cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1400
title: Data from: Biogeography of the livebearing fish Poecilia gillii in Costa Rica: are phylogeographic breaks congruent with fish community boundaries?

description: One of the original goals of phylogeography was to use genetic data to
 identify historical events that might contribute to breaks among
 communities. In this study, we examine the phylogeography of a common
 livebearing fish (Poecilia gillii) from Costa Rica. Our goal was to
 determine if phylogeographic breaks in this species were congruent with
 previously-defined boundaries among four fish community provinces. We
 hypothesized that if abiotic factors influence both community boundaries
 and genetic structuring in P. gillii then we might find four clades within
 our focal species that were geographically separated along community
 boundary lines. Similarly, we expected to find most of the genetic
 variation in P. gillii partitioned among these four geographic regions. We
 generated DNA sequence data (mitochondrial cyt b and nuclear S7 small
 ribosomal subunit) for 260 individuals from 42 populations distributed
 across Costa Rica. We analyzed these data using phylogenetic (parsimony
 and likelihood) and coalescent approaches to estimate phylogenetic
 relationships among haplotypes, patterns of gene flow, and effective
 population size. Contrary to our expectations, we did not find four
 monophyletic groups that mapped cleanly to our geographic community
 provinces. However, one of our clades was restricted to a single province,
 suggesting that common earth history events could be responsible for both
 genetic structuring in P. gillii and fish community composition in this
 area. However, our results show a complex pattern of gene flow throughout
 other regions in Costa Rica where genetic structuring is not predicted by
 community province boundaries.
description: Pgillii.cytb.nexAligned cyt b data for all individuals with the taxa labels in nexus file format.Pgillii.S7.nexAligned S7 data for all individuals with the taxa labels in nexus file format.redundanttaxa.xlsThis spreadsheet contains three worksheets. The first is labeled 'Localities' and gives the province, locality number, locality name, Field ID, and Drainage for each locality. the first three columns are available in the publication and associated online supplementary material. The Field ID corresponds to the taxa labels used in the nexus files. The first two numbers are the year they were collected and the last numbers are the collection number. Thus, a taxa label that reads 'PG0701.04' would be the species Poecilia gillii collected in 2007 in the first collection locality and the fourth fish from that locality. The second and third worksheet provide the taxa labels with their associated haplotype as found in the publication for each of the respective loci.
DOI: 10.5061/dryad.13jc4
title: Data from: Population genomics shed light on the demographic and adaptive histories of European invasion in the Pacific oyster, Crassostrea gigas

description: Crassostrea gigas originated from the Pacific coast of Asia but was
 introduced into several European countries in the early 1970s. Natural
 populations have now spread the length of the western seaboard of Europe.
 To elucidate the demographic and selective processes at play during this
 rapid expansion, genome-scan analysis was performed on different
 populations. High diversities and low differentiation were observed
 overall, but significant genetic differentiation was found among
 newly-established populations and between the newly-established northern
 group and a nearly panmictic group composed of southern European
 populations and a population from Japan. Loss of genetic diversity was
 also seen in the north, likely caused by founder events during
 colonisation. The few strongly supported outlier loci revealed a genetic
 structure uncorrelated with the north/south differentiation, but grouping
 two samples from the Danish Fjords (northern group) and one from the Dutch
 Scheldt estuary (southern group) with the one from Japan. These findings
 might reflect: (i) parallel adaptation to similar environmental pressures
 (Fjord-like environment) within each of the two groups or (ii) a footprint
 of a secondary introduction of an alternative genomic background
 maintained by multifarious isolation factors. Our results call for a
 closer examination of adaptive genetic structure in the area of origin.
description: AFLP genotypes from C.
 gigas populationsAFLP
 data.txtSNP genotypes from C.
 gigas populationsSNP
 data.txtmicrosatellite genotypes
 from C. gigas populationsmicrosatellite
 data.txt
DOI: 10.5061/dryad.2s5t6
title: Data from: The interface of ecological novelty and behavioral context in the formation of ecological traps

description: Ecological traps occur when rapid environmental change causes animals to
 actually prefer inferior habitats. Traps increase the likelihood of
 species extinction, but our understanding of how evolved behavioral
 algorithms interface with increasingly novel ecosystems to trigger them
 remains limited. Both polarized and unpolarized light are increasingly
 common forms of light pollution known to cause maladaptive behavior for
 both water-seeking and entirely terrestrial insects by maladaptively
 triggering innate habitat selection and navigation preferences,
 respectively. We designed a nocturnal, field-based experiment to
 investigate how diverse nocturnal insect taxa use and contextualize these
 cues when they are placed in evolutionarily novel proximity, and so test
 the hypothesis that cues that originally evolved to guide navigation
 behavior can enhance or hinder the ability of different nocturnal insects
 to avoid maladaptive behavior within the context of habitat selection.
 Unpolarized light created more attractive ecological traps, even for
 aquatic taxa known to use polarized light as their sole habitat selection
 cue. We found that these cues could, in aquatic taxa, act both additively
 and synergistically to increase the attraction of ecological traps. While
 one family showed evidence of partitioning their response to these 2 forms
 of light within their respective behavioral contexts (navigation, habitat
 selection), our results indicate that the novel proximity of cues from
 separate behavioral contexts can act to enhance the attractiveness of
 ecological traps within a focal context.
description: Raw capture database_PLP
 vs. ULP_dryadThis database includes
 the abundance and biomass of individual insects captured in oil-filled
 traps that vary in the degree of polarized vs. unpolarized light
 associated with them.PLP_ULP_DATABASE_040617_dryad.xlsx
DOI: 10.5061/dryad.9nb56
title: Data from: The impact of weather and storm water management ponds on the transmission of West Nile virus

description: West Nile virus (WNV) is the most widely distributed arbovirus in the
 world and the spread is influenced by complex factors including weather
 conditions and urban environmental settings like storm water management
 ponds (SWMP). The purpose of this work was to develop an ordinary
 differential equation model to explore the impacts of SWMP, temperature
 and precipitation on WNV vector abundance and the transmission of WNV
 between mosquito and bird populations. The model was used to analyse how
 weather conditions and SWMP can influence the basic reproduction number.
 The results found that an excess of precipitation and fiercer
 intraspecific competition will reduce vector population and the peak value
 of infectious vectors and birds. This information can be used to identify
 measures that would be useful to control larval abundance in SWMP and the
 transmission of WNV.
description: Daily weather data in
 2006 in the Greater Toronto Areawea.csvR0.mA function m-file named R0.m related to sensitive analysisODE_WNV.mA function m-file named ODE_WNV.m related to sensitive analysis to define the dynamical systemLHS_Call.mA function m-file named LHS_Call.m related to sensitive analysisPara_settings.mM-file named Para_settings.m related to sensitive analysisPRCCM.mA function m-file named PRCCM.m related to sensitive analysisPRCCR0.mA function m-file named PRCCR0.m related to sensitive analysisMain script named Model.mMain script (related to sensitive analysis) calls functions R0.m, ODE_WNV.m, LHS_Call.m, PRCCM.m, PRCCR0.m and Para_settings.m.Model.mWeather.mA function m-file named Weather.m to define a weather-driven dynamical systemWeatherCases.mA function m-file named WeatherCases.m related to comparison of two cases (a region with multiple SWMPs)WeatherKappa.mA function m-file named WeatherKappa.m to show the role of intraspecific competitionMain script named WeatherSWMP.mMain script named WeatherSWMP calls functions Weather.m, WeatherCases.m, WeatherSWMP.m to show the influence of weather and SWMP on mosquito abundance and the transmission of WNV.WeatherSWMP.mWNV_SWMP_R0.mvA maple file named WNV_SWMP_R0.mw to show the variation of basic reproduction number R_0 along with combinations of weather conditions or SWMP properties.WNV_SWMP_R0.mw
DOI: 10.5281/zenodo.15586552
title: Allostery is a widespread cause of loss-of-function variant pathogenicity - raw data

description: Supplemental raw data for the preprint: Liao, X., & Lehner, B. (2025). Allostery is a widespread cause of loss-of-function variant pathogenicity. bioRxiv, 2025-06.   



thermompnn_outs.tar.gz: raw human proteome-wide ThermoMPNN predictions.
DOI: 10.5281/zenodo.18381534
title: Allostery is a widespread cause of loss-of-function variant pathogenicity - raw data

description: Supplemental raw data for the preprint: Liao, X., & Lehner, B. (2025). Allostery is a widespread cause of loss-of-function variant pathogenicity. bioRxiv, 2025-06.   



thermompnn_outs.tar.gz: raw human proteome-wide ThermoMPNN predictions.
DOI: 10.5061/dryad.qp1f6h0s
title: Data from: Cross-sectional versus longitudinal research: a case study of trees with hollows and marsupials in Australian forests

description: How different are insights based on cross-sectional studies from those of
 longitudinal investigations? We addressed this question using a detailed
 case study encompassing a rare suite of inter-connected cross-sectional
 and longitudinal investigations that have spanned the past two decades and
 included work on (1) the decay and collapse of large cavity forest trees
 (termed trees with hollows), (2) populations of a suite of species of
 arboreal marsupials which are reliant on trees with hollows as nesting and
 denning sites, and (3) relationships between the abundance, type and
 condition of trees with hollows and the presence, abundance and species
 richness of these animals. Our case study was from the montane ash
 eucalypt forests of the Central Highlands of Victoria, south-eastern
 Australia. Our longitudinal studies led to new insights that either would
 not have been possible from a cross-sectional study or which were
 unexpected because they did not conform, or only partially conformed, to
 postulated responses made at the outset based on the results of earlier
 research. These new insights included (1) a substantial slowing in rates
 of tree fall between 1997 and 2006 which were significantly lower than
 predicted from earlier data gathered between 1983 and 1993, (2) no
 evidence for a decline in populations of almost all species of arboreal
 marsupials between 1997 and 2007, despite the loss of nearly 14% of the
 measured population of trees with hollows in that time, (3) changes in
 nest tree selection by some species of arboreal marsupials in response to
 these changes in hollow availability, (4) concentration effects, in which
 populations of animals used the declining tree hollow resource more
 intensively, and (5) evidence for significant rainfall effects on temporal
 changes in animal abundance. Our case study underscored the additional
 ecological insights that can be generated from longitudinal studies,
 including how relationships between biota and their habitat can change
 over time. Understanding these temporal changes is essential for informed
 forest management and biodiversity conservation and points towards the
 need for greater use of longitudinal datasets in ecology.
description: yearsiteanimalswatchtreeIndividual tree datarain
DOI: 10.5061/dryad.nk33c06
title: Data from: Influence of clay licks on the diversity and structure of an Amazonian forest

description: The spatial heterogeneity of resource availability is a major driver of
 biodiversity patterns. Some environmental conditions and resources are
 characterized by large-scale patterns of variation within the landscape.
 Clumped local discontinuities or discrete elements also increase spatial
 heterogeneity, romoting local “biodiversity hot-spots” by modifying
 habitat characteristics and promoting plant-animal interactions. Clay
 licks are faunal attractors owing to their role in the nutritional ecology
 of the user species; nevertheless, the effect of their presence on the
 surrounding vegetation has been poorly quantified. Here, we use data from
 100 x 10 m transects and evaluate the effects of the presence of clay
 licks on forest diversity and structure at local and landscape scales. In
 clay lick areas, there was a higher abundance of certain species, which
 helps to homogenize species composition between localities counteracting
 the natural distance-decay of compositional similarity between transects
 without clay lick influence (controls). Compared to control sites, clay
 lick´s forests had higher palm densities, shorter but more variable
 individuals in the canopy and understory, a thinner canopy layer, and
 denser herbaceous and ground level covers. These differences were found
 along the whole length of transects in both sampled areas types. These
 results reveal that the presence of discrete elements (i.e. clay licks)
 may help to explain the compositional and structural heterogeneity of
 Amazonian forests influencing ecological processes such as seed dispersal
 and trampling. These considerations may be relevant for other biomes where
 clay licks are present and give weight to their inclusion in conservation
 initiatives in tropical forests.
description: Inventory_sppSpecies invetontory of each plot of each transect at clay licks and non clay licks areas.Plot_coverage_StructurePlant covers of each plot of each transect in clay lick and non clay lick areasPlot_Trees_StructureStrucutural attributes of individuals of each plot of each transect in clay lick and non clay lick areas
DOI: 10.5061/dryad.rc454pc
title: Data from: The achaete-scute complex contains a single gene that controls bristle development in the semi-aquatic bugs

description: The semi-aquatic bugs (Heteroptera, Gerromorpha) conquered water surfaces
 worldwide and diversified to occupy puddles, ponds, streams, lakes,
 mangroves, and even oceans. Critical to this life style is the evolution
 of sets of hairs that allow these insects to maintain their body weight on
 the water surface and protect the animals against wetting and drowning. In
 addition, the legs of these insects are equipped with various grooming
 combs that are important for cleaning and tidying the hair layers for
 optimal functional efficiency. Here we show that the hairs covering the
 legs of water striders represent innervated bristles. Genomic and
 transcriptomic analyses revealed that in water striders the achaete-scute
 complex, known to control bristle development in flies, contains only the
 achaete-scute homologue (ASH) gene due to the loss of the gene asense.
 Using RNA interference, we show that ASH plays a pivotal role in the
 development of both bristles and grooming combs in water striders. Our
 data suggest that the ASH locus may have contributed to the adaptation to
 water surface lifestyle through shaping the hydrophobic bristles that
 prevent water striders from wetting and allow them to exploit water
 surface tension.
description: concatenated
 alignment_amino acids_Figure2concatenated
 alignment_amino acids_Figure4Figure
 S2_BayesianFigure
 S3_BayesianFigure S2_Maximum
 LikelihoodFigure S3_Maximum
 Likelihood
DOI: 10.5061/dryad.21517
title: Data from: Habitat preference facilitates successful early breeding in an open-cup nesting songbird

description: Selecting breeding habitats that ameliorate environmental limits on
 fitness and facilitate successful reproduction should benefit individual
 animals. This is particularly true in the temperate zone, where breeding
 early in a season presents a unique series of environmental challenges
 that can limit an individual's fitness. While many studies document
 links between habitat quality and reproductive success, few identify the
 cues used to assess habitat quality or the components of reproduction most
 influenced by occupying higher quality habitat, particularly during the
 early breeding season. We used detailed spatial maps and observations of
 all early season nesting attempts in an insular song sparrow (Melospiza
 melodia) population over 38 years to estimate the influence of nest-site
 preference on reproductive success and to test whether relative
 microclimate or food availability may act as cues for early season site
 selection. Female sparrows in preferred early season nest sites had
 earlier laying dates, exhibited more energetically efficient incubation
 behaviour and produced more offspring that recruited to the population
 than those nesting in less-preferred sites. Preference for potential
 nesting sites was positively related to leaf damage by Lepidopteran
 larvae, an indicator of food abundance, negatively related to early season
 microclimate, likely due to greater vegetation cover, and unrelated to
 site-specific plant phenology. Our findings show that breeding in
 preferred, high-quality habitat may offer females a fitness advantage by
 facilitating early laying and the production of offspring more likely to
 recruit to the population at a lower potential reproductive cost to the
 parent. We provide a clear demonstration of potential links between
 habitat preference and quality and their contributions to the ecology and
 life history of animals in seasonal environments.
description: Reproductive,
 incubation, micro-climate, and phenology dataThis Microsoft Excel
 file contains 10 tabs, 5 of which contain data and 5 a description of
 variables. These include: all data associated with components of
 reproduction (Table 1), measures of incubation behaviour (Table 2), plant
 phenology and insect abundance (Results), and cell-specific micro-climate
 (Table 3, Fig S3).Germain_et.al_FunctionalEcology_Data.xlsx
DOI: 10.5061/dryad.637
title: Data from: Australian Lasioglossum + Homalictus Form a Monophyletic Group: Resolving the "Australian Enigma"

description: The bee genus Lasioglossum includes over 1000 species of bees distributed
 on all continents except Antarctica. Lasioglossum is a major component of
 the bee fauna in the Holarctic, Ethiopian, and Oriental regions, and is an
 important group for investigating the evolution of social behavior in
 bees. Given its cosmopolitan distribution, the historical biogeography of
 the genus is of considerable interest. We reconstructed phylogenetic
 relationships among the subgenera and species within Lasioglossum s.s.
 using DNA sequence data from a slowly evolving nuclear gene, EF-1α. The
 entire data set includes over 1604 aligned nucleotide sites (including
 three exons plus two introns) for 89 species (17 outgroups plus 72
 ingroups). Parsimony and maximum likelihood analyses provide strong
 evidence that the primarily Indoaustralian subgenera (Homalictus,
 Chilalictus, Parasphecodes) form a monophyletic group. Bootstrap support
 for the Australian clade ranged from 73% to 77% (depending on the method
 of analysis). Monophyly of the Australian Lasioglossum suggests that a
 single colonization event (via Southeast Asia and New Guinea) gave rise to
 a lineage of over 350 native Indoaustralian bees. We discuss the
 implications of Australian monophyly for resolving the "Australian
 enigma" -- similarity in social behavior among the Australian
 halictine bees relative to Holarctic groups.
description: Gap Coded Alignment Data
 SetGap.coded.alignment.nexusDNA Sequence Alignment Data SetDNA.sequence.alignment.nexus
DOI: 10.5061/dryad.np321
title: Data from: Notch and Nodal control expression of a forkhead factor in the specification network of a multipotent progenitor population in sea urchin

description: Indirect development, where embryogenesis gives rise to a larval form,
 requires that some cells retain developmental potency until they
 contribute to the different tissues in the adult, including the germ line,
 in a later, post-embryonic phase. In sea urchins, the coelomic pouches are
 the major contributor to the adult but how coelomic pouch cells (CPCs) are
 specified during embryogenesis is unknown. We here identify the key
 signaling inputs into the CPC specification network and show the forkhead
 factor foxY is the first transcription factor specifically expressed in
 CPC progenitors. Through dissection of its cis-regulatory apparatus we
 determine that the foxY expression pattern is the result of two signaling
 inputs: First, Delta/Notch signaling activates foxY in CPC progenitors
 and, second, Nodal signaling restricts its expression to the left side,
 where the adult rudiment will form, through direct repression by the Nodal
 target pitx2. A third signal, Hedgehog, is required for coelomic pouch
 morphogenesis and institution of laterality but does not directly affect
 foxY transcription. Knockdown of foxY results in failure to form coelomic
 pouches and disrupts expression of virtually all transcription factors
 known to be expressed in this cell type. Our experiments place foxY at the
 top of the regulatory hierarchy underlying specification of a cell type
 maintaining developmental potency.
description: ArchiveGene expression data and analysis. Data was collected on the Nanostring nCounter.CODESET-INFORMATIONCode set definition for the Nanostring probe set used to quantify mRNA abundance.CODESET-INFORMATIONCode set information. Excel format.PERTURBATION-DATAData analysis for all our expression data collected with the Nanostring nCounter under all the conditions applied in our experiments.PERTURBATION-DATAData analysis excel format.