cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cd62n
title: Data from: Acute artificial light diminishes central Texas Anuran calling behavior

description: Male anuran (frog and toad) advertisement calls associate with fitness and
 can respond to environmental cues such as rain and air temperature.
 Moonlight is thought to generally decrease call behaviors – perhaps as a
 response to increased perceived risk of predation – and this study sought
 to determine if artificial lighting produces a similar pattern. Using a
 handheld spotlight, light was experimentally introduced to natural anuran
 communities in ponds and streams. Custom call surveys where then used to
 measure anuran calls in paired unlit and lit conditions at six locations
 in central Texas. Among seven species heard, the number of frogs calling
 and call index declined in response to the acute light input. Local
 weather conditions could not explain differences between numbers of frogs
 calling between species, sites, survey order, or lighting order suggesting
 the main effect on number calling was light treatment. It appears acute
 artificial light alone can change calling behavior within several species
 in natural, mixed species assemblages.
description: Anurans2010_Data.csvRaw tabular data collected throughout this experiment. The data are unfiltered. All variables described within the file.Anurans2010_Rdata.csvMatrix data with a header row as used by R for linear mixed models. Variables are explained in the readme.Anurans2010_MeanComparisonData.csvMatrix data with a header row as used by SPSS (or R) for comparisons of anuran calling behavior between lit and unlit conditions. Includes some weather data. Variables explained in the readme. Missing data are blank cells. Rows with missing data should be removed if replicating the published analyses.Anurans2010_LogRegressionData.csvMatrix data with a header row in computing the log regression between call index and number heard calling. Only non-zero data were included to accommodate the log relationship.history.txtVerbatim R code with markup used to generate the linear mixed models.
DOI: 10.5061/dryad.250c3s47
title: Data from: Population size and major valleys explain microsatellite variation better than taxonomic units for caribou in western Canada

description: Identifying conservation units below the species level is becoming
 increasingly important, particularly when limited resources necessitate
 prioritization for conservation among such units. This problem is
 exemplified with caribou, a mammal with a circum-Arctic distribution that
 is exposed to a broad spectrum of ecological conditions, but is also
 declining in many parts of its range. We used microsatellite markers to
 evaluate the suitability of existing intra-specific taxonomic designations
 to act as population units for conservation, and contrasted this with
 landscape features that were independent of taxonomy. We also quantified
 the relationship between genetic differentiation and subpopulation size, a
 factor that has been under-represented in landscape genetic research. Our
 dataset included three subspecies and three ecotypes of caribou that
 varied in population size by five orders of magnitude. Our results
 indicated that genetic structure did not correspond to existing taxonomic
 designation, particularly at the level of ecotype. Instead, we found that
 major valleys and population size were the strongest factors associated
 with substructure. There was a negative exponential relationship between
 population size and FST between pairs of adjacent subpopulations,
 suggesting that genetic drift was the mechanism causing the structure
 among the smallest subpopulations. A genetic assignment test revealed that
 movement among subpopulations was a fraction of the level needed to
 stabilize smaller subpopulations, indicating little chance for demographic
 rescue. Such results may be broadly applicable to landscape genetic
 studies, because population size and corresponding rates of drift have the
 potential to confound interpretations of landscape effects on population
 structure.
description: all the
 data_dryad318 Microsatellite loci.
 Alleles coded by three digits, six digits for the diploid organism are in
 each cell. Collected in the field. Columns are: subpopulation (pop),
 Subspecies, Ecotype, Individual ID, followed by the 18
 markers.
DOI: 10.5061/dryad.v32df
title: Data from: The potential of electricity transmission corridors in forested areas as bumblebee habitat

description: Declines in pollinator abundance and diversity are not only a conservation
 issue, but also a threat to crop pollination. Maintained infrastructure
 corridors, such as those containing electricity transmission lines, are
 potentially important wild pollinator habitat. However, there is a lack of
 evidence comparing the abundance and diversity of wild pollinators in
 transmission corridors with other important pollinator habitats. We
 compared the diversity of a key pollinator group, bumblebees (Bombus
 spp.), between transmission corridors and the surrounding semi-natural and
 managed habitat types at 10 sites across Sweden's Uppland region. Our
 results show that transmission corridors have no impact on bumblebee
 diversity in the surrounding area. However, transmission corridors and
 other maintained habitats such as roadsides have a level of bumblebee
 abundance and diversity comparable to semi-natural grasslands and host
 species that are important for conservation and ecosystem service
 provision. Under the current management regime, transmission corridors
 already provide valuable bumblebee habitat, but given that host plant
 density is the main determinant of bumblebee abundance, these areas could
 potentially be enhanced by establishing and maintaining key host plants.
 We show that in northern temperate regions the maintenance of transmission
 corridors has the potential to contribute to bumblebee conservation and
 the ecosystem services they provide.
description: Bumblebee occurrence
 along different habitatsThis data contains
 bumblebee occurrences in different habitats in 10 sites along Sweden. Five
 of the sites have powerlines on it.powerlines3.csv
DOI: 10.5061/dryad.681sn
title: Data from: Evolution of the vertebrate goose-type lysozyme gene family

description: Background: Lysozyme g is an antibacterial enzyme that was first found in
 the eggs of some birds, but recently has been found in additional species,
 including non-vertebrates. Some previously characterized lysozyme g
 sequences are suggested to have altered secretion potential and enzymatic
 activity, however the distribution of these altered sequences is unknown.
 Duplicated copies of the lysozyme g gene exist in some species; however,
 the origins of the duplicates and their roles in altered function are
 unclear. Results: We identified 234 lysozyme g sequences from 118
 vertebrate species, including 181 sequences that are full or near full
 length representing all vertebrate classes except cartilaginous fish.
 Phylogenetic analysis shows that most lysozyme g gene duplicates are
 recent or lineage specific events, however three amplification events are
 more ancient, those in an early amniote, an early mammal, and an early
 teleost. The older gene duplications are associated with changes in
 function, including changes in secretion potential and muramidase
 antibacterial enzymatic activity. Conclusions: Lysozyme g is an essential
 muramidase enzyme that is widespread in vertebrates. Duplication of the
 lysozyme g gene, and the retention of non-secreted isozymes that have lost
 enzymatic activity indicate that lysozyme g has an activity other than the
 muramidase activity associated with being an antibacterial enzyme.
description: lysozyme g coding
 sequencesFull-length and near
 full-length lysozyme g coding sequences used in this analysis are
 presented in fasta format with shortened species names. Ns are added to
 the beginning of some sequences to generate correct reading
 frames.Lyg
 coding sequences.txt
DOI: 10.13140/rg.2.2.28721.03689
title: The code about R2-L2 strategy Physics-Informed Neural Network for Chloride Diffusion
DOI: 10.5061/dryad.52j07
title: Data from: Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogen Plasmopara viticola

description: Biologic invasions can have important ecological, economic and social
 consequences, particularly when they involve the introduction and spread
 of plant invasive pathogens, as they can threaten natural ecosystems and
 jeopardize the production of human food. Examples include the grapevine
 downy mildew, caused by the oomycete Plasmopara viticola, an invasive
 species native to North America, introduced into Europe in the 1870s. We
 investigated the introduction and spread of this invasive pathogen, by
 analysing its genetic structure and diversity in a large sample from
 European vineyards. Populations of P. viticola across Europe displayed
 little genetic diversity, consistent with the occurrence of a bottleneck
 at the time of introduction. Bayesian coalescent analyses revealed a clear
 population expansion signal in the genetic data. We detected a weak, but
 significant, continental-wide population structure, with two
 geographically and genetically distinct clusters in Western and Eastern
 European vineyards. Approximate Bayesian computation, analyses of clines
 of genetic diversity and of isolation-by-distance patterns provided
 evidence for a wave of colonization moving in an easterly direction across
 Europe. This is consistent with historical reports, first mentioning the
 introduction of the disease in Bordeaux vineyards (France) and
 sub-sequently documenting its rapid spread across Europe. This initial
 introduction in the west was probably followed by a ‘leap-frog’ event into
 Eastern Europe, leading to the formation of the two genetic clusters we
 detected. This study shows that recent population genetics methods within
 the Bayesian and coalescence frameworks are extremely powerful for
 increasing our understanding of pathogen population dynamics and invasion
 histories.
description: Microsatellite_data_SPAGEDIMicrosatellite data set (n=938) follows the SPAGEDI input file format. It contains codes for localities, latitude-longitude coordinates as well as projected coordinates using a Gnomonic projection.spagedi_mathilde.txt
DOI: 10.5061/dryad.5cm32
title: Data from: Contrasting influences of geographic range and distribution of populations on patterns of genetic diversity in two sympatric Pilbara Acacias

description: The influence of geographic range on species persistence has long been of
 interest and there is a need for a better understanding of the genetic
 consequences for species with restricted distributions, particularly with
 the increasing rate of global species extinctions. However, the genetic
 effects of restricted range are often confounded by the impacts of
 population distribution. We compared chloroplast and nuclear genetic
 diversity and differentiation in two acacias, the restricted, patchily
 distributed Acacia atkinsiana and the widespread, semi-continuously
 distributed A. ancistrocarpa. Lower intra-population diversity and higher
 differentiation between populations were seen in A. atkinsiana compared to
 its widespread congener, A. ancistrocarpa. There was little evidence of
 geographical influences on population genetic structure in A.
 ancistrocarpa whereas A. atkinsiana exhibited nuclear genetic structure
 with isolation by distance, differentiation of near-coastal populations
 from those in the ranges, and differentiation of peripheral populations
 from those in the centre of the distribution. These results are consistent
 with expectations of the effect of geographic range and population
 distribution on genetic diversity, but indicate that distribution of
 populations rather than geographic range has influenced the observed
 genetic structure. The contrasting patterns observed here demonstrate that
 conservation approaches for species management and ecological restoration
 need to consider the distribution of populations in geographically
 restricted species.
description: A.atkinsiana and
 A.ancistrocarpa genotypesMicrosatellite genotypes
 and population locations for A.atkinsiana and A. ancistrocarpa in Genalex
 formatA.ancistrocarpa sequence
 dataChloroplast sequence
 data for A. ancistrocarpa in Nexus formatA.atkinsiana sequence
 dataChloroplast sequence
 data for A. atkinsiana in Nexus format
DOI: 10.5061/dryad.156ss6b
title: Data from: Grab my tail: evolution of dazzle stripes and colourful tails in lizards

description: Understanding the functions of animal coloration has been a long-standing
 question in evolutionary biology. For example, the widespread occurrence
 of striking longitudinal stripes and colourful tails in lizards begs for
 an explanation. Experiments have suggested that colourful tails can
 deflect attacks towards the tail (the ‘deflection’ hypothesis), which is
 sacrificable in most lizards, thereby increasing the chance of escape.
 Studies also suggest that in moving lizards, longitudinal body stripes can
 redirect predators’ strikes towards the tail through the ‘motion dazzle’
 effect. Despite these experimental studies, the ecological factors
 associated with the evolution of such striking colourations remain
 unexplored. Here, we investigated if predictions from motion dazzle and
 attack deflection could explain the widespread occurrence of these
 striking marks using comparative methods and information on
 eco-physiological variables (caudal autotomy, diel activity, microhabitat,
 and body temperature) potentially linked to their functioning. We found
 both longitudinal stripes and colourful tails are associated with diurnal
 activity and with the ability to lose the tail. Compared to stripeless
 species, striped species are more likely to be ground-dwelling and have
 higher body temperature, emphasizing the connection of stripes to mobility
 and rapid escape strategy. Colourful tails and stripes have evolved
 multiple times in a correlated fashion, suggesting that their functions
 may be linked. Overall, our results together with previous experimental
 studies support the notion that stripes and colourful tails in lizards may
 have protective functions based on deflective and motion dazzle effects.
description: Data_file
DOI: 10.5061/dryad.qt174
title: Data from: Contribution of cell proliferation to axial elongation in the red flour beetle Tribolium castaneum

description: Most arthropods generate their posterior bodies by adding segments
 periodically, as the embryo grows, from a posteriorly located region
 called the segment addition zone. This mode of segmentation is shared with
 vertebrates and relies on oscillatory mechanisms, where the temporal
 periodicity of a clock is translated into repetitive spatial patterns.
 This ordered anterior-to-posterior pattern is achieved at the same time as
 the tissue elongates, opening the question of the functional coordination
 between the mechanisms of segmental patterning and posterior growth. The
 study of these processes in different arthropods has played an important
 role in unravelling some of the molecular mechanisms of segment formation.
 However, the behavior of cells during elongation and how cellular
 processes affect this segmental patterning has been poorly studied. Cell
 proliferation together with cell rearrangements are presumed to be the
 major forces driving axis elongation in the red flour beetle Tribolium
 castaneum. However, there still no strong evidence about the role and
 distribution of cell proliferation within the embryo. In this study, we
 propose to address these questions by using whole embryo cultures and
 pharmacological manipulation. We show that considerable cell proliferation
 occurs during germband elongation, measured by incorporation of the
 nucleoside analog of thymidine 5-Ethynyl-2’-deoxyuridine, EdU. Moreover,
 proliferating cells appeared to be spread along the elongating embryo with
 a posterior bias at early segmentation. In addition, when we blocked cell
 division, treated germbands were always shorter than controls and in some
 cases not able to fully elongate, even when control embryos already
 started to retract and leg buds are evident. Finally, we found that the
 absence of cell proliferation has no apparent effect on segmental
 patterning, as evidenced by Tc-engrailed (Tc-en) gene expression.
description: Total data
 tablesTable 1. Data germband
 length APH-HU 2 and 3 HTable 1. Data germband length
 APH-HU 2 y 3 H.xlsxTable 2. FI SAZ vs Trunk
 Early and mid-elongationTable 3. Data SAZ width
 APH+HUTable
 3. Data ZAS width APH+HU.xlsxTable 4. Data germband
 length mid-elongationTable 5. Data Tc-en
 stripesTable 6. Data APH+HU
 injectedTable 7. Data segment
 length
DOI: 10.5061/dryad.pf21m
title: Data from: Signatures of selection in mammalian clock genes with coding trinucleotide repeats: implications for studying the genomics of high-pace adaptation

description: Climate change is predicted to affect the reproductive ecology of
 wildlife; however, we have yet to understand if and how species can adapt
 to the rapid pace of change. Clock genes are functional genes likely
 critical for adaptation to shifting seasonal conditions through shifts in
 timing cues. Many of these genes contain coding trinucleotide repeats,
 which offer the potential for higher rates of change than single
 nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate
 to faster rates of adaptation in changing environments. We characterized
 repeats in 22 clock genes across all annotated mammal species and
 evaluated the potential for selection on repeat motifs in three clock
 genes (NR1D1, CLOCK, and PER1) in three congeneric species pairs with
 different latitudinal range limits: Canada lynx and bobcat (Lynx
 canadensis and L. rufus), northern and southern flying squirrels
 (Glaucomys sabrinus and G. volans), and white-footed and deer mouse
 (Peromyscus leucopus and P. maniculatus). Signatures of positive selection
 were found in both the interspecific comparison of Canada lynx and bobcat,
 and intraspecific analyses in Canada lynx. Northern and southern flying
 squirrels showed differing frequencies at common CLOCK alleles and a
 signature of balancing selection. Regional excess homozygosity was found
 in the deer mouse at PER1 suggesting disruptive selection, and further
 analyses suggested balancing selection in the white-footed mouse. These
 preliminary signatures of selection and the presence of trinucleotide
 repeats within many clock genes warrant further consideration of the
 importance of candidate gene motifs for adaptation to climate change.
description: Prentice et al.
 2017_DATAThis data set contains
 neutral microsatellite and coding trinucleotide repeat genotype data for
 deer mouse, white-footed mouse, northern flying squirrels and southern
 flying squirrels. Data for Canada lynx and bobcat will be made accessible
 with a follow-up publication.
DOI: 10.5061/dryad.pp67h
title: Data from: Territory configuration moderates the frequency of extra-group mating in superb fairy-wrens

description: The frequency of extra-pair paternity (EPP) in socially monogamous birds
 varies substantially between and within species, but ecological drivers of
 this variation remain poorly understood. Habitat configuration could
 influence EPP by moderating access to extra-pair mates, because species
 occupying territories in a clustered ‘honeycomb’ configuration have a
 larger pool of potential extra-group mates in their immediate
 neighbourhood than those living in linearly arranged territories (e.g.
 along narrow strips of riparian or fragmented habitat). We exploited
 variation in the spatial arrangement of territories due to anthropogenic
 modification of habitat of the cooperatively breeding superb fairy-wren
 Malurus cyaneus to test whether habitat configuration influenced the
 frequency of EPP. In this species, most paternity is obtained by males
 outside the social group (extra-group paternity, EGP). We found that the
 frequency of EGP among groups living in linear strips of roadside
 vegetation (41% of 44 offspring) was lower than it was for groups living
 in clustered territories within continuous habitat (59% of 70 offspring).
 Differences in group size and pair relatedness did not explain differences
 in EGP associated with territory configuration, though the frequency of
 EGP was negatively correlated with pair relatedness. Our finding suggests
 that territory configuration can influence rates of EGP and that
 anthropogenic habitat fragmentation has the potential to limit access to
 extra-pair mates, affecting mating systems and ultimately fitness.
description: Bain et al
 dataAll data from this
 study, organised into four tabs: ReadMe, Broods, Chicks and
 GenotypesFinalAnalysesR script containing all code necessary to repeat the analyses reported in the paper.
DOI: 10.5061/dryad.53hv6
title: Data from: Males in seemingly female-like plumage do not mimic females: UV reflectance reveals temporal cryptic dimorphism in a manakin species exhibiting delayed plumage maturation

description: Manakins (Pipridae) are neotropical birds that usually exhibit delayed
 plumage maturation (DPM). Thus, while plumage of most adult male manakins
 is brightly conspicuous, subadult males and females are basically
 dull-olive green. Although sexual dichromatism in some bird species may be
 evident only through UV reflectance, this phenomenon, known as hidden
 sexual dichromatism, has not been previously studied in manakins to
 compare subadult males and females. Within this framework, we carried out
 spectrophotometric analyses in searching for hidden sexual dichromatism in
 the white-bearded manakin Manacus manacus, through comparison of UV
 spectra in females and subadult males in green plumage. Our results
 revealed UV reflectance in both sexes in green plumage. Moreover, we found
 UV spectral differences in homologous color patches between sexes,
 particularly at belly. Since the observed differences may allow
 intraspecific sex recognition of individuals in green plumage, our results
 do not support the female-mimicry hypothesis to explain delayed plumage
 maturation in the white-bearded manakin. Although our findings dismiss the
 female mimicry hypothesis, we cannot state whether these results support
 the non-mutually exclusive cryptic and status signaling hypotheses. We
 propose then, that dull coloration of subadult males may serve both as a
 cryptic trait and to limit the energetic costs of acquiring the adult
 plumage before sexual maturity. Meanwhile, differential UV color traits
 between sexes in green plumage may allow adult males to avoid unnecessary
 energy expenditures in courtship displays in the presence of males near
 leks, and to selectively focus their the courtship displays on females. In
 accordance with the signaling status hypothesis, subadult males can be
 recognized both as males and subordinates and consequently may practice
 courtship displays without suffering aggressions by adult males. Our
 results highlight the importance to include a wider range of
 spectrophotometric information analyses for testing hypotheses regarding
 delayed plumage maturation.
description: Table S1. Museum data
 for the white-bearded manakin specimens in green plumage collected along
 the Magdalena River Valley and the Eastern Llanos in
 Colombia.Museum data for the
 white-bearded manakin specimens in green plumage collected along the
 Magdalena River Valley and the Eastern Llanos in Colombia. Hyphen
 indicates absence of geographic coordinates in the specimen label. The
 data correspond to specimens of the ornithological collections held in
 Instituto de Ciencias Naturales de la Universidad Nacional de Colombia
 (ICN) and Museo de Historia Natural de la Universidad de los Andes,
 Colombia (ANDES).Table_S1_jav_01467.pdf