cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b8gtht7dw
title: Script and data used in: A lot of convergence, a bit of divergence: environment and interspecific interactions shape body color patterns in Lissotriton newts

description: Coexistence with related species poses evolutionary challenges to which
 populations may react in diverse ways. When exposed to similar
 environments, sympatric populations of two species may adopt similar
 phenotypic trait values. However, selection may also favor trait
 divergence as a way to reduce competition for resources or mates. The
 characteristics of external body parts, such as coloration and external
 morphology, are involved to varying degrees in intraspecific signaling as
 well as in the adaptation to the environment, and consequently may be
 diversely affected by interspecific interactions in sympatry. Here, we
 studied the effect of sympatry on various color and morphological traits
 in males and females of two related newt species Lissotriton helveticus
 and L. vulgaris. Importantly, we did not only estimate how raw trait
 differences between species respond to sympatry, but also the marginal
 responses after controlling for environmental variation. We found that
 dorsal and caudal coloration converged in sympatry, likely reflecting
 their role in adaptation to local environments, especially concealment
 from predators. In contrast, aspects of male and female ventral
 coloration, which harbours sexual signals in both species, diverged in
 sympatry. This divergence may reduce opportunities for interspecific
 sexual interactions and the associated loss of energy, suggesting
 reproductive character displacement (RCD). Our study emphasizes the
 contrasting patterns of traits involved in different functions and calls
 for the need to consider this diversity in evolutionary studies.
DOI: 10.5061/dryad.q2bvq83mj
title: Tree_seedling_survival_growth_leaf_traits_in_disturbed_conditions

description: 1.              Restoration of tropical montane cloud forest landscapes is urgently required. Assisting the regeneration of endangered and shade tolerant tree species is essential for both the recovery of this vulnerable group and of ecological processes. However, there is limited species-specific information regarding tree performance under different disturbance conditions with which to implement effective interventions.  2.              We assessed the performance of shade tolerant tree seedlings in restoration plantings under different disturbance settings and determined whether leaf mass area (LMA) and leaf dry mass content (LDMC) – functional traits typically associated with resource capture or stress tolerance – could serve as predictors of survival and growth among species. Since conservative leaf morphological traits can maximize survival, we expected species with higher LMA and LDMC to present higher survival. For a set of eight native cloud forest species, a total of 2202 seedlings were planted in four pastures, five secondary forests and three forests subjected to traditional selective logging, in tropical montane cloud forest landscapes in Eastern Mexico. 3.              Seedling survival was high after three years: 62% in pastures, 80% in secondary forests and 88% in logged forests. Growth rates were lowest in pastures, followed by secondary forests and highest in logged forests. LMA was a strong predictor of seedling survival in all of the environments; tree species with higher LMA presented greater survival. LDMC was related to seedling survival in the three environments, although to a lesser extent than LMA. In the pastures, higher LMA and LDMC were linked to lower growth. 4.              Synthesis and applications. This study support the potential of shade tolerant tree species in restoration efforts to assist the recovery of this important functional group and to accelerate succession across altered environments. Our results support the notion that conservative leaf functional traits are linked to a higher probability of survival, not only in the shaded understorey, but also under high solar radiation in transformed habitats. Leaf Mass Area (LMA) in particular is a reliable predictor of seedling survival for shade tolerant species. Species selection based on LMA could thus improve restoration initiative outcomes: tree species with high LMA present higher survival probability and can be introduced into pastures, secondary forests and selectively logged forests.
description: Description of methodology available in Toledo-Aceves et al.
 2022. Leaf functional traits predict shade tolerant tree performance in
 cloud forest restoration plantings. Journal of Applied Ecology. https://doi.org/10.1111/1365-2664.14128  
description: For Relative Growth Rate data missing values are denoted as
 n/a
DOI: 10.5061/dryad.w3r2280sd
title: Congruence among multiple indices of habitat preference for species facing human-induced rapid environmental change: A case study using the Brewer’s sparrow

description: Accurate evaluations of habitat preference are key to understanding
 optimal conditions for wildlife survival and reproduction. Habitat
 selection, however, usually is evaluated using a single index of
 preference, and congruence among multiple, relevant indices of preference
 is examined rarely. We assessed the concordance between patterns of
 habitat preference using three different indices of breeding site
 preference in a migratory songbird. Specifically, we compared the
 chronology of territorial establishment, pair formation, and reproductive
 initiation of the Brewer’s sparrow (Spizella breweri) along a gradient of
 surface disturbance associated with natural gas development in Wyoming,
 USA during 2019. We expected all three indices to demonstrate a preference
 for breeding sites with less surface disturbance, where reproductive
 success typically is higher. By contrast, all indices suggested suboptimal
 preference with respect to surface disturbance, with some discrepancy
 among them. The chronology of settlement and pairing did not vary across
 the disturbance gradient, whereas nest initiation tended to occur earlier
 at sites with more disturbance. If the pattern of suboptimal selection of
 breeding sites that we identified is generalizable across other
 populations of migratory birds affected by energy development, the
 resultant lower fitness in those areas may exacerbate population declines.
 Our results suggest that traditional, single-index approaches to the study
 of habitat selection, if chosen carefully, may provide adequate inference
 on habitat preferences. Different metrics, however, can lead to at least
 subtle differences in patterns of habitat selection. The simultaneous
 examination of multiple indices of preference across a diversity of
 systems would help clarify the contexts under which preference metrics can
 become decoupled.
DOI: 10.5061/dryad.nvx0k6dtx
title: Earth and life evolve together from something ancestral — reply to Britz et al

description: Ricefishes of the family Adrianichthyidae are considered to have dispersed
 eastward “out-of-India” after the collision of the Indian subcontinent
 with Eurasia and subsequently diversified in Southeast-East Asia. In this
 study, we reconstructed ancestral areas of Adrianichthyidae with
 BioGeoBEARS, expanding the scope to include Cyprinodontiformes, the
 outgroup of Beloniformes to which Adrianichthyidae belongs. The
 results again supported the “out-of-India” dispersal scenario. The dataset
 contained all files necessary for the BioGeoBEARS analysis.
DOI: 10.5061/dryad.x95x69pkm
title: Mississippi River Baton Rouge water quality

description: We investigated how physical and chemical factors affect Chlorophyll a
 concentrations in the Mississippi River, the largest river in North
 America, by sampling 878 times from February 1997 to December 2018 near
 its terminus at Baton Rouge, Louisiana. Measured values included
 temperature, light (secchi disk), suspended sediments, and nutrients
 (nitrate+nitrite, phosphate, TP, TN, ammonium, silicate) that may affect
 phytoplankton communities. The data are available for unrestricted use.
description: Water samples were taken from a wharf overhanging the left
 descending riverbank of the Mississippi River in Baton Rouge, LA, USA
 (30<sup>o</sup> 26’ 34”N, 91<sup>o</sup>11’ 29”W),
 located 233 km (365 km of river distance) from the debouching
 end. Sampling started February 1997 and ended December 2018 for a total of
 878 collection events occurring at least once monthly. Chl a measured with
 a Turner Designs fluorometer after extraction in DMSO:Acetone, adjusted
 for flourometer lamp aging. Sample analysis used a Technicon Autoanalyzer
 II or LaChat Quick Chem analyzer for inorganic nutrients. Suspended solids
 were measure gravimetrically. A Secchi disk was used for water
 clarity.
description: no restrictions on data set use.
DOI: 10.5061/dryad.zs7h44jbh
title: Soil chemical variables improve models of understory plant species distributions

description: Aim To determine the importance of soil variables relative to more
 commonly used topo-climatic or remotely sensed variables in species
 distribution models (SDMs) for understory plants.   Location
 White Mountain National Forest, New Hampshire, U.S.A.   Methods
 We fit models for presence of 41 forest understory plant species across
 158 plots using soil, topographic, and spectral predictors to determine
 the relative contribution of different predictor types. We determined (a)
 if the potential importance of soil variables is greater than generally
 described in SDM literature, (b) which predictors are most important, and
 (c) if a standard subset of predictors can be used to effectively model
 all species.   Results Models containing all three predictor
 types performed best. Soil and topographic variables had comparable
 importance; spectral variables were of lesser importance. The best
 predictor variable was B horizon carbon to nitrogen ratio (B C:N),
 followed by topographic position index, elevation, and B horizon
 exchangeable calcium (B Ca). No standard subset effectively modeled all
 species.   Main conclusions  Our results and those of
 other SDMs that include in-situ soil geochemical data suggest that soil
 variables are increasingly important with more detailed descriptions of
 soils. Soil fertility data, such as B C:N and B Ca, are particularly
 important in acidic, forest soils where pH is a poor indicator of
 fertility. Commonly used topo-climatic variables provide meaningful
 predictions but are limited by their use of indirect predictor variables,
 inhibiting transferability and interpretability. The poor performance of
 models created using standard subsets of variables highlights the
 uniqueness of each species’ niche and the need to combine flexible model
 building techniques with a variety of predictor variables.
description: This data does not include plot locations to preserve the
 integrity of US Forest Service long-term monitoring plots.
DOI: 10.5061/dryad.sj3tx966g
title: Plant species richness on the Tibetan Plateau: Patterns and determinants

description: Whether current hypotheses for geographic patterns of species richness
 (SR) have a strong explanatory power for the Tibetan Plateau (TP) with
 extreme climatic conditions remains unclear. In comparison with the
 classic “water–energy dynamics hypothesis”, the unique climate factors
 (e.g., extreme low temperature and low oxygen partial pressure) on the TP
 likely significantly affect the spatial variation of SR. Here, we
 investigate geographic patterns and determinants of SR on the TP through a
 systematic field investigation. We systematically analyzed a total of
 2,013 plant communities covering 11 different vegetation types on the TP.
  The SR per 400 m2 in the forests and shrubs and that per 1 m2 in
 alpine grasslands and deserts was 62.76 (±1.80 SE), 44.53 (±7.57 SE),
 16.84 (±0.39 SE), and 3.62 (±0.55 SE), respectively. Unique climate
 factors, such as extremely low temperature, mean diurnal temperature, and
 oxygen partial pressure, act synergistically with water–energy dynamics
 and influence the spatial pattern of SR on the TP. Our findings provide
 novel insights into the mechanisms underlying the spatial variation in
 plant diversity, especially on plateaus and in high-latitude regions. Our
 findings and the SR map with 1 km resolution provide important benchmarks
 for biodiversity conservation and may help to improve predictions of the
 effect of climate change on biodiversity.
description: Field sampling was conducted
 during the high growth period of mid-July to late August in 2018,
 2019, and 2020. We divided
 the entire Tibetan Plateau
 according to the latitude and longitude into 1,000 grids with equal area
 (0.5° × 0.5°). For the field investigation of the alpine grasslands and
 deserts, we selected the dominant plant communities via visual observation
 in each grid and randomly set up three 1 m × 1 m plots located at least 20
 m apart (most commonly plot-size for these
 grasslands). If two or
 more types of plant communities were abundant in a given grid, the
 vegetation type was then randomly selected (the same rules apply to
 forests and shrubs). The “shoot presence” method was used to record the
 presence of species, whereby an individual is recorded as present if any
 part of its stem or leaf is inside the plot. For the forests and shrubs in the southeast,
 three 20 m × 20 m plots located at least 100 m apart were randomly
 established in each grid.
  We recorded all vascular
 plants (including juveniles and seedlings) in these plots including tree,
 shrub, and herb species.  A total of 2,013 field plots were investigated.
 The depopulated zone was not investigated due to access
 limitations.
DOI: 10.5061/dryad.bg79cnpcc
title: Data from: Molecular identification of an avian predator of mimetic salamanders

description: Natural field observations of salamander predation are uncommon, in some
 cases limiting the ability of scientists to study the evolution of
 toxicity, aposematism, and mimicry in these amphibians. Here, we document
 field observations of a recently depredated Pseudotriton ruber (Red
 Salamander) and two Gyrinophilus porphyriticus (Spring Salamanders),
 members of a putative Müllerian mimetic complex involving Notophthalmus
 viridescens (Eastern Newts). We use molecular methods to identify the
 likely avian predator of the Spring Salamanders and underscore the
 opportunities for future research enabled by the pairing of traditional
 natural history with modern molecular techniques.
DOI: 10.5061/dryad.70rxwdc00
title: NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype

description: Hypertension is the most important cause of death and disability in the
 elderly. In 9 out of 10 cases, the molecular cause, however, is unknown.
 One mechanistic hypothesis involves impaired endothelium-dependent
 vasodilation through reactive oxygen species (ROS) formation. Indeed, ROS
 forming NADPH oxidase (Nox) genes associate with hypertension, yet target
 validation has been negative. We re-investigate this association by
 molecular network analysis and identify NOX5, not present in rodents, as a
 sole neighbor to human vasodilatory endothelial nitric oxide (NO)
 signaling. In hypertensive patients, endothelial microparticles indeed
 contained higher levels of NOX5—but not NOX1, NOX2, or NOX4—with a bimodal
 distribution correlating with disease severity. Mechanistically, mice
 expressing human Nox5 in endothelial cells developed—upon aging—severe
 systolic hypertension and impaired endothelium-dependent vasodilation due
 to uncoupled NO synthase (NOS). We conclude that NOX5-induced uncoupling
 of endothelial NOS is a causal mechanism and theragnostic target of an
 age-related hypertension endotype. Nox5 knock-in (KI) mice represent the
 first mechanism-based animal model of hypertension.
description: CD144+ microparticles were isolated as described with
 modifications (see paper). Briefly, Dynabeads G (Invitrogen, Carlsbad, CA)
 were washed with PBS containing 0.1% BSA and then reconstituted with PBS.
 Anti-CD144 antibody (Santa Cruz Biotechnology, Dallas, TX), which
 specifically targets endothelial cells, was mixed with prewashed Dynabeads
 G for 2 hours and then incubated with plasma samples at 1:200 dilution
 overnight at 4°C. After precipitation, Dynabeads G were washed with PBS
 and 1% Tween-20 three times. The purity of CD144+ MPs, determined by FACS
 analysis, was 70% ± 5.6%. With the use of FITC-conjugated beads as size
 references, the size of such particles was assessed to be &lt;0.5 μm
 in diameter. The baseline characteristics of those patients are listed in
 S1 Table. The values provided for Fig. S1 in the article’s S1 Data file
 are ng/mL values calculated from optical density (O.D.)
 measurements.
description: The dataset contains repeated values for Fig. S1A because NOX1
 concentrations were very close to the limit of detection, i.e., close to
 the O.D. of the buffer control for which we obtained a value of 0.09. The
 repeated values in the 0.07-0.16 range were interpreted as essentially
 negative results, and from these data we concluded that NOX1 was not
 detectable using this assay for most subjects. Only one normotensive and
 two hypertensive patients with microalbuminuria yielded O.D. readings
 above the 0.07-0.16 range.
DOI: 10.5061/dryad.bcc2fqzdq
title: Distinct decision-making properties underlying the species specificity of group formation of flies

description: Many animal species form groups. Group characteristics differ between
 species, suggesting that the decision-making of individuals for grouping
 varies across species. However, the actual decision-making properties that
 lead to interspecific differences in group characteristics remain unclear.
 Here, we compared the group formation processes of two Drosophilinae fly
 species, Colocasiomyia alocasiae and Drosophila melanogaster, which form
 dense and sparse groups, respectively. A high-throughput tracking system
 revealed that C. alocasiae flies formed groups faster than D. melanogaster
 flies, and the probability of C. alocasiae remaining in groups was far
 higher than that of D. melanogaster. C. alocasiae flies joined groups even
 when the group size was small, whereas D. melanogaster flies joined groups
 only when the group size was sufficiently large. C. alocasiae flies
 attenuated their walking speed when the inter-individual distance between
 flies became small, whereas such behavioural properties were not clearly
 observed in D. melanogaster. Furthermore, depriving C. alocasiae flies of
 visual input affected grouping behaviours, resulting in a severe reduction
 in group formation. These findings show that C. alocasiae decision-making
 regarding grouping, which greatly depends on vision, is significantly
 different from D. melanogaster, leading to species-specific
 group-formation properties.
DOI: 10.5061/dryad.hmgqnk9jk
title: Conflict over the eukaryote root resides in strong outliers, mosaics and missing data sensitivity of site-specific (CAT) mixture models

description: Abstract Phylogenetic reconstruction using concatenated loci
 (“phylogenomics” or “supermatrix phylogeny”) is a powerful tool for
 solving evolutionary splits that are poorly resolved in single
 gene/protein trees (SGTs). However, recent phylogenomic attempts to
 resolve the eukaryote root have yielded conflicting results, along with
 claims of various artefacts hidden in the data. We have investigated these
 conflicts using two new methods for assessing phylogenetic conflict.
 ConJak uses whole marker (gene or protein) jackknifing to assess deviation
 from a central mean for each individual sequence, while ConWin uses a
 sliding window to screen for incongruent protein fragments (mosaics). Both
 methods allow selective masking of individual sequences or sequence
 fragments in order to minimize missing data, an important consideration
 for resolving deep splits with limited data. Analyses focused on a set of
 76 eukaryotic proteins of bacterial-ancestry previously used in various
 combinations to assess the branching order among the three major divisions
 of eukaryotes: Amorphea (mainly animals, fungi and Amoebozoa),
 Diaphoretickes (most other well-known eukaryotes and nearly all algae) and
 Excavata, represented here by Discoba (Jakobida, Heterolobosea, and
 Euglenozoa). ConJak analyses found strong outliers to be concentrated in
 under-sampled lineages, while ConWin analyses of Discoba, the most
 under-sampled of the major lineages, detected potentially incongruent
 fragments scattered throughout. Phylogenetic analyses of the full data
 using an LG-gamma model support a Discoba sister scenario
 (neozoan-excavate root), which rises to 99-100% bootstrap support with
 data masked according to either protocol. However, analyses with two
 site-specific (CAT) mixture models yielded widely inconsistent results and
 a striking sensitivity to missing data. The neozoan-excavate root places
 Amorphea and Diaphoretickes as more closely related to each other than
 either is to Discoba, a fundamental relationship that should remain
 unaffected by additional taxa.
DOI: 10.5061/dryad.j9kd51cf2
title: Divergent natural selection alters male sperm competition success in Drosophila melanogaster

description: Sexually selected traits may also be subject to non-sexual selection.
 If optimal trait values depend on environmental conditions, then
 “narrow sense” (i.e., non-sexual) natural selection can lead to
 local adaptation, with fitness in a certain environment being
 highest among individuals selected under that environment. Such
 adaptation can in turn drive ecological speciation via sexual
 selection. To date, most research on the effect of narrow-sense
 natural selection on sexually selected traits has focused on
 precopulatory measures like mating success.
 However, postcopulatory traits, such as sperm function, can also
 be under nonsexual selection, and have the potential to
 contribute to population divergence between different
 environments. Here, we investigate the effects of narrow-sense
 natural selection on male postcopulatory success in Drosophila
 melanogaster. We chose two extreme environments, low oxygen (10%,
 hypoxic) or high CO2 (5%, hypercapnic) to detect small effects.
 We measured the sperm defensive (P1) and offensive
 (P2) capabilities of selected and control males in the
 corresponding selection environment and under control conditions.
 Overall, selection under hypoxia decreased both P1 and P2, while
 selection under hypercapnia had no effect. Surprisingly, P1 for
 both selected and control males was higher under both ambi-ent
 hypoxia and ambient hypercapnia, compared to control conditions,
 while P2 was lower under hypoxia. We found limited evidence for
 local adaptation: the positive environmental effect of hypoxia on
 P1 was greater in hypoxia-selected males than in controls. We
 discuss the implications of our findings for the evolution
 of postcopulatory traits in response to non-sexual and sexual
 selection.