cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.69kq2
title: Data from: Can terrestrial laser scanners (TLSs) and hemispherical photographs predict tropical dry forest succession with liana abundance?

description: Tropical dry forests (TDFs) are ecosystems with long drought periods, a
 mean temperature of 25 °C, a mean annual precipitation that ranges from
 900 to 2000 mm, and that possess a high abundance of deciduous species
 (trees and lianas). What remains of the original extent of TDFs in the
 Americas remains highly fragmented and at different levels of ecological
 succession. It is estimated that one of the main fingerprints left by
 global environmental and climate change in tropical environments is an
 increase in liana coverage. Lianas are non-structural elements of the
 forest canopy that eventually kill their host trees. In this paper we
 evaluate the use of a terrestrial laser scanner (TLS) in combination with
 hemispherical photographs (HPs) to characterize changes in forest
 structure as a function of ecological succession and liana abundance. We
 deployed a TLS and HP system in 28 plots throughout secondary forests of
 different ages and with different levels of liana abundance. Using a
 canonical correlation analysis (CCA), we addressed how the VEGNET, a
 terrestrial laser scanner, and HPs could predict TDF structure. Likewise,
 using univariate analyses of correlations, we show how the liana abundance
 could affect the prediction of the forest structure. Our results suggest
 that TLSs and HPs can predict the differences in the forest structure at
 different successional stages but that these differences disappear as
 liana abundance increases. Therefore, in well known ecosystems such as the
 tropical dry forest of Costa Rica, these biases of prediction could be
 considered as structural effects of liana presence. This research
 contributes to the understanding of the potential effects of lianas in
 secondary dry forests and highlights the role of TLSs combined with HPs in
 monitoring structural changes in secondary TDFs.
description: SR-EMSS
 BiogeosciencesLocation of selected
 sampling sites at the Santa Rosa National Park Environmental Monitoring
 Super Site. Data represents three levels of information: Terrestrial
 Scanner derived Information, Hemispherical Photos Derived information, and
 structural forest parameters. Data provides also latitude and longitude of
 each plot.Biogeosciences Santa Rosa TLS
 plots.xlsx
DOI: 10.5061/dryad.td453
title: Data from: Weak geographical structure in sperm morphology across the range of two willow warbler Phylloscopus trochilus subspecies in Scandinavia

description: Sperm morphology is highly diversified among species and at higher
 taxonomic levels. In birds, there is also increasing evidence of
 geographical differentiation in sperm traits within species, especially in
 those with strong sperm competition. Geographical divergences in sperm
 traits might imply the formation of a reproductive barrier in a speciation
 process. Here we study sperm morphology variation of willow warblers
 Phylloscopus trochilus in a geographical context in Scandinavia, across
 the range of two subspecies that are differentiated in certain genetic
 markers, morphology and migratory routes. We describe geographical
 patterns in genotypes (two previously described single-nucleotide
 polymorphism (SNP) markers and four polymorphic microsatellites); in wing
 length, tarsus length and body mass; and in sperm traits of 330 male
 willow warblers sampled at 33 localities across Norway (58°N–69°N). Birds
 were on average larger and longer-winged in the north (spp. acredula) than
 in the south (spp. trochilus), and showed a sigmoid change in the SNP
 allele frequencies and body morphology around 65°N. We found no evidence
 of genetic structuring in the microsatellites. There was no geographical
 variation in sperm traits across Norway, except that sperm heads were on
 average longer in the south. Sperm head length was also associated with
 the two SNP markers, with longer sperm heads for the southern alleles, and
 midpiece length was weakly associated with one of the SNP markers. Similar
 among-male variances in total sperm length among the 33 sampling sites
 indicate uniform levels of sperm competition across Norway. We conclude
 that sperm morphology remains a rather undifferentiated trait between the
 two willow warbler subspecies in Scandinavia, which is consistent with a
 pattern of a shallow genetic divergence. This indicates that sperm
 morphology is not a reproductive barrier maintaining the narrow hybrid
 zone.
description: Average site
 valuesThis file contains
 average values (SD) for each of the 33 sites used in the study. The
 variables are latitude, longitude, elevation, tarsus length, wing length,
 body mass, sperm head length, sperm midpiece length, sperm tail length,
 sperm total length, CVbm, WW1 allele frequency, WW2 allele frequency, and
 length of the Clock gene.sitevalues.xlsx
DOI: 10.5061/dryad.8c3h2
title: Data from: Trends and determinants of gastric bacterial colonization of preterm neonates in a NICU setting

description: Background: Newborn gastrointestinal (GI) tract is considered sterile but
 rapidly acquires a diverse microbiota from its intimate environment. Early
 acquisition of a bacterial species in the upper GI tract may play a role
 in establishing the colonic microbiota. There is paucity of molecular data
 on the upper GI tract microbiota in preterm neonates. Methods: Gastric
 aspirates from 22 neonates with an average gestational age 27.7 weeks
 (±2.8), weighing 973.2 grams (±297.9) admitted to a neonatal intensive
 care unit were collected prospectively from weeks 1-4 of life. All samples
 were evaluated for microbiota using 16S rRNA-based Denaturing Gradient Gel
 Electrophoresis. Bacterial species colonization and its association with
 maternal and neonatal demographics, and neonatal clinical characteristics
 were analyzed. Results: Bacteroides spp. was the predominant species in
 all four weeks. Bifidobacterium spp. colonization was significantly higher
 in exclusively breast milk fed compared to partially breast milk (PBM) fed
 neonates in first (p = 0.03) and third (p = 0.03) week of life. Anaerobic
 bacteria colonization decreased from first through fourth week of life (p
 = 0.03). Aerobic bacteria colonization was highly dynamic throughout the
 four week period. Premature rupture of membrane (p = 0.05) and birth
 outside of study hospital (p = 0.006) influenced the acquisition of
 bacteria in the first week of life. Birth weight was positively correlated
 with total number of bacterial species (p = 0.002) and anaerobes (p =
 0.004) in PBM-fed neonates during the fourth week of life. H. pylori and
 Ureaplasma were not detected in any of our samples. Conclusion: Gastric
 bacterial colonization in preterm neonates is unstable during early weeks
 of life. Delayed oral feeding and use of antibiotics may be responsible
 for paucity of bacterial species. Monitoring of the gastric microbiota and
 concurrent examination of stool microbiota may yield important information
 on the utility of gastric signature patterns for predicting colon
 microbiota that may drive GI and immune dysfunctions.
description: PLoSOne GApaper
 dataThis data file consists
 raw data used to generate results published in PLOS ONE article titled
 "Trends and determinants of gastric bacterial colonization of preterm
 neonates in a NICU setting"
DOI: 10.5061/dryad.5d68n
title: Data from: Female behavior and the interaction of male and female genital traits mediate sperm transfer during mating.

description: Natural selection and post-copulatory sexual selection, including sexual
 conflict, contribute to genital diversification. Fundamental first steps
 in understanding how these processes shape the evolution of specific
 genital traits are to determine their function experimentally and to
 understand the interactions between female and male genitalia during
 copulation. Our experimental manipulations of male and female genitalia in
 red-sided garter snakes (Thamnophis sirtalis parietalis) reveal that
 copulation duration and copulatory plug deposition, as well as total and
 oviductal/vaginal sperm counts, are influenced by the interaction between
 male and female genital traits and female behaviour during copulation. By
 mating females with anesthetized cloacae to males with spine-ablated
 hemipenes using a fully factorial design, we identified significant
 female–male copulatory trait interactions and found that females prevent
 sperm from entering their oviducts by contracting their vaginal pouch.
 Furthermore, these muscular contractions limit copulatory plug size,
 whereas the basal spine of the male hemipene aids in sperm and plug
 transfer. Our results are consistent with a role of sexual conflict in
 mating interactions and highlight the evolutionary importance of female
 resistance to reproductive outcomes.
description: Female behavior and the
 interaction of male and female genital traits mediate sperm transfer
 during mating
DOI: 10.5061/dryad.s6k44
title: Data from: Ontogeny of aerial righting and wing flapping in juvenile birds

description: Mechanisms of aerial righting in juvenile chukar partridge (Alectoris
 chukar) were studied from hatching to 14 days-post-hatching (dph).
 Asymmetric movements of the wings were used from 1 to 8 dph to effect
 progressively more successful righting behaviour via body roll. Following
 8 dph, wing motions transitioned to bilaterally symmetric flapping that
 yielded aerial righting via nose-down pitch, along with substantial
 increases in vertical force production during descent. Ontogenetically,
 the use of such wing motions to effect aerial righting precedes both
 symmetric flapping and a previously documented behaviour in chukar (i.e.
 wing-assisted incline running) hypothesized to be relevant to incipient
 flight evolution in birds. These findings highlight the importance of
 asymmetric wing activation and controlled aerial manoeuvres during bird
 development and are potentially relevant to understanding the origins of
 avian flight.
description: Raw data and R code for
 plottingData and R code to
 produce figure 2, which gives (a) Percent righting (N=26 birds, number of
 drops as indicated) and (b) righting mode (N=26 birds, number of
 successful rightings as indicated), and (c) vertical force production (N=5
 birds, except for N=1 at 14 dph; data represent mean ± 1 s.d.) versus age
 in Chukar Partridge. Righting via roll, as accomplished by asymmetric wing
 and leg movements, is used prior to 14 dph. Around 9 dph, birds switch to
 righting via pitch using symmetric wing motions, and vertical force
 production increases concomitantly.data.tar.gz
DOI: 10.5061/dryad.9rt50
title: Data from: A consensus method for ancestral recombination graphs

description: We propose a consensus method for ancestral recombination graphs (ARGs)
 that generates a single ARG representing commonalities among a cloud of
 ARGs defined for the same genomic region and set of taxa. Our method,
 which we call “threshold consensus,” treats a genomic location as a
 potential recombination breakpoint only if the number of ARGs in the cloud
 possessing a breakpoint at that location exceeds a chosen threshold. The
 estimate is further refined by ignoring recombinations that do not change
 the local tree topologies, as well as collapsing breakpoint locations
 separated only by invariant sites. We test the threshold consensus
 algorithm, using a range of threshold values, on simulated ARGs inferred
 by a genealogy sampling algorithm, and evaluate accuracy of breakpoints
 and local topologies in the resulting consensus ARGs.
description: Software for computing
 the ARG consensusThis is a tar gzip
 archive of all programs needed to compute the ARG consensus as described
 in our paper, and a documentation file explaining how they are used. In
 order to use this archive you will need access to a Python interpreter and
 a C++ compiler. A shell script linking the steps is included, but is
 optional.argconsense_software.tgz
DOI: 10.5061/dryad.074r6
title: Data from: Linking disturbance and resistance to invasion via changes in biodiversity: a conceptual model and an experimental test on rocky reefs

description: Biological invasions threaten biodiversity worldwide. Nonetheless, a
 unified theory linking disturbance and resistance to invasion through a
 mechanistic understanding of the changes caused to biodiversity is
 elusive. Building on different forms of the disturbance-biodiversity
 relationship and on the Biotic Resistance Hypothesis (BRH), we constructed
 conceptual models showing that, according to the main biodiversity
 mechanism generating invasion resistance (complementary vs. identity
 effects), disturbance can either promote or hinder invasion. Following the
 Intermediate Disturbance Hypothesis (IDH), moderate levels of disturbance
 (either frequency or intensity) are expected to enhance species richness.
 This will promote invasion resistance when complementarity is more
 important than species identity. Negative effects of severe disturbance on
 invasion resistance, due to reductions in species richness, can be either
 overcompensated or exacerbated by species identity effects, depending on
 the life-traits becoming dominant within the native species pool.
 Different invasion resistance scenarios are generated when the
 diversity-disturbance relationship is negative or positive monotonic.
 Predictions from these models were experimentally tested on rocky reefs.
 Macroalgal canopies differing in species richness (1 vs. 2 vs. 3) and
 identity, were exposed to either a moderate or a severe pulse disturbance.
 The effects of different canopy-forming species on the seaweed, Caulerpa
 cylindracea, varied from positive (Cystoseira crinita) to neutral
 (Cystoseira barbata) to negative (Cystoseira compressa). After 2 years,
 severely disturbed plots were monopolized by C. compressa and supported
 less C. cylindracea. Our study shows that the effects of disturbance on
 invasion depend upon its intensity, the main mechanism through which
 biodiversity generates invasion resistance and the life-traits selected
 within the native species pool. Disturbance can sustain invasion
 resistance when promoting the dominance of competitively subordinate
 species possessing traits that allow outperforming invaders.
description: DatasetThis Excel file reports data from a field experiment. The first 8 columns (A-H) report conditions established at the beginning of the experiment. In column F, cri = crinita, bar = barbata; com = compressa. Columns K to L report the percentage cover of Caulerpa cylindracea, Cystoseira compressa, Cystoseira barbata and Cystoseira crinita in experimental plots at the end of the experiment.
DOI: 10.5061/dryad.fg7v4
title: Data from: Does predation risk affect mating behavior? An experimental test in dumpling squid (Euprymna tasmanica)

description: Introduction: One of the most important trade-offs for many animals is
 that between survival and reproduction. This is particularly apparent when
 mating increases the risk of predation, either by increasing
 conspicuousness, reducing mobility or inhibiting an individual’s ability
 to detect predators. Individuals may mitigate the risk of predation by
 altering their reproductive behavior (e.g. increasing anti-predator
 responses to reduce conspicuousness). The degree to which individuals
 modulate their reproductive behavior in relation to predation risk is
 difficult to predict because both the optimal investment in current and
 future reproduction (due to life-history strategies) and level of
 predation risk may differ between the sexes and among species. Here, we
 investigate the effect of increased predation risk on the reproductive
 behavior of dumpling squid (Euprymna tasmanica). Results: Females, but not
 males, showed a substantial increase in the number of inks (an
 anti-predator behavior) before mating commenced in the presence of a
 predator (sand flathead Platycephalus bassensis). However, predation risk
 did not affect copulation duration, the likelihood of mating, female
 anti-predator behavior during or after mating or male anti-predator
 behavior at any time. Conclusions: Inking is a common anti-predator
 defense in cephalopods, thought to act like a smokescreen, decoy or
 distraction. Female dumpling squid are probably using this form of defense
 in response to the increase in predation risk prior to mating. Conversely,
 males were undeterred by the increase in predation risk. A lack of change
 in these variables may occur if the benefit of completing mating outweighs
 the risk of predation. Prioritizing current reproduction, even under
 predation risk, can occur when the chance of future reproduction is low,
 there is substantial energetic investment into mating, or the potential
 fitness payoffs of mating are high.
description: Franklin et al 2014 PLOS
 ONE dataDoes predation risk
 affect mating behavior? An experimental test in dumpling squid (Euprymna
 tasmanica), PLOS ONE, datafileFranklin et al
 2014.xlsx
DOI: 10.15468/dl.8sj473
title: Occurrence Download

description: A dataset containing 25209 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((4.465458123046558 50.80945925027852, 4.465054616471967 50.812090263047224, 4.463848624026548 50.81462083575098, 4.461886378476872 50.81695369644477, 4.459243212240388 50.81899915942145, 4.456020673927599 50.82067857713844, 4.452342629980305 50.82192736892543, 4.448350500588839 50.82269750911806, 4.444197813569968 50.82295937803403, 4.44004428723655 50.822702903840536, 4.436049672264774 50.82193795088239, 4.432367592301042 50.82069393935378, 4.429139623101666 50.819018711119114, 4.42648984036166 50.81697668581517, 4.424520047507081 50.814646378910915, 4.4233058674575085 50.81211737807022, 4.422893847933862 50.80948689497787, 4.423299689802861 50.806856025958304, 4.424507663926474 50.80432586563483, 4.4264712358456135 50.80199362317126, 4.429114871215076 50.799948890154866, 4.432336950003039 50.798270202998395, 4.436013675726113 50.79702203115088, 4.44000382888162 50.79625230589657, 4.44415418251684 50.79599058374712, 4.448305373555493 50.79624691419146, 4.452298006848929 50.79701145476927, 4.455978760443339 50.7982548480676, 4.459206260510091 50.799929346341926, 4.461856502775279 50.8019706410854, 4.463827613854229 50.804300328050225, 4.465043770139613 50.80682891395268, 4.465458123046558 50.80945925027852))",
 "KingdomKey is one of (Animalia, Fungi, Plantae)",
 "Year is one of (2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024, 2025, 2026)"
 ]
}

 The dataset includes 25209 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001282-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.vk5176r
title: Data from: The effects of diet and mating system on reproductive (and post-reproductive) lifespan in a freshwater snail

description: The length of the reproductive lifespan, along with the
 number/frequency/magnitude of reproductive events, quantifies an
 individual’s potential contribution to the next generation. By examining
 reproductive lifespan, and distinguishing it from somatic lifespan, we
 gain insight into critical aspects of an individual’s potential fitness as
 well as reproductive and somatic senescence. Additionally, differentiating
 somatic and reproductive lifespans can provide insight into the existence
 of a post-reproductive period and factors that shape its duration. Given
 the known importance of diet and mating system on resource allocation, I
 reared individual freshwater snails (Physa acuta) from 22 full-sib
 families under a 2x2 factorial design that crossed mate availability
 (available [outcrossing] or not [selfing]) and diet (Spirulina or lettuce)
 and quantified aspects of the entire life history enabling me to
 distinguish reproductive and somatic lifespans, determine the total number
 of reproductive events, and evaluate how the reproductive rate changes
 with age. Overall, mated snails experienced shorter reproductive and
 somatic lifespans; a diet of Spirulina also shortened both reproductive
 and somatic lifespans. A post-reproductive period existed in all
 conditions; its duration was proportional to somatic but not reproductive
 lifespan. I evaluate several hypotheses for the existence and duration of
 the post-reproductive period, including a novel hypothesis that the
 post-reproductive period may result from an increase in reproductive
 interval with age. I conclude that the post-reproductive period may be
 indicative of a randomly timed death occurring as the interval between
 reproductive events continues to increase. As such, a “post-reproductive”
 period can be viewed as a by-product of a situation where reproductive
 senescence outpaces somatic senescence.
description: Auld
 DataFamily, mate treatment,
 diet treatment, age at first reproduction (d), age at last reproduction
 (d), and age at death (d)
DOI: 10.15468/dl.7xn4rc
title: Occurrence Download

description: A dataset containing 689 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Elliottia bracteata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 689 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001283-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fs24q30
title: Data from: Mate choice vs mate preference: inferences about color-assortative mating differ between field and lab assays of poison frog behavior

description: Co-divergence of mating traits and mate preferences can lead to behavioral
 isolation among lineages in early stages of speciation. However, mate
 preferences only limit gene flow when expressed as mate choice, and
 numerous factors might be more important than preferences in nature. In
 the extremely color polytypic strawberry poison frog (Oophaga pumilio),
 female mate preferences have co-diverged with color in most allopatric
 populations tested. Whether these lab-assayed preferences predict mating
 (gene flow) in the wild remains unclear. We observed courting pairs in a
 natural contact zone between red and blue lineages until oviposition or
 courtship termination. We found color-assortative mating in a disturbed
 habitat with high population density, but not in a secondary forest with
 lower density. Our results suggest color-assortative O. pumilio mate
 choice in the wild, but also mating patterns that do not match those
 predicted by lab-assayed preferences.
description: MateChoiceThe compressed folder contained an R markdown file (MateChoice_for archive.rmd) with codes for all analyses and figures, and the two data sets that would be read into R when performing analyses.