cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k3j9kd5b8
title: Uncovering circuit mechanisms of current sinks and sources with biophysical simulations of primary visual cortex

description: Local field potential (LFP) recordings reflect the dynamics of the current
 source density (CSD) in brain tissue. The synaptic, cellular and circuit
 contributions to current sinks and sources are ill-understood. We
 investigated these in mouse primary visual cortex using public Neuropixels
 recordings and a detailed circuit model based on simulating the
 Hodgkin-Huxley dynamics of &gt;50,000 neurons belonging to 17 cell
 types. The model simultaneously captured spiking and CSD responses and
 demonstrated a two-way dissociation: Firing rates are altered with minor
 effects on the CSD pattern by adjusting synaptic weights, and CSD is
 altered with minor effects on firing rates by adjusting synaptic placement
 on the dendrites. We describe how thalamocortical inputs and recurrent
 connections sculpt specific sinks and sources early in the visual
 response, whereas cortical feedback crucially alters them in later stages.
 These results establish quantitative links between macroscopic brain
 measurements (LFP/CSD) and microscopic biophysics-based understanding of
 neuron dynamics and show that CSD analysis provides powerful constraints
 for modeling beyond those from considering spikes.
description: Collected by simulations on a biophysically detailed model of
 mouse primary visual cortex. Output data files are unprocessed.
description: Data analysis pipeline is set up in Python and is available at
 https://github.com/atleer/CINPLA_Allen_V1_analysis.git.
DOI: 10.5061/dryad.mcvdnck41
title: Data from: Pervasive introgression during rapid diversification of the European mountain genus Soldanella (L.) (Primulaceae)

description: Hybridization is a key mechanism involved in lineage diversification and
 speciation, especially in ecosystems that experienced repeated
 environmental oscillations. Recently radiated plant groups, which have
 evolved in mountain ecosystems impacted by historical climate change
 provide an excellent model system for studying the impact of gene flow on
 speciation. We combined organellar (whole plastome) and nuclear genomic
 data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the
 effects of hybridization and introgression on evolution and speciation in
 the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has
 already occurred among ancestral lineages of snowbells and has persisted
 throughout the entire evolutionary history of the genus, regardless of the
 ecology, cytotype, or distribution range size of the affected species. The
 highest extent of introgression has been detected in the Carpathian
 species, which is also reflected in their extensive karyotype variation.
 Introgression occurred even between species with dysploid and euploid
 cytotypes, which were considered to be reproductively isolated. The
 magnitude of introgression detected in snowbells is unprecedented in other
 mountain genera of the European Alpine System investigated hitherto. Our
 study stresses the prominent evolutionary role of hybridization in
 facilitating speciation and diversification on the one hand, but also
 enriching previously isolated genetic pools. 
description: Libraries for Rad sequencing were sequenced on an Illumina HiSeq
 2500 at the sequencing facility of the Vienna BioCenter Core
 Facilities. Plastome data represents genome skimming
 data generated by the sequencing project PhyloAlps.
description: Word, Excel, FigTree
DOI: 10.5517/ccdc.csd.cc2mhz15
title: CCDC 2428417: Experimental Crystal Structure Determination

description: Related Article: Jose M. Sansano|2025|CSD Communication|||
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5061/dryad.m37pvmd56
title: Invasive plant species that experience lower herbivory pressure may evolve lower diversities of chemical defence compounds in the exotic range

description: ABSTRACT PREMISE Invasive plant species often escape from specialist
 herbivore species and are likely to experience herbivory mostly from
 generalist herbivore species in the exotic range. Consequently, the
 Shifting Defence Hypothesis (SDH) predicts that invasive plants will
 express higher concentrations of qualitative defence compounds to deter
 dominant generalist herbivores in the exotic range. Here, I additionally
 propose a Reduced Chemical Diversity Hypothesis (RCDH), which predicts
 that reduced herbivory pressure will select for invasive plant genotypes
 that produce lower diversities of defence compounds in the exotic range.
 METHODS I tested whether: (1) Invasive Brassica nigra populations express
 a lower diversity and an overall higher concentration of glucosinolate
 compounds than native-range B. nigra; (2) Brassica nigra individuals that
 express high diversities and concentrations of glucosinolates are more
 attractive to specialist and deterrent to generalist herbivores; (3)
 Tissues of invasive B. nigra are less palatable to two generalist
 herbivores Theba pisana and Helix aspersa than tissues of native-range B.
 nigra. RESULTS Invasive B. nigra populations expressed a significantly
 lower diversity of glucosinolate compounds and a marginally higher
 concentration of total glucosinolate compounds. Leaf tissues of the
 invasive B. nigra were significantly less palatable to T. pisana and
 marginally less so to H. aspersa. Brassica nigra individuals that
 expressed high concentrations of total glucosinolate compounds were
 visited by a low diversity of generalist herbivore species in the field.
 CONCLUSIONS The biogeographical differences in glucosinolate profiles of
 invasive and native-range populations of B. nigra may be the result of
 differential herbivore selection pressures in the respective ranges.
DOI: 10.5061/dryad.41ns1rnhn
title: Patterns of reef fish taxonomic and functional diversity in the Eastern Tropical Pacific

description: A core challenge in ecology is identifying the factors that determine
 species distribution and functional diversity of species assemblages. Reef
 fish are the most diverse group of vertebrates, form taxonomically rich
 and functionally diverse communities and represent a key source of food
 for humans. We examine regional distribution patterns of reef fish species
 richness and functional diversity and investigate how these are determined
 by historical, biogeographic, energetic, and anthropogenic factors. We
 compiled data from 3,312 underwater visual censuses (UVCs) performed at
 122 locations comprising rocky and coral reefs along of the Eastern
 Tropical Pacific (ETP). We used Generalized Linear Mixed-effects Models
 (GLMM) implemented in a Bayesian framework to investigate whether distance
 from quaternary refugia, distance from mainland, shelf area, primary
 productivity, sea surface temperature, human population gravity and
 conservation status influence reef fish species richness and functional
 diversity in the ETP. Species richness and functional richness (FRic)
 peaked towards the center of the ETP and our null model suggests that FRic
 followed a spatial pattern than would be predicted by species richness.
 Additionally, functional evenness (FEve) was highest at higher latitudes
 whereas functional dispersion (FDis) was homogeneous throughout the ETP.
 Species richness was negatively influenced by shelf area and distance from
 the mainland but positively influenced by sea surface temperature and
 conservation status. FEve was influenced by human population gravity and
 FDis by shelf area, respectively. Reef fish species richness and
 functional diversity in the ETP exhibited a strong division within the
 region mainly mediated by sea surface temperature and human population
 gravity. Our results also suggest that dominant species in large areas
 share more common traits than dominant species in small areas. This study
 provides previously unknown regional patterns of reef fish functional
 diversity and new insights into how historical, biogeographic, energetic,
 and anthropogenic factors influence complementary biodiversity facets.
description: We compiled data from 3,312
 underwater visual censuses ‘UVCs’ of fish conducted at 122 locations
 comprising rocky and coral reefs along of the ETP between 2004 and 2020.
 The total area surveyed per location varied between 320 and
 74,000 m<sup>2</sup>. During visual censuses, the surveyor
 identified and counted all actinopterygian fish species observed in the
 water column and on the bottom of belt transects.
description: All analyses and figures were
 implemented using the R environment ver. 4.0.2.
DOI: 10.5061/dryad.q83bk3jm5
title: Evolution of physical linkage between loci: simulations output

description: Coupling of multiple barriers to gene-flow, such as divergent local
 adaptation and reproductive isolation, facilitates speciation. However,
 alleles at loci that contribute to barrier effects can be dissociated by
 recombination. Models of linkage between diverging alleles often consider
 elements that reduce recombination, such as chromosomal inversions and
 alleles that modify recombination rate between existing loci. In contrast,
 here we consider the evolution of linkage due to close proximity of loci
 on the same chromosome. Examples of such physical linkage exist in several
 species, but in other cases strong associations are maintained without
 physical linkage. We use an individual-based model to study the conditions
 under which physical linkage between loci controlling ecological traits
 and mating preferences might be expected to evolve. We modelled a single
 locus controlling an ecological trait that acts also as a mating cue.
 Mating preferences are controlled by multiple loci, formed by mutations
 that are randomly placed in the “genome”, within varying distances from
 the ecological trait locus, allowing us to examine which genomic
 architectures spread across the population. 
description: The dataset details results of simulations of an individual-based
 model, which was designed to explore evolutionary changes in the relative
 location of loci contributing to reproductive isolation due to selection
 pressure against intermediate phenotypes. The model was
 impelemented in NetLogo. The model files, including source code and model
 description (following the ODD protocol) are available for public review
 at the NetLogo User community website, via the following link:
 http://ccl.northwestern.edu/netlogo/models/community/physical_linkage_one_trait_locus Specifically, simulations were run with the following parameters: Selection coefficients (s) of 0.5, 0.6, 0.7 and 0.8. Preference strength factors (pf) of 0.3, 0.6, 1.2 and 2.4. As a control, additional simualtions were run separately with no recombination applied on offspring chromosomes, (s = 0.5, pf = 0.3). The output measures were recorded every generation for the duration of 3000 generations.
description: The data file can be oppened by any program that supports CSV
 files.
DOI: 10.5061/dryad.rfj6q57dp
title: A combined microbial and biogeochemical dataset from high-latitude ecosystems with respect to methane cycle

description: High latitudes are experiencing intense ecosystem changes with climate
 warming. The underlying methane (CH4) cycling dynamics remain unresolved,
 despite its crucial climatic feedback. Atmospheric CH4 emissions are
 heterogeneous, resulting from local geochemical drivers, global climatic
 factors, and microbial production/consumption balance. Holistic studies
 are mandatory to capture CH4 cycling complexity. Here, we report a large
 set of integrated microbial and biogeochemical data from 396 samples,
 using a concerted sampling strategy and experimental protocols. The study
 followed international standards to ensure inter-comparisons of data
 amongst three high-latitude regions: Alaska, Siberia and Patagonia. The
 dataset encompasses different representative environmental features (e.g.
 lake, wetland, tundra, forest soil) of these high-latitude sites and their
 respective heterogeneity (e.g. characteristic microtopographic patterns).
 The data included physicochemical parameters, greenhouse gas
 concentrations and emissions, organic matter characterization, trace
 elements and nutrients, isotopes, microbial quantification and
 composition. This dataset addresses the need for a robust physicochemical
 framework to conduct and contextualize future research on the interactions
 between climate change, biogeochemical cycles and microbial communities at
 high-latitudes.
description: This study focused on three
 regions located in subantarctic, arctic and subarctic
 latitudes.  The field campaigns were conducted in 2016,
 during the respective summer for each region: January-February in Chilean
 Patagonia, June-July in Alaska and July-August in Siberia. For every site included in the present study, a
 set of nine qualitative environmental and/or ecological site-scale
 descriptors was selected and adapted from ENVO Environment
 Ontology, which included
 for example permafrost state, biome, environmental feature and vegetation
 type.  The environmental features that are representative for
 the three regions were considered: lakes, wetlands,
 broadleaf/coniferous/mixed forest soils, grassland, tundra and palsa. All
 the metadata is included in the submitted dataset. A specific sampling
 strategy was defined for each kind of ecosystem, i.e. lakes, soils and
 wetlands.  Details for field sampling, in situ
 (physiochemical analyses, dissolved CH<sup>4</sup> and
 CO<sup>2</sup> concentrations, atmospheric CH4 and CO2
 emission rates, sample processing in the field) and laboratory analyses
 (moisture and organic matter content, suspended solids, filtration, pore
 water extraction, total and dissolved organic carbon, anions and cations,
 trace elements, optical properties, isotopes, DNA extraction, qPCR assays,
 high-throughput amplicon sequencing) are described in the Scientific Data
 manuscript. 
description: MS Word for ReadMe file; CSV for Dataset.
DOI: 10.5061/dryad.1zcrjdfvm
title: Latitudinal influences on bryozoan calcification through the Paleozoic

description: Bryozoans are active non-phototrophic biomineralizers that precipitate
 their calcareous skeletons in sea-water. Carbonate saturation states vary
 temporally and spatially in Paleozoic oceans, and we used the Bryozoan
 Skeletal Index (BSI) to investigate whether bryozoan calcification is
 controlled by seawater chemistry in Paleozoic trepostome and cryptostome
 bryozoans. Our results show that cryptostome bryozoan genera are
 influenced by ocean chemistry throughout the Paleozoic and precipitate the
 most calcite per autozooid at lower latitudes, where carbonate saturation
 states are generally higher, and less in mid-latitudes where carbonate
 will be relatively undersaturated. Trepostome bryozoan genera show a
 similar, but weaker, trend for the Ordovician to Devonian, suggesting that
 like the cryptostomes they are unable to metabolically overcome falling
 saturation states and simply precipitate less robust skeletons at
 higher-latitudes. Carboniferous to Triassic trepostomes differ however and
 show a trend toward increased calcification at higher latitudes,
 indicating they are able to overcome unfavorable carbonate saturation
 states. Analysis of Permian trepostomes, at the species level, indicates
 this is most pronounced in the southern hemisphere where calcification is
 matched by increased feeding capacity. It is proposed that this increased
 feeding capacity allowed them to metabolically overcome unfavorable
 carbonate saturation states. The differing responses of trepostome and
 cryptostome bryozoans to carbonate saturation states suggest that
 bryozoans should not be considered as a single group in climate driven
 marine extinctions. Likewise, it would suggest that modern stenolaemate
 and gymnolaemate bryozoans should be treated separately when considering
 their response to modern ocean chemistry changes.
description: The data is supplied as a CSV file and may be opened in Excel,
 PAST or other software. No specialist software is required to access the
 data files.
DOI: 10.5061/dryad.wh70rxwqx
title: Data from: Weedy and seedy: The rapid evolution of life-history characteristics in an introduced daisy

description: Despite the importance of life-history characteristics in determining a
 species’ success, we still lack basic information about some fundamental
 life-history elements found across the life cycle of introduced plants.
 Our study assesses rapid evolutionary divergence in life-history
 characteristics of the beach daisy, Arctotheca populifolia, by comparing
 introduced Australian and source South African plants and measuring eight
 key variables including seed mass, germination, reproductive output and
 survival. This is the first study that compares the life history of an
 introduced plant species with its single original source population,
 providing a precise and powerful method for detecting evolutionary
 divergence. We found that introduced A. populifolia has evolved a suite of
 weedy life-history characteristics in less than 90 years: the introduced
 plants use a live-fast die-young strategy of germination and survival and
 produce significantly more inflorescences and more seeds that germinate
 faster. This knowledge adds to the remarkable data that we already have on
 the rapid evolutionary divergence occurring in the morphology, physiology
 and defence of this introduced plant and highlights the speed and scope of
 evolutionary divergence possible in plants. To fully understand and manage
 the future of our plant species, we must consider their potential for
 ongoing change in key aspects of life history.
description: Please see the published article at https://doi.org/10.1093/aobpla/plac038 for method information: Brandenburger CR, Maslen B, Sherwin WB, Moles AT. 2022. Weedy and seedy: the rapid evolution of life-history characteristics in an introduced daisy. <em>AoB PLANTS.</em>
description: Microsoft Excel R statisical software (R Core
 Team)
DOI: 10.15468/dl.8egfxp
title: Occurrence Download

description: A dataset containing 2348 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Anthene emolus"
 ]
}

 The dataset includes 2348 records from 33 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003184-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5hqbzkh8h
title: The evolution of immune function in decorated crickets

description: While dietary macronutrients are known to regulate insect immunity, few
 studies have examined their evolutionary effects. Here, we evaluate this
 relationship in the cricket Gryllodes sigillatus by maintaining replicate
 populations on four diets differing in protein (P) to carbohydrate (C)
 ratio (P- or C-biased) and nutritional content (low- or high-nutrition)
 for &gt;37 generations. We split each population into two; one
 maintained on their evolution diet and the other switched to their
 ancestral diet. We also maintained populations exclusively on the
 ancestral diet (baseline). After three generations, we measured three
 immune parameters in males and females from each population. Immunity was
 higher on P-biased than C-biased diets and on low- versus high-nutrition
 diets, although the latter was most likely driven by compensatory feeding.
 These patterns persisted in populations switched to their ancestral diet,
 indicating genetic divergence. Crickets evolving on C-biased diets had
 lower immunity than the baseline, whereas their P-biased counterparts had
 similar or higher immunity than the baseline, indicating that populations
 evolved with dietary manipulation. While females exhibited superior
 immunity for all assays, the sexes showed similar immune changes across
 diets. Our work highlights the important role that macronutrient intake
 plays in the evolution of immunity in the sexes.
description: We measured immune parameters (hemocyte count, zone of inhibition
 and PO activity) in male and female crickets from replicate populations
 that have been evolving on diets differing in the ratio of protein to
 carbohydrates and total caloric content. Data on these immune parameters
 were compressed to a mean for each sex per population for final data
 analysis.
description: Data can be open in Microsoft Excel. The data is contained in two
 separate tabs. The first tab contains all the data from the evolution diet
 populations. The second tab contains all the data pertaining to the
 control populations (SCD).
DOI: 10.5061/dryad.gqnk98srh
title: Data from: Climate warming leads to advanced fruit development period of temperate woody species but divergent changes in its length

description: Climate warming has significantly altered the phenology of plants in
 recent decades. However, in contrast to the widely reported
 warming-induced extension of vegetative growing season, the response of
 fruit development period (FDP) from flowering to fruiting remains largely
 unexplored, particularly for woody plants. Analyzing &gt;560,000 in
 situ observations of both flowering and fruiting dates for six temperate
 woody species across 2958 European phenological observations sites during
 1980 – 2013, we found that in all species both flowering and fruiting
 phenology, i.e., the FDP, advanced with climate warming. However, the
 advancing rates of the two events were not necessarily equal for any given
 species, resulting in divergent changes in the length of FDP among species
 with climate warming. During 1980 – 2013, not only the temperature during
 FDP but also the forcing requirement for fruit development increased, both
 affecting the length of FDP. The shortened FDP was mainly due to elevated
 temperature, thus accelerating the accumulation of forcing, whereas the
 prolonged FDP was primarily caused by the substantial increase of the
 forcing requirement of fruiting, which could be fulfilled only in a longer
 time and thus slowed down the advance of fruiting. This study provides
 large-scale empirical evidence of warming-induced advances of FDP but
 divergent changes in its length in temperate woody species. Our findings
 demonstrate the contrasting reproductive phenological strategies among
 temperate woody species under the pressure of warming climate, contrary to
 the lengthening of vegetative growing season, which is by and largely
 similar with different woody species.