cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3b2q4g1m
title: Data from: Discordant introgression in a rapidly expanding hybrid swarm

description: The erosion of species boundaries can involve rapid evolutionary change.
 Consequently, many aspects of the process remain poorly understood,
 including the formation, expansion and evolution of hybrid swarms.
 Biological invasions involving hybridization present exceptional
 opportunities to study the erosion of species boundaries because timelines
 of interactions and outcomes are frequently well known. Here, we examined
 clinal variation across codominant and maternally inherited genetic
 markers as well as phenotypic traits to characterize the expansion and
 evolution of a hybrid swarm between native Cyprinella venusta and invasive
 C. lutrensis minnows. Discordant introgression of phenotype,
 microsatellite multilocus genotype and mtDNA haplotype indicate that the
 observable expansion of the C. venusta x C. lutrensis hybrid swarm is a
 false invasion front. Both parental and hybrid individuals closely
 resembling C. lutrensis are numerically dominant in the expansion wake,
 indicating that the non-native parental phenotype may be selectively
 favored. These findings show that cryptic introgression can extend beyond
 the phenotypic boundaries of hybrid swarms, and that hybrid swarms likely
 expand more rapidly than can be documented from phenotypic variation
 alone. Similarly, dominance of a single parental phenotype following an
 introduction event may lead to instances of species erosion being mistaken
 for species displacement without hybridization.
description: Cyprinella hybrid zone
 dataFile includes raw
 morphology, mtDNA and microsatellite data. Locality and collection site
 information is also included.
DOI: 10.5061/dryad.963hr
title: Data from: A large and phylogenetically diverse class of type 1 opsins lacking a canonical retinal binding site

description: Opsins are photosensitive proteins catalyzing light-dependent processes
 across the tree of life. For both microbial (type 1) and metazoan (type 2)
 opsins, photosensing depends upon covalent interaction between a retinal
 chromophore and a conserved lysine residue. Despite recent discoveries of
 potential opsin homologs lacking this residue, phylogenetic dispersal and
 functional significance of these abnormal sequences have not yet been
 investigated. We report discovery of a large group of putatively
 non-retinal binding opsins, present in a number of fungal and microbial
 genomes and comprising nearly 30% of opsins in the Halobacteriacea, a
 model clade for opsin photobiology. We report phylogenetic analyses,
 structural modeling, genomic context analysis and biochemistry, to
 describe the evolutionary relationship of these recently described
 proteins with other opsins, show that they are expressed and do not bind
 retinal in a canonical manner. Given these data, we propose a hypothesis
 that these abnormal opsin homologs may represent a novel family of sensory
 opsins which may be involved in taxis response to one or more non-light
 stimuli. If true, this finding would challenge our current understanding
 of microbial opsins as a light-specific sensory family, and provides a
 potential analogy with the highly diverse signaling capabilities of the
 eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2
 opsins are a light-specific sub-clade.
description: SI_Dataset_1_Haloarcheal_opsin_seqsFasta file containing 170 haloarchaeal opsin sequences recovered by BLASTp searches of haloarchaeal genomes, after correcting for incorrectly called start sites. Sequences are marked with tags noting differences from corresponding NCBI records. Long = sequence is longer than corresponding NCBI record. ID_to = sequence perfectly matches multiple NCBI records, Not_ID = sequence is not identical to corresponding NCBI record, Cap = sequence has alternative annotation as “capsular polysaccharide biosynthesis protein”.SI_Dataset_2_Haloarchaeal_opsins_treeNexus formatted phylogeny file for 170 haloarchaeal opsins included in this study. Best opened with FigTree v1.4.0. Corresponds to Fig 2A and SI Fig. 5.SI_Dataset_3_Alignment_halo_trimmedFasta formatted alignment file for 170 haloarchaeal opsins included in this study after manual trimming. Remaining 204 positions were used for phylogenetic inference with MrBayes.SI_Dataset_4_Opsin_related_genes_queriesFasta formatted file containing query sequences used in BLASTp searches for brp, crtE, crtB, crtI, and crtY.SI_Dataset_5_Universal_opsins_treeNexus formatted phylogeny file for 1077 Class I opsins collected from the NCBI nr and env_nr databases. Best opened with FigTree v1.4.0. Corresponds to Fig 2C and SI Fig 3.SI_Dataset_6_Plasmid_sequences.fastaFasta formatted file containing sequences for expression vectors pMTFCHIS2 and pDJLCHIS.
DOI: 10.5061/dryad.0q13g
title: Data from: Environmental quality predicts optimal egg size in the wild

description: Parents can maximize their reproductive success by balancing the trade-off
 between investment per offspring and fecundity. According to theory,
 environmental quality influences the relationship between investment per
 offspring and offspring fitness, such that well-provisioned offspring fare
 better when environmental quality is lower. A major prediction of classic
 theory, then, is that optimal investment per offspring will increase as
 environmental quality decreases. To test this prediction, we release over
 30,000 juvenile Atlantic salmon (Salmo salar) into eight wild stream
 environments, and we monitor subsequent growth and survival of juveniles.
 We estimate the shape of the relationship between investment per offspring
 (egg size) and offspring fitness in each stream. We find that optimal egg
 size is greater when the quality of the stream environment is lower (as
 estimated by a composite index of habitat quality). Across streams, the
 mean size of stream gravel and the mean amount of incident sunlight are
 the most important individual predictors of optimal egg size. Within
 streams, juveniles recaptured in stream subsections that featured larger
 gravels and greater levels of sunlight also grew relatively quickly, an
 association that complements our cross-stream analyses. This study
 provides the first empirical verification that environmental quality
 alters the relationship between investment per offspring and offspring
 fitness, such that optimal investment per offspring increases as
 environmental quality decreases.
description: Economy_ReleasesRelease and recapture data for juvenile Atlantic salmon released in all streams in the Economy River. See Excel file for a description of column headers.Stewiacke_ReleasesRelease and recapture data for juvenile Atlantic salmon released in streams in the Stewiacke River. See Excel file for details on column headings.GreatVillage_ReleasesRelease and recapture data for all juvenile Atlantic salmon released into streams in the Great Village River. See Excel file for a description of column headers.Growth_and_HabitatGrowth of individual Atlantic salmon juveniles recaptured from eight different streams near the Minas Basin, Nova Scotia. Habitat measurements were performed within 5 meters of each juvenile collected, and all measurements are described in the Excel file.R_Script_for_estimaing_offspring_fitness_curvesThis script can be used in R, in conjunction with the dryad data "Economy_Releases.xls", "Stewiacke_Releases.xls" and "GreatVillage_Releases.xls", to estimate the relationship between egg size and offspring fitness in eight streams near the Minas Basin, Nova Scotia.
DOI: 10.5061/dryad.20407
title: Data from: Evidence for selection-by-environment but not genotype-by-environment interactions for fitness-related traits in a wild mammal population

description: How do environmental conditions influence selection and genetic variation
 in wild populations? There is widespread evidence for
 selection-by-environment interactions (S*E), but we reviewed studies of
 natural populations estimating the extent of genotype-by-environment
 interactions (G*E) in response to natural variation in environmental
 conditions, and found that evidence for G*E appears to be rare within
 single populations in the wild. Studies estimating the simultaneous impact
 of environmental variation on both selection and genetic variation are
 especially scarce. Here, we used 24 years of data collected from a wild
 Soay sheep population to quantify how an important environmental variable,
 population density, impacts upon (1) selection through annual contribution
 to fitness and (2) expression of genetic variation, in six morphological
 and life-history traits: body weight; hind leg length; parasite burden;
 horn length; horn growth; and testicular circumference. Our results
 supported the existence of S*E: selection was stronger in years of higher
 population density in all traits apart from horn growth, with directional
 selection being stronger under more adverse conditions. Quantitative
 genetic models revealed significant additive genetic variance for body
 weight, leg length, parasite burden, horn length and testes size, but not
 for horn growth or our measure of annual fitness. However, random
 regression models found variation between individuals in their responses
 to the environment in only three traits, and did not support the presence
 of G*E for any trait. Our analyses of St Kilda Soay sheep data thus
 concurs with our cross-study review that, while natural environmental
 variation within a population can profoundly alter the strength of
 selection on phenotypic traits, there is less evidence for its effect on
 the expression of genetic variance in the wild.
description: Phenotypic data
 fileThe phenotypic data
 analysed, including individual identities, years of measurement,
 morphological and fitness data.Hayward et al Soay S and
 GxE_Data.txtPedigree
 fileThe pedigree (individual
 identities and parents) used for quantitative genetic
 analysesHayward et al Soay S and
 GxE_Pedigree.txt
DOI: 10.5281/zenodo.18381690
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Shelley A. James, https://orcid.org/0000-0003-1105-1850. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.7920c
title: Data from: Tillage and fertilizer effects on crop yield and soil properties over 45 years in southern Illinois

description: Reducing soil disturbance may limit erosion, but many still consider
 tillage essential for seedbed preparation, particularly on poorly drained
 soils. Our objective was to quantify tillage and fertilizer management
 effects after 45 yr {21 in continuous corn [Zea mays L.] [CC] and 24 in
 corn–soybean [Glycine max (L.) Merr.] [CS] rotation} on a somewhat poorly
 drained silt loam near Belleville, IL. Four tillage (moldboard plow [MP],
 chisel tillage [ChT], alternate tillage [AT], and no-till [NT]) and five
 fertilizer (no fertilization, N-only, N+NPK starter, NPK+NPK starter, and
 NPK broadcast) treatments were evaluated. With N, P, and K fertilizer,
 yields were similar for tilled and NT treatments, averaging 8.73 Mg ha–1
 for CC and 11.93 Mg ha–1 and 3.70 Mg ha–1 for rotated corn and soybean.
 Below recommended soil-test values resulted in NT yielding less than
 tilled treatments even though soil test P, K, and pH were similar. No-till
 with N, P, and K increased soil organic matter (OM) to 27.6 g kg–1 (20.5 g
 kg–1 in all other treatments), with the greatest increase from 0- to 5-cm.
 No-till treatments showed stratification of P and K, but it had no effect
 on yield. No excessive pH stratification was observed. Overall, fertilizer
 management predominantly influenced crop yield and with complete NPK
 management non-tilled yields were similar to tilled, even on flat,
 somewhat-poorly drained soils. No-till with NPK management therefore may
 allow farmers to maintain high yields while reducing soil and nutrient
 losses.
description: Tillage x Fertility Crop
 Yields 1970-2015, Soils, and Plant TissueThese data represent
 crop yield data from 1970 to 2015 for the long-term Tillage x Fertility
 trial started by Dr. George Kapusta at the Southern Illinois University
 Belleville Research Center in Belleville, IL. Some other agronomic data
 are also included.BRC_TxF_yield_1970-2015.csvTxF soils increment data 1990 and 2013These data were used for the Cook and Trlica 2016 publication. Soil plow layer (0-15 cm) was constructed from 5-cm increments. Metadata is included with the yield README file.BRC_TxF_soils_increments_1990_2013.csvTxF Corn plant tissue 1990 and 2014These data were analyzed for the Cook and Trlica 2016 publication. Metadata are found in the yield README file.BRC_TxF_Plant_tissue_1990_2014 Corn.csvTxF historic soils composites 1978 1983 1990 1999 2011 2013These data were NOT included in the Cook and Trlica 2016 publication. Curation for the historic soils data was imperfect and any use of this data should be considered not completely reliable. A thorough explanation of data processing and data issues is included in the README file. The composite samples were for the most part collected and analyzed at 0-15 cm soil cores.BRC_TxF_soils_composite_78 83 90 99 2011 2013.csv
DOI: 10.5281/zenodo.3235490
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Shelley A. James, https://orcid.org/0000-0003-1105-1850. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.qd53c
title: Data from: Shaping the latitudinal diversity gradient: New perspectives from a synthesis of paleobiology and biogeography

description: An impediment to understanding the origin and dynamics of the latitudinal
 diversity gradient (LDG) -- the most pervasive large-scale biotic pattern
 on Earth -- has been the tendency to focus narrowly on a single causal
 factor, when a more synthetic, integrative approach is needed. Using
 marine bivalves as a model system, and drawing on other systems where
 possible, we review paleobiologic and biogeographic support for two
 supposedly opposing views, that the LDG is shaped primarily by (a) local
 environmental factors that determine the number of species and higher taxa
 at a given latitude (in-situ hypotheses), or (b) the entry of lineages
 arising elsewhere into a focal region (spatial-dynamics hypotheses).
 Support for (a) includes the fit of present-day diversity trends in many
 clades to environmental factors such as temperature, and the correlation
 of extinction intensities in Pliocene bivalve faunas with net regional
 temperature changes. Support for (b) includes the age-frequency
 distribution of bivalve genera across latitudes, which is consistent with
 an out-of-the-tropics dynamic, as are the higher species diversities in
 temperate southeast Australia and southern Japan than in the tropical
 Caribbean. Thus, both in-situ and spatial-dynamics processes must shape
 the bivalve LDG, and are likely to operate in other groups as well. The
 relative strengths of the two processes may differ among groups showing
 similar LDGs, but dissecting their effects will require improved methods
 of integrating fossil data with molecular phylogenies. We highlight
 several potential research directions, and argue that many of the most
 dramatic biotic patterns, past and present, are likely to have been
 generated by diverse, mutually reinforcing drivers.
description: JablonskiEtAlShapingLatDivGradientSupplTables1&2Table 1 - Geologic ages of extant marine bivalves, Arctic, Tropical, and Antarctic faunas, with supporting references; Table 2 - extant marine bivalve species in SE Japan and SE Australia, with supporting references
DOI: 10.5061/dryad.45dn8
title: Data from: Slow development as an evolutionary cost of long life

description: Life-history theory predicts a trade-off between early-life fitness and
 life span. While the focus traditionally has been on the fecundity-life
 span trade-off, there are strong reasons to expect trade-offs with growth
 rate and/or development time. We investigated the roles of growth rate and
 development time in the evolution of life span in two independent
 selection experiments in the outcrossing nematode Caenorhabditis remanei.
 First, we found that selection under heat-shock leads to the evolution of
 increased life span without fecundity costs, but at the cost of slower
 development. Thereafter, the putative evolutionary links between
 development time, growth rate, fecundity, heat-shock resistance and life
 span were independently assessed in the second experiment by directly
 selecting for fast or slow development. This experiment confirmed our
 initial findings, since selection for slow development resulted in the
 evolution of long life span and increased heat-shock resistance. Because
 there were no consistent trade-offs with growth rate or fecundity, our
 results highlight the key role of development rate – differentiation of
 the somatic cells per unit of time – in the evolution of life span. Since
 development time is under strong selection in nature, reduced somatic
 maintenance resulting in shorter life span may be a widespread cost of
 rapid development.
description: Juvenile data
 femalesDevelopment time to
 maturation, area at maturation and juvenile growth rate for females from
 development-selected lines.devselected_juvenile_female.xlsxJuvenile data malesDevelopment time to maturation, area at maturation and juvenile growth rate for males from development-selected lines.devselected_juvenile_males.xlsxAge-specific reproduction and size - femalesAge-specific size and reproduction for females. Day 0 = day of maturation. Size was not measured every day.female size repr.xlsxTotal reproduction and lambda - femalesTotal reproduction over lifespan and lambda for individual females.female totrep lambda.xlsxHeatshock resistance males and femalesHeatshock resistance (alive/dead) per plate for both males and femalesheatshock.xlsxAge-specific reproduction and size - malesAge-specific size and reproduction for development-selected males. Note that traits were not measured every day.males size repr.xlsxTotal reproduction and lambda - malesTotal reproduction and lambda for males. Note that this is based upon the subset of times measured.males totrep lambda.xlsxMortality-selected lines: juvenile traitsDevelopment time (h), area at maturity and juvenile growth rate of females from mortality-selected lines.mortalityselected.xlsxSurvival: matricide includedSurvival of development-selected lines. Matricide treated as dead. See other file for matricide censored.survival_incl_matricide.xlsxSurvival: matricide censoredSurvival of development-selected lines. Worms dying of matricide are censored in this dataset.survival.xlsx
DOI: 10.5061/dryad.61r43kd
title: Data from: Interpersonal variations in gut microbiota profiles supersedes the effects of differing fecal storage conditions

description: Due to ease of acquisition, fecal samples are often used in studies
 investigating gut microbiota. Improper handling of these samples can lead
 to bacterial growth and alter bacterial composition. While freezing
 samples at −80 °C is considered gold standard, this is not suitable for
 studies utilizing self-sampling by lay participants or field studies. Thus
 to effectively prevent bacterial growth, techniques that allow efficient
 fecal storage outside laboratory facilities are needed. Fecal samples were
 collected from three donors. From each donor feces, 45 samples were
 collected and stored either freshly frozen at −80 or −20 °C, or in three
 separate storage buffers at room temperature or 4 °C for 24 or 72 hours.
 Bacterial composition was analyzed using Illumina amplicon sequencing of
 the V4 region of the 16 S rRNA gene. While storage conditions did affect
 bacterial composition and diversity compared to storage at −80 °C, the
 variation between donors superseded the variations introduced by storage.
 Samples stored at −20 °C most closely resembled those stored at −80 °C.
 When investigating variations in bacterial composition between separate
 study populations, fecal samples can efficiently be stored in −20 °C
 freezers or in one of the presented storage buffers, without severe
 alterations in bacterial composition.
description: Supplementary_MetadataMetadata describing information regarding each sample included in the study. The metadata includes sequence ID, DNA yield following DNA extraction and library generation, storage conditions, DNA quality and donor.Supplementary_OTUtableOTUtable with OTUs generated during this study. For each sample, sequence ID matching that of Supplementary_Metadata, the total number of OTUs belonging to different bacterial taxonomic groups as assigned by the RDP classifier, are listed.
DOI: 10.5061/dryad.q9c98
title: Data from: How differential management strategies affect Ips typographus L. dispersal

description: Bark beetle outbreaks have a devastating effect on economically important
 forests worldwide, thus requiring extensive application of management
 control strategies. The presence of unmanaged protected areas in close
 proximity to managed forests can instigate concerns that bark beetle
 infestations may spread from unmanaged into managed stands. We studied the
 impact of differential management of forest stands on the dispersal
 dynamics of the European spruce bark beetle, Ips typographus, making use
 of inferential population genetics on mitochondrial and nuclear genomes.
 Bayesian inferences of migration rates and a most parsimonious dispersal
 tree show that outgoing gene flow was consistently higher from managed to
 unmanaged areas. Reason for that is likely the thorough removal of
 potential breeding material in managed forests and thus the dispersal of
 the base stock beetles from these areas to unmanaged areas where breeding
 material is available. Our study suggests that the potential threat posed
 by unmanaged to managed forests in regard to I. typographus infestation
 needs to be carefully re-considered.
description: STRs_lengthIndividual genotypes of bark beetle populations for STRs lociSRR_050714.xlsxmtDNA_sequencesCOI_gene individual sequences of bark beetle populationsmtDNA.fas