cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fxpnvx0rq
title: Wildlife-vehicle collisions at 42 Florida State Parks, 2005-2015

description: Peninsular Florida, USA: 9,254 WVC survey records collected by Florida
 State Parks personnel at 42 parks during a decade (2005-2015). Data
 represent observations of wildlife-vehicle collisions for birds (138
 species), mammals (35 species), and reptiles (64 species). The 42 state
 parks encompassed a variety of Florida’s ecosystems on the peninsula and
 keys (and North, but not the Florida panhandle) from barrier islands and
 the Everglades to pine flatwoods, sandhills, and urban areas. Climate
 ranged from subtropical in South Florida to warm temperate in North
 Florida.
description: Florida State Park personnel
 collected WVC data as part of a statewide program, where data forms
 included date, general location (not GPS coordinates), species, and number
 of individuals for organisms killed on roads. Parks varied in how data
 were collected (staff or volunteers, temporal frequency and extent, roads)
 but all surveys were conducted while driving (i.e., none were conducted by
 walking road margins). Taxonomic identifications are to species level for
 birds, mammals, and reptiles. Data were iteratively cleaned to assure
 consistency (e.g., taxonomy, road names, etc.).
description: Each row represents one observation
 event - see metadata tab in xls for explanations of columns. Note NAs in
 some parks for attendance. Please see the file named "data
 summary.txt" for an overview using the summary(data) command in
 R.
DOI: 10.5061/dryad.2z34tmpmg
title: Effects of tree species on root exudation and mineralization of organic acids in a tropical forest

description: Habitat differentiation of diverse tropical tree species is supported by
 different root strategies of nutrient acquisition from the highly
 weathered soils. In the rhizosphere (soil affected by roots), tree species
 modify carbon (C) and nutrient cycles directly through root exudation and
 indirectly through increased microbial activity. We test whether root
 exudation and rhizosphere C fluxes of organic acids and sugars differ
 between dominant dipterocarp trees and pioneer trees (Macaranga gigantea).
 To quantify the C fluxes of organic acids in the rhizosphere soils, we
 measured in situ root exudation from mature trees, concentrations of
 organic acids (acetate, oxalate, malate, and citrate) and monosaccharides
 in the rhizosphere and bulk soil fractions, and mineralization kinetics of
 14C-radiolabelled substrates. Dipterocarp roots release greater amounts of
 malate than pioneer tree roots, while monosaccharides are dominant
 exudates of pioneer trees. Organic acid exudation increases with
 increasing root surface area and with decreasing soil pH. Microbial
 activities of malate mineralization are enhanced in the rhizosphere both
 under Dipterocarp and Macaranga trees, but the C fluxes of malate
 mineralization by rhizosphere microbes exceeded root exudation due to
 microbial malate production in rhizosphere of Dipterocarp trees. Tree
 species affects both root exudation composition and rhizosphere microbe
 activities that increase malate production at lower soil pH, likely for
 phosphorus solubilization, aluminum detoxification, and lignin
 degradation.
DOI: 10.5061/dryad.95x69p8kc
title: More than just a pretty face? The relationship between immune function and perceived facial attractiveness

description: It has long been hypothesized that attractiveness provides a cue to a
 target’s health and immunocompetence. However, much of the research
 testing this hypothesis has relied on a small number of indirect proxies
 of immune function and the results of this research have been mixed. Here,
 we build on this past research, examining the relationship between target
 attractiveness and: (a) self-reported health, (b) in vivo measures of
 inflammation and white blood cell count / composition, and (c) in vitro
 tests of targets’ immune function, including (c1) leukocyte proliferation
 in response to immunological stimulants, (c2) phagocytosis of Escherichia
 coli bioparticles, (c3) NK cell-mediated lysis of target tumor cells, and
 (c4) Staphylococcus aureus growth in isolated plasma. Results revealed
 multiple, sometimes sex-differentiated, relationships between targets’
 immune function and others’ perceptions of their attractiveness. Together,
 this work suggests complex, often sex-differentiated relationships between
 immune function, health, and attractiveness.
DOI: 10.5061/dryad.7d7wm37v1
title: Sex-specific plasticity and the nutritional geometry of insulin-signaling gene expression in Drosophila melanogaster

description: Background Sexual-size dimorphism (SSD) is replete among animals, but
 while the selective pressures that drive the evolution of SSD have been
 well studied, the developmental mechanisms upon which these pressures act
 are poorly understood. Ours and others’ research has shown that SSD
 in D. melanogaster reflects elevated levels of nutritional
 plasticity in females versus males, such that SSD increases with dietary
 intake and body size, a phenomenon called sex-specific plasticity (SSP).
 Additional data indicate that while body size in both sexes responds to
 variation in protein level, only female body size is sensitive to
 variation in carbohydrate level. Here, we explore whether these difference
 in sensitivity at the morphological level are reflected by differences in
 how the insulin/IGF-signaling (IIS) and TOR-signaling pathways respond to
 changes in carbohydrates and proteins in females versus males, using a
 nutritional geometry approach. Results The IIS-regulated transcripts
 of 4E-BP and InR most strongly
 correlated with body size in females and males, respectively, but neither
 responded to carbohydrate level and so could not explain the sex-specific
 response to body size to dietary carbohydrate. Transcripts regulated by
 TOR-signaling did, however, respond to dietary carbohydrate in a
 sex-specific manner. In females, expression
 of dILP5 positively correlated with body size, while
 expression of dILP2,3 and 8, was
 elevated on diets with a low concentration of both carbohydrate and
 protein. In contrast, we detected lower levels of dILP2 and 5 protein in
 the brains of females fed on low concentration diets. We could not detect
 any effect of diet on dILP expression in males.
 Conclusion Although females and males show sex-specific transcriptional
 responses to changes in protein and carbohydrate, the patterns of
 expression do not support a simple model of the regulation of body-size
 SSP by either insulin- or TOR-signaling. The data also indicate a complex
 relationship between carbohydrate and protein
 level, dILP expression and dILP peptide levels in the
 brain. In general, diet quality and sex both affect the transcriptional
 response to changes in diet quantity, and so should be considered in
 future studies that explore the effect of nutrition on body size.
description: The data are morphological measurements on wing, palp, leg and
 thorax size, and gene expression analysis of insulin/TOR-signaling
 genes of <em>Drosophila melanogaster </em>reared across a
 nutritional landscape varying in proteins and carbohydrate levels. Details
 of the methods to collect the data are described in the published
 paper.
description: The data are in .csv format. There are two data sets: one for
 morphological data and one for gene expression data. All the data are log
 transformed from their raw values and can be analyzed directly with the R
 scripts provided. Missing values are given as 'NA'.
DOI: 10.5061/dryad.4b8gthtcg
title: Phylogenomics and fossil data inform the systematics and geographic range evolution of a diverse Neotropical ant lineage

description: Recent advances in phylogenomics allow for the use of large amounts of
 genetic information in phylogenetic inference. Ideally, the increased
 resolution and accuracy of such inferences facilitate improved
 understanding of macroevolutionary processes. Here, we integrate
 ultraconserved elements (UCEs) with fossil and biogeographic range data to
 explore diversification and geographic range evolution in the diverse
 turtle ant genus Cephalotes. We focus on the potential role of the uplift
 of the Panamanian land bridge and the putative ephemeral GAARlandia land
 bridge linking South America and the Antilles in shaping the evolution in
 this group. Our phylogenetic analyses provide new resolution to the
 backbone of the turtle ant phylogeny. We further found that a majority of
 geographic range shifts between the South America and Central America
 regions were temporally consistent with the development of the Panamanian
 land bridge, while we did not find support for the GAARlandia land bridge.
 Additionally, we did not infer any shifts in diversification rates
 associated with our focal land bridges, or any other historical events (we
 inferred a single diversification rate regime across the genus). Our
 findings highlight the impact of the Panamanian land bridge for Cephalotes
 geographic range evolution as well as the influence of taxonomic sampling
 on macroevolutionary inferences. Keywords: Formicidae, Hymenoptera,
 Biogeography, Biology, Evolution, Phylogeny, Systematics
description: See associated manuscript for dataset collection
 information.
description: UCE contig files (including .zip for trimmed-unfiltered contigs
 and .zip for trimmed-filtered contigs [75% taxon complete contigs]), tree
 files, data, and R scripts associated with manuscript by Price et
 al. (submitted) on <em>Cephalotes</em> diversification and
 biogeography.
DOI: 10.5061/dryad.bcc2fqzc7
title: Dataset S1 - Noelaerhabdaceae organic carbon isotope culture data compilation

description: The carbon isotope fractionation in algal organic matter (Ep), including
 the long-chain alkenones produced by the coccolithophorid family
 Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The
 conventional proxy linearly relates Ep to changes in cellular carbon
 demand relative to diffusive CO2 supply, with larger Ep values occurring
 at lower carbon demand relative to supply (i.e. abundant CO2). 
 However, the response of Gephyrocapsa oceanica, one of the dominant
 alkenone producers of the last few million years, has not been studied
 closely. Here we subject G. oceanica to various CO2 levels by increasing
 pCO2 in the culture headspace, as opposed to increasing dissolved
 inorganic carbon (DIC) and alkalinity concentrations at constant pH. We
 note no substantial change in physiology, but observe an increase in Ep as
 carbon demand relative to supply decreases, consistent with DIC
 manipulations. We compile existing Noelaerhabdaceae Ep data and show that
 the diffusive model poorly describes the data. A meta-analysis of
 individual treatments (unique combinations of lab, strain, and light
 conditions) shows that the slope of the Ep response depends on the light
 conditions and range of carbon demand relative to CO2 supply in the
 treatment, which is incompatible with the diffusive model. We model Ep as
 a multilinear function of key physiological and environmental variables
 and find that both photoperiod duration and light intensity are critical
 parameters, in addition to CO2 and cell size. While alkenone carbon
 isotope ratios indeed record CO2 information, irradiance and other factors
 are also necessary to properly describe alkenone Ep.
description: G. oceanica RCC1303 was cultivated in triplicate batch culture at
 five different pCO<sub>2</sub> levels.
 CO<sub>2</sub> modification was achieved by continuously
 aerating the headspace of the culture flask. Alkenones were extracted
 using accelerated solvent extraction and carbon isotope ratios were
 measured by GC-IRMS. CO<sub>2</sub> concentrations were
 calculated from measurements of pH, total alkalinity, temperature, and
 salinity. Cell sizes were measured by flow cytometry. Existing data were
 compiled from the literature. Cell sizes and carbon content were
 standardized to the middle of the photoperiod, where applicable.
  
description: Missing values are noted with “NaN.” Data sources are listed in
 the references and explanatory columns (e.g. “Source of cell radius
 data”). Information in columns titled “Note on XYZ” (e.g. “Note on
 d13C_POC uncertainty”) reflect the source of information in the original
 publication.
DOI: 10.5061/dryad.fbg79cnv1
title: CPCP-1: Thermal demagnetization data

description: The Colorado Plateau Coring Project Phase 1 (CPCP-1) acquired three
 continuous drill cores from Petrified Forest National Park (PFNP),
 Arizona, U.S.A. Two cores, CPCP-PFNP13-1A and CPCP-PFNP13-2B, hereafter
 CPCP-1A and CPCP-2B; respectively, intersected the Upper Triassic
 Chinle Formation, Lower(?)-Middle Triassic Moenkopi Formation (MF) and
 Permian Coconino Sandstone. We examined CPCP-1A and CPCP-2B cores to
 construct a high-resolution magnetostratigraphy of Moenkopi Formation
 strata. These data files contain progressive thermal demagnetization data
 collected from the specimens from cores CPCP-1A and CPCP-2B.
description: The progressive thermal demagnetization data was generated by
 heating specimens in ASC TD-48 furnaces stored in a magnetically shielded
 room with a peak magnetic field of less than 10 nT. At
 each demagnetization step, the NRM and remanence were measured using
 either a 2G-Enterprises cryogenic magnetometer equipped with DC-squids or
 AGICO JR6A spinner magnetometers housed in a magnetically shielded room.
 AGICO data reduction software "Remasoft 3.0" was used to process
 the data and to calculate the characteristic remanent magnetization (ChRM)
 directions.
description: All the thermal demagnetization data is in "Remasoft3
 file(s) (*.rs3)" format and can be opened in AGICO "Remasoft
 3.0" paleomagnetic data processing software. The data files
 those name that starts with CPCP-1A contain thermal demagnetization data
 from core CPCP-1A and other files contain thermal demagnetization data
 from the core CPCP-2B. To view the data in geographic coordinate use an
 azimuth/hade of 135°/90° (CPCP-1A) and 113°/90° (CPCP-2B) and the
 following orientation parameters in Remasoft 3.0 (P1= 12; P2= 0; P3= 12;
 P4= 0 or 90).
DOI: 10.5061/dryad.j0zpc86dp
title: Underlying microevolutionary processes parallel macroevolutionary patterns in ancient Neotropical Mountains - Ecological Niche Modeling and Corridors files

description: Aim Ancient climatic fluctuations are invoked as the main driving force
 that generates the astonishing biodiversity in ancient mountains. As a
 result, endemism and spatial turnover are usually high and few species are
 widespread among entire mountain ranges, precluding the understanding of
 origins of macroevolutionary patterns. Here, we used a species endemic to,
 but widespread in, one of the most species-rich ancient mountains on the
 globe to test how environmental changes acted on them and how their
 macroevolutionary patterns were shaped. Location Espinhaço Range, Eastern
 Brazil. Taxon Vriesea oligantha species complex (Bromeliaceae). Methods We
 compiled data for plastidial regions and nuclear microsatellites to assess
 genetic diversity, population structure, migration rates and phylogenetic
 relationships. Using temperature and precipitation variables we modeled
 suitable areas for the present and the past, estimating corridors between
 isolated populations. We also implemented Bayesian demographic analyses to
 estimate ancient populations dynamics. Finally, we tested if population
 structure is driven by isolation by environment or by distance using a
 Bayesian modeling approach. Results Our results showed that the
 intraspecific divergence events of V. oligantha are older than those
 associated with the latest Pleistocene climatic oscillations, supporting
 the view that Quaternary climatic fluctuations are key components for
 understanding its population differentiation processes.  Species
 distribution modeling estimated corridors between populations in the past,
 as also shown in the demographic analyses, depicting a major spatial
 reorganization during colder climates. Besides, the high genetic structure
 estimated results from both models of isolation by distance and by
 environment. Main conclusions V. oligantha is a remarkable model to test
 the effects of climatic oscillations over the biological community, since
 this species originated in the early-Pleistocene, prevailing over several
 cycles of climatic fluctuations until today. The estimated demographic
 dynamics of V. oligantha agrees with the species-pump mechanism,
 suggesting it as the main cause of speciation within the Espinhaço Range.
 Moreover, the phylogeographic patterns of V. oligantha reflect previously
 recognized spatial and temporal macroevolutionary patterns in the
 Espinhaço Range, providing insights into how microevolutionary processes
 may have given rise to this astonishing mountain biodiversity.
DOI: 10.6078/d1gt5s
title: Temporal shifts in antibiotic resistance elements govern phage-pathogen conflicts

description: Bacteriophage predation selects for diverse anti-phage systems that
 frequently cluster on mobilizable defense islands in bacterial genomes.
 However, there remains a lack of molecular insight into the reciprocal
 dynamics of phage-bacterial adaptations in nature, particularly in
 clinical contexts where there is need to inform phage therapy efforts and
 understand how phages drive pathogen evolution. Here,  we used
 time-shift assays to evaluate whether clinical Vibrio cholerae isolates
 were susceptible to infection by phage from past, future or
 contemporaneous patient samples. Across a 34-month sampling period, we
 discover that phage resistance is governed by fluctuations in SXT
 integrative and conjugative elements (ICEs), which notoriously also confer
 antibiotic resistance. We further demonstrate potential trade-offs for
 having SXT ICEs, as we show they can also can restrict beneficial mobile
 genetic elements. We discover phage counter-adaptation to SXT-mediated
 restriction in clinical samples, and show that flux of SXT ICEs in V.
 cholerae over time allows for re-emergence of phage resistance. We find
 that SXT ICEs, which are widespread in Gammaproteobacteria, invariably
 encode phage defense and function to protect other genera from phage
 attack following conjugation. Further, we find that phage infection
 stimulates high frequency SXT ICE conjugation, leading to the concurrent
 dissemination of phage and antibiotic resistance.
description: WYL-domain proteins and the downstream flanking gene encoding the
 conjugative relaxase TraI were extracted from all identifiable hotspot
 5's encoded by SXT ICEs. MUSCLE alignments were performed on the
 nucleotide sequence for each unique gene, and a phylogenetic tree was
 constructed using PhyML with 100 bootstrap iteractions. Phylogenetic trees
 were visualized in FigTree v1.4.4.
description: The unique genes sequences for each WYL-domain protein are
 uploaded as an Excel spreasheet. The datasheet indicates which WYL-domain
 protein encoding genes are identical between SXT ICEs, and the tree was
 only constructed using one of the unique WYL-domain proteins. Of note: The
 tree displays the WYL-domain protein encoding gene for ICEVchCHN1605, yet
 the published manuscript is showing this node labelled ICEVchCHN956. These
 two WYL-domain protein containing genes are identical, and these two SXT
 ICEs are so similar that the cut-offs for our BLASTn analysis identified
 them as the same SXT ICE. The trees are uploaded in the NEWICK file
 format.
DOI: 10.25338/b85s7m
title: Data from: Validation of 1-0 and instantaneous sampling for quantifying oral behaviors in milk-fed dairy calves

description: Oral behaviors, including feeding, drinking, grooming, and non-nutritive
 behaviors, are used as indicators of health and welfare in dairy calves,
 but continuous measurement of these behaviors can be labor intensive.
 Instantaneous sampling is often used to save labor but has only been
 validated for feeding behavior in calves. One-zero sampling may be an
 appropriate strategy well suited to capturing the rapid performance of
 non-nutritive behaviors. Our objective was to validate 1-0 and
 instantaneous sampling for measurement of oral behaviors around the time
 of bottle delivery against true values. Eleven Holstein heifer calves were
 housed individually, provided water and fed a diet of starter grain and
 milk replacer (4.8 – 5.6 L/d step-up) via a bottle. When calves were 23 ±
 7 d old, they were video recorded for 30 min before and after the morning
 2.5 ± 0.2 L milk meal from approximately 0900 – 1000 h. We measured
 ruminating, eating, drinking water, sucking milk, grooming, non-nutritive
 oral manipulation, and tongue flicks continuously and with instantaneous
 and 1-0 sampling at 5-, 10-, 30-, and 60-s intervals. We also examined the
 effect of instantaneous timing within these intervals. Estimates obtained
 through subsampling were compared to true values with regression analysis.
 The subsampling interval was determined to represent true values if the
 coefficient of determination ≥ 0.9, slope = 1, intercept = 0, and relative
 error &lt; 10%. Ruminating, drinking water, and eating were not
 performed by all 11 calves and were not included in the analysis. The
 proportion of time performing non-nutritive oral manipulation, grooming,
 and tongue flicks generated by continuous and 1-0 sampling were highly
 correlated but were consistently overestimated by 1-0 sampling, especially
 as calves spent more time engaged in these behaviors. Sucking milk was
 accurately represented at intervals of less than 30 s, likely due to most
 sucking bouts continuing for at least 150 s at a time, and low
 between-calf variability compared to the other behaviors. Different start
 times within a given instantaneous interval resulted in wide variance in
 discrepancies between subsampling and continuous recording for all
 behaviors. We conclude that around milk feeding, 1-0 sampling is an
 appropriate choice to represent stimulus-elicited behavior, such as
 sucking milk in a milk-restricted system. However, time engaged in short,
 highly variable, or intermittent behaviors is not reliably captured via
 instantaneous or 1-0 sampling in the hour around bottle delivery.
description: Methodological details are described in the associated journal
 article as well as RMarkdown.
description: Each RMarkdown file contains a description of how to use these
 datasets. This Dryad entry also includes Supplemental
 Figures S1-S4.