cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5066/p1damsmx
title: Concentration results for per- and polyfluoroalkyl substances (PFAS) analyzed in fish tissue, bed sediment, and biofilm samples, Montana, 2023

description: This data release contains the concentration results of per- and polyfluoroalkyl substances (PFAS) collected in fish tissue and whole blood, bed sediment and biofilm samples from water bodies in and surrounding the Little Bighorn River (LBHR) in Montana in July 2023. A total of 29 filets and whole blood samples were collected from 10 brown trout, 10 catfish, 6 rock bass, and 3 goldeye specimens collected by U.S. Geological Survey personnel and community volunteers in two locations along the LBHR. Bed sediment samples were collected from the top 2.54 centimeters in depositional zones in 12 sampling locations where surface-water-quality samples also were collected (Romanok and others, 2023). Biofilm scrapings were collected from rocks at five locations on the LBHR where bed-sediment and surface-water-quality samples were collected. Fish filet, whole blood, and biofilm samples were analyzed for 28 PFAS at RTI Laboratories, Inc., Livonia, Michigan, following EPA method 537.1 (liquid chromatography, tandem mass spectrometry). Bed-sediment samples were analyzed for 40 PFAS at SGS AXYS, Sidney, British Columbia, Canada, also using EPA method 537.1. References cited: Romanok, K.M., Bradley, P.M., Smalling, K.L., Doyle, J.T., Eggers, M.J., Gray, J.L., Hladik, M.L., Kanagy, L.K., McCleskey, R.B., Meppelink, S.M., Richards, C.L., and Roth, D.A., 2023, Target-chemical concentrations and microbiological results in surface water and tapwater, Montana, 2022-23 (ver. 2.0, December 2025): U.S. Geological Survey data release, https://doi.org/10.5066/P9R7MV6I.
DOI: 10.5061/dryad.984fn
title: Data from: Tisaniba, a new genus of marpissoid jumping spiders from Borneo (Araneae: Salticidae)

description: Six new species of marpissoid jumping spiders from Sarawak, Borneo, are
 described in the new genus Tisaniba Zhang & Maddison. They are the
 type species, T. mulu Zhang & Maddison sp. nov., as well as the
 species T. bijibijan Zhang & Maddison sp. nov., T. dik Zhang
 & Maddison sp. nov., T. kubah Zhang & Maddison sp. nov.,
 T. selan Zhang & Maddison sp. nov., and T. selasi Zhang &
 Maddison sp. nov. The spiders are small and brown to black, living in leaf
 litter in the tropical forest. Phylogenetic analyses based on 28s and
 16sND1 genes indicate that they are a distinctive group within the
 marpissoids. Diagnostic illustrations and photographs of living spiders
 are provided for all species.
description: Tisaniba-ZhangMaddison2014Contains alignments for 28s and 16sND1 for both the broad sample dataset and the marpissoid dataset, and trees for both.
DOI: 10.5061/dryad.4013p
title: Data from: Reproductive assurance drives transitions to self-fertilization in experimental Caenorhabditis elegans

description: Background: Evolutionary transitions from outcrossing between individuals
 to selfing are partly responsible for the great diversity of animal and
 plant reproduction systems. The hypothesis of ‘reproductive assurance’
 suggests that transitions to selfing occur because selfers that are able
 to reproduce on their own ensure the persistence of populations in
 environments where mates or pollination agents are unavailable. Here we
 test this hypothesis by performing experimental evolution in
 Caenorhabditis elegans. Results: We show that self-compatible
 hermaphrodites provide reproductive assurance to a male-female population
 facing a novel environment where outcrossing is limiting. Invasions of
 hermaphrodites in male-female populations, and subsequent experimental
 evolution in the novel environment, led to successful transitions to
 selfing and adaptation. Adaptation was not due to the loss of males during
 transitions, as shown by evolution experiments in exclusively
 hermaphroditic populations and in male-hermaphrodite populations. Instead,
 adaptation was due to the displacement of females by hermaphrodites.
 Genotyping of single-nucleotide polymorphisms further indicated that the
 observed evolution of selfing rates was not due to selection of standing
 genetic diversity. Finally, numerical modelling and evolution experiments
 in male-female populations demonstrate that the improvement of male
 fitness components may diminish the opportunity for reproductive
 assurance. Conclusions: Our findings support the hypothesis that
 reproductive assurance can drive the transition from outcrossing to
 selfing, and further suggest that the success of transitions to selfing
 hinges on adaptation of obligate outcrossing populations to the
 environment where outcrossing was once a limiting factor.
description: elegans.assuranceexcel file with multiple sheets, see readme text file for description of the data
DOI: 10.5061/dryad.8jf2k
title: Data from: The breakdown of static and evolutionary allometries during climatic upheaval

description: The influence of within-species variation and covariation on evolutionary
 patterns is well established for generational and macroevolutionary
 processes, most prominently through genetic lines of least resistance.
 However, it is not known whether intraspecific phenotypic variation also
 directs microevolutionary trajectories into the long term when a species
 is subject to varying environmental conditions. Here we present a
 continuous, high-resolution bivariate record of size and shape changes
 among 12,633 individual planktonic foraminifera of a surviving and an
 extinct-going species over 500 thousand years. This time interval spans
 the late Pliocene to earliest Pleistocene intensification of Northern
 Hemisphere glaciation, an interval of profound climate upheaval that can
 be divided into three phases of increasing glacial intensity. We found
 that within each of these three Plio-Pleistocene climate phases the
 within-population allometries predict evolutionary change from one
 time-step to the next, and that the within-phase among-population (i.e.
 evolutionary) allometries match their corresponding static
 (within-population) allometries. However, the evolutionary allometry
 across the three climate phases deviates significantly from the static and
 phase-specific evolutionary allometries in the extinct-going species.
 Although intraspecific variation leaves a clear signature on mean
 evolutionary change from one time-step to the next, our study suggests
 that the link between intraspecific variation and longer-term micro- and
 macroevolutionary phenomena is prone to environmental perturbation that
 can overcome constraints induced by within-species trait covariation.
description: Shall area and aspect
 ratio of G. puncticulata and T. crassaformisShell size and shape of
 the planktonic foraminifera species Globoconella puncticulata and
 Truncorotalia crassaformis are presented, with sample ID. Sample age as
 determined by the age model by Bolton et al., 2010
 (Paleoceanography).Data Brombacher et
 al.xlsx
DOI: 10.5061/dryad.p069231
title: Data from: A simulation-based approach to statistical alignment

description: Classic alignment algorithms utilize scoring functions which maximize
 similarity or minimize edit distances. These scoring functions account for
 both insertion-deletion (indel) and substitution events. In contrast,
 alignments based on stochastic models aim to explicitly describe the
 evolutionary dynamics of sequences by inferring relevant probabilistic
 parameters from input sequences. Despite advances in stochastic modeling
 during the last two decades, scoring-based methods are still dominant,
 partially due to slow running times of probabilistic approaches. Alignment
 inference using stochastic models involves estimating the probability of
 events, such as the insertion or deletion of a specific number of
 characters. In this work, we present SimBa-SAl, a simulation-based
 approach to statistical alignment inference, which relies on an explicit
 continuous Markov process for both indels and substitutions. SimBa-SAl has
 several advantages. First, using simulations, it decouples the estimation
 of event probabilities from the inference stage, which allows the
 introduction of accelerations to the alignment inference procedure.
 Second, it is general and can accommodate various stochastic models of
 indel formation. Finally, it allows computing the maximum-likelihood
 alignment, the probability of a given pair of sequences integrated over
 all possible alignments, and sampling alternative alignments according to
 their probability. We first show that SimBa-SAl allows accurate estimation
 of parameters of the long-indel model previously developed by Miklós,
 Lunter and Holmes in 2004. We next show that SimBa-SAl is more accurate
 than previously developed pairwise alignment algorithms, when analyzing
 simulated as well as empirical datasets. Finally, we study the
 goodness-of-fit of the long-indel and TKF91 models. We show that while the
 long-indel model fits the datasets better than TKF91, there is still room
 for improvement concerning the realistic modeling of evolutionary sequence
 dynamics.
description: SimBa_SAl_Supplementary_InformationSupplementary InformationSimBa_SAl_Supp_Revised.docx
DOI: 10.5061/dryad.qb4gs
title: Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis

description: Mosquito-borne infectious diseases are emerging in many regions of the
 world. Consequently, surveillance of mosquitoes and concomitant infectious
 agents is of great importance for prediction and prevention of
 mosquito-borne infectious diseases. Currently, morphological
 identification of mosquitoes is the traditional procedure. However,
 sequencing of specified genes or standard genomic regions, DNA barcoding,
 has recently been suggested as a global standard for identification and
 classification of many different species. Our aim was to develop a genetic
 method to identify mosquitoes and to study their relationship. Mosquitoes
 were captured at collection sites in northern Sweden and identified
 morphologically before the cytochrome c oxidase subunit I (COI) gene
 sequences of 14 of the most common mosquito species were determined. The
 sequences obtained were then used for phylogenetic placement, for
 validation and benchmarking of phenetic classifications, and finally to
 develop a hierarchical PCR-based typing scheme based on single nucleotide
 polymorphism sites (SNPs) to enable rapid genetic identification,
 circumventing the need for morphological characterization. The results
 showed that exact phylogenetic relationships between mosquito taxa were
 preserved at shorter evolutionary distances, but at deeper levels they
 could not be inferred with confidence by using COI gene sequence data
 alone. Fourteen of the most common mosquito species in Sweden were
 identified by the SNP/PCR-based typing scheme, demonstrating that genetic
 typing using SNPs of the COI gene is a useful method for identification of
 mosquitoes with potential for worldwide application.
description: 5P_COI_MSA3P_COI_MSAMosquito_COI
DOI: 10.5061/dryad.d1d30
title: Data from: Carbon stocks in the Guinea savanna of Ghana: estimates from three protected areas

description: Savannas are widespread in sub-Saharan Africa (SSA) and unarguably play
 major role in the global carbon balance. Extensive quantification of
 carbon stocks of the savannas in SSA will therefore contribute
 significantly to the global carbon budget in the era of climate change. In
 this study, we investigated the spatial distribution of carbon stocks of
 different soil fractions from the dominant tree species (Vitellaria
 paradoxa) of three forest reserves in the Guinea savanna of Ghana as well
 as the tree and non-tree carbon stocks. The study was carried out in
 Kenikeni, Sinsablegbinni and Klupene forest reserves using nested plot
 design. Higher soil carbon stock (SCS) was associated with the silt +clay
 fraction than the microaggregates and small macroaggregates of all three
 protected areas. Soil carbon stocks ranged from 2.99 to 15.89 Mg C /ha in
 the surface soil of 0-10 cm depth. The highest SCS was recorded at the
 sub-canopy (SC), drip line (DL) and 2(SC + DL) zones from the dominant
 tree of the Klupene, Sinsablegbinni and Kenikeni forest reserves,
 respectively. The highest tree carbon stock of 60.57 Mg C/ha was recorded
 in Kenikeni as compared to 26.98 Mg C/ha of Sinsablegbinni, which had the
 highest stocking density. Average carbon capture by a single tree ranged
 from 0.04 to 0.34 Mg C. Grass C stock in the above- ground biomass ranged
 from 0.09 to 0.29 Mg C /ha whilst the below ground carbon stock ranged
 from 0.03 to 0.44 Mg C /ha. Accumulation of carbon in the aboveground
 grass biomass increased with decreasing forest cover, whereas that of the
 below ground biomass increased with increasing forest cover with
 implications for forest management in the savanna.
description: JAB
 FINAL2_Logah_Biotropica
DOI: 10.5061/dryad.9rj26
title: Data from: Why we need more nature at work: effects of natural elements and sunlight on employee mental health and work attitudes

description: This study investigated the effects of natural elements and direct and
 indirect sunlight exposure on employee mental health and work attitudes.
 We recruited participants via an online panel from the United States and
 India, and analyzed data from 444 employees. Natural elements and sunlight
 exposure related positively to job satisfaction and organizational
 commitment, and negatively to depressed mood and anxiety. Direct sunlight
 was a dominant predictor of anxiety; indirect sunlight was a dominant
 predictor of depressed mood, job satisfaction, and organizational
 commitment. Natural elements buffered the relationship between role
 stressors and job satisfaction, depressed mood, and anxiety. We also found
 that depressed mood partially mediated the relationship between natural
 elements and job satisfaction. We discuss scientific and policy
 implications of these findings.
description: PHE&RoleStress_FinalThis data set is for PHE study. It includes variables, Sunlight, Natural elements (Greenery), role stressors, job satisfaction, organizational commitment (or satisfaction), depression and anxiety. In addition, data were collected from two countries, U.S and India (name of variable: Country).SI files_table, figure and scale. PHEIt is a collection of the supporting files for PHE, including tables, figures and scales.
DOI: 10.5061/dryad.kh356
title: Data from: Movement responses of caribou to human-induced habitat edges lead to their aggregation near anthropogenic features

description: The assessment of disturbance effects on wildlife and resulting mitigation
 efforts are founded on edge-effect theory. According to the classical
 view, the abundance of animals affected by human disturbance should
 increase monotonically with distance from disturbed areas to reach a
 maximum at remote locations. Here we show that distance-dependent movement
 taxis can skew abundance distributions toward disturbed areas. We develop
 an advection-diffusion model based on basic movement behavior commonly
 observed in animal populations and parameterize the model from
 observations on radio-collared caribou in a boreal ecosystem. The model
 predicts maximum abundance at 3.7 km from cutovers and roads.
 Consistently, aerial surveys conducted over 161,920 km2 showed that the
 relative probability of caribou occurrence displays nonmonotonic changes
 with the distance to anthropogenic features, with a peak occurring at 4.5
 km away from these features. This aggregation near disturbed areas thus
 provides the predators of this top-down-controlled, threatened herbivore
 species with specific locations to concentrate their search. The
 edge-effect theory developed here thus predicts that human activities
 should alter animal distribution and food web properties differently than
 anticipated from the current paradigm. Consideration of such nonmonotonic
 response to habitat edges may become essential to successful wildlife
 conservation.
description: Average Vector
 DirectionData used to evaluate
 changes in the orientation of caribou with respect to the nearest road or
 cut block as a function of distance from these anthropogenic features
 (Fig. B1 Online Appendix B).AvgVectorDirection.xlsxData for GAM analysisData used to model the relative probability of occurrence of caribou track networks in winter as a function of the distance from the nearest anthropogenic disturbance (Table 1). Landscape features (distance from the nearest cut block or road, various land cover types) are provided at observed track network locations and at random locations.GAM.xlsHome RangeCharacteristics of home ranges of GPS-collared caribou in managed boreal forests. Home ranges were delineated using the Brownian bridge kernel method.Distance to human disturbances for VHF dataDistances between the centroid locations of VHF-collared caribou and the nearest cut, the nearest primary road and the nearest secondary road, according to whether the information was gathered in the current year (Year 0) and the following year (Year 1).VHF.xls
DOI: 10.5061/dryad.2d53k
title: Data from: The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean

description: Uncovering the genetic basis of phenotypic variation and the population
 history under which it established is key to understand the trajectories
 along which local adaptation evolves. Here, we investigated the genetic
 basis and evolutionary history of a clinal plumage color polymorphism in
 European barn owls (Tyto alba). Our results suggest that barn owls
 colonized the Western Palearctic in a ring-like manner around the
 Mediterranean and meet in secondary contact in Greece. Rufous coloration
 appears to be linked to a recently evolved non-synonymous derived variant
 of the melanocortin-1-receptor (MC1R) gene, which according to
 quantitative genetic analyses evolved under local adaptation during or
 following the colonization of Central Europe. Admixture patterns and
 linkage disequilibrium between the neutral genetic background and color
 found exclusively within the secondary contact zone suggest limited
 introgression at secondary contact. These results from a system
 reminiscent of ring species provide a striking example of how local
 adaptation can evolve from derived genetic variation.
description: Per-individual
 microsatellite and MC1R genotypes, coloration, and sex
 dataColumns contain the
 following data: Individual ID, Population, Sex, Brown chroma (coloration),
 MC1R genotype at amino acid position 126 (Ile126Val polymorphism),
 Microsatellite genotypes (the two alleles of each locus are given in two
 subsequent rows)DRYAD_msat&MC1R-genotypes_sex_coloration.txtMC1R sequencesColumns contain the following data: Individual ID, Population, MC1R sequence (unphased, heterozygous positions are provided in IUPAC degenerate code)DRYAD_MC1R-sequences.txtND6 haplotypesColumns contain the following data: Individual ID, Population, ND6 haplotypeDRYAD_ND6-haplotypes.txt
DOI: 10.5061/dryad.162
title: Data from: Compensatory evolution in RNA secondary structures increases substitution rate variation among sites

description: There is growing evidence that interactions between biological molecules
 (e.g., RNA-RNA, protein-protein, RNA-protein) place limits on the rate and
 trajectory of molecular evolution. Here, by extending Kimura's model
 of compensatory evolution at interacting sites, we show that the ratio of
 transition to transversion substitutions (κ) at interacting sites should
 be equal to the square of the ratio at independent sites. Because
 transition mutations generally occur at a higher rate than transversions,
 the model predicts that κ should be higher at interacting sites than at
 independent sites. We tested this prediction in 10 RNA secondary
 structures by comparing phylogenetically derived estimates of κ in paired
 sites within stems (κ(p)) and unpaired sites within loops (κ(u)). Eight of
 the 10 structures showed an excellent match to the quantitative
 predictions of the model, and 9 of the 10 structures matched the
 qualitative prediction κ(p) &gt; κ(u). Only the Rev response element
 from the human immunovirus (HIV) genome showed the reverse pattern, with
 κ(p) &lt; κ(u). Although a variety of evolutionary forces could
 produce quantitative deviations from the model predictions, the reversal
 in magnitude of κ(p) and κ(u) could be achieved only by violating the
 model assumption that the underlying transition (or transversion) mutation
 rates were identical in paired and unpaired regions of the molecule. We
 explore the ability of the APOBEC3 enzymes, host defense mechanisms
 against retroviruses, which induce transition mutations preferentially in
 single-stranded regions of the HIV genome, to explain this exception to
 the rule. Taken as a whole, our findings suggest that kappa may have
 utility as a simple diagnostic to evaluate proposed secondary structures.
description: 23S Alignment and
 Tree23SandTREE.nexIRES Alignment and TreeIRESandTREE.nextRNA Mammalian Alignment and TreetRNA_mammalianANDtree.nexRNase P_10 Alignment and TreeRNaseP_10andTREE.nex12S rRNA Alignment and Tree12SrRNAandTREE.nexCRE Alignment and TreeCREandTREE.nexRRE Alignment and TreeRREandTREE.nex5S Alignment and Tree5SandTREE.nextRNA Amphibian Alignment and TreetRNA_amphibianANDtree.nexPartition Informationparttioninfo.txt16S Alignment and Tree16SandTREE.nex
DOI: 10.5061/dryad.85q6j
title: Data from: Utility of pooled sequencing for association mapping in non-model organisms

description: High density genome-wide sequencing increases the likelihood of
 discovering genes of major effect and genomic structural variation in
 organisms. While there is an increasing availability of reference genomes
 across broad taxa, the greatest limitation to whole-genome sequencing of
 multiple individuals continues to be the costs associated with sequencing.
 To alleviate excessive costs, pooling multiple individuals with similar
 phenotypes and sequencing the homogenized DNA (Pool-Seq) can achieve high
 genome coverage, but at the loss of individual genotypes. Although
 Pool-Seq has been an effective method for association mapping in model
 organisms, it has not been frequently utilized in natural populations. To
 extend bioinformatic tools for rapid implementation of Pool-Seq data in
 non-model organisms, we developed a pipeline called PoolParty and
 illustrate its effectiveness in genetic association mapping. Alignment
 expectations based on five pooled Chinook salmon (Oncorhynchus
 tshawytscha) libraries showed that approximately 48% genome coverage per
 library could be achieved with reasonable sequencing effort. We
 additionally examined male and female O. tshawytscha libraries to
 illustrate how Pool-Seq techniques can successfully map known genes
 associated with functional differences among sexes such as growth hormone
 2. Finally, we compared pools of individuals of different spawning ages
 for each sex to discover novel genes involved with age at maturity in O.
 tshawytscha such as opsin4 and transmembrane protein19. While not
 appropriate for every system, Pool-Seq data processed by the PoolParty
 pipeline is a practical method for identifying genes of major effect in
 non-model organisms when high genome coverage is necessary and cost is a
 limiting factor.
description: Modified NebNext PoolSeq
 ProtocolCurrent version of
 NEBNext ultra fragmentase protocol for pooled
 sequencing.NEBNEXT_poolseq_protocol.docx