cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4qrfj6q8h
title: Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species

description: Polyploidization is pervasive in plants, but little is known about the
 niche divergence of wild allopolyploids (species that harbor polyploid
 genomes originating from different diploid species) relative to their
 diploid progenitor species and the gene expression patterns that may
 underlie such ecological divergence. We conducted a fine-scale empirical
 study on habitat and gene expression of an allopolyploid and its diploid
 progenitors.  We quantified soil properties and light
 availability of habitats of an allotetraploid Cardamine flexuosa and its
 diploid progenitors C. amara and C. hirsuta in two seasons. We analyzed
 expression patterns of genes and homeologs (homeologous gene copies in
 allopolyploids) using RNA-seq. We detected niche divergence between the
 allopolyploid and its diploid progenitors along water availability
 gradient at a fine scale: the diploids in opposite extremes and the
 allopolyploid in a broader range between diploids, with limited overlap
 with diploids at both ends. Most of the genes whose homeolog expression
 ratio changed among habitats in C. flexuosa varied spatially and
 temporally.  These findings provide empirical evidence for niche
 divergence between an allopolyploid and its diploid progenitor species at
 a fine scale and suggest that divergent expression patterns of homeologs
 in an allopolyploid may underlie its persistence in diverse habitats.
description: The data was collected
 manually at study sites (Figure 1) and used for principal component
 analysis (Figure 2), logistic regressions (Table 1), and plotting (Figures
 3, S2, and S4).
description: Data on soil properties and light availability of Cardamine sites
 in Switzerland analysed in the study. README sheet explains the structure
 of the data in Dryad_Cardamine_habitat_data.xlsx
DOI: 10.5061/dryad.rbnzs7h9m
title: Whole feeding apparatus 3D landmarks

description: The kinetic skull is a key innovation that allowed snakes to capture,
 manipulate, and swallow prey exclusively using their heads using the
 coordinated movement of 8 bones. Despite these unique feeding behaviors,
 patterns of evolutionary integration and modularity within the feeding
 bones of snakes in a phylogenetic framework have yet to be addressed.
 Here, we use a dataset of 60 µCT scanned skulls and high-density geometric
 morphometric methods to address the origin and patterns of variation and
 integration in the feeding bones of aquatic-foraging snakes. By comparing
 alternate superimposition protocols allowing us to analyze the entire
 kinetic feeding system simultaneously, we find that the feeding bones are
 highly integrated, driven predominantly by functional selective pressures.
 The most supported pattern of modularity contains four modules, each
 associated with distinct functional roles: the mandible, the
 palatopterygoid arch, the maxilla, and the suspensorium. Further, the
 morphological disparity of each bone is not linked to its magnitude of
 integration, indicating that integration within the feeding system does
 not strongly constrain morphological evolution, and that adequate
 biomechanical solutions to a wide range of feeding ecologies and behaviors
 are readily evolvable within the constraint due to integration in the
 snake feeding system.
description: For each bone, anatomical and curve landmarks were placed by hand
 on each model. Surface semi-landmarks were placed on a template bone and
 then projected and slided onto the other specimens. After sliding,
 specimens from the same species were averaged to obtain 1 set of bones per
 species. The attached file is a TPS file of the mean shapes per species of
 all the bones (i.e. 8 bones for 1 species). 36 species of snakes are
 included in this dataset. Landmarks number for each
 bone:   dentary = 1:180  <br>   compound
 =181:368<br>   quadrate = 369:638<br>   supratemporal
 = 639:731<br>   pterygoid = 732:885<br>   ectopterygoid
 = 886:996<br>   palatine = 997:1108<br>   maxilla
 = 1109:1335
DOI: 10.5061/dryad.n2z34tmvj
title: Data from: Can variation in seed removal patterns of Neotropical pioneer tree species be explained by local ant community composition?

description: Many plants depend on animals for seed dispersal, and ants commonly fill
 this role. We examined if heterogeneity in ant community composition among
 sites, between above- and below-ground foraging guilds, or between seasons
 predicts observed variation in seed removal rates for 12 nonmyrmecochorous
 Neotropical pioneer tree species on Barro Colorado Island, Panama. We also
 investigated if ants associated with removing seeds differed in specific
 morphological characters from the larger ant community. We observed
 ant-seed interactions at caches to determine which ants removed seeds of
 12 tree species. We also sampled ant community composition by placing 315
 pitfall traps and 160 subterranean traps across the five sites where seed
 removal rates were quantified. Above-ground ant community composition
 varied by site but not season. Among-site variation in ant composition did
 not predict seed removal patterns at these same sites. Below-ground ant
 communities differed from above-ground ant communities but were not
 structured by either site or seed cache type. Finally, ants that removed
 seeds did not differ morphologically from the broader ant community.
 Overall, our results suggest ant communities vary over relatively small
 spatial scales but exhibit a high degree of functional redundancy in terms
 of seed removal services provided for Neotropical pioneer tree species.
description: The data was collected at five sites on Barro Colorado Island, in
 the Republic of Panama. Data on seed removal for 12 Neotropical pioneer
 tree species and the ants observed removing those seeds were collected
 once during the dry season and once during the wet season of 2013. These
 data were collected by observing seed caches consisting of 10 seeds placed
 within the lid of a petri dish on the forest floor over 47 hours. Data on
 seed removal for 6 Neotropical pioneer tree species and the associated
 ants were collected once in the wet season of 2013. These data were
 collected by placing seed caches of 10 seeds within the topsoil and
 pairing these with associated subterranean traps to catch ants. Data on
 the above-ground ant community was captured using pitfall traps placed
 during the wet season of 2013 and the dry season of 2014.
description: To access the R project associated with this data deposition
 please
 see https://github.com/sruzi24/Ruzi_etal_seed_removal_and_ant_communities.
DOI: 10.5061/dryad.h70rxwdh0
title: Ancestral genetic variation in phenotypic plasticity underlies rapid evolutionary changes in resurrected populations of waterfleas

description: The role that phenotypic plasticity plays in adaptive evolution has been
 debated for decades. This is because the strength of natural selection is
 dependent upon the direction and magnitude of phenotypic responses to
 environmental signals. Therefore, the connection between plasticity and
 adaptation will depend on the patterns of plasticity harbored by ancestral
 populations prior to a change in the environment. Yet, few studies have
 directly assessed ancestral variation in plasticity and tracked phenotypic
 changes over time. Here we resurrected historic propagules of Daphnia
 spanning multiple species and lakes in Wisconsin following the invasion
 and proliferation of a novel predator (spiny waterflea, Bythotrephes
 longimanus). This approach revealed extensive genetic variation in
 predator-induced plasticity in ancestral populations of Daphnia. It is
 unlikely that the standing patterns of plasticity shielded Daphnia from
 selection to permit long-term coexistence with a novel predator. Instead,
 this variation in plasticity provided the raw materials for
 Bythotrephes-mediated selection to drive rapid shifts in Daphnia behavior
 and life history. Surprisingly, there was little evidence for the
 evolution of trait plasticity as genetic variation in plasticity was
 maintained in the face of a novel predator. Such results provide new
 insights into the link between plasticity and adaptation and highlight the
 importance of quantifying genetic variation in plasticity when evaluating
 the drivers of evolutionary change in the wild.
DOI: 10.5061/dryad.h70rxwdh1
title: The impact of urbanization on body size of Barn Swallows Hirundo rustica gutturalis

description: Urbanization implies a dramatic impact on ecosystems, which may lead to
 drastic phenotypic differences between urban and non-urban individuals.
 For instance, urbanization is associated with increased metabolic costs,
 which may constrain body size, but urbanization also leads to habitat
 fragmentation, which may favour increases in body mass when for
 instance it correlates with dispersal capacity. However, this
 apparent contradiction has rarely been studied. This is particularly
 evident in China where the urbanization process is currently occurring at
 an unprecedented scale. Moreover, no study has addressed this issue across
 large geographical areas encompassing locations in different climates. In
 this regard, Barn Swallows (Hirundo rustica) are a suitable model to study
 the impact of urbanization on wild animals because they are a widely
 distributed species tightly associated with humans. Here, we collected
 body mass and wing length data for 359 breeding individuals of Barn
 Swallow (H. r. gutturalis) from 128 sites showing different levels of
 urbanization around the whole China. Using a set of linear mixed-effects
 models, we assessed how urbanization and geography influenced body size
 measured using body mass, wing length and their regression residuals.
 Interestingly, we found that the impact of urbanization was sex-dependent,
 negatively affecting males’ body mass, its regression residuals, and
 females’ wing length. We also found that northern and western individuals
 were larger, regarding both body mass and wing length, than southern and
 eastern individuals. Females were heavier than males, yet males had
 slightly longer wings than females. Overall, our results showed that body
 mass of males was particularly sensitive trait to urbanization, latitude
 and longitude, while it only showed a weak response to latitude in
 females. Conversely, while wing length showed a similar geographical
 pattern, it was only affected by urbanization in the case of females.
 Further research is needed to determine if these phenotypic differences
 are associated with negative effects of urbanization or potential
 selective advantages.
description: See README file.
DOI: 10.5061/dryad.5x69p8d1v
title: Facile fabrication of polymer network using click chemistry and their computational study

description: Click reaction is a very fast, high yield with no byproduct,
 biocompatible, tolerant to surrounded medium, and very specific
 cycloaddition reaction between azides and alkynes to form triazole. They
 are widely being employed in the synthesis of various polymeric materials.
 Here, the design, fabrication, and characterization of hydrogel prepared
 using click reaction have been reported. At first telechelic acetylene
 precursor for click reaction is prepared from diisocyanatohexane and
 propargyl alcohol in the presence of triethylamine. The azide derivatives
 of poly(hydroxyethylmethacrylate), i.e., poly(HEMA), are successfully
 prepared following two different routes.  In route 1,
 esterification of bromopropionic acid is performed with HEMA monomer using
 N, N′-Dicyclohexylcarbodiimide/4-Dimethylaminopyridine (DCC/DMAP) as a
 catalyst followed by replacing bromide by azide moiety. Free radical
 polymerization of the fabricated monomer is then performed under N2
 atmosphere using Azobisisobutyronitrile (AIBN) as an initiator. In route
 2, polymerization of HEMA has been carried out first, then modification of
 the polymer with azide group via successive steps to obtain azide
 derivative polymer for click reaction. The hydrogel is prepared by a very
 fast, highly specific, and simple click reaction between azide derivative
 polymer and telechelic acetylene precursor using copper as a catalyst. The
 structures of derivatives of azide functionalized HEMA, acetylene
 precursors, and hydrogels are confirmed by FTIR and 1H-NMR spectroscopy.
 The optimized structure of each precursor is determined, and their
 chemical and thermodynamic parameters are computationally studied in
 detail.
description: Fourier transform infrared (FT-IR) spectrophotometer (FTIR-8400,
 Shimadzu, Japan) 400 MHz Bruker BPX-400, 1HNMR
 spectrometer Thermogravimetry-Differential Scanning
 Calorimetry (STA/TG-DSC) of STA 449 F3 Jupiter®, NETZSCH-Gerätebau GmbH,
 Germany The VAMP code of Material studio version 8.0
 was employed for optimization and calculation based on DFT
DOI: 10.15468/dl.57nm52
title: Occurrence Download

description: A dataset containing 81 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Copaifera officinalis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 81 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002658-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25338/b8t32q
title: Retention of green leaves not brown leaves increases spring cynipid diversity on large valley oaks

description: Plants can retain either physiologically active green leaves or inactive
 brown leaves over winter. Research has suggested that leaf retention
 incurs a cost due to higher herbivore load in the following year; however,
 no distinction has, thus, far been made between retention of green and
 brown leaves. We surveyed the over-winter retention of physiologically
 active green and inactive brown leaves of valley oaks (Quercus lobata) and
 examined their relationship with the diversity and density of 15
 gall-making cynipid wasp species. Cynipid diversity in the spring was
 8.2-fold greater on larger trees with more green leaf retention. Brown
 leaf retention was not associated with spring cynipid diversity, but was
 related to a substantial 20-fold reduction in spring cynipid densities on
 large trees. Retention of either leaf type was generally a poor predictor
 of summer cynipid diversity and density. Overall, green leaf retention
 better explained cynipid diversity, but brown leaf retention better
 explained cynipid densities. These differing effects may be explained by
 the fact that green leaves provide a common cue used by herbivores to find
 a suitable host. Retained brown leaves, however, may be an ecological trap
 for over-winter gall wasps that normally drop to the ground.
description: See article.
description: See article.
DOI: 10.25338/b8pd2k
title: The consequence of leaf life span to virus infection of herbivorous insects

description: Many herbivorous insects die of pathogen infections, though the role of
 plant traits in promoting the persistence of these pathogens as an
 indirect interaction is poorly understood. We tested whether winter leaf
 retention of bush lupines (Lupinus arboreus) promotes the persistence of
 nucleopolyhedroviruses, thereby increasing the infection risk of
 caterpillars (Arctia virginalis) feeding on the foliage during spring. We
 also investigated whether winter leaf retention reduces viral exposure of
 younger caterpillars that live on the ground, as leaf retention prevents
 contaminated leaves from reaching the ground. We surveyed winter leaf
 retention of 248 lupine bush canopies across twelve sites and examined how
 it related to caterpillar infection risk, herbivory, and inflorescence
 density. We also manipulated the amount of lupine litter available to
 young caterpillars in a feeding experiment to emulate litterfall exposure
 in the field. Greater retention of contaminated leaves from the previous
 season increased infection rates of caterpillars in early spring. Higher
 infection rates reduced herbivory and increased plant inflorescence
 density by summer. Young caterpillars exposed to less litterfall were more
 likely to starve to death but less likely to die from infection, further
 suggesting foliage-mediated exposure to virus. We speculate that longer
 leaf life span may be an unrecognized trait that indirectly mediates
 top-down control of herbivores by facilitating epizootics.
description: See paper.
DOI: 10.5061/dryad.vdncjsxsk
title: Complex sensory environments alter mate choice outcomes

description: Noise is a common problem in animal communication. We know little,
 however, about how animals communicate in noise using multimodal signals.
 Multimodal signals are hypothesized to be favoured by evolution because
 they increase the efficacy of detection/discrimination in noisy
 environments. We tested the hypothesis that female túngara frogs’
 responses to attractive male advertisement calls are improved in noise
 when a visual cue is added. We tested this at two levels of decision
 complexity (two and three choices). In a two-choice test, the
 presence of noise did not reduce female preferences for attractive calls.
 The visual cue of a calling male, associated with an unattractive call,
 also did not reduce preference for attractive calls in the absence of
 noise. In the presence of noise, however, females were more likely to
 choose an unattractive call coupled with the visual cue. In three-choice
 tests, the presence of noise alone reduced female responses to attractive
 calls and this was not strongly affected by the presence or absence of
 visual cues. The responses in these experiments fail to support the
 multimodal signal efficacy hypothesis. Instead, the data suggest that
 audio-visual perception and cognitive processing, related to mate choice
 decisions, are dependent on the complexity of the sensory scene.
DOI: 10.5061/dryad.q2bvq83hp
title: Neurophysiological coordination of duet singing

description: Cooperation is critical for survival and reproduction in many animal
 species. Coordination of behavior for cooperative performances often
 relies on linkages mediated by sensory cues exchanged between
 participants. How neurophysiological responses to sensory information
 affect motor programs to coordinate behavior between individuals is not
 known. We investigated how plain-tailed wrens (Pheugopedius euophrys) use
 acoustic feedback to coordinate extraordinary duet performances in which
 females and males rapidly take turns singing. We made simultaneous
 neurophysiological recordings in a song control area
 'HVC' in pairs of singing wrens at a field site in
 Ecuador. HVC is a premotor area that integrates auditory feedback and is
 necessary for song production. We found that spiking activity of HVC
 neurons in each sex increased for production of its own syllables. As
 acoustic feedback is critical for the coordination of duet performances,
 we expected neurons to respond to singing cues from the partner bird.
 Surprisingly, these `heterogenous' cues resulted in decreases in HVC
 activity during duet singing, potentially coordinating the pattern
 generating circuit in HVC in each bird through inhibition. To examine the
 role of acoustic feedback in the absence of motor activity, we recorded
 responses of HVC neurons to playbacks in anesthetized wrens. Neurons
 showed significant excitatory responses to heterogenous cues within duets.
 These data suggest that HVC integrates information across partners during
 duets, and that rapid turn-taking is mediated, in part, by inhibition from
 heterogenous cues.
description: See README files.
DOI: 10.15468/dl.x342jj
title: Occurrence Download

description: A dataset containing 368 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Dipterocarpus turbinatus"
 ]
}

 The dataset includes 368 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002659-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0gb5mkm04
title: Genome-wide association and genomic prediction for a reproductive index summarizing fertility outcomes in U.S. Holsteins

description: Subfertility represents one major challenge to enhancing dairy production
 and efficiency. Herein, we use a reproductive index (RI) expressing the
 predicted probability of pregnancy following artificial insemination with
 Illumina 778K genotypes to perform single and multi-locus genome-wide
 association analyses (GWAA) on 2,448 geographically diverse U.S. Holstein
 cows and produce genomic heritability estimates. Moreover, we use genomic
 best linear unbiased prediction (GBLUP) to investigate the potential
 utility of the RI by performing genomic predictions with cross-validation.
 Notably, genomic heritability estimates for the U.S. Holstein RI were
 moderate ( 0.1654± 0.0317 – 0.2550 ± 0.0348), while single and multi-locus
 GWAA revealed overlapping quantitative trait loci (QTL) on BTA6 and BTA29,
 including known QTL for daughter pregnancy rate (DPR) and cow conception
 rate (CCR). Multi-locus GWAA revealed seven additional QTL, including one
 on BTA7 (60 Mb) which is adjacent to a known heifer conception rate (HCR)
 QTL (59 Mb). Positional candidate genes for the detected QTL included male
 and female fertility loci (i.e., spermatogenesis, oogenesis), meiotic and
 mitotic regulators, and genes associated with immune response, milk yield,
 enhanced pregnancy rates, and the reproductive-longevity pathway.
  Based on the proportion of phenotypic variance explained (PVE),
 all detected QTL (n = 13; P ≤ 5e-05) were estimated to have moderate (1.0%
 &lt; PVE ≤ 2.0%) or small effects (PVE ≤ 1.0%) on the predicted
 probability of pregnancy.  Genomic prediction using GBLUP with
 cross-validation (k = 3) produced mean predictive abilities
 (0.1692–0.2301) and mean genomic prediction accuracies (0.4119–0.4557)
 that were similar to bovine health and production traits previously
 investigated.
description: Summary data from single-locus and multi-locus genome wide
 association analyses are summarized in Additional File 1 and Additional
 File 2, respectively. Summary data from GBLUP-based
 genomic predictions with k-fold cross-validation are summarized in
 Additional File 3.  Summary statistics for milk yield (up to 90 days of
 lactation, MAVG90kg) in high-fertility and low-fertility individuals are
 described in Additional File 4.
description: The files are annotated in detail and self-explanatory when
 evaluated within the context of the manuscript.  See the ReadMe.
DOI: 10.5061/dryad.0vt4b8gx9
title: Extreme rainfall events and cooling of sea turtle clutches: implications in the face of climate warming

description: Understanding how climate change impacts species and ecosystems is
 integral to conservation. When studying impacts of climate change, warming
 temperatures are a research focus, with much less attention given to
 extreme weather events and their impacts. Here we show how localized,
 extreme rainfall events can have a major impact on a species that is
 endangered in many parts of its range. We report incubation temperatures
 from the world’s largest green sea turtle rookery, during a breeding
 season when two extreme rainfall events occurred. Rainfall caused nest
 temperatures to drop suddenly and the maximum drop in temperature for each
 rain-induced cooling averaged 3.6°C (n = 79 nests, min = 1.0°C, max =
 7.4°C). Since green sea turtles have temperature-dependent sex
 determination, with low incubation temperatures producing males, such
 major rainfall events may have a masculinization effect on primary sex
 ratios. Therefore, in some cases, extreme rainfall events may provide a
 “get-out-of-jail-free card” to avoid complete feminization of turtle
 populations as climate warming continues.