cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gf1vhhmpv
title: Rapid evolutionary divergence of a songbird population following recent colonization of an urban area

description: Colonization of a novel environment by a small group of individuals can
 lead to rapid evolutionary change, yet evidence of the relative
 contributions of neutral and selective factors in promoting divergence
 during the early stages of colonization remain scarce. Here, we use
 genome-wide SNP data to test the role of neutral and selective forces in
 driving the divergence of a unique urban population of the Oregon junco
 (Junco hyemalis oreganus), which became established on the campus of the
 University of California at San Diego (UCSD) in the early 1980s. Previous
 studies based on microsatellite loci documented significant genetic
 differentiation of the urban population as well as divergence in sexual
 signaling and life-history traits relative to nearby montane populations.
 However, the geographic origin of the colonization and the factors
 involved in the onset of the differentiation process remained uncertain.
 Our genome-wide SNP dataset confirmed the marked genetic differentiation
 of the UCSD population, and phylogenomic analysis identified the coastal
 subspecies pinosus from central California as its sister group instead of
 the neighboring mountain population. Demographic inference based on site
 frequency spectra recovered a time of separation from pinosus as recent as
 20 to 32 generations, and a strong bottleneck at the time of colonization,
 suggesting a relevant role of founder effects and drift in the genetic
 differentiation of the UCSD population. However, we also found significant
 associations between environmental parameters characterizing the urban
 habitat of UCSD and genome-wide variants linked to functional genes. Some
 of the identified gene functions, like heavy metal detoxification and
 high-pitched hearing, have been reported as potentially adaptive in birds
 inhabiting urban environments. These results suggest that the interplay
 between founder events and directional selection may result in rapid
 shifts in both neutral and adaptive loci across the genome, and reveal the
 UCSD population of juncos as an ongoing case of divergence following the
 colonization of an anthropic environment.
description: All methods and protocols are described in detail in the
 article.
description: All methods and protocols are described in detail in the
 article.
DOI: 10.5061/dryad.qfttdz0h5
title: Parasitoid communities in the variable agricultural environments of blueberry production in the Southeastern USA

description: In blueberry crops, there are multiple pest species, and some of those can
 be suppressed by natural enemies including parasitoid wasps and predators.
 Parasitoid wasps occur within the environment often tracking pest species
 for food resources to complete their lifecycle. These small wasps are also
 sensitive to agricultural environments including agrichemicals, habitat
 availability, and climate. We investigated how the structure of parasitoid
 communities varied between organic and conventional blueberry systems, and
 how the communities of these parasitoids varied within field spatial
 scales (forested border vs edge vs interior). With lower intensity of
 agricultural interventions occurring in organic systems and forested
 borders, we predicted more stable parasitoid numbers that would be
 insulated from predicted climate variability. In our study, parasitoids
 were observed in low abundance in each cropping system, with community
 structure dependent on both management practice and field position.
 Unmanaged blueberry fields and forested field borders contained more
 parasitoid families, and in conventional systems we saw
 fewer families present in the field interior as compared to field
 borders. In this first study to characterize Southern parasitoid
 communities in blueberry production systems, we observed over 50 genera of
 parasitoids, with a few dominant families (Braconidae and Ichneumonidae)
 that would contribute to biological control in blueberry systems. Overall,
 we captured few parasitoids, which indicates potential vulnerability in
 biological control, and the need for further research using other sampling
 techniques to better understand these parasitoid communities. 
description: Data collected from commerical blueberry fields using suction
 sampling. Parsitoids collected were identified using COI molecular
 barcoding. All samples with high quality paired-end reads forming contigs
 were loaded to GenBank.
description: See manuscript in the Journal of Economic Entomology.
 Important columns in dataset: GenBank
 Accession #: sequence archiving
DOI: 10.5061/dryad.ns1rn8psn
title: Impacts of beekeeping on wild bee diversity and pollination networks in the Aegean Archipelago

description: Maintaining the diversity of wild bees is a priority for preserving
 ecosystem function and promoting stability and productivity of
 agroecosystems. However, wild bee communities face many threats and
 beekeeping could be one of them, because honey bees may have a strong
 potential to outcompete wild pollinators when placed at high densities.
 Yet, we still know little about how beekeeping intensity affects wild bee
 diversity and their pollinator interactions. Here, we explore how honey
 bee density relates to wild bee diversity and the structure of their
 pollination networks in 41 sites on 13 Cycladic Islands (Greece) with
 similar landscapes but differing in beekeeping intensity. Our large-scale
 study shows that increasing honey bee visitation rate had a negative
 effect on wild bee species richness and abundance, although the latter
 effect was relatively weak compared to the effect of other landscape
 variables. Competition for flowering resources (as indicated by a resource
 sharing index) increased with the abundance of honey bees, but the effect
 was more moderate for wild bees in family Apidae than for bees in other
 families, suggesting a stronger niche segregation in Apidae in response to
 honey bees. Honey bees also influenced the structure of wild bee
 pollination networks indirectly, through changes in wild bee richness. Low
 richness of wild bees in sites with high honey bee abundance resulted in
 wild bee networks with fewer links and lower linkage density. Our results
 warn against beekeeping intensification in these islands and similar
 hotspots of bee diversity, and shed light on how benefits to pollination
 services of introducing honey bees may be counterbalanced by detriments to
 wild bees and their ecosystem services.
DOI: 10.5061/dryad.pzgmsbcm1
title: Interactions between local and global drivers determine long-term trends in boreal forest understory vegetation

description: Aim: Global change effects on forest ecosystems are increasingly claimed
 to be context dependent, indicated by interactions between global and
 local environmental drivers. Most examples of such context dependencies
 originate from temperate systems, while limited research comes from the
 boreal biome. Here we set out to test if interactions between climate
 warming, nitrogen deposition, land-use change resulting in increasing
 forest density and soil pH drive long-term changes of understory
 vegetation in boreal forests. Location: Sweden Time period: 1953-2012
 Major taxa studied: Vascular plants Methods: We used long-term (50 years)
 National Forest Inventory data on forest understory vegetation in Sweden
 to model the combined effects of climate warming, nitrogen deposition,
 increase in forest density (tree basal area) and soil pH. Results: Our
 results identify increasing temperature, nitrogen deposition and denser,
 shadier forest conditions as main drivers of understory vegetation changes
 during this time period. More importantly, we found that these effects
 varied with local conditions, i.e. that the change towards a more
 nitrophilic understory vegetation was more pronounced at low than high
 soil pH. Forest density was an important modulator of nitrogen deposition
 and temperature increase, with effects generally decreasing with density.
 Decreased cover of ericaceous dwarf shrubs was driven by both forest
 density and nitrogen deposition, with a stronger effect at low than at
 high pH. Main conclusions: Our results highlight that to understand forest
 ecosystems´ response to global change, and to make adequate management
 decisions to mitigate the effects of global change, we need to understand
 how changes in local environmental factors (forest density and soil pH)
 interact with global-scale drivers (nitrogen deposition and climate
 warming). Neglecting such interactions will lead to incorrect estimations
 of effects. In our case, we would e.g. have underestimated the
 eutrophication effects on acid soils, which constitute a considerable part
 of the boreal biome. --
description: The variables Rich_Forb_increase, Low_Cover_increase,
 Tall_Forb_increase and Low_Forb_increase indicate if a vegetation type has
 increase in a spatial unit (1=increase).
 Dwarf_Shrub_Cover_change indicates the change over time in the
 aggregated cover of dwarf shrubs (0.01=1% cover). The
 basal areas are in m<sup>2</sup> per ha.
 Nitrogen deposition is in mg N per
 m<sup>2</sup>. Temperature change is in
 Celsius degrees. Spatial coordinates are in SWEREF 99
 TM.
DOI: 10.57992/nmrxiv.p160
title: Preliminary Work for: A Straightforward Synthesis of a Diene From a Homoallylic Bromide to Access Cycloadducts to Elucidate Michael Acceptors as Antimicrobial Motifs - Nmr Data

description: Diels-Alder reaction from a methyl enol ether derivative of isopulegone with para-benzoquinone.
DOI: 10.57992/nmrxiv.p160.s1621
title: KVXIII-078B_DMP_isopulegone_11_13_23_FULL

description: This dataset contains NMR spectra obtained for the sample -KVXIII-078B_DMP_isopulegone_11_13_23_FULL Nucleus: 1H NMR Solvent: CDCl3 NMR Probe: Z149001_0004 (CPP BBO 500S1 BB-H&F-05 Z) NMR Pulse Sequence: 1d Temperature: 298.1454 Observed Frequency: 500.13 Magnetic Field Strength: 11.746350800110099 Number of Scans: 8 NMR Pulse Sequence: zg30 Spectral Width: 19.9946778845251 Number of Data Points: 32768 Relaxation Delay: 1 Observed Frequency: 500.133088302
DOI: 10.57992/nmrxiv.p160.s1621.d7283
title: KVXIII-078B_DMP_isopulegone_11_13_23_FULL[1]

description: 1
DOI: 10.57992/nmrxiv.p160.s1622
title: KVXIII-082E_MeOMeTPP_isopulegone_11_13_23

description: This dataset contains NMR spectra obtained for the sample -KVXIII-082E_MeOMeTPP_isopulegone_11_13_23 Nucleus: 1H NMR Solvent: CDCl3 NMR Probe: Z149001_0004 (CPP BBO 500S1 BB-H&F-05 Z) NMR Pulse Sequence: 1d Temperature: 298.1452 Observed Frequency: 500.13 Magnetic Field Strength: 11.746350800110099 Number of Scans: 8 NMR Pulse Sequence: zg30 Spectral Width: 19.9946778845251 Number of Data Points: 32768 Relaxation Delay: 1 Observed Frequency: 500.133088302
DOI: 10.5061/dryad.kwh70rz3p
title: Niche differences in co-occurring cryptic coral species (Pocillopora spp.)

description: Cryptic species that are morphologically similar co-occur because either
 the rate of competitive exclusion is very slow, or because they
 are not, in fact, ecologically similar. The processes that
 maintain cryptic local diversity may, therefore, be particularly
 subtle and difficult to identify. Here, we uncover differences
 among several cryptic species in their relative abundance across
 a depth gradient within a dominant and ecologically important
 genus of hard coral, Pocillopora. From extensive sampling unbiased
 towards morphological characters, at multiple depths on the
 forereef around the island of Mo’orea, French Polynesia, we
 genetically identified 673 colonies in the Pocillopora species
 complex. We identified 14 mitochondrial Open Reading
 Frame haplotypes (mtORFs, a well-studied and informative species
 marker used for pocilloporids), which included at least six
 nominal species, and uncovered differences among haplotypes in
 their relative abundance at 5, 10, and 20 m at four sites
 around the island. Differences in relative haplotype abundance
 across depths were greater than differences among sites separated
 by several kilometers. The four most abundant species are often
 visibly indistinguishable at the gross colony level, yet they
 exhibited stark differences in their associations with light
 irradiance and daily water temperature variance. The pattern of
 community composition was associated with frequent cooling in
 deeper versus shallower water more than warmer temperatures in shallow
 water. Our results indicate that these cryptic species are not
 all ecologically similar. The differential abundance of
 Pocillopora cryptic species across depth should promote
 their coexistence at the reef scale, as well as promote
 resilience through response diversity.
DOI: 10.57992/nmrxiv.p160.s1622.d7284
title: KVXIII-082E_MeOMeTPP_isopulegone_11_13_23[1]

description: 1
DOI: 10.57992/nmrxiv.p160.s1623
title: KVXIII-082D_MeOMeTPP_isopulegone_11_13_23

description: This dataset contains NMR spectra obtained for the sample -KVXIII-082D_MeOMeTPP_isopulegone_11_13_23 Nucleus: 1H NMR Solvent: CDCl3 NMR Probe: Z149001_0004 (CPP BBO 500S1 BB-H&F-05 Z) NMR Pulse Sequence: 1d Temperature: 298.1487 Observed Frequency: 500.13 Magnetic Field Strength: 11.746350800110099 Number of Scans: 8 NMR Pulse Sequence: zg30 Spectral Width: 19.9946778845251 Number of Data Points: 32768 Relaxation Delay: 1 Observed Frequency: 500.133088302
DOI: 10.57992/nmrxiv.p160.s1623.d7285
title: KVXIII-082D_MeOMeTPP_isopulegone_11_13_23[1]

description: 1
DOI: 10.57992/nmrxiv.p160.s1624
title: KVXIII-083B_DMP_methylenolether_11_14_23_H_and_C

description: This dataset contains NMR spectra obtained for the sample -KVXIII-083B_DMP_methylenolether_11_14_23_H_and_C Nucleus: 1H NMR Solvent: CDCl3 NMR Probe: Z149001_0004 (CPP BBO 500S1 BB-H&F-05 Z) NMR Pulse Sequence: 1d Temperature: 298.1494 Observed Frequency: 500.13 Magnetic Field Strength: 11.746350800110099 Number of Scans: 8 NMR Pulse Sequence: zg30 Spectral Width: 19.9946778845251 Number of Data Points: 32768 Relaxation Delay: 1 Observed Frequency: 500.133088302 Nucleus: 13C NMR Solvent: CDCl3 NMR Probe: Z149001_0004 (CPP BBO 500S1 BB-H&F-05 Z) NMR Pulse Sequence: 1d Temperature: 298.1479 Observed Frequency: 125.757788526 Magnetic Field Strength: 11.744561760260211 Number of Scans: 64 NMR Pulse Sequence: udeft Spectral Width: 236.636865340793 Number of Data Points: 21424 Relaxation Delay: 4 Observed Frequency: 125.770364305
DOI: 10.57992/nmrxiv.p160.s1624.d7286
title: KVXIII-083B_DMP_methylenolether_11_14_23_H_and_C[1]

description: 1
DOI: 10.57992/nmrxiv.p160.s1624.d7287
title: KVXIII-083B_DMP_methylenolether_11_14_23_H_and_C[2]

description: 2
DOI: 10.57992/nmrxiv.p160.s1625.d7288
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[1]

description: 1
DOI: 10.57992/nmrxiv.p160.s1625.d7289
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[2]

description: 2
DOI: 10.57992/nmrxiv.p160.s1625.d7290
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[3]

description: 3
DOI: 10.57992/nmrxiv.p160.s1625.d7291
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[4]

description: 4
DOI: 10.57992/nmrxiv.p160.s1625.d7292
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[5]

description: 5
DOI: 10.57992/nmrxiv.p160.s1625.d7293
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[6]

description: 6
DOI: 10.57992/nmrxiv.p160.s1625.d7294
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[7]

description: 7
DOI: 10.57992/nmrxiv.p160.s1625.d7295
title: KVXIII-093D_Pd_BQ_methylenolether_DA_11_17_2023_FULL[8]

description: 8
DOI: 10.5061/dryad.q573n5thx
title: Managed logging negatively affects the density and abundance of some dry forest specialist bird species of northeastern Brazil

description: The Caatinga, the largest region of seasonally dry tropical forest in the
 Neotropics, suffers high rates of deforestation and habitat degradation,
 mostly due to wood extraction. As an alternative to illegal logging,
 governments have looked at more sustainable management schemes, allowing
 natural regeneration after logging through relatively long (~ 25-yr)
 harvest rotations. We investigated the impacts of forest management at a
 1,700-ha privately-owned area located at the Araripe Plateau, in the
 semi-arid interior of northeastern Brazil, focusing on the population
 parameters of eight avian species. The property was subdivided into 22
 forest stands, where a different stand has been logged every year since
 2004. By 2016, when we sampled the avifauna, 12 forest stands had already
 been logged and allowed to regrow, creating a landscape of logged and
 unlogged stands and a 12-yr forest recovery chrono-sequence. We conducted
 distance-based sampling along transects to estimate the density and
 abundance of these species in logged and unlogged stands. We found that
 logging impacted three of the target species. Two of them (Megaxenops
 parnaguae and Synallaxis scutata) were less abundant,
 whereas another (Sclerurus cearensis) disappeared altogether from logged
 areas. We also found a positive correlation between the NDVI and avian
 density of the affected species. However, we failed to observe any
 significant relationship between forest recovery or NDVI and species
 densities, suggesting that even after 12-yr of forest recovery, species
 abundance remains lower in logged than in unlogged areas. We found that
 logging impacted birds in a species-specific manner, with five species
 unaffected and three species declining. Although our sampling occurred
 halfway through the regeneration cycle, we found no evidence of recovery
 for those species most affected. We suggest keeping unlogged areas
 intermingled with logged stands, allowing the survival and potential
 recovery of species in regenerating forests.   
  
description: These data were collected
 from acoustic bird census using the distance sampling method. This method
 was applied to 11 trails that divide a dry forest area in the Brazilian
 Caatinga under a forest management regime. In the field, bird individuals
 were monitored across the transects and the following data were collected:
 species, type of detection, distance and angle of the transect, the total
 length of the transect, the numbers of the forest stands on each side of
 the transect, the logging status of each forest stand and the extent of
 the logged and unlogged area for forest management. All data were obtained
 in both the wet and dry seasons of 2016.
description: Readme file is included with the dataset.
DOI: 10.5061/dryad.b8gtht7cj
title: Coordinates for traces of predation in Meoma tests from San Salvador Island

description: Here, we examine interactions between the spatangoid echinoid Meoma
 ventricosa and the drilling predatory gastropod Cassis tuberosa from a
 shallow tropical marine habitat (San Salvador Island, Bahamas) to assess
 the impact of drilling predation on the fossilization potential of
 echinoids, estimate drilling frequency, characterize drill hole
 morphology, and evaluate size and site selectivity of predators. Cassid
 gastropods commonly attack sea urchins today, creating a distinct circular
 hole in the urchin exoskeleton using the radula, often in conjunction with
 the application of acid secreted by the accessory boring organ to weaken
 the test, which can result in a serrated hole. In some cases, radula
 rasping traces were also present around the hole. Data include size
 measurements of M. ventricosa tests and drill holes on the test made by C.
 tuberosa. In addition, two-dimensional landmark co-ordinates are provided
 to determine the location of the drill hole on the test.
description: When using these data please cite Tyler, C.L.,<b>
 </b>Dexter, T.A., Portell, R.W., Kowalewski, M., 2018.
 Predation-Facilitated Preservation of Echinoids in a Tropical Marine
 Environment. <i>PALAIOS</i>
 <i>33(10):478-486.</i><b> </b>https://doi.org/10.2110/palo.2018.046
DOI: 10.5061/dryad.wstqjq2m5
title: Data from: Contrasting effects of land cover on nesting habitat use and reproductive output for bumble bees

description: Understanding habitat quality is central to understanding the
 distributions of species on the landscape, as well as to conserving and
 restoring at-risk species. Although it is well-known that many species
 require different resources throughout their life cycles, pollinator
 conservation efforts focus almost exclusively on forage resources. In this
 study, we evaluate nesting habitat for bumble bees by locating nests
 directly on the landscape. We compared colony density and colony
 reproductive output for Bombus impatiens, the common eastern bumble bee,
 across three different land cover types (hay fields, meadows, and
 forests). We also assessed nesting habitat associations for all Bombus
 nests located during surveys to tease apart species-specific patterns of
 habitat use. We found that B. impatiens nested under the ground in two
 natural land cover types, forests and meadows, but found no B. impatiens
 nests in hay fields. Though B. impatiens nested at similar densities in
 both meadows and forests, colonies in forests had much higher reproductive
 output. In contrast, B. griseocollis tended to nest on the
 surface of the ground and was almost always found in meadows. B. perplexis
 was the only species to nest in all three habitat types, including hay
 fields. For some bumble bee species in this system, meadows, the habitat
 type with abundant forage resources, may be sufficient to maintain them
 throughout their life cycles. However, B. impatiens might benefit from
 heterogeneous landscapes with forests and meadows. Results for B.
 impatiens emphasize the longstanding notion that habitat use is not always
 positively correlated with habitat quality (as measured by reproductive
 output). Our results also show that habitat selection by bumble bees at
 one spatial scale may be influenced by resources at other scales. Finally,
 we demonstrate the feasibility of direct nest searches for understanding
 bumble bee distribution and ecology.
description: This publication contains
 data and R code to perform the analyses described in the main text of this
 manuscript, and analyses described in Appendix S1 and Appendix S3. Please
 see the main text of the manuscript and the attached ReadMe file for
 further detail.
DOI: 10.5061/dryad.ns1rn8psq
title: Quaternary equatorial Atlantic deep-sea ostracodes: evidence for a distinct tropical fauna in the deep sea

description: Low latitude, deep-sea faunas remain poorly understood and described. Here
 we systematically describe Quaternary deep-sea ostracodes from the Ocean
 Drilling Program (ODP) Site 925 (Ceara Rise; 4°12.2'N,
 43°29.3'W; 3040 m water depth) in the equatorial Atlantic Ocean.
 Twenty-six genera and 52 species were examined and illustrated with
 high-resolution scanning electron microscopy images. Six new species are
 described herein: Pseudocythere spinae, Hemiparacytheridea zarikiani,
 Pedicythere canis, Xylocythere denticulata, Paracytherois obtusa, and
 Poseidonamicus sculptus. The results show that deep-sea ostracodes have a
 tropical faunal element that is distinctive from higher latitude
 ostracodes, and that is globally distributed in low latitudes. This
 tropical faunal component is possibly a Tethyan legacy of a fauna that was
 widely distributed in tropical and extratropical latitudes in deep waters
 during greenhouse conditions in the Cretaceous and early Cenozoic. Global
 cooling thereafter shrank its distribution, limiting it to tropical
 latitudes, perhaps with the relatively warm uppermost bathyal area acting
 as the source or refuge of this faunal component. Since similar
 present-day biogeographic patterns (i.e., presence and wide distribution
 of tropical deep-sea fauna) are known in other deep-sea benthic groups,
 this scenario might be applicable to the deep-sea benthos more broadly.
description: High-resolution figures of ostracod SEM images (Figs 2–13,
 15–17)