduction as indicated by similar life-time
 fecundity of CS and NS flies from selected populations, while the Control
 CS flies significantly lower life-time fecundity compared to Control NS
 flies. The flies from selected populations seem to achieve longevity
 comparable to control flies despite being significantly smaller in size-
 thus resource constrained due to faster pre-adult development.
description: 1) Life history assays- Adults- Body size measurement by dry
 weight measurement, Fecundity assay, longevity assay was estimated as
 described in research article (manuscript) 2)
 Biochemical estimation was performed on larval stages.
 3) Statistical analysis was done on raw data.
DOI: 10.5061/dryad.k0p2ngf68
title: Color polymorphism is a driver of diversification

description: Color polymorphism – two or more heritable color phenotypes maintained
 within a single breeding population – is an extreme type of intra-specific
 diversity widespread across the tree of life. Color polymorphism is
 hypothesized to be an engine for speciation, where morph loss or
 divergence between distinct color morphs within a species results in the
 rapid evolution of new lineages, and thus, color polymorphic lineages are
 expected to display elevated diversification rates. Multiple species in
 the lizard family Lacertidae are color polymorphic, making them an ideal
 group to investigate the evolutionary history of this trait and its
 influence on macroevolution. Here, we produce a comprehensive
 species-level phylogeny of the lizard family Lacertidae to reconstruct the
 evolutionary history of color polymorphism and test if color polymorphism
 has been a driver of diversification. Accounting for phylogenetic
 uncertainty, we estimate an ancient origin of color polymorphism (111 MYA)
 within the Lacertini tribe (subfamily Lacertinae). Color polymorphism most
 likely evolved few times in the Lacertidae and has been lost at a much
 faster rate than gained. Evolutionary transitions to color polymorphism
 are associated with shifts in increased net diversification rate in this
 family of lizards. Taken together, our empirical results support
 long-standing theoretical expectations that color polymorphism is a driver
 of diversification.
description: GENETIC DATA All genetic data were downloaded
 from GenBank and are publicly available.  PHENOTYPIC
 TRAIT DATA Phenotypic trait data were collected by
 Kinsey M. Brock and Indiana E. Madden from the literature and photos of
 lizards publicly available at lacertid.de and inaturalist.org.
DOI: 10.5061/dryad.2547d7wp2
title: Data from: Exotic species drive patterns of plant species diversity in 93 restored tallgrass prairies

description: A primary goal of restoration ecology is to understand the factors that
 generate variability in species diversity and
 composition among restorations. Plant communities may
 assemble deterministically towards a common community type, or they may
 assemble stochastically, ending differently because of weather conditions
 during establishment, soil legacy effects,
 or exotic species propagule pressure. To test
 these alternative hypotheses, we
 sampled plant communities and soil
 at 93 randomly
 selected restored prairies distributed
 throughout Iowa, USA. Five remnant sites were sampled as a reference. We
 tested our hypotheses using multiple regressions and investigated the
 strength of direct and indirect effects
 on species diversity and richness using
 structural equation models. The prairie restorations were highly variable
 in their age, size, diversity, soil characteristics, and how they
 were managed post-seeding. The strongest predictor
 of plant species richness
 and diversity was the degree of invasion, as measured by
 the abundance of exotic species. Restorations planted
 with species-rich seed mixes had
 reduced exotic species abundance, which led
 indirectly to higher species richness of
 restorations.  Sites with higher organic matter and a more linear
 shape had a direct positive effect on exotic abundance,
 which in turn decreased diversity. We found little support for
 deterministic assembly, and diversity did not increase
 with the age of planting.  Our results indicate
 that restored prairie communities tend to assemble into
 states of high or low diversity, driven by invasion
 from exotic plant species.  Management
 of exotic species is essential for
 maximizing species diversity in temperate
 grassland restorations.
description: Please seed methods in corresponding manuscript for details.
description: Here we provide raw data on plant community composition for 93
 tallgrass prairie restorations and 5 prairie remnants in Iowa, USA. For
 prairie restorations, we also provide data on soil characteristics, site
 age, site shape and size, weather conditions during the first two years of
 establishment, land use history, management actions, and composition of
 the initial seed mix. Any missing values are noted by
 periods "." in all files.
DOI: 10.25338/b81918
title: Data from: Resilience of an integrated crop-livestock system to climate change: a simulation analysis of cover crop grazing in southern Brazil

description: Integrated crop-livestock systems are a form of sustainable
 intensification of agriculture that rely on synergistic relationships
 between plant and animal components to bolster critical agroecosystem
 processes. We simulated cash crop and cover crop productivity dynamics in
 an integrated beef-soybean cover crop grazing system typical of southern
 Brazil to gain a better understanding of the impacts of livestock
 integration on system performance. Long-term historical simulations in
 APSIM showed that the integrated system resulted in greater system-wide
 productivity than a specialized control system in 77% of simulated years.
 Although soybean yields were typically lower in the integrated system,
 additional forage and livestock production was obtained. Under simulated
 future climate conditions (RCP8.5 scenario from 2020-2060), integrated
 system productivity exceeded specialized system productivity in 95% of
 years despite declines in average soybean yield and cover crop aboveground
 biomass production. While the integrated system provided a productivity
 buffer against chronic climate stress, its resilience to annual weather
 anomalies depended on disturbance type and timing. This study demonstrates
 the potential advantages of cover crop grazing as a sustainable
 intensification strategy, using process-based modeling tools to explore
 biophysical proxies for resilience in field-level agroecosystem functions.
DOI: 10.15468/dl.phrb9b
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-81.22378 -5.06183,-74.91817 -5.06183,-74.91817 2.24743,-81.22378 2.24743,-81.22378 -5.06183))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dormitator latifrons",
 "Year 2000-2026"
 ]
}

 The dataset includes 18 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002543-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9kd51c5f3
title: Cryptic lineages respond differently to coral bleaching

description: Coral cover is decreasing worldwide largely as a result of a rise in
 seawater temperatures that triggers coral bleaching and induces coral
 mortality. How coral reefs will respond to climate change will be a
 function of genetic variation and how it is partitioned within and among
 species. A critical initial step is to accurately delineate species and
 quantify their physiological potential to cope with heat stress. Cryptic
 species are morphologically similar but genetically distinct and may
 respond physiologically different to climate change. A dominant Caribbean
 reef builder severely affected by climate change is the mountainous star
 coral, Orbicella faveolata. Recently, Dziedzic et al. (2019) reported
 quantitative genetic variation in the physiological response to thermal
 stress in a single population of this species, suggesting that variation
 within populations will allow these corals to adapt to rising ocean
 temperatures. We reanalyzed their data and found multiple cryptic lineages
 rather than a single panmictic population, with one of the lineages being
 not heat-tolerant. While different cryptic lineages co-occur in certain
 locations, there is at least one lineage that occurs only in a single
 location. Our finding of hidden lineages within a threatened species
 highlights the varying extinction risks faced by these independently
 evolving groups, especially when the prospects of survival under warmer
 oceans seem favorable for some of them only.
description: Code and files needed to reproduce analyses in the associated
 publication
DOI: 10.5061/dryad.95x69p8hk
title: Westward range expansion from middle latitudes explains the Mississippi River discontinuity in a forest herb of eastern North America

description: It is often expected that temperate plants have expanded their geographic
 ranges northward from primarily southern refugia. Evidence for this
 hypothesis is mixed in eastern North American species, and there is
 increasing support for colonization from middle latitudes. We studied
 genome-wide patterns of variation in RADseq loci to test hypotheses
 concerning range expansion in a North American forest herb (Campanula
 americana). First, spatial patterns of genetic differentiation were
 determined. Then phylogenetic relationships and divergence times were
 estimated. Spatial signatures of genetic drift were also studied to
 identify the directionality of recent range expansion and its geographic
 origins. Finally, spatially explicit scenarios for the spread of plants
 across the landscape were compared, using variation in the population
 mutation parameter and Tajima's D. We found strong longitudinal
 subdivision, with populations clustering into groups west and east of the
 Mississippi River. While the southeastern region was likely part of a
 diverse Pleistocene refugium, there is little evidence that range
 expansion involved founders from these southern locales. Instead, declines
 in genetic diversity and the loss of rare alleles support a westward
 colonization wave from a middle latitude refugium near the southern
 Appalachian Mountains, with subsequent expansion from a Pleistocene
 staging ground in the Mississippi River Valley (0.51 - 1.27 Mya). These
 analyses implicate stepping stone colonization from middle latitudes as an
 important mechanism of species range expansion in eastern North America.
 This study further demonstrates the utility of population genetics as a
 tool to infer the routes traveled by organisms during geographic range
 expansion.
description: This dataset contains R scripts necessary to generate the results
 in our paper. All scripts are custom.
description: Users will need sequence data (BioProject ID: PRJNA560272) and
 some knowledge of iPyrad parameterization (see Supporting Table
 1).