cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6t1g1jww0
title: Phylogenomics of piranhas and pacus (Serrasalmidae) uncovers how dietary convergence and parallelism obfuscate traditional morphological taxonomy

description: The Amazon and neighboring South American river basins harbor the world’s
 most diverse assemblages of freshwater fishes. One of the most prominent
 South American fish families is the Serrasalmidae (pacus and piranhas),
 found in nearly every continental basin. Serrasalmids are keystone
 ecological taxa, being some of the top riverine predators as well as the
 primary seed dispersers in the flooded forest. Despite their widespread
 occurrence and notable ecologies, serrasalmid evolutionary history and
 systematics are controversial. For example, the sister taxon to
 serrasalmids is contentious, the relationships of major clades within the
 family are inconsistent across different methodologies, and half of the
 extant serrasalmid genera are suggested to be non-monophyletic. We
 analyzed exon capture to reexamine the evolutionary relationships among 63
 (of 99) species across all 16 serrasalmid genera and their nearest
 outgroups, including multiple individuals per species to account for
 cryptic lineages. To reconstruct the timeline of serrasalmid
 diversification, we time-calibrated this phylogeny using two different
 fossil-calibration schemes to account for uncertainty in taxonomy with
 respect to fossil teeth. Finally, we analyzed diet evolution across the
 family and comment on associated changes in dentition, highlighting the
 ecomorphological diversity within serrasalmids. We document widespread
 non-monophyly of genera within Myleinae, as well as
 between Serrasalmus and Pristobrycon, and
 propose that reliance on traits like teeth to distinguish among genera is
 confounded by ecological homoplasy, especially among herbivorous and
 omnivorous taxa. We clarify the relationships among all serrasalmid
 genera, propose new subfamily affiliations, and support hemiodontids as
 the sister taxon to Serrasalmidae.
description: These data comprise the Supplemental Files for submission to
 Systematic Biology S1 - Previous phylogenetic
 hypotheses for the relationships of Serrasalmidae. S2 -
 Description of the fossil calibration schemes and rationale for assignment
 of those fossils to nodes. S3 - References for
 S2. S4 - Diet classification of extant serrasalmids
 based on literature review. S5 - References for
 S4. S6 - Stochastic Character mapping transition matrix
 for diet states. S7 - Taxonomic recommendations for
 Serrasalmidae: new subfamilies and paraphyly of most extant
 genera.
description: Dryad tree files.zip includes: ASTRAL
 coalescent tree Nucleotide & amino acid
 concatenated trees & matrices Scheme 1
 & Scheme 2 time-calibrated trees (generated from BEAST2)
DOI: 10.5061/dryad.ffbg79cr5
title: Data from: Salinity stress increases the severity of ranavirus epidemics in amphibian populations

description: The stress-induced susceptibility hypothesis, which predicts chronic
 stress weakens immune defenses, was proposed to explain increasing
 infectious disease-related mass mortality and population declines.
 Previous work characterized wetland salinization as a chronic stressor to
 larval amphibian populations. Thus, we combined field observations with
 experimental exposures quantifying epidemiological parameters to test the
 role of salinity stress in the occurrence of ranavirus-associated mass
 mortality events. Despite ubiquitous pathogen presence (94%), populations
 exposed to salt runoff had slightly more frequent ranavirus related mass
 mortality events, more lethal infections, and 117-times greater pathogen
 environmental DNA. Experimental exposure to chronic elevated salinity
 (0.8-1.6 g/L Cl-) reduced tolerance to infection, causing greater
 mortality at lower doses. We found a strong negative relationship between
 splenocyte proliferation and corticosterone in ranavirus-infected larvae
 at a moderate elevation of salinity, supporting glucocorticoid-medicated
 immunosuppression, but not at high salinity. Salinity alone reduced
 proliferation further at similar corticosterone levels and infection
 intensities. Finally, larvae raised in elevated salinity had 10-times more
 intense infections and shed 5-times as much virus with similar viral decay
 rates, suggesting increased transmission. Our findings illustrate how a
 small change in habitat quality leads to more lethal infections and
 potentially greater transmission efficiency, increasing the severity of
 ranavirus epidemics.
DOI: 10.5061/dryad.2rbnzs7jp
title: A catastrophic tropical drought kills hydraulically vulnerable tree species

description: Drought-related tree mortality is now a widespread phenomenon predicted to
 increase in magnitude with climate change. However, the patterns of which
 species and trees are most vulnerable to drought, and the underlying
 mechanisms have remained elusive, in part due to the lack of relevant data
 and difficulty of predicting the location of catastrophic drought years in
 advance. We used long‐term demographic records and extensive databases of
 functional traits and distribution patterns to understand the responses of
 20 to 53 species to an extreme drought in a seasonally dry tropical forest
 in Costa Rica, which occurred during the 2015 El Niño Southern Oscillation
 event. Overall, species-specific mortality rates during the drought ranged
 from 0% to 34%, and varied little as a function of tree size. By contrast,
 hydraulic safety margins correlated well with probability of mortality
 among species, while morphological or leaf economics spectrum traits did
 not. This firmly suggests hydraulic traits as targets for future research.
description: The dataset contains annual observations of tree mortality in
 different 18 plots, expanded sampling for mortality during 2015, and
 datasets of plant functional and hydraulic traits.  Please refer to the
 publication for exact methods.  All data come from Guanacaste, Costa
 Rica.
description: All data and associated R scripts are contained in the files. The
 R scripts refer to the three main questions asked in the associated
 publication.
DOI: 10.6078/d1z41q
title: Coalescent-based species delimitation is sensitive to geographic sampling and isolation by distance

description: Species are a fundamental unit of biodiversity that are delimited via
 genetic data and coalescent-based methods with increasing frequency.
 Despite the widespread use of coalescent-based species delimitation, we do
 not fully understand the sensitivity of these methods to potential sources
 of bias and violations of their underlying assumptions. One implicit
 assumption of coalescent-based species delimitation is that geographic
 sampling is adequate and representative of genetic variation among
 populations within the lineage of interest. Yet exhaustive geographic
 sampling is logistically difficult, if not impossible, for many taxa that
 span large geographic expanses or occupy remote regions. Here, we examine
 the impact of geographic sampling on the output of Bayes-factor
 delimitation with SNAPP, a popular coalescent-based species delimitation
 pipeline. First, we demonstrate the problematic nature of sparse
 geographic sampling and isolation by distance for species delimitation
 using simulated data sets of populations connected by different levels of
 gene flow. We then examine whether similar trends are present in an
 empirical dataset of Andesiops mayflies (Ephemeroptera: Baetidae) from a
 high elevation transect in the Ecuadorian Andes. In both the simulated and
 empirical analyses, we systematically exclude geographically intermediate
 sites to quantify the impact of geographic sampling and isolation by
 distance on coalescent-based species delimitation. We find that removing
 intermediate sites with genetically admixed individuals incorrectly favors
 multi-species delimitation scenarios. Oversplitting is especially
 pronounced when isolation by distance is strong, but exists even when gene
 flow among neighboring populations is relatively high. These findings
 highlight the importance of adequate geographic sampling in species
 delimitation and urge caution in interpreting the output of such methods
 when species’ distributions are sparsely sampled and in systems
 characterized by strong patterns of isolation by distance.
description: This data set is a combination of empirical and simulated data.
 As described in the methods section, the empirical data is from a genus of
 Mayflies, <em>Andesiops</em>, that are distributed along a
 high-elevation drainage in the Andes of Ecuador. The data come from a
 ddRAD experiment, while loci were assembled with Stacks. The simulated
 data set were generated with the program msLandscape.
DOI: 10.5061/dryad.qnk98sfcj
title: Rapid adaptation (or not) in restored plant populations

description: Mismatches between the traits of a colonizing population and a novel
 habitat can generate strong selection, potentially resulting in rapid
 adaptation. However, for most colonization events, it can be difficult to
 detect rapid adaptation or distinguish it from non-adaptive evolutionary
 changes. Here I take advantage of a replicated prairie restoration
 experiment to compare recently established plant populations in two
 closely-located restored prairies to each other and to their shared source
 population to test for rapid adaptation. Using a reciprocal transplant
 experiment six years after the populations were established, I found that
 one restored plant population showed evidence of adaptation, outperforming
 the other restored population when grown at its home site. In contrast, I
 detected no evidence for adaptation at the other site. These findings
 demonstrate that while rapid adaptation can occur in colonizing plant
 populations, it may not be the rule. Better understanding of when
 adaptation may or may not occur in these contexts may help us use
 evolution to our advantage, potentially improving establishment of
 desirable species in restored habitats.
DOI: 10.5061/dryad.hdr7sqvdz
title: A survey of small-scale waves and wave-like phenomena in Jupiter's atmosphere detected by JunoCam

description: In the first 20 orbits of the Juno spacecraft around Jupiter, we have
 identified a variety of wave-like features in images made by its
 public-outreach camera, JunoCam.  Because of Juno’s unprecedented
 and repeated proximity to Jupiter’s cloud tops during its close
 approaches, JunoCam has detected more wave structures than any previous
 surveys.  Most of the waves appear in long wave packets, oriented
 east-west and populated by narrow wave crests.  Spacing between
 crests were measured as small as ~30 km, shorter than any previously
 measured.  Some waves are associated with atmospheric features,
 but others are not ostensibly associated with any visible cloud phenomena
 and thus may be generated by dynamical forcing below the visible cloud
 tops.    Some waves also appear to be
 converging and others appear to be overlapping, possibly at different
 atmospheric levels.  Another type of wave has a series of fronts
 that appear to be radiating outward from the center of a
 cyclone.  Most of these waves appear within 5° of latitude from
 the equator, but we have detected waves covering planetocentric latitudes
 between 20°S and 45°N.   The great majority of the waves
 appear in regions associated with prograde motions of the mean zonal
 flow.   Juno was unable to measure the velocity of wave
 features to diagnose the wave types due to its close and rapid
 flybys.  However, both by our own upper limits on wave motions
 and by analogy with previous measurements, we expect that the waves
 JunoCam detected near the equator are inertia-gravity waves.
description: These are measurements of physical properites of waves and
 wave-like features in Jupiter's atmosphere measured from cylindrical
 projections of JunoCam imaging in close approaches to Jupiter by the Juno
 spacecraft. 
description: The measurments are limited to Jupiter orbits from 1 through 20,
 a period covering 2016 August 27 through 2019 May 29.  They correspond to
 values plotted in Figures 16 and 17 of the main article, and Figures SI3-2
 and SI3-3 of the Supplemental Information associated with this article.  
 The table replicates the values shown in the Table of the Supplemental
 Information file. The term ‘wavelength’ in column 8
 refers to the distance between wave crests or discrete clouds. The tilt
 angle in column 9 is defined as 0º at the eastward direction of the wave
 packet to 180º in the westward direction of the wave packet.  Thus, wave
 crests oriented more-or-less orthogonally to the direction of the wave
 packet, such as those shown in Figure 2 of the main article, have tilt
 angles close to 90º.
DOI: 10.15468/dl.jfuvhj
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Grahamichthys radiata",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 31 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002253-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zgmsbcc7d
title: Combined cues of male competition influence spermatozoal investment in a moth

description: Male animals usually raise their sperm allocation after detecting sperm
 competition risk. To date, only a few studies have investigated the cues
 used by males to sense and respond to rivals. Yet, it is still largely
 unknown whether males respond to single or combined cues and whether they
 can increase their lifetime spermatozoal investment after a perception of
 rival cue(s). Here we postulate that males increase ejaculation and
 production of sperm after detecting combined cues from rivals, but such
 response quickly diminishes after the cues are removed. We exposed newly
 emerged and virgin focal males of the moth Ephestia kuehniella to various
 rival cues and then permanently removed the cues. We introduced a virgin
 female to an exposed focal male and an unexposed focal male, respectively,
 per day and counted the number of sperm transferred by the focal males in
 each mating and recovered in their body after death. We demonstrate that
 males significantly increased their lifetime sperm allocation and
 production after premating detection of either single (acoustic or
 chemical) or combined cues (acoustic + chemical, or acoustic + chemical +
 tactile) from their rivals with combined cues (acoustic + chemical +
 tactile) somewhat strengthening such response in eupyrene production. The
 number of sperm ejaculated by males significantly decreased over
 successive matings in their lifetime regardless of whether they were
 exposed to rival cues, but the decline was significantly faster in
 rival-cue exposed males than in unexposed ones. This suggests that the
 increase of spermatogenesis cannot fully compensate for that of sperm
 expenditure in response to rival cues. We show that 10-h premating rival
 exposure was sufficient to maximise males’ response in sperm ejaculation
 and production. The impact of the rival perception on sperm transfer
 persisted for most of males’ reproductive life, suggesting that the moth
 males have a long-term memory of sperm competition risk experienced in the
 early adulthood.
description: Through experiments. In Excel.
DOI: 10.25338/b86g7t
title: Data from: Forests do not limit bumble bee foraging movements in a montane meadow complex

description: Understanding the roles of habitat fragmentation and resource availability
 in shaping animal movement are integral for promoting species persistence
 and conservation. For insects like bumble bees, their movement patterns
 affect the survival and reproductive potential of their colonies as well
 as the pollen flow of plant species. However, our understanding of their
 mobility or the impact of putative barriers in natural environments is
 limited due to the technical difficulties of studying wild populations. We
 used genetic mark-recapture to estimate the foraging distance, resource
 use, and site connectivity of two bumble bee species in a montane meadow
 complex composed of open meadows within a matrix of forest. There was no
 evidence that forests or changes in landcover function as barriers to
 fine-scale movement for either species. We found substantially greater
 colony-specific foraging distances for Bombus vosnesenskii (maximum: 1867
 m) compared to B. bifarius (maximum: 362 m). Despite this difference in
 absolute range, we detected both species across putative forest barriers
 at frequencies expected by uninhibited movement. Siblings separated by
 greater distances were more likely to be foraging on different floral
 species, potentially suggesting a resource-based motivation for movement.
 These results suggest that bumble bee foraging patterns are influenced by
 species-specific differences in movement capacity, with little influence
 of matrix composition between resource patches. They also support the
 perspective that habitat conservation for bumble bees should prioritize
 providing abundant and diverse patches of resources within
 species-specific movement radii with less emphasis on matrix composition.
description: Genetic data are available as BAM files in the NCBI Short Read
 Archive (accession no. PRJNA610901). Full methods for data collection are
 described in the manuscript. The provided data files were processed using
 COLONYv2.0 and joined with the field collected data.
description: All further code for generation of the manuscript figures and
 results can be found on github at: https://github.com/John-Mola/bb-forage-mvmt-eco-ent
DOI: 10.5061/dryad.05qfttf05
title: Identification and characterization of N9-methyltransferase involved in converting caffeine into non-stimulatory theacrine in tea

description: Caffeine is a major component of xanthine alkaloids and commonly consumed
 in many popular beverages. Due to its occasional side effects, reduction
 of caffeine in a natural way is of great importance and economic
 significance. Recent studies reveal that caffeine can be converted into
 non-stimulatory theacrine in the rare tea plant Camellia assamica var.
 kucha (Kucha), which involves oxidation at the C8 and methylation at the
 N9 positions of caffeine. However, the underlying molecular mechanism
 remains unclear. Here, we identify the theacrine synthase CkTcS from
 Kucha, which possesses novel N9-methyltransferase activity using
 1,3,7-trimethyluric acid but not caffeine as a substrate, confirming that
 C8 oxidation takes place prior to N9-methylation. The crystal structure of
 the CkTcS complex reveals the key residues that are required for the
 N9-methylation, providing insights into how caffeine N-methyltransferases
 in tea plants have evolved to catalyze regioselective N-methylation
 through fine tuning of their active sites. These results may guide the
 future development of decaffeinated drinks.
description: Transcriptome sequencing performed at the Novogene Bioinformatics
 Institute (Novogene, Beijing, China). Briefly, mRNA was purified from the
 total RNA of tea leaves (<em>Camellia assamica var. kucha</em>
 and <em>Camellia sinensis var.assamica</em>) and used to
 construct sequencing libraries using a NEBNext<sup>®</sup>
 Ultra<sup>™</sup> RNA Library Prep Kit for
 Illumina<sup>®</sup> (NEB, USA) according to the
 manufacturer’s recommendations. The index codes were added to attribute
 sequences to each sample. After the qualities of sequencing libraries were
 confirmed on the Agilent Bioanalyzer 2100 system, clustering of the
 index-coded samples was performed on a cBot Cluster Generation System
 using TruSeq PE Cluster Kit v3-cBot-HS (Illumia, San Diego, CA, USA)
 according to the manufacturer’s instructions. The library preparations
 were then sequenced on an Illumina Hiseq 2500 platform (Illumina, San
 Diego, CA, USA) and paired-end reads were generated. Transcriptome
 assembly was accomplished based on the left.fq and right.fq using Trinity
 with min_kmer_cov set to 2 by default and all other parameters set
 default.
DOI: 10.5061/dryad.4f4qrfj86
title: Self-organising cicada choruses respond to the local sound and light environment

description: 1. Periodical cicadas exhibit an extraordinary capacity for
 self-organising spatially synchronous breeding behavior. The regular
 emergence of periodical cicada broods across the US is a phenomenon of
 longstanding public and scientific interest, as the cicadas of each brood
 emerge in huge numbers and briefly dominate their ecosystem. During the
 emergence, the 17-year periodical cicada species Magicicada cassini is
 found to form synchronised choruses, and we investigated their chorusing
 behavior from the standpoint of spatial synchrony. 2. Cicada choruses were
 observed to form in trees, calling regularly every five seconds. In order
 to determine the limits of this self-organising behaviour, we set out to
 quantify the spatial synchronisation between cicada call choruses in
 different trees, and how and why this varies in space and time. 3. We
 performed 20 simultaneous recordings in Clinton State Park, Kansas, in
 June 2015 (Brood IV) with a team of citizen-science volunteers using
 consumer equipment (smartphones). We use a wavelet approach to show in
 detail how spatially synchronous, self-organised chorusing varies across
 the forest. 4. We show how conditions that increase the strength of audio
 interactions between cicadas also increase the spatial synchrony of their
 chorusing. Higher forest canopy light levels increase cicada activity,
 corresponding to faster and higher-amplitude chorus cycling and to greater
 synchrony of cycles across space. We implemented a
 relaxation-oscillator-ensemble model of interacting cicadas, finding that
 a tendency to call more often, driven by light levels, results in all
 these effects. 5. Results demonstrate how the capacity to self-organise in
 ecology depends sensitively on environmental conditions. Spatially
 correlated modulation of cycling rate by an external driver can also
 promote self-organisation of phase synchrony.
description: Data was collected and processed as described in Materials and
 Methods of <em>Self-organising cicada choruses respond to the local
 sound and light environment (2020) Ecology and
 Evolution.</em> Further details are provided in
 the Supplementary Information S2 and S3, and in the supplementary figure
 S26. The 20 cicada sound volume time-series represent
 0.1 second segments of data, aligned and filtered as described (the final
 stage in figure S26, prior to wavelet transformation; step X).
 The normalised (smoothed) forest canopy brightness profile is as
 shown in figure 3c. Latitude and longitude for the 20
 recording locations (derived from multiple GPS devices) are as depicted in
 supplementary figure S22 and elsewhere.
description: Data is presented in csv format, output from MATLAB in Windows
 10.