cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cvdncjt1g
title: Data from: Increased glucocorticoid concentrations in early life cause mitochondrial inefficiency and short telomeres

description: Telomeres are DNA structures that protect chromosome ends. However,
 telomeres shorten during cell replication and at critically low lengths
 can reduce cell replicative potential, induce cell senescence and decrease
 fitness. Stress exposure, which elevates glucocorticoid hormone
 concentrations, can exacerbate telomere attrition. This phenomenon has
 been attributed to increased oxidative stress generated by glucocorticoids
 ("oxidative stress hypothesis"). We recently instead suggested
 that glucocorticoids increase telomere attrition during stressful periods
 by reducing the resources available for telomere maintenance through
 changes in the metabolic machinery ("metabolic telomere attrition
 hypothesis"). Here we tested whether experimental increases in
 glucocorticoid levels affected telomeres and mitochondrial function in
 wild great tit (Parus major) nestlings during the energy-demanding early
 growth. We monitored resulting corticosterone (Cort) concentrations in
 plasma, and in red blood cells telomere lengths and mitochondrial
 metabolism (metabolic rate, proton leak, oxidative phosphorylation,
 maximal mitochondrial capacity and mitochondrial inefficiency). We
 assessed oxidative damage caused by reactive oxygen species (ROS)
 metabolites as well as the total non-enzymatic antioxidant protection in
 plasma. Compared with control (Ctrl) nestlings, Cort-nestlings had higher
 baseline corticosterone, shorter telomeres and higher mitochondrial
 metabolic rate. Importantly, Cort-nestlings showed increased mitochondrial
 proton leak, leading to a decreased ATP production efficiency. Treatment
 groups did not differ in oxidative damage or antioxidants. Hence,
 glucocorticoid-induced telomere attrition is associated with changes in
 mitochondrial metabolism, but not with ROS production. These findings
 support the "metabolic telomere attrition hypothesis" which
 proposes an active regulation of telomere length by glucocorticoids during
 stressful periods, which is mediated through metabolic rearrangements.
DOI: 10.5061/dryad.7pvmcvdq7
title: Data from: Appearances can be deceptive: bizarre shell microanatomy and histology in a new Triassic turtle (Testudinata) from Argentina at the dawn of turtles

description: The origin and homology of the turtle shell are one of the most
 captivating topics in amniote evolution. In this contribution, we present
 a new species of turtle from the Late Triassic of Argentina whose
 peripheral plates question the homology of these bones in turtles. The
 external morphology of the peripheral plates of Waluchelys cavitesta gen.
 et sp. nov. (Testudinata: Australochelyidae) is as in any other turtle,
 however, appearances can be deceiving. Internally, these plates exhibit an
 unexpected internal cavity. The absence of structural similarities and of
 ontogenetic or phylogenetic transitional forms between the peripheral
 plates of W. cavitesta and other testudinatans might suggest that the
 periphery of turtles represents a case of deep homology. Furthermore, the
 present and recent findings suggest that the structure and ossification
 patterns of the periphery of the turtle shell were more plastic and
 subject to variation than other elements of the shell, at least in the
 earliest stages of turtle evolution. These findings also suggest that the
 “typical” mesochelydian turtle shell could have been acquired in a
 two-stage process.
DOI: 10.5061/dryad.kwh70rz1d
title: Pathotype complexity and genetic characterization of Phytophthora sojae populations in Illinois, Indiana, Kentucky, and Ohio

description: Phytophthora sojae, the causal agent of Phytophthora root and stem rot of
 soybean, has been managed with single Rps genes since the 1960’s, but has
 subsequently adapted to many of these resistance genes, rendering them
 ineffective. The objective of this study was to examine the pathotype and
 genetic diversity of P. sojae from soil samples across Illinois, Indiana,
 Kentucky, and Ohio by assessing which Rps gene(s) were still effective and
 identifying possible population clusters. There were 218 pathotypes
 identified from 473 P. sojae isolates with an average of 6.7 out of 15
 differential soybean lines exhibiting a susceptible response for each
 isolate. Genetic characterization of 103 P. sojae isolates from across
 Illinois, Indiana, Kentucky, and Ohio with 19 simple sequence repeat
 markers identified 92 multilocus genotypes. There was a moderate level of
 population differentiation among these four states, with pairwise FST
 values ranging from 0.026 to 0.246. There was also moderate to high levels
 of differentiation between fields, with pairwise FST values ranging from
 0.071 to 0.537. Additionally, cluster analysis detected the presence of P.
 sojae population structure across neighboring states. The level of
 pathotype and genetic diversity, in addition to the identification of
 population clusters, supports the hypothesis of occasional outcrossing
 events that allow for an increase in diversity and the potential to select
 for a loss in avirulence to specific resistance genes within regions. The
 trend of suspected gene flow among neighboring fields is expected to be an
 ongoing issue with current agricultural practices.
DOI: 10.15468/dl.bwakuz
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "CatalogNumber" : [
 "is one of (PDD 90497, PDD 90806, PDD 91700, PDD 91659, K-M000195442, K-M000122116, K-M000235255, K-M000951276, K-M000193562, K-M000195452, K-M000822505, K-M000235135, PDD 91131, PDD 90660, PDD 86101, K-M000948317, K-M001441780, K-M000081495, K-M000769762)"
 ]
}

 The dataset includes 19 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002351-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5qfttdz2b
title: Demographic analysis for article Hurricane-induced demographic changes in a nonhuman primate population

description: Major disturbance events can have large impacts on the demography and
 dynamics of animal populations. Hurricanes are one example of an extreme
 climatic event, predicted to increase in intensity due to climate change,
 and thus expected to be a considerable threat to population viability.
 However, little is understood about the underlying
 demographic mechanisms shaping population response following these extreme
 disturbances. Here, we analyze 45 years of the most comprehensive
 free-ranging nonhuman primate demographic dataset to determine the effects
 of major hurricanes on the variability and maintenance
 of long-term population fitness. For this, we use
 individual-level data to build matrix population models and perform
 perturbation analyses. Despite reductions in population growth
 rate mediated through reduced fertility, our study reveals a
 demographic buffering during hurricane years. As long as survival does not
 decrease, our study shows that hurricanes do not result in detrimental
 effects at the population level, demonstrating the unbalanced contribution
 of survival and fertility to population fitness in long-lived animal
 populations.
description: The demographic dataset of Cayo Santiago rhesus macaques was
 shared by the Caribbean Primate Research Center, University of Puerto
 Rico.
description: This folder contains all the required data and codes to reproduce
 the main study results. Codes were built in R version 3.5.1. These codes
 use packages “popbio”, “tidyverse”, “ggplot2”, “scales”, and “gamm4” for
 demographic data management and analysis. The data contains the
 following: 
 Morcillo_et_al_nonhurricane_transitions.csv contains every
 individual transition during non-hurricane years; including age and stage
 at time t and fate or stage at time t+1.
 Morcillo_et_al_hurricane_transitions.csv contains every
 individual transition during hurricane years; including age and stage at
 time t and fate or stage at time t+1.
 Morcillo_et_al_nonhurricane_bootstrap.csv contains the bootstrap
 transition matrix for a non-hurricane year.
 Morcillo_et_al_hurricane_bootstrap.csv contains the bootstrap
 transition matrix for a hurricane year.
 Morcillo_et_al_annual_matrices.RData contains annual transition
 matrices from 1973 to 2018.
 Morcillo_et_al_gamm_model.RData contains the generalized
 additive mixed top model output 
 Specifically, the codes provide calculations for:
 Mean matrix populations models for non-hurricane and
 hurricane years from individual-level transition data.
 Eigen analysis for matrix models Life table
 response experiment Bootstrap and Kolmogorov-Smirnov
 test Generalized additive mixed model
 Figures
DOI: 10.5061/dryad.tqjq2bvvx
title: Data from: Socially foraging bats discriminate between group members based on search-phase echolocation calls

description: Animals have evolved diverse strategies to use social information for
 increasing foraging success and efficiency. Echolocating bats, for
 example, can eavesdrop on bats foraging nearby, because they shift from
 search-phase calls to feeding buzzes when they detect prey. Feeding buzzes
 can directly convey information about prey presence, but it is unknown
 whether search-phase calls also convey social information. Here we
 investigated whether search-phase echolocation calls, distinct calls
 produced by some bat species to scan large open areas for prey, can
 additionally convey individual identity. We tested this in Molossus
 molossus, a neotropical insectivorous bat that forages with group members,
 presumably to find ephemeral insect swarms more efficiently. We caught M.
 molossus from six different social groups and recorded their search-phase
 calls during a standardized release procedure, then recaptured and tested
 19 marked bats with habituation-dishabituation playback experiments. We
 showed that they can discriminate between group members based on
 search-phase calls, and our statistical analysis of call parameters
 supported the presence of individual signatures in search-phase calls.
 Individual discrimination is a prerequisite of individual recognition,
 which may allow M. molossus to maintain contact with group members while
 foraging without using specialized signals for communication.
DOI: 10.5061/dryad.7sqv9s4q0
title: Heterogeneous timing of asexual cycles in Plasmodium falciparum quantified by extended time-lapse microscopy

description: Malarial fever arises from the synchronous bursting of human red blood
 cells by the Plasmodium parasite. The released parasites re-infect
 neighboring red blood cells and undergo another asexual cycle of
 differentiation and proliferation for 48 hours, before again bursting
 synchronously. The synchrony of bursting is lost during in vitro culturing
 of the parasite outside the human body, presumably because the asexual
 cycle is no longer entrained by host-specific circadian cues. Therefore,
 most in vitro malaria studies have relied on the artificial
 synchronization of the parasite population. However, much remains unknown
 about the degree of timing heterogeneity of asexual cycles and how
 artificial synchronization may affect this timing. Here, we combined
 time-lapse fluorescence microscopy and long-term culturing to follow
 single cells and directly measure the heterogeneous timing of in vitro
 asexual cycles. We first demonstrate that unsynchronized laboratory
 cultures are not fully asynchronous and the parasites exhibit a bimodal
 distribution in their first burst times. We then show that synchronized
 and unsynchronized cultures had similar asexual cycle periods, which
 indicates that artificial synchronization does not fundamentally perturb
 asexual cycle dynamics. Last, we demonstrate that sibling parasites
 descended from the same schizont exhibited significant variation in
 asexual cycle period, although smaller than the variation between
 non-siblings. The additional variance between non-siblings likely arises
 from the variable environments and/or developmental programs experienced
 in different host cells.
description: We used timelapse fluorescence microscopy of GFP-expressing
 <em>P. falciparum</em> to quantify the timing and variability
 of the asexual cycle in in vitro culturing conditions.  We measured the
 timing of GFP-parasite bursting across two asexual cycles for
 unsynchronized and sorbitol-shock synchronized cultures (two biological
 replicates).  Dataset consists of one example timelapse fluorescence movie
 of GFP-labelled parasites (Movie S1), data of first-burst time,
 second-burst time, and asexual cycle time of synchronized and
 unsynchronized parasites for both biological replicates (Dataset S1), and
 timecourse data of ring, trophozoite, schizont counts for a synchronized
 GFP culture released into control and light condition (Dataset
 S2).
DOI: 10.5061/dryad.47d7wm39m
title: Data from: Phylogenomics, biogeography and morphometrics reveal rapid phenotypic evolution in pythons after crossing Wallace’s line

description: Ecological opportunities can be provided to organisms that cross stringent
 biogeographic barriers towards environments with new ecological niches.
 Wallace’s and Lyddeker’s lines are arguably the most famous biogeographic
 barriers, separating the Asian and Australo-Papuan biotas. One of the most
 ecomorphologically diverse groups of reptiles, the pythons, is distributed
 across these lines, and are remarkably more diverse in phenotype and
 ecology east of Wallace’s line in Australo-Papua. We used an anchored
 hybrid enrichment approach, with near complete taxon sampling, to extract
 mitochondrial genomes and 376 nuclear loci to resolve and date their
 phylogenetic history. Biogeographic reconstruction demonstrates that they
 originated in Asia around 38-45 Ma and then invaded Australo-Papua around
 23 Ma. Australo-Papuan pythons display a sizeable expansion in
 morphological space, with shifts towards numerous new adaptive optima in
 head and body shape, coupled with the evolution of new micro-habitat
 preferences. We provide an updated taxonomy of pythons and our study also
 demonstrates how ecological opportunity following colonization of novel
 environments can promotemorphological diversification in a formerly
 ecomorphologically conservative group.
DOI: 10.5061/dryad.zw3r2285t
title: Effect of tomato-fruit cultivar and ripening stage on Bactrocera tryoni (Froggatt) egg and larval survival

description: In studies of frugivorous tephritids, determining when offspring (i.e. egg
 and three larval instars) mortality occurs within the fruit can greatly
 improve the mechanistic understanding of the fly/host
 interaction.  Previous research has demonstrated that the
 Queensland fruit fly, Bactrocera tryoni, has differential offspring
 performance in two tomato cultivars Cherry and Roma, but when juvenile
 mortality was occurring was not determined.  We examined B.
 tryoni egg and larval survival in three different ripening stages
 (immature-green (IG), colour-break (CB) and fully-ripe (FR)) of Cherry and
 Roma tomato cultivars through destructive fruit sampling at 72 and 120 hrs
 for eggs, and 48 (1st instar), 96 (2nd instar) and 120 hours (3rd instar)
 after fruit inoculation with neonates for larvae. Cultivar and ripening
 stage had no significant effect on egg survival, nor larval survival at 48
 hrs: egg survival was high across all treatments, while 1st instar larval
 was low across all treatments.  At 96 and 120 hrs, there were
 significant cultivar and ripening stage impacts on larval survival. In
 fully-ripe fruit, no further significant mortality happened after the
 first instar. However, in colour-break fruit, after the initial 1st instar
 mortality, high mortality also occurred in third instar larvae. 
 In immature-green fruits nearly all mortality occurred during the first
 and second instars. The difference in timing of larval mortality with
 ripening stage provides indirect evidence of active fruit defense which is
 strongest in immature-green fruit, less in colour-break fruit and absent
 in fully-ripe fruit. Increased knowledge of fruit defenses against fruit
 flies is a starting point for developing fruit fly resistant crops.
description: Data set collected by dissecting tomato fruits and observation
 (counting) samples under streo microscope.
DOI: 10.5061/dryad.3ffbg79fk
title: Data from: Nighttime warming enhances ecosystem carbon-use efficiency in a temperate steppe

description: 1. Reductions in the diurnal temperature range (DTR), e.g., greater
 increases in daily minimum than maximum temperatures, have occurred for
 several decades and are projected to continue over this century, which
 could affect terrestrial carbon (C) cycling. Carbon-use efficiency of
 plants (CUEp) and ecosystems (CUEe) represents the capacity of plants to
 capture C and ecosystems to store C fixed from the atmosphere,
 respectively. Few studies have examined how grassland CUE responds to
 asymmetric warming. 2. As part of a long-term (2006-2016) field experiment
 that simulated daytime and nighttime warming in a semiarid temperate
 steppe on the Mongolian Plateau, this study was conducted to examine the
 effects of daytime and nighttime warming on CUEp and CUEe. 3. Nighttime
 warming, unlike daytime warming, increased CUEe by 54.2%, whereas neither
 nighttime nor daytime warming affected CUEp. Ecosystem-level CUE linearly
 increased with soil moisture but declined with soil temperature variation
 (CVST). The suppressed ER, which might have been driven by the reduced
 CVST, primarily contributed to the higher CUEe under nighttime warming. 4.
 These observations indicate that a reduced DTR, associated with a warmer
 night under asymmetric diurnal climate warming, could increase the
 capacity of the temperate steppe transferring C into ecosystems by
 elevating CUEe, resulting more C sequestration.
DOI: 10.5061/dryad.jh9w0vt7z
title: Data from: Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

description: The number of male gametes is critical for reproductive success and varies
 between and within species. The evolutionary reduction of the number of
 pollen grains encompassing the male gametes is widespread in selfing
 plants. Here, we employ genome-wide association study (GWAS) to identify
 underlying loci and to assess the molecular signatures of selection on
 pollen number-associated loci in the predominantly selfing plant
 Arabidopsis thaliana. Regions of strong association with pollen number are
 enriched for signatures of selection, indicating polygenic selection. We
 isolate the gene REDUCED POLLEN NUMBER1 (RDP1) at the locus with the
 strongest association. We validate its effect using a quantitative
 complementation test with CRISPR/Cas9-generated null mutants in
 nonstandard wild accessions. In contrast to pleiotropic null mutants, only
 pollen numbers are significantly affected by natural allelic variants.
 These data support theoretical predictions that reduced investment in male
 gametes is advantageous in predominantly selfing species.
DOI: 10.5061/dryad.00000001j
title: Influence of annealing atmosphere on performances of CIGS film by sputtering from quaternary targets

description: Quaternary sputtering without additional selenization is a low-cost
 alternative method for the preparation of Cu(InGa)Se2 (CIGS) thin film for
 photovoltaics. However, the device efficiency without selenization is much
 lower than that with selenization. To illuminate the issue, we compared
 the properties of absorbers including the morphology, depth profile,
 composition, electrical properties and the recombination mechanism
 comprehensively. The results revealed that the superficial Se of CIGS film
 annealed in Se-free atmosphere is less than that annealed in Se-containing
 atmosphere，and the loss of Se reduced the carrier concentration and
 enhanced the resistivity of CIGS film. Besides, the loss of Se caused the
 dominant recombination mechanism to be CIGS/CdS interface recombination.
 The increase of interface recombination was considered to be the reason
 for the reduced efﬁciency of the device annealed in Se-free atmosphere.
description: The depth direction distributions were measured by
 secondary ion mass spectroscopy (SIMS, ION-TOF GmbH instrument, TOF.SIMS
 5-100) and the sputtering was provided by bismuth primary ion bombardment
 at 30 keV. The electrical properties were characterized by Hall
 measurement (Hall, HL5500PC, Nanometric). The temperature dependent J-V
 measurements were conducted under AM1.5 (100
 mW/cm<sup>2</sup>) illumination using a solar simulator to
 examining the recombination mechanisms.
DOI: 10.5061/dryad.zkh189376
title: Data from: Contrasting leaf trait responses of conifer and broadleaved seedlings to altered resource availability are linked to resource strategies

description: (1) Understanding tree seedling responses to water, nutrient and light
 availability is crucial to precisely predict potential shifts in
 composition and structure of forest communities under future climatic
 conditions. (2) We exposed seedlings of widespread central European tree
 species with contrasting leaf habit, deciduous broadleaves (DB) and
 evergreen conifers (EC), to factorial combinations of manipulated
 precipitation (100% and 50% of ambient), shade (40% and 60% of full
 sunlight) and nutrient availability (low and high NPK), and measured
 specific leaf area, C/N ratio, soluble sugars, starch and non-structural
 carbohydrate concentration, and δ13C of the leaves. (3) We found
 contrasting effects of water and nutrient availability on foliar traits of
 the two species groups: EC exhibited higher tolerance to low resource
 availability but also less plasticity in foliar traits, which is congruent
 with a "slow" resource strategy. In contrast, foliage of DB
 reacted particularly to altered nutrient availability, corresponding to a
 "fast" resource strategy with high foliar plasticity and rapid
 adjustments to resource fluctuations, commonly adopted by species with
 high growth rates. (4) We conclude that DB will respond to environmental
 change with foliar acclimation, while EC will either tolerate, to some
 extent, or shift their distribution range in response to environmental
 change.
description: See Zhang et al. 2020,
 https://dx.doi.org/10.3390/plants9050621
description: This file contains measurements of leaf traits of single tree
 seedlings and traits derived from measured data as described in the
 publication and the ReadMe file.