cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r2280gb8x
title: Dual function of epaxial musculature for swimming and suction feeding in largemouth bass

description: The axial musculature of many fishes generates the power for both swimming
 and suction feeding. In the case of the epaxial musculature, unilateral
 activation bends the body laterally for swimming, and bilateral activation
 bends the body dorsally to elevate the neurocranium for suction feeding.
 But how does a single muscle group effectively power these two distinct
 behaviors? Prior electromyographic (EMG) studies have identified fishes’
 ability to activate dorsal and ventral epaxial regions independently, but
 no studies have directly compared the intensity and spatial activation
 patterns between swimming and feeding. We measured EMG activity throughout
 the epaxial musculature during swimming (turning, sprinting, and
 fast-starts) and suction feeding (goldfish and pellet strikes) in
 largemouth bass (Micropterus salmoides). We found that swimming involved
 obligate activation of ventral epaxial regions whereas suction feeding
 involved obligate activation of dorsal epaxial regions, suggesting
 regional specialization of the epaxial musculature. However, during
 fast-starts and suction feeding on live prey, bass routinely activated the
 whole epaxial musculature, demonstrating the dual function of this
 musculature in the highest performance behaviors. Activation intensities
 in suction feeding were substantially lower than fast-starts which, in
 conjunction with suboptimal shortening velocities, suggests that bass
 maximize axial muscle performance during locomotion and underutilize it
 for suction feeding.
description: These files contain EMG data (normalized peak signal amplitude)
 for locomotion and feeding in three largemouth bass. Peak pressure data
 (in kPa) are also included for suction feeding. Data file names correspond
 to the figure they were used for.
DOI: 10.5061/dryad.wpzgmsbh8
title: Data from: Phenological synchrony shapes pathology in host–parasite systems

description: A key challenge surrounding ongoing climate shifts is to identify how they
 alter species interactions, including those between hosts and parasites.
 Because transmission often occurs during critical time windows, shifts in
 the phenology of either taxa can alter the likelihood of interaction or
 the resulting pathology. We quantified how phenological synchrony between
 vulnerable stages of an amphibian host (Pseudacris regilla) and infection
 by a pathogenic trematode (Ribeiroia ondatrae), determined infection
 prevalence, parasite load, and host pathology. By tracking hosts and
 parasite infection throughout development between low- and high-elevation
 regions (San Francisco Bay Area and the Southern Cascades [Mt. Lassen]),
 we found that when phenological synchrony was high (Bay Area), each
 established parasite incurred a 33% higher probability of causing severe
 limb malformations relative to areas with less synchrony (Mt. Lassen). As
 a result, hosts in the Bay Area had up to a 50% higher risk of pathology
 even while controlling for mean infection load. Our results indicate that
 host-parasite interactions and the resulting pathology were the joint
 product of infection load and phenological synchrony, highlighting the
 sensitivity of disease outcomes to forecasted shifts in climate.
DOI: 10.15468/dl.h9axjt
title: Occurrence Download

description: A dataset containing 12749 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudophycis bachus",
 "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 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 12749 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002113-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kd51c5b2c
title: Data from: How important is it to consider lineage diversification heterogeneity in macroevolutionary studies? lessons from the lizard family Liolaemidae

description: Macroevolutionary and biogeographical studies commonly apply multiple
 models to test state-dependent diversification. These models track the
 association between states of interest along a phylogeny, although many of
 them do not consider whether different clades might be evolving under
 different evolutionary drivers. Yet, they are still commonly applied to
 empirical studies without careful consideration of possible lineage
 diversification heterogeneity along the phylogenetic tree. A recent
 biogeographic study has suggested that orogenic uplift of the southern
 Andes has acted as a species pump, driving diversification of the lizard
 family Liolaemidae (307 described species), native to temperate southern
 South America. Here, we argue against the Andean uplift as main driver of
 evolution in this group. We show that there is a clear pattern of
 heterogeneous diver- sification in the Liolaemidae, which biases state-
 and environment-dependent analyses in, respectively, the GeoSSE and RPANDA
 programs. We show here that there are two shifts to accelerated speciation
 rates involving two clades that have both been classified as having
 “Andean” distri- butions. We incorporated the Geographic Hidden-State
 Speciation and Extinction model (GeoHiSSE) to accommo- date unrelated
 diversification shifts, and also re-analyzed the data in RPANDA program
 after splitting biologically distinct clades for separate analyses, as
 well as including a more appropriate set of models. We demonstrate that
 the “Andean uplift” hypothesis is not supported when the het- erogeneous
 diversification histories among these lizards is considered. We use the
 Liolaemidae as an ideal system to demonstrate potential risks of ignoring
 clade-specific dif- ferences in diversification patterns in
 macroevolutionary studies. We also implemented simulations to
 show that, in agreement with previous findings, the HiSSE approach can
 effectively and substantially reduce the level of distribution-dependent
 models receiving the highest AIC weights in such scenarios. However, we
 still find a relatively high rate (15%) of distribution-dependent models
 receiving the highest AIC weights, and provide recommendations re- lated
 to the set of models included in the analyses that reduce these rates by
 half. Finally, we demonstrate that trees including clades following
 different dependent-drivers affect RPANDA analyses by producing different
 outcomes, ranging from partially correct models to completely mis- leading
 results. We provide recommendations for the implementation of both
 programs.
DOI: 10.5061/dryad.sbcc2fr2t
title: Population Genomics 'Beta vulgaris'

description: Population Genomic data sets from several papers descibing genetic
 diversity of beet crop types. 1) Genetic diversity among cultivated beets
 (Beta vulgaris) assessed via population-based whole genome sequences (BMC
 Genomics paper )
DOI: 10.5061/dryad.m63xsj3xv
title: Reduced biodiversity in modernised villages: a conflict between sustainable development goals

description: 1. Despite large conservation efforts to halt the loss of farmland
 biodiversity in Europe, negative population trends are still observed,
 especially for common species. Old villages and human settlements are
 biodiversity hotspots and important breeding habitats for farmland birds,
 but recent requirements for energy saving measures and improved living
 comfort have changed their architecture and habitats. Consequently,
 modernisation of villages may negatively affect bird diversity due to the
 loss of nesting and foraging sites. 2. We investigated how the abundance
 and diversity of birds breeding in 104 Polish villages varied in relation
 to the degree of modernisation as estimated by the proportion of new and
 renovated homesteads. 3. Abundance of building-nesting species, but not
 tree-nesting species, declined by 50% across a gradient of old to highly
 modernised villages. The contribution of new vs. renovated houses to the
 observed decline was similar. 4. Applications and synthesis. Rural
 modernisation has a dramatic effect on abundance of birds nesting in/on
 buildings, thus may be an important and overlooked contributor to farmland
 bird population declines in Europe. Villages and rural properties may fall
 outside of current conservation policy as they are neither protected areas
 nor agricultural lands (where AES can be applied). Therefore, bird
 diversity declines in rural landscapes could continue unchecked. The
 observed conflict between sustainability goals such as increased building
 energy efficiency and biodiversity conservation suggests that sustainable
 rural development should better link modernisation with conservation
 measures, e.g. by constructing nesting sites when renovating and building
 new houses.
DOI: 10.5061/dryad.1zcrjdfnw
title: Differential migration in Chesapeake Bay striped bass

description: Differential migration - greater migration level with increasing
 individual size - is common in migratory species. Like other forms of
 partial migration, it provides spatial buffering against regional
 differences in habitat quality and sources of mortality. We investigated
 differential migration in striped bass, a species with well-known
 plasticity in migration behaviors.  A size-stratified sample of
 Potomac River (Chesapeake Bay) striped bass was implanted with acoustic
 transmitters and their subsequent coastal migrations recorded over a 4-yr
 period by telemetry receivers throughout the Mid-Atlantic Bight and
 Southern New England. A logistic regression predicted that ≥ 50% of both
 males and females depart the Chesapeake Bay at large sizes &gt; 80 cm
 total length. Egressing striped bass exited through both the Chesapeake
 Bay and Delaware Bay (C&D Canal), favoring the former. All large
 fish migrated to Massachusetts coastal waters and in subsequent years
 repeatedly returned to regions within Massachusetts and Cape Cod Bays.
 Within this dominant behavior, minority behaviors included straying,
 skipped spawning, and residency by large individuals. Analysis of last day
 of transmission indicated that small resident striped bass experienced
 nearly 2-fold higher loss rates (70% yr-1) than coastal emigrants (37%
 yr-1). The study confirmed expectations for a threshold size at emigration
 and different mortality levels between Chesapeake Bay (resident) and ocean
 (migratory) population contingents; and supported the central premise of
 the current assessment and management framework of a two-contingent
 population: Chesapeake Bay and ocean contingents discriminated by size. An
 improved understanding of differential migration thus affords an
 opportunity to specify stock assessments according to different population
 sub-components, and tailor reference points and control rules between
 regions and fishing stakeholder groups.
DOI: 10.5061/dryad.x95x69pdm
title: Dust and grit matter: abrasives of different size lead to opposing dental microwear textures in experimentally fed sheep (Ovis aries)

description: External abrasives ingested along with the herbivore diet are considered
 main contributors to dental wear, though how different abrasive sizes and
 concentrations influence wear remains unclear. Dental microwear texture
 analysis (DMTA) is an established method for dietary reconstruction which
 describes a tooth’s surface topography on a micrometre scale. The method
 has yielded conflicting results as to the effect of external abrasives. In
 the present study, a feeding experiment was performed on sheep (Ovis
 aries), fed seven diets of different abrasiveness. Our aim was to discern
 the individual effects of abrasive size (4 , 50 and 130 µm) and
 concentration (0, 4 and 8 % of dry matter) on dental wear, applying DMTA
 to four tooth positions. Microwear textures differed between individual
 teeth, but surprisingly, showed no gradient along the molar tooth row, and
 the strongest differentiation of experimental groups was achieved when
 combining data of all maxillary molars. Overall, a pattern of increasing
 height, volume, and complexity of the tooth’s microscopic surface appeared
 with increasing dietary abrasive size, and when compared to the control,
 the small abrasive diets showed a polishing effect. Results indicate that
 a diet’s abrasive size is more important for DMT traces than its abrasive
 concentration, and that different sizes can have opposing effects on the
 dietary signal. The latter finding possibly explains conflicting evidence
 from previous experimental DMTA application. Further exploration is
 required to understand if indeed, and how microscopic traces created by
 abrasives translate quantitatively to tissue loss.
description: Boxplots and descriptive statistics for all individual
 measurements are provided in the supplemental information (Tables S1-9,
 Figure S1). We also provide the original dataset in the
 form of an excel file. DMTA values were derived from four scans per facet
 (a single facet per tooth) and a median is then calculated from the four
 measures for each DMTA parameter. Original code also
 available upon request.
DOI: 10.25338/b88w32
title: Data from: Using an arbitrary moment predictor to investigate the optimal choice of prognostic moments in bulk cloud microphysics schemes

description: Most bulk cloud microphysics schemes predict up to three standard
 properties of hydrometeor size distributions, namely, the mass mixing
 ratio, number concentration, and reﬂectivity factor in order of increasing
 scheme complexity. However, it is unclear whether this combination of
 properties is optimal for obtaining the best simulation of clouds and
 precipitation in models. In this study, a bin microphysics scheme has been
 modiﬁed to act like a bulk microphysics scheme. The new scheme can predict
 an arbitrary combination of two or three moments of the hydrometeor size
 distributions. As a ﬁrst test of the arbitrary moment predictor (AMP), box
 model simulations of condensation, evaporation, and collision‐coalescence
 are conducted for a variety of initial cloud droplet distributions and for
 a variety of conﬁgurations of AMP. The performance of AMP is assessed
 relative to the bin scheme from which it was built. The results show that
 no double‐ or triple‐moment conﬁguration of AMP can simultaneously
 minimize the error of all cloud droplet distribution moments. In general,
 predicting low‐order moments helps to minimize errors in the cloud droplet
 number concentration, but predicting high‐order moments tends to minimize
 errors in the cloud mass mixing ratio. The results have implications for
 which moments should be predicted by bulk microphysics schemes for the
 cloud droplet category.
description: Simulation output. See the manuscript for details.
description: Igel 2019 AMP Data <strong>Notes on
 the directory naming conventions:</strong><br> Folders are
 named as follows: nu#_N#_M# where<br> the number after nu indicates
 the value of the shape parameter,<br> the number after N indicates
 the initial droplet concentration (#/cm3),<br> and the number after
 M indicates the initial droplet mass mixing ratio (g/kg).
 <strong>Notes on the file naming
 convention:</strong><br> There are two files per simulation.
 File names indicate the two moments <br> that were predicted in
 addition to the 3rd moment. Double-moment simulations<br> are
 indicated by a repetation of the moment value. E.g. M0M0 is a
 double-moment<br> simulation with the 0th and 3rd moments predicted.
 M0M2 is a triple-moment <br> simulation with the 0th, 2nd, and 3rd
 moments predicted.  <strong>Notes on the two file
 types:</strong><br> cM#M#.txt files contain the 0th-9th
 moments of the cloud and rain distributions<br> plus the shape
 parameter obtained by the distribution initialization.
 cpdf*.txt files contain the binned water distributions at the end
 of each time step. Also see the README file.
DOI: 10.5061/dryad.k0p2ngf4k
title: A novel role for Eip74EF in male reproduction in promoting sperm elongation at the cost of fecundity

description: Spermatozoa are the most morphologically variable cell type, yet little is
 known about genes controlling natural variation in sperm shape. Drosophila
 fruit flies have evolved the longest sperm known, which are evolving under
 postcopulatory sexual selection, driven by sperm competition and cryptic
 female choice. Long sperm outcompete short sperm but primarily when
 females have long seminal receptacles (SRs), the primary sperm storage
 organ. Thus, selection on sperm length is mediated by SR length, and the
 two traits are coevolving across the Drosophila lineage, driven by a
 genetic correlation and fitness advantage of long sperm and long SR
 genotypes in both males and females. Ecdysone induced protein 74EF
 (Eip74EF) is rapidly evolving under positive selection in Drosophila, and
 it is expressed during post-meiotic stages of spermatogenesis, when
 spermatid elongation occurs. Partial knockdown of Eip74EF leads to shorter
 sperm but does not affect SR length, suggesting that Eip74EF is involved
 in promoting spermatid elongation but is not a genetic driver of
 male-female coevolution. We also found that Eip74EF knockdown has opposing
 effects on fecundity in males and females, with an increase in fecundity
 for males but a decrease in females, consistent with its documented role
 in oocyte maturation. It is possible that knockdown males produce more
 sperm that are also shorter, which would explain the increase in
 fecundity, but this hypothesis remains to be tested. Our results document
 a novel function of Eip74EF in spermatogenesis and demonstrates that this
 gene influences both male and female reproductive success.
DOI: 10.5061/dryad.z08kprr8r
title: Recreating giants impacts in the laboratory: Shock compression of MgSiO3 bridgmanite to 14 Mbar

description: Understanding giant impacts requires accurate description of how extreme
 pressures and temperatures affect the physical properties of the
 constituent materials. Here, we report shock experiments on two polymorphs
 of  MgSiO3: enstatite and bridgmanite (perovskite)
 crystals.  We obtain pressure-density shock equation of state to
 14 Mbar and more than 9 g/cm3 a 40 % increase in density from previous
 data on MgSiO3. Density-functional-theory molecular dynamics (DFT-MD)
 simulations provide predictions for the shock Hugoniot curves for
 bridgmanite and enstatite and suggest that the Gruneisen parameter
 decreases with increasing density. The good agreement between the
 simulations and the experimental data, including for the shock temperature
 along the enstatite Hugoniot reveals that DFT-MD  simulations
 reproduce well the behavior of dense fluid MgSiO3. We also reveal a high
 optical reflectance indicative of a metal-like electrical conductivity
 which supports the hypothesis that magma oceans may contribute to
 planetary magnetic field generation.
description: This dataset contains equation of state and optical properties
 data on the mineral MgSiO3 that is reported in an upcoming paper in
 Geophysical Review Letters titled: <i>Recreating giants impacts in
 the laboratory: Shock compression of MgSiO<sub>3</sub>
 bridgmanite to 14 Mbar.</i> All data are gathered
 in a single Excel spreadsheet with multiple tabs. Data
 include Laser-driven shock equation of state experimental measurements and
 density-functional-theory computer simulations.
description: Abbreviations:
 Pressure P, Density rho, Energy u or E, Temperature
 T, shock velocity Us, particle velocity up, Gruneisen parameter Gamma,
 reflectivity R  
 Prepared by LLNL under Contract DE-AC52-07NA27344.
DOI: 10.5061/dryad.rr4xgxd5f
title: Cryptic and extensive hybridization between ancient lineages of American crows

description: Most species and therefore most hybrid zones have historically been
 defined using phenotypic characters. However, both speciation and
 hybridization can occur with negligible morphological differentiation.
 Recently developed genomic tools provide the means to better understand
 cryptic speciation and hybridization. The Northwestern Crow (Corvus
 caurinus) and American Crow (Corvus brachyrhynchos) are continuously
 distributed sister taxa that lack reliable traditional characters for
 identification. In this first population genomic study of Northwestern and
 American crows, we use genomic SNPs (nuDNA) and mtDNA to investigate the
 degree of genetic differentiation between these crows and the extent to
 which they may hybridize. Our results indicate that American and
 Northwestern crows have distinct evolutionary histories, supported by two
 nuDNA ancestry clusters and two 1.1%-divergent mtDNA clades dating to the
 late Pleistocene, when glacial advances may have isolated crow populations
 in separate refugia. We document extensive hybridization, with geographic
 overlap of mtDNA clades and admixture of nuDNA across &gt;900 km of
 western Washington and western British Columbia. This broad hybrid zone
 consists of late-generation hybrids and backcrosses, but not recent (e.g.,
 F1) hybrids. Nuclear DNA and mtDNA clines had concordant widths and were
 both centered in southwestern British Columbia, farther north than
 previously postulated. Overall, our results suggest a history of
 reticulate evolution in American and Northwestern crows, perhaps due to
 recurring neutral expansion(s) from Pleistocene glacial refugia followed
 by lineage fusion(s). However, we do not rule out a contributing role for
 more recent potential drivers of hybridization, such as expansion into
 human-modified habitats.
DOI: 10.15468/dl.q4vg9k
title: Occurrence Download

description: A dataset containing 3257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (6ea87510-0561-11d8-b851-b8a03c50a862, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, c2ecae57-6701-485e-9ebd-5f87b2945cb2)",
 "TaxonKey is Melanoplus bivittatus",
 "Year 1900-2026"
 ]
}

 The dataset includes 3257 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002114-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.