cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pg4f4qrn2
title: Frog tongue segmentation data for a realistic vascular structure in modelling

description: In the last decade, numerical models have been an increasingly important
 tool in biological and medical science both for the fundamental
 understanding of physiology as well as the potential for novel diagnostics
 and treatments tools in clinical application. In this paper, a nonlinear
 multi-scale model framework is developed for blood flow distribution in
 the full vascular system of an organ. We couple a quasi 1D vascular graph
 model to represent blood flow in larger vessels and a porous media model
 to describe flow in smaller vessels and capillary bed. The vascular model
 is based on Poiseuille’s law, with pressure correction by elasticity and
 pressure drop estimation at vessels junctions. The porous capillary bed is
 modelled as a two-compartment domain (artery and venous) using Darcy’s
 law. The fluid exchange between the artery and venous capillary bed
 compartments are defined as blood perfusion.  The numerical
 experiments show that the proposed model for blood circulation: 1) is
 closely dependent on the structure and parameters of both the vascular
 vessels and of the capillary bed, and 2) it provides a realistic blood
 circulation in the organ. The advantage of the proposed model is that it
 is complex enough to reliably capture the main underlying physiological
 function, yet highly flexible as it offers the possibility of
 incorporating various local effects. Furthermore, the numerical
 implementation of the model is straightforward and allows for simulations
 on a regular desktop computer. 
description: The vascular system was segmented from an image in a classical
 medical textbook, Cohnheim JF. 1872 Untersuchungen über die embolischen
 Prozesse. Berlin: Hirschwald. Segmentation based on
 Hanson EA, Lundervold A. 2013 Local/non-local regularized image
 segmentation using graph-cuts. International Journal of Computer Assisted
 Radiology and Surgery 8, 1073–1084.
DOI: 10.5061/dryad.2bvq83bnx
title: Morning glory species co-occurrence is associated with asymmetrically decreased and cascading reproductive isolation

description: Hybridization between species can affect the strength of the reproductive
 barriers that separate those species. Two extensions of this effect are:
 (1) the expectation that asymmetric hybridization or gene flow will have
 asymmetric effects on reproductive barrier strength and (2) the
 expectation that local hybridization will affect only local reproductive
 barrier strength and could therefore alter within-species compatibility.
 We tested these hypotheses in a pair of morning glory species that exhibit
 asymmetric gene flow from highly selfing Ipomoea lacunosa into
 mixed-mating I. cordatotriloba in regions where they co-occur. Because of
 the direction of this gene flow, we predicted that reproductive barrier
 strength would be more strongly affected in I. cordatotriloba than I.
 lacunosa. We also predicted that changes to reproductive barriers in
 sympatric I. cordatotriloba populations would affect compatibility with
 allopatric populations of that species.  We tested these
 predictions by measuring the strength of a reproductive barrier to seed
 set across the species’ ranges. Consistent with our first prediction, we
 found that sympatric and allopatric I. lacunosa produce the same number of
 seeds in crosses with I. cordatotriloba, whereas crosses between sympatric
 I. cordatotriloba and I. lacunosa are more successful than crosses between
 allopatric I. cordatotriloba and I. lacunosa. This difference in
 compatibility appears to reflect an asymmetric decrease in the strength of
 the barrier to seed set in sympatric I. cordatotriloba, which could be
 caused by I. lacunosa alleles that have introgressed into I.
 cordatotriloba. We further demonstrated that changes to sympatric I.
 cordatotriloba have decreased its ability to produce seeds with allopatric
 populations of the same species, in line with our second prediction. Thus,
 in a manner analogous to cascade reinforcement, we suggest that
 introgression associated with hybridization not only influences
 between-species isolation but can also contribute to isolation within a
 species.
description: These data were generated by growing morning glory plants from
 multiple populations of two species in a common environment and making
 crosses between the individuals (see Ostevik et al. 2020 for details). We
 recorded whether crosses produced a fruit. In cases where a fruit was
 produced, we further recorded the weight of the fruit, the number of seeds
 inside the fruit, and the weight of those seeds. The data have been
 lightly filtered to remove unreliable crosses (e.g., cases in which the
 plant died between pollination and fruit set and cases in which the flower
 was damaged in some way).
DOI: 10.5061/dryad.tx95x69w7
title: Life‐stage‐dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas

description: Among highly migratory fish species, nursery areas occupied by juveniles
 often differ from adult habitats. To better understand the spatial
 dynamics of Canada’s Northern cod stock, juveniles caught off the east
 coast of Newfoundland and Labrador were compared to adults from the same
 region as well as individuals from other areas in Atlantic Canada using
 ddRAD-derived SNPs. A reduced proportion of homozygotes with a chromosomal
 inversion located in LG1 was detected between juvenile and adult samples
 in the Northern cod stock region, potentially indicating age-dependent
 habitat use or ontogenetic selection for attributes associated with the
 many genes located in LG1. No neutral genetic differences were found
 between samples from the Northern cod stock; however, significant
 differences were found between some of these samples and cod collected
 from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian
 Shelf. Clustering analysis of variants at neutral loci provided evidence
 for three major genetic units: 1) the Newfoundland Atlantic Coast, 2)
 eastern and southern Gulf of St. Lawrence and Burgeo Bank, and 3) the Bay
 of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and
 neutral population structure within the Northern cod stock should be
 considered by managers to promote rebuilding.
description: DNA was prepared using a ddRAD protocol and 125PE sequenced 60-96
 individuals/lane on an Illumina HiSeq2500. SNPs were selected using STACKS
 and various software described in "Life-stage dependent supergene haplotype
 frequencies and metapopulation neutral genetic patterns of Atlantic cod,
 <i>Gadus morhua</i>, from Canada’s Northern cod stock region
 and adjacent areas." Please refer to publication for
 individual codes.
DOI: 10.5061/dryad.jwstqjq7h
title: Long-term effects of antibiotic treatments on honeybee colony fitness – a modelling approach

description: 1. Gut microbiome disequilibrium is increasingly implicated in host
 fitness reductions, including for the economically important and
 disease-challenged western honey bee, Apis mellifera. In lab experiments
 the antibiotic tetracycline, which is used to prevent American Foulbrood
 Disease in countries including the US, elevates honey bee mortality by
 disturbing the microbiome. It is unclear however, how elevated individual
 mortality affects colony level fitness. 2. We used an agent-based model
 (BEEHAVE) and empirical data to assess colony level effects of
 antibiotic-induced worker bee mortality, by measuring colony size. We
 investigated the relationship between the duration that the
 antibiotic-induced mortality probability is imposed for and colony size.
 3. We found that when simulating antibiotic-induced mortality of worker
 bees from just 60 days per year, up to a permanent effect, the colony is
 reduced such that tetracycline treatment would not meet the European Food
 Safety Authority’s (EFSA) honey bee protection goals. When antibiotic
 mortality was imposed for the hypothetical minimal exposure time, which
 assumes that antibiotics only impact the bee’s fitness during the
 recommended treatment period of fifteen days in both spring and autumn,
 the colony fitness reduction was only marginally under the EFSA’s
 threshold. 4. Synthesis and Applications: Modelling colony level impacts
 of antibiotic treatment shows that individual antibiotic-induced honey bee
 worker mortality can lead to colony mortality. To assess the full impact,
 the persistence of antibiotic-induced mortality in honey bees must be
 determined experimentally, in vivo. We caution that as the domestication
 of new insect species increases, maintaining healthy gut microbiomes is of
 paramount importance to insect health and commercial productivity. The
 recommendation from this work is to limit prophylactic use of antibiotics
 and to not exceed recommended treatment strategies for domesticated
 insects. This is especially important for highly social insects as excess
 antibiotic use will likely decrease colony growth and an increase in
 colony mortality.
description: See README file 
description: See README file
DOI: 10.5061/dryad.dr7sqv9wt
title: Acoustic indices perform better when applied at ecologically meaningful time and frequency scales

description: Abstract: 1. Acoustic indices are increasingly employed in the analysis of
 soundscapes to ascertain biodiversity value. However, conflicting results
 and lack of consensus on best practices for their usage has hindered their
 application in conservation and land-use management contexts. Here we
 propose that the sensitivity of acoustic indices to ecological change and
 fidelity of acoustic indices to ecological communities are severely
 impacted by signal masking. Signal masking can occur when acoustic
 responses sensitive to the effect being monitored are masked by less
 sensitive acoustic groups, or target taxa sonification is masked by
 non-target noise. We argue that by calculating acoustic indices at
 ecologically appropriate time and frequency bins, masking effects can be
 reduced and the efficacy of indices increased. 2. We test this on a large
 acoustic dataset collected in Eastern Amazonia spanning a disturbance
 gradient including undisturbed, logged, burned, logged-and-burned, and
 secondary forests. We calculated values for two acoustic indices: the
 Acoustic Complexity Index and the Bioacoustic Index, across the entire
 frequency spectrum (0-22.1 kHz), and four narrower subsets of the
 frequency spectrum; at dawn, day, dusk and night. 3. We show that signal
 masking has a large impact on the sensitivity of acoustic indices to
 forest disturbance classes. Calculating acoustic indices at a range of
 narrower time-frequency bins substantially increases the classification
 accuracy of forest classes by random forest models. Furthermore, signal
 masking led to highly misleading correlations, including spurious inverse
 correlations, between biodiversity indicator metrics and acoustic index
 values compared to correlations derived from manual sampling of the audio
 data. 4. Consequently, we recommend that acoustic indices are calculated
 either at a range of time and frequency bins, or at a single narrow bin,
 predetermined by a priori ecological understanding of the soundscape.
description: Detailes of data collection are provided in the paper. Species
 richness and other diversity metrics are calculated in the vegan package
 in R. 
description: Read me file uploaded with description of data.
DOI: 10.5061/dryad.z612jm69p
title: CA10 regulates neurexin heparan sulfate addition via a direct binding in the secretory pathway

description: Neurexins are presynaptic adhesion molecules that shape the molecular
 composition of synapses. Diversification of neurexins in numerous isoforms
 is believed to confer synapse-specific properties by engaging with
 distinct ligands. For example, a subset of neurexin molecules carry a
 heparan sulfate (HS) glycosaminoglycan that controls ligand binding, but
 how this posttranslational modification is controlled is not known. Here,
 we observe that CA10, a ligand to neurexin in the secretory pathway,
 regulates neurexin-HS formation. CA10 is exclusively found on non-HS
 neurexin and CA10 expressed in neurons is sufficient to suppress HS
 addition and attenuate ligand binding and synapse formation induced by
 ligands known to recruit HS. This effect is mediated by a direct
 interaction in the secretory pathway that blocks the primary step of HS
 biosynthesis: xylosylation of the serine residue. NMR reveals that CA10
 engages residues on either side of the serine that can be HS-modified,
 suggesting that CA10 sterically blocks xylosyltransferase access in Golgi.
 These results suggest a mechanism for the regulation of HS on neurexins
 and exemplify a new mechanism to regulate site-specific glycosylations.
DOI: 10.5061/dryad.xwdbrv1c8
title: The evolutionary genetics of paternal care: how good genes and extra-pair copulation affect the trade-off between paternal care and mating success

description: We investigate the evolution of a gene for paternal care, with pleiotropic
 effects on male mating fitness and offspring viability, with and without
 extra pair copulations (EPCs). We develop a population genetic model to
 examine how pleiotropic effects of a male mating advantage and paternal
 care are affected by ‘good genes’ and EPCs. Using this approach, we show
 that the relative effects of each on fitness do not always predict the
 evolutionary change. We then find the line of combinations of mating
 success and paternal care that bisects the plane of possible values into
 regions of positive or negative gene frequency change. This line shifts
 when either good genes or EPCs are introduced, thereby expanding or
 contracting the region of positive gene frequency change and significantly
 affecting the evolution of paternal care. Predictably, a direct viability
 effect of ‘good genes’ that enhances offspring viability constrains or
 expands the parameter space over which paternal care can evolve, depending
 on whether the viability effect is associated with the paternal care
 allele or not. In either case, the effect of a ‘good gene’ that enhances
 offspring viability is substantial; when strong enough, it can even
 facilitate the evolution of poorpaternal care, where males harm
 their young. When non-random mating is followed by random EPCs, the
 genetic regression between sire and offspring is reduced and,
 consequently, the relative strengths of selection are skewed away from
 paternal care and toward the male mating advantage. However, when random
 mating is followed by non-random EPCs, a situation called “trading up” by
 females, we show that selection is skewed in the opposite direction, away
 from male mating advantage and toward paternal care across the natural
 range of EPC frequencies.
description: No empirical data. These files are mathematica notebooks which
 are used to solve equations and to generate simulations. 
description: All files are legible and excecutable in Wolfram Mathematica, and
 include annotation.
DOI: 10.5061/dryad.tdz08kpz0
title: Data from: Integration and harmonization of trait data from plant individuals across heterogeneous sources

description: Trait data represent the basis for ecological and evolutionary research
 and have relevance for biodiversity conservation, ecosystem management and
 earth system modelling. The collection and mobilization of trait data has
 strongly increased over the last decade, but many trait databases still
 provide only species-level, aggregated trait values (e.g. ranges, means)
 and lack the direct observations on which those data are based. Thus, the
 vast majority of trait data measured directly from individuals remains
 hidden and highly heterogeneous, impeding their discoverability, semantic
 interoperability, digital accessibility and (re-)use. Here, we integrate
 quantitative measurements of verbatim trait information from plant
 individuals (e.g. lengths, widths, counts and angles of stems, leaves,
 fruits and inflorescence parts) from multiple sources such as field
 observations and herbarium collections. We develop a workflow to harmonize
 heterogeneous trait measurements (e.g. trait names and their values and
 units) as well as additional information related to taxonomy, measurement
 or fact and occurrence. This data integration and harmonization builds on
 vocabularies and terminology from existing metadata standards and
 ontologies such as the Ecological Trait-data Standard (ETS), the Darwin
 Core (DwC), the Thesaurus Of Plant characteristics (TOP) and the Plant
 Trait Ontology (TO). A metadata form filled out by data providers enables
 the automated integration of trait information from heterogeneous
 datasets. We illustrate our tools with data from palms (family Arecaceae),
 a globally distributed (pantropical), diverse plant family that is
 considered a good model system for understanding the ecology and evolution
 of tropical rainforests. We mobilize nearly 140,000 individual palm trait
 measurements in an interoperable format, identify semantic gaps in
 existing plant trait terminology and provide suggestions for the future
 development of a thesaurus of plant characteristics. Our work thereby
 promotes the semantic integration of plant trait data in a
 machine-readable way and shows how large amounts of small trait data sets
 and their metadata can be integrated into standardized data products.
description: Data integration of individual trait measurements from multiple
 sources such as field observations and herbarium collections
description: See the Readme file and the accompanying publication in
 Ecological Informatics for details.
DOI: 10.15468/dl.e5u9vp
title: Occurrence Download

description: A dataset containing 2121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Caryota mitis"
 ]
}

 The dataset includes 2121 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002629-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5068/d17t1w
title: Population structure, inbreeding and stripe pattern abnormalities in plains zebras

description: One of the most iconic wild equids, the plains zebra occupies a broad
 region of sub-Saharan Africa and exhibits a wide range of phenotypic
 diversity in stripe patterns that have been used to classify multiple
 sub-species. After decades of relative stability, albeit with a loss of at
 least one recognized subspecies, the total population of plains zebras has
 undergone an approximate 25% decline since 2002. Individuals with abnormal
 stripe patterns have been recognized in recent years but the extent to
 which their appearance is related to demography and/or genetics is
 unclear. Investigating population genetic health and genetic structure are
 essential for developing effective strategies for plains zebra
 conservation. We collected DNA from 140 plains zebra, including 7 with
 abnormal stripe patterns, from 9 locations across the range of plains
 zebra, and analyzed data from restriction site-associated and whole genome
 sequencing (RAD-seq, WGS) libraries to better understand the relationships
 between population structure, genetic diversity, inbreeding, and abnormal
 phenotypes. We find that genetic structure does not coincide with
 described subspecific variation, but does distinguish geographic regions
 in which anthropogenic habitat fragmentation is associated with reduced
 gene flow and increased evidence of inbreeding, especially in certain
 parts of East Africa. Further, zebras with abnormal striping exhibited
 increased levels of inbreeding relative to normally striped individuals
 from the same populations. Our results point to a genetic cause of stripe
 pattern abnormalities, and dramatic evidence of the consequences of
 habitat fragmentation.
description: SNPs were generated from RADseq data created using the
 restrictioin enzyme SBFI. Processing details can be found in Larison et.
 al 2020. Population structure, inbreeding and stripe pattern abnormalities
 in plains zebras. Molecular Ecology 
description: Details about the samples can be found in Larison et. al 2020.
 Population structure, inbreeding and stripe pattern abnormalities in
 plains zebras. Molecular Ecology
DOI: 10.5061/dryad.sj3tx9638
title: IOB-2020-008_HouseSparrow

description: The climatic variability hypothesis (CVH) posits that more flexible
 phenotypes should provide a fitness advantage for organisms experiencing
 more variable climates. While typically applied across geographically
 separated populations, whether this principle applies across seasons or
 other conditions (e.g., open vs. sheltered habitats) which differ in
 climatic variability remains essentially unstudied. In north-temperate
 climates, climatic variability in winter usually exceeds that in summer,
 so extending the CVH to within-population seasonal variation predicts that
 winter phenotypes should be more flexible than summer phenotypes. We
 tested this prediction of the within-season extension of the CVH by
 acclimating summer and winter-collected house sparrows (Passer domesticus)
 to 24, 5 and -10°C and measuring basal (BMR) and summit (Msum = maximum
 cold-induced) metabolic rates before and after acclimation. To examine
 mechanistic bases for metabolic variation, we measured flight muscle and
 heart masses and citrate synthase and β-hydroxyacyl coA-dehydrogenase
 activities. BMR and Msum were higher for cold-acclimated than for
 warm-acclimated birds and BMR was higher in winter than in summer birds.
 Contrary to our hypothesis of greater responses to cold acclimation in
 winter birds, metabolic rates generally decreased over the acclimation
 period for winter birds at all temperatures but increased at cold
 temperatures for summer birds. Flight muscle and heart masses were not
 significantly correlated with season or acclimation treatment, except for
 supracoracoideus mass, which was lower at -10°C in winter, but flight
 muscle and heart masses were positively correlated with BMR and flight
 muscle mass was positively correlated with Msum. Catabolic enzyme
 activities were not clearly related to metabolic variation. Thus, our data
 suggest that predictions of the CVH may not be relevant when extended to
 seasonal temperature variability at the within-population scale. Indeed,
 these data suggest that metabolic rates are more prominently upregulated
 in summer than in winter in response to cold. Metabolic rates tended to
 decrease during acclimation at all temperatures in winter, suggesting that
 initial metabolic rates at capture (higher in winter) influence metabolic
 acclimation for captive birds.
description: House Sparrows acclimated to different temperature conditions
 (24, 5, and -10 C) for six weeks in both summer and winter.
 Data collected included basal and summit metabolic rates (pre,
 mid and post-acclimation), ultrasound flight muscle width (pre and
 post-acclimation), and tissue masses and catabolic enzyme activities
 (post-acclimation).
description: There are scattered missing values for some of these variables.
 They appear as blank cells in the Excel file.