cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.026np03
title: Data from: Ongoing hybridization obscures phylogenetic relationships in the Drosophila subquinaria species complex

description: Inferring evolutionary relationships among recently diverged lineages is
 necessary to understand how isolating barriers produce independent
 lineages. Here we investigate the phylogenetic relationships between three
 incompletely isolated and closely related mushroom-feeding Drosophila
 species. These species form the Drosophila subquinaria species complex and
 consist of one Eurasian species (D. transversa) and two widespread North
 American species (D. subquinaria and D. recens) that are sympatric in
 central Canada. While patterns of pre- and post-mating isolation among
 these species are well characterized, previous work on their phylogenetic
 relationships is limited and conflicting. In this study, we generated a
 multi-locus dataset of 29 loci from across the genome sequenced in a
 population sample from each species, and then we inferred species
 relationships and patterns of introgression. We find strong statistical
 support that D. subquinaria is paraphyletic, showing that samples from the
 geographic region sympatric with D. recens are most closely related to D.
 recens whereas samples from the geographic region allopatric with D.
 recens are most closely related to D. transversa. We present several lines
 of evidence that both incomplete lineage sorting and gene flow are causing
 phylogenetic discordance. We suggest that ongoing gene flow primarily from
 D. recens into D. subquinaria in the sympatric part of their ranges causes
 phylogenetic uncertainty in the evolutionary history of these species. Our
 results highlight how population genetic data can be used to disentangle
 the sources of phylogenetic discordance among closely related species.
description: MrBayes
 analysesSequence alignments with
 command blocks for all phylogenetic analyses using MrBayes
 3.6.1MrBayes.zipQuartet_samplingPhylogenies in newick format with sequence alignments in phylip format and accompanying commands used for analyses.*Beast .xml files*Beast v2.5.1 .xml files for three independent runs later combined in final results.StarBeast.zipMigrate-n analysesParameter files for final Migrate-n v3.6.11 runs. Start parameters are estimated from data or from medians of previous runs. Models are designated as free: all parameters free to vary; StoR: migration from D. recens to D. subquinaria set to zero; RtoS: migration from D. subquinaria to D. recens set to zero; and symmetric: migration rates are constrained to be symmetric. Sequence alignments in modified phylip format are included.Migrate-n.zipABBA BABA testsSequence alignments by species for nuclear concatenation (except Y-linked loci) and by locus with R script for analysis using evobiR package.ABBA_BABA.zip
DOI: 10.6073/pasta/eec234feca4c123dce9f999fb8f09ac6
title: GCE-LTER Altamaha River Plant Community Monitoring Survey in October 2024

description: A quadrat survey was conducted in October 2024 to measure the species and size distribution of plants at 3 sampling sites on the creekbank of the Altamaha River. The sites were chosen to capture the transition from Spartina alterniflora to Spartina cynosuroides (site SCSA) and the transition from Spartina cynosuroides to Zizaniopsis miliacea (sites ZSC1 and ZSC2). The quadrats were established as permanent plots in October 2012 by placing PVC stakes along the creekbank at each site. Plots were evenly spaced, but were not randomly located because the goal was to start with mixtures of vegetation in most of the plots, and vegetation was distributed in patches along the creekbanks. Therefore, these plots provide useful measures of vegetation change, but are not a random sample of the vegetation at the site. Plots will be replaced each year as necessary to replace any lost to disturbance. The plots were visually surveyed and the species, shoot height, and flowering status was recorded individually for each shoot over 10 cm in height present in each plot. Observations from plots exhibiting signs of disturbance were noted in a separate data set. This survey will be repeated annually to assess changes in plant distribution and biomass in relation to environmental changes documented by other GCE LTER monitoring efforts.
DOI: 10.5061/dryad.6kg1sd7
title: Data from: Association of diabetic retinopathy and diabetic macular edema with renal function in southern Chinese patients with type 2 diabetes mellitus: a single-center observational study

description: Background and Objectives: The association of diabetic retinopathy (DR)
 and diabetic macular edema (DME) with renal function in southern Chinese
 diabetic patients is poorly understood. So we aimed to study the
 correlation between stage of DR and DME with stage of eGFR (estimated
 glomerular filtration rate) and stage of UACR (urine albumin to creatinine
 ratio), and to explore the systemic risk factors for DR and DME. Design
 and Setting: Single-center retrospective observational study.
 Participants: 413 southern Chinese patients with type two diabetes
 mellitus (T2DM). Outcome Measures: The correlations between stage of DR
 and DME with stage of eGFR/UACR were assessed by spearman or Χ² analyses
 and represented with histograms. Risk factors associated with the
 occurrence of DR and DME were performed by logistic regression and
 represented with nomograms. Results: Stage of DR had a positive
 correlation with stage of eGFR (r=0.264, p＜0.001) and stage of UACR
 (r=0.542, p＜0.001). With the stage of eGFR/UACR being more severe, the
 prevalence of DME became higher as well (both p＜0.001). The risk factors
 for DR were DM duration (OR, 1.072; 95% CI, 1.032–1.114; P＜0.001), stage
 of UACR (OR, 2.001; 95% CI, 1.567-2.555; P＜0.001) and LDL (OR, 1.301; 95%
 CI, 1.139-1.485; P＜0.001), while risk factors for DME were stage of UACR
 (OR, 2.308; 95% CI, 1.815-2.934; P＜0.001) and LDL (OR, 1.460; 95% CI,
 1.123–1.875; P=0.008). Conclusions: Among southern Chinese patients, stage
 of DR and DME were positively correlated with renal function, while stage
 of UACR performed a better relevance than stage of eGFR.
description: datas
DOI: 10.5061/dryad.99sq846
title: Data from: LiDAR and RGB-image analysis to predict hairy vetch biomass in breeding nurseries

description: Hairy vetch is a fall seeded annual legume that can be used as a forage
 and cover crop. As a cover crop, it can provide numerous ecosystem
 services, such as soil erosion reduction, carbon sequestration, and
 pollinator habitat, but also agronomic services such as weed suppression
 and N fixation via soil rhizobium species. To improve cover crop function,
 traits such as biomass production are especially relevant, making it a
 first priority trait for cover crop breeders. However, direct phenotypic
 methods for biomass production are destructive. Breeders have thus relied
 on subjective, visual scoring methods for biomass, which are generally
 correlative, but are not quantitative or absolute. In this study, we
 evaluated two low-cost remote sensing tools, LiDAR and RGB-image analysis,
 for their effectiveness at predicting biomass in vivo. We evaluated these
 tools in two common forage breeding scenarios, spaced-plant and sward-plot
 nurseries, at three Minnesota locations following the winter of 2016/2017.
 Ground cover, determined from RGB image binarization using the Canopeo
 application, had a significant and linear relationship with above-ground
 biomass in spaced-plants (R2=0.93), and sward-plots (R2=0.89). Once the
 image area became saturated with vegetative pixels, a near-exponential
 relationship with biomass would occur. Because of the low-growth habit of
 hairy vetch, RGB image analysis was more appropriate at lower plant
 densities, such as spaced-plant nurseries. LiDAR measures of sward-plot
 height were also linearly and strongly related to dry-matter biomass in
 sward-plots (R2=0.80). The dimensionality of LiDAR sensing gave it greater
 predictive ability at higher plant densities, where RGB analysis could not
 detect vertical increases in biomass production. Lastly, we combined RGB
 and LiDAR data to predict sward-plot biomass in a multiple mixed-effect
 regression model. By doing so, we were able to explain more biomass
 variation than with use of either phenotypic tool as a single predictor
 (R2=0.94).
description: LiDAR and RGB canopy
 cover relationship with biomass in hairy vetchLiDAR and RGB canopy
 cover estimates were evaluated for predictive ability of hairy vetch dry
 matter biomass in spaced or sward plot breeding nurseries. All necessary
 files are within the ZIP file. See the README file for greater detail. R
 scripts and html data analysis output are provided.2019_wiering_etal.zip
DOI: 10.5061/dryad.647b5h6
title: Data from: Partner’s age, not social environment, predicts extrapair paternity in wild great tits (Parus major)

description: An individual’s fitness is not only influenced by its own phenotype, but
 by the phenotypes of interacting conspecifics. This is likely to be
 particularly true when considering fitness gains and losses caused by
 extrapair matings, as they depend directly on the social environment.
 While previous work has explored effects of dyadic interactions, limited
 understanding exists regarding how group-level characteristics of the
 social environment affect extrapair paternity (EPP) and cuckoldry. We use
 a wild population of great tits (Parus major) to examine how, in addition
 to the phenotypes of focal parents, two neighborhood-level traits – age
 and personality composition – predict EPP and cuckoldry. We used the
 well-studied trait “exploration behavior” as a measure of the
 reactive-proactive personality axis. Because breeding pairs inhabit a
 continuous “social landscape”, we first established an ecologically
 relevant definition of a breeding “neighborhood” through genotyping
 parents and nestlings in a 51-ha patch of woodland and assessing the
 spatial predictors of EPP events. Using the observed decline in likelihood
 of EPP with increasing spatial separation between nests, we determined the
 relevant neighborhood boundaries, and thus the group phenotypic
 composition of an individual’s neighborhood, by calculating the point at
 which the likelihood of EPP became negligible. We found no evidence that
 “social environment” effects (i.e. neighborhood age or personality
 composition) influenced EPP or cuckoldry. We did, however, find that a
 female’s own age influenced the EPP of her social mate, with males paired
 to older females gaining more EPP, even when controlling for the social
 environment. These findings suggest that partner characteristics, rather
 than group phenotypic composition, influence mating activity patterns at
 the individual level.
description: Nestbox
 CoordinatesThis file contains the
 GPS coordinates for the nestboxes in the Marley Wood and Marley Plantation
 sections of Wytham Woods, Oxfordshire.Nestbox.Coordinates.csvBreeding IndividualsThis file contains the identities of the male and female great tits breeding at each occupied nest, for each year.Breeding.Individuals.csvExtrapair Paternity and CuckoldryThis file contains binary data on whether breeding males obtained extrapair paternity and whether they were cuckolded. 1= Yes; 0 = No.EPP.Cuckoldry.csvAge DataThis file contains data on the age of breeding individuals for each study year.Age.Data.csvPersonality DataThis file contains data on the personality scores of breeding individuals.Personality.Data.csv
DOI: 10.5061/dryad.n4ts139
title: Data from: Close kin mating, but not inbred parents, reduces hatching rates and offspring quality in a threatened tortoise

description: Inbreeding depression, the reduction of fitness due to mating of related
 individuals, is of particular conservation concern in species with small,
 isolated populations. Although inbreeding depression is widespread in
 natural populations, long-lived species may be buffered from its effects
 during population declines due to long generation times, and thus are less
 likely to have evolved mechanisms of inbreeding avoidance than species
 with shorter generation times. However, empirical evidence of the
 consequences of inbreeding in threatened, long-lived species is limited.
 In this study, we leverage a well-studied population of gopher tortoises,
 Gopherus polyphemus, to examine the role of inbreeding depression and the
 potential for behavioral inbreeding avoidance in a natural population of a
 long-lived species. We tested the hypothesis that increased parental
 inbreeding leads to reduced hatching rates and offspring quality.
 Additionally, we tested for evidence of inbreeding avoidance. We found
 that high parental relatedness results in offspring with lower quality,
 and that high parental relatedness is correlated with reduced hatching
 success. However, we found that hatching success and offspring quality
 increase with maternal inbreeding, likely due to highly inbred females
 mating with more distantly-related males. We did not find evidence for
 inbreeding avoidance in males and outbred females, suggesting sex-specific
 evolutionary tradeoffs may have driven the evolution of mating behavior.
 Our results demonstrate inbreeding depression in a long-lived species and
 that the evolution of inbreeding avoidance is shaped by multiple selective
 forces.
description: Clutch Data
 2015-2016Metadata on clutches
 collected in 2015 and 2016 including inferred dam and sire, parental
 relatedness, parental inbreeding, clutch size, and hatching success. Both
 raw and quality controlled data.Clutch_Data_2015-16.xlsxGenotype dataMicrosatellite genotype calls for all genotyped individuals from Archbold Biological Station including hatchlings and eggs from clutches examined in this study.Genotypes_Gpolyphemus_ABS.txtHatchling phenotypic dataPhenotypic data for all viable hatchlings collected for this study. Carapace and plastron measurements (in mm) and mass was measured for both the 2015 and 2016 cohort. Locomotor performance data on a 1m track was measured for the 2016 cohort only. Locomotor data (latency time, total time, initial speed, average speed, and max speed) is averaged across trials for each individual.Full_Hatchling_Data_2016_QC.txt
DOI: 10.5061/dryad.2bg7pk5
title: Data from: Pollination and fruit set in two rewardless slipper orchids and their hybrids (Cypripedium, Orchidaceae): large yellow flowers outperform small white flowers in the northern tall grass prairie

description: • Species with rewardless flowers often have low fruit to flower ratios,
 although wide temporal and spatial variation in fruiting success can
 occur. We compared floral phenotypes, insect visitors, and fruiting
 success in four populations of the small white (Cypripedium candidum) and
 yellow lady’s slipper orchids (C. parviflorum) and their hybrids near the
 northern extent of North America’s tall grass prairie. • Flower and fruit
 numbers were observed for two seasons on marked individuals (n = 1811).
 Floral traits were measured on 82-140 individuals per taxon, and analyzed
 in relation to fruiting success. All insects found inside flowers were
 collected, inspected for pollen smears, and measured for comparison to
 floral features. • Among orchid taxa, C. candidum had the smallest
 flowers, lowest number and variety of insect visitors, and lowest fruit to
 flower ratios. These measures were intermediate in hybrids and highest in
 C. parviflorum, despite low flower numbers in the latter. Within orchid
 taxa, fruit number was positively related to flower number, but fruit to
 flower ratios decreased slightly, as would be expected if pollinators left
 unrewarding patches. Potential pollinators included the dipteran
 Odontomyia pubescens and hymenopterans Andrena spp., Apis mellifera, and
 Lasioglossum zonulum. • Cypripedium parviflorum had a reproductive
 advantage over C. candidum across multiple populations and years. Hybrids
 showed segregation for floral traits, and hybrid fruiting success
 increased with a deeper intensity of yellow pigment and larger escape
 routes for floral visitors. These same attributes likely contributed to
 the relatively high fruit set in C. parviflorum in the study region.
description: Cypripedium flower
 measurements 2010 2011367 genets with a
 complete set of floral measurements. Flower colour ranged from 1 (white)
 to 8 (deep yellow). Data correspond to Fig. 2, Fig 3 and Table S2. 337
 genets have fruiting data. These data correspond to Fig. 6 and Table
 S3.Cypripedium fruiting
 survey 2010 2011Flowering and Fruiting
 data for 1811 genets. Data correspond to Fig. 4, Fig. 5, and Table
 S3Cypripedium insect
 visitors 2010 2011Measurements of 117
 insect visitors found in Cypripedium flowers. Of these 112 had complete
 data. Data for the most common insect taxa (n=96) are in Table 1 and Fig.
 3. Body width in the Figure refers to insect abdominal width. Pollen
 smears were on the thorax unless otherwise noted. A yes for exit success
 indicates direct observation of an insect leaving a flower through the
 exit (see description in text).
DOI: 10.15468/dl.jtpfw3
title: Occurrence Download

description: A dataset containing 6386 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Rhincodon typus"
 ]
}

 The dataset includes 6386 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001842-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dydp9k
title: Occurrence Download

description: A dataset containing 15622 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-85.23043 41.02386,-83.43004 41.02386,-83.43004 41.73115,-85.23043 41.73115,-85.23043 41.02386))",
 "OccurrenceStatus is Present",
 "TaxonKey is Odonata",
 "Year 2014-2024"
 ]
}

 The dataset includes 15622 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001843-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p3hry6
title: Occurrence Download

description: A dataset containing 11471 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tremarctos"
 ]
}

 The dataset includes 11471 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001844-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mn9vvg
title: Occurrence Download

description: A dataset containing 421 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "NetworkKey is 99d66b6c-9087-452f-a9d4-f15f2c2d0e7e",
 "TaxonKey is Chordata"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Petrochelidon pyrrhonota [GBIF Backbone Taxonomy])",
 "Preparations is one of (tissue, tissue only, tissue 4122, tissue only, tissue 4099, tissue only, tissue 4081, tissue only, tissue 4068, tissue only, tissue 4067, tissue - 1; skin - 1, tissue - 100, tissue (frozen), tissue - 10, tissue - 1, muscle (frozen), whole organism (frozen), tiss, skin, study; tissue (frozen), skin - 1; tissue - 100, round/wing/tissue, heart, liver, muscle (frozen); skin, round/tissue, skeleton; tissue (frozen), carcass; muscle (frozen), feather; skin study; tissue; toepad, heart, muscle (frozen), liver (frozen); muscle (frozen); wing, muscle (frozen); skeleton, skeleton; tissue (frozen); wing (dry), feather; muscle (frozen), muscle (frozen); tissue (frozen), skeleton; skin; stomach; tissue (frozen), wing/tissue, heart, muscle (frozen); liver (frozen), heart, liver, muscle (frozen); skin; tissue (frozen), heart, liver, muscle (frozen); lung (frozen); skin, heart, kidney, muscle (frozen); liver (frozen); whole organism (ethanol), heart, kidney, liver (frozen); muscle (frozen); skull, heart, kidney (frozen); liver (frozen); muscle (frozen); tissue; whole organism (ethanol), skin; tissue (frozen), blood (frozen); brain (frozen); heart, liver, muscle (frozen); skin, blood_donna_l._dittmann_4827_05-06-1995_p1-4,42,e6; mhlo_donna_l._dittmann_4827_05-06-1995_p1-3,54,f9; study skin_donna_l._dittmann_4827_05-06-1995, bone sample; skin study; tissue, heart, kidney, muscle (frozen); liver (frozen); skeleton; skin, study, heart, kidney, muscle (frozen); liver (frozen); skeleton, heart, kidney, muscle (frozen); liver (frozen); muscle (frozen), heart, kidney, liver, muscle (frozen); skeleton; wing, heart, kidney, liver, muscle (frozen); skeleton; skin, study, heart, kidney (frozen); liver (frozen); muscle (frozen); skin, study, heart, kidney (frozen); liver (frozen); skeleton (postcranial); skin, study, heart, kidney (frozen); liver (frozen); skin; tissue (frozen), heart, kidney, liver (frozen); muscle (frozen), heart, kidney, liver (frozen); muscle (frozen); skeleton (postcranial); skin, study, heart, kidney, liver (frozen); muscle (frozen); wing, lung (frozen); muscle (frozen); wing (dry), kidney, muscle (frozen), heart, liver, muscle (frozen); skeleton; skin, blood)",
 "Country is one of (United States of America)"
 ]
 }
 ]
}

 The dataset includes 421 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001846-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9v6xu5
title: Occurrence Download

description: A dataset containing 1028 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melursus ursinus"
 ]
}

 The dataset includes 1028 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001847-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.64yveg
title: Occurrence Download

description: A dataset containing 69 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Macrosaccus morrisella",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 69 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001850-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.