cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qbzkh18f4
title: Data from: To bee or not to bee: the “raison d’être” of toxic secondary compounds in the pollen of Boraginaceae

description: This dataset contains all data analyzed in the article "To bee or not
 to bee: The “raison d’être” of toxic secondary compounds in the pollen of
 Boraginaceae", by V. Trunz et al, published in Functional Ecology.
 List of files: in "PGLS" folder, "PA_values.csv" gives
 the transformed PA values for pollen and corolla. "Group" stands
 for Borago-Group (1) or other species (0). The tree
 ("tree_Boraginaceae.txt") is in Nexus format. This dataset can
 be used for CAPER and mv-morph analyses. The tree needs to be pruned for
 analyzing corolla data, or for the analysis of the relationship between PA
 levels and the number of specialist bees on a given plant taxon. in
 "Raw-data" folder: the table "PA_values_all.xlsx"
 gives the raw data of all PA values for each plant species and replicate.
 It corresponds to Table S2 in the paper. in "Survival" Folder:
 "bicornis.csv" and "rapunculi.csv" give the survival
 data for Osmia bicornis and Chelostoma rapunculi, respectively. For each
 larva the following information is given: treatment (C = control, T =
 PA-supplemented), number of days alive (Days_alive) and whether mortality
 occurred (Death = 1) larva.
DOI: 10.5061/dryad.rxwdbrv5f
title: Data from: Gene flow and species delimitation in fishes of Western North America: Flannelmouth (Catostomus latipinnis) and Bluehead sucker (C. Pantosteus discobolus)

description: The delimitation of species-boundaries, particularly those obscured by
 reticulation, is a critical step in contemporary biodiversity assessment.
 It is especially relevant for conservation and management of indigenous
 fishes in western North America, represented herein by two species with
 dissimilar life-histories co-distributed in the highly modified Colorado
 River (i.e., Flannelmouth Sucker, Catostomus latipinnis; Bluehead Sucker,
 C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine
 proposed taxonomic revisions, we first employed double-digest
 restriction-site associated DNA sequencing (ddRAD), yielding 39,755
 unlinked SNPs across 139 samples. These were subsequently evaluated with
 multiple analytical approaches and by contrasting life history data. Three
 phylogenetic methods and a Bayesian assignment test highlighted similar
 phylogenomic patterns in each, but with considerable difference in
 presumed times of divergence. Three lineages were detected in Bluehead
 Sucker, supporting elevation of C. (P.) virescens to species-status, and
 recognizing C. (P.) discobolus yarrowi (Zuni Bluehead Sucker) as a
 discrete entity. Admixture in the latter necessitated a reevaluation of
 its contemporary and historic distributions, underscoring how biodiversity
 identification can be confounded by complex evolutionary histories. In
 addition, we defined three separate Flannelmouth Sucker lineages as ESUs
 (Evolutionarily Significant Units), given limited phenotypic and genetic
 differentiation, contemporary isolation, and lack of concordance (per the
 genealogical concordance component of the phylogenetic species concept).
 Introgression was diagnosed in both species, with the Little Colorado and
 Virgin rivers in particular. Our diagnostic methods, and the agreement of
 our SNPs with previous morphological, enzymatic, and mitochondrial work,
 allowed us to partition complex evolutionary histories into requisite
 components, such as isolation versus secondary contact.
description: ddRAD data sorted processed in pyRAD.
description: Raw fastq files for all individuals are included along with a
 folder of alignments used for analyses. Alignments included phylip
 formated concatened loci (.phy), phylip formated concatenation of SNPs
 (.allsnps), phylip formatted concatenated unlinked SNPS as generated by
 pyRAD (.unlinked_snps), Structure formatted unlinked SNPs (.str), and SNPs
 split by locus as generated by pyRAD (.snps).
DOI: 10.5061/dryad.69p8cz8z7
title: Data from: Sustainability management of short-lived freshwater fish in human-altered ecosystems should focus on adult survival

description: Fish populations globally are susceptible to endangerment through
 exploitation and habitat loss. We present theoretical simulations to
 explore how reduced adult survival (age truncation) might affect
 short-lived freshwater fish species in human-altered contemporary
 environments. Our simulations evaluate two hypothetical "average
 fish" and five example fish species of age 1 or age 2 maturity. From
 a population equilibrium baseline representing a natural, unaltered
 environment we impose systematic reductions in adult survival and quantify
 how age truncation affects the causes of variation in population growth
 rate. We estimate the relative contributions to population growth rate
 arising from simulated temporal variation in age-specific vital rates and
 population structure. At equilibrium and irrespective of example species,
 population structure (first adult age class) and survival probability of
 the first two adult age classes are the most important determinants of
 population growth. As adult survival decreases, the first reproductive age
 class becomes increasingly important to variation in population growth.
 All simulated examples show the same general pattern of change with age
 truncation as known for exploited, longer-lived fish species in marine and
 freshwater environments. This implies age truncation is a general
 potential concern for fish biodiversity across life history strategies and
 ecosystems. Managers of short-lived, freshwater fishes in contemporary
 environments often focus on supporting reproduction to ensure population
 persistence. However, a strong focus on water management to support
 reproduction may reduce adult survival. Sustainability management needs a
 focus on mitigating adult mortality in human-altered ecosystems. A
 watershed spatial extent embracing land and water uses may be necessary to
 identify and mitigate causes of age truncation in freshwater species.
 Achieving higher adult survival will require paradigm transformations in
 society and government about water management priorities.
description: Data were generated by computer simulation. Details are contained
 within individual R scripts. Summary data sets of mean contributions for
 Figs 2 and 3 of Hatch et al. are given individually in subfolders for each
 example.
description: This supporting file to Hatch et al. (2020) is a ZIP archive of
 folders and subfolders containing R scripts (.R) and simulation results
 (.Rdata) for all simulations reported in the aforementioned publication.
 The ZIP file contains two parts for simulations of age 1 maturity (a) and
 simulations for age 2 maturity life histories. Full simulation results are
 provided for five example species (Enteromius motebensis, Hybognathus
 amarus, Hybognathis argyritis, Iberochondrostoma lusitanicum, and
 Pseudobarbus burchelli) and two representations of an "average
 fish". Consult R scripts (.R) in each
 folder.
DOI: 10.5061/dryad.3xsj3txcn
title: The hidden costs of dietary restriction: implications for its evolutionary and mechanistic origins

description: Dietary restriction (DR) extends life span across taxa. Despite
 considerable research, universal mechanisms of DR have not been
 identified, limiting its translational potential. Guided by the conviction
 that DR evolved as an adaptive, pro-longevity physiological response to
 food scarcity, biomedical science has interpreted DR as an activator of
 pro-longevity molecular pathways. Current evolutionary theory predicts
 that organisms invest in their soma during DR, and thus when resource
 availability improves, should outcompete rich-fed controls in survival
 and/or reproduction. Testing this prediction in Drosophila melanogaster (N
 &gt; 66,000 across 11 genotypes), our experiments revealed
 substantial, unexpected mortality costs when flies returned to a rich diet
 following DR. The physiological effects of DR should therefore not be
 interpreted as intrinsically pro-longevity, acting via somatic
 maintenance. We suggest DR could alternatively be considered an escape
 from costs incurred under nutrient-rich conditions, in addition to costs
 associated with DR.
description: Csvs have been broken down by experimental date and analysis, for
 ease of use.
DOI: 10.5061/dryad.2v6wwpzjc
title: Data from: Climate change and pathways of vessel traffic create marine protected area networks of invasion

description: Establishment of protected areas to maintain biodiversity requires
 identification, prioritization, and management of stressors that may
 undermine conservation goals. Nonindigenous species and climate change are
 critical ecosystem stressors that need greater attention in the context of
 spatial planning and management of protected areas. Risk of invasion into
 protected areas needs to be quantified under current and projected climate
 conditions in conjunction with prioritization of key vectors and
 vulnerable areas to enable development of effective management strategies.
 We assessed the likelihood of invasion across networks of marine protected
 areas (MPAs) to determine how invaded MPAs may compromise MPA networks by
 sharing nonindigenous species. We evaluated invasion risk in 83 MPAs along
 Canada’s Pacific coast for eight nonindigenous species based on
 environmental suitability under current and future (average conditions
 from 2041-2070) climate conditions and association with shipping and
 boating pathways. We applied species distribution models and network
 analysis of vessel tracking data for 805 vessels in 2016 that connected
 MPAs. The probability of occurrence within MPAs and the proportion of MPA
 area that is suitable to the modelled species significantly increased
 under future climate conditions, with six species reaching over 90%
 predicted occurrence across MPAs and over 70% of suitable area within
 MPAs. Vessel traffic created four network clusters of 61 highly connected
 MPAs that spanned the coastline. Occupancy of over 90% of the MPAs within
 the clusters was predicted for most species. Synthesis and applications.
 Our results indicate a high likelihood of marine protected area (MPA)
 network invasion based on current and future environmental conditions and
 vectors of spread, and the potential for extensive nonindigenous species
 distributions within MPAs. Our approach highlights how interacting
 stressors can exacerbate MPA susceptibility to nonindigenous species,
 adding further challenges for protected area management. Management
 planning that invests in understanding connectivity and vector processes
 (human behaviors) is more likely to derive effective policies to stem the
 flow of nonindigenous species under both current and future conditions. In
 particular, biosecurity measures including vessel biofouling regulations
 and MPA- and MPA network-specific plans for prevention, monitoring, and
 mitigation of nonindigenous species are needed.
description: See Iacarella et al. (2020) Climate change and vessel traffic
 create networks of invasion in marine protected areas. <em>Journal
 of Applied Ecology.</em>
description: Data provided are specific to the anlayses conducted on
 environmental suitability of eight modeled nonindigenous species and
 vessel traffic within marine protected areas in British Columbia,
 Canada.
DOI: 10.5061/dryad.p8cz8w9mg
title: Post-disturbance conifer tree-ring δ15N reflects openness of the nitrogen cycle across temperate coastal rainforests

description: 1. Post-disturbance losses in nitrogen (N) may diminish forest
 productivity, and soils with inherently ‘open’ N cycles (high
 nitrification rates) are considered the most vulnerable to leaching losses
 of NO3-.  Monitoring ongoing N depletion from soil profiles is
 challenging, but tree-ring δ15N of regenerating stands may offer an
 effective method for assessing site-specific, long-term soil N
 dynamics.  Evidence to date is mixed, however, and includes
 increasing, unchanging, or decreasing tree-ring δ15N in young stands
 following stand-level disturbances, possibly because of contrasting soil
 fertility among study sites.  In addition, a consensus on
 post-disturbance N trajectories is hampered by the sometimes inconsistent
 patterns in tree-ring δ15N found between tree species of differing
 mycorrhizal association. 2. We compared tree-ring δ15N of two conifer
 species (Picea sitchensis with ectomycorrhizal fungi and Thuja plicata
 with arbuscular mycorrhiza) from a replicated silviculture trial across
 temperate rainforests of Vancouver Island (Canada).  A natural
 gradient in soil fertility across the six sites, driven largely by
 topography and parent materials, was confirmed by an in situ increase in N
 mineralization and nitrification rates with declining C:N ratios for both
 organic horizons and mineral soils.  3. Five decades after
 logging, the overall trend in tree-ring δ15N was positive, but among
 individual plots there was a wide range in δ15N slopes, ranging from
 nearly 0 to 0.13.  We found the gains in tree-ring δ15N over time
 were consistent between mycorrhizal types and escalated sharply (up to 6‰)
 with increasing N mineralization rates, although less so on flat terrain
 with seasonal water tables.  The most recent sapwood was also
 enriched in 15N as soil N mineralization rates increased, perhaps slightly
 more so for T. plicata than P. sitchensis.  4. Synthesis. The
 correspondence of tree-ring δ15N with soil fertility may be especially
 strong in regenerating forests because of tree ontogeny effects, including
 the expansion of rooting depth and differences in N resorption efficiency
 with stand age.  Sharp increases in tree-ring d15N underscore the
 vulnerability of low C:N soils with open N cycles to post-disturbance N
 losses, and highlight how repeated, frequent harvest cycles may risk
 substantial N depletion from these productive rainforest ecosystems.
DOI: 10.5061/dryad.kprr4xh25
title: Data used to estimate the influence of habitat protection, habitat heterogeneity, and periodic flooding on species richness and abundance of waterbirds of the lower Paraná River, Argentina

description: Interest has grown in how birds respond to environmental characteristics
 of river systems, motivated by the high biodiversity and biomass of
 waterbirds in these systems and the importance of waterbirds in hunting
 for sport or sustenance. We studied the influence of natural (water level
 fluctuations and environmental heterogeneity) and human-related (cattle
 grazing and hunting) factors on waterbirds in the Pre-Delta region of the
 Paraná River system during three years. Our objectives were to evaluate
 which are the main environmental factors that influence the assemblages of
 waterbirds and whether these variables explain differences in waterbird
 assemblages between protected and non-protected areas. Both species
 richness and abundance of waterbirds increased with the surface of open
 water and the number of environmental units. The larger surface of open
 water in the non-protected area contributed to explaining the higher
 species richness and abundance of waterbirds, including of species with
 hunting pressure, in this area. During flood stages the protected area
 maintained a high abundance of water birds, probably because the higher
 proportion of trees and aquatic vegetation in this area provided perches
 and foraging sites. We recommend enlarging protected areas in the
 Pre-Delta region because of their role of sheltering waterbirds during
 floods. Our results showed that the presence of both protected and
 non-protected areas increased the diversity of waterbirds in the region
 due to the species turnover, so it is recommendable to keep a mixture of
 both in the region.
DOI: 10.5061/dryad.ngf1vhhr0
title: Data from: Adaptation to monogamy influences parental care but not mating behavior in the burying beetle, Nicrophorus vespilloides

description: The mating system is expected to have an important influence on the
 evolution of mating and parenting behaviors. Although many studies have
 used experimental evolution to examine how mating behaviors evolve under
 different mating systems, this approach has seldom been used to study the
 evolution of parental care. We used experimental evolution to test whether
 adaptation to different mating systems involves changes in mating and
 parenting behaviors in populations of the burying beetle, Nicrophorus
 vespilloides. We maintained populations under monogamy or promiscuity for
 six generations. This manipulation had an immediate impact on reproductive
 performance and adult survival. Compared to monogamy, promiscuity reduced
 brood size and adult (particularly male) survival during breeding. After
 six generations of experimental evolution, there was no divergence between
 monogamous and promiscuous populations in mating behaviors. However, we
 found that parents from the promiscuous populations (especially males)
 displayed less care than parents from the monogamous populations. Our
 results are consistent with the hypothesis that male care will increase
 with the certainty of paternity. However, it appears that this change is
 not associated with a concurrent change in mating behaviors.
DOI: 10.5061/dryad.dv41ns1vg
title: Data from: The complete mitochondrial genome of Schoutedenia ralumensis Rübsaamen, 1905 (Hemiptera: Aphididae: Greenideinae)

description: We sequenced the complete mitochondrial genome of Schoutedenia ralumensis.
 The mitogenome is 16,051 bp long with an A+T content of 84.5%, including
 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, a
 control region and an aphid-specific repeat region located between trnE
 and trnF. All protein-coding genes are initiated by ATN and terminated
 with TAA or TAG except for cox1 and nad5. All transfer RNAs display the
 typical clover-leaf secondary structure except for trnS (AGN). The unique
 repeat region is 974 bp long, in which a 305-bp repeat unit repeats 3.19
 times. The phylogenetic tree supports a sister relationship of S.
 ralumensis and Greenidea psidii.
description: Phylogenetic analysis
DOI: 10.25338/b8fg9r
title: Insect diversity over 36 years at a protected Sierra Nevada (California) site

description: Recent authors have suggested that declines of insect abundance or
 diversity, documented first for particular insect taxa of high interest
 (e.g., butterflies, bees), may apply to insect diversity more
 generally.  This has led to an urgent call for analysis of
 additional longitudinal datasets to examine trends in general insect
 diversity.  Here we present a dataset gathered from 1982-2018 by
 advanced undergraduate students and graduate students enrolled in a
 taxonomy course that involved collecting as many insect families as
 possible over a 5-week period at a high-elevation protected forested site,
 the Sagehen Creek Field Station, in the Sierra Nevada Mountains,
 California, USA. 
description: Individual students collected insects for a 5-week summer period
 and used dichotomous keys to identify them to family.  Each student
 strived to collect as many insect families as possible, using a diversity
 of collecting methods (hand collecting, sweep netting, blacklights,
 malaise traps, and leaf litter samples).
DOI: 10.5061/dryad.ttdz08kv4
title: Data from: Biomimicry of iridescent, patterned insect cuticles: comparison of biological and synthetic, cholesteric microcells using hyperspectral imaging

description: Biological systems inspire the design of multifunctional materials and
 devices. However, current syynthetic replicas rarelyy capture the range of
 structural complexityy observed in natural materials. Prior to the
 definition of a biomimetic design, a dual investigation with a common set
 of criteria for comparing the biological material and the replica is
 required. Here, we deal with this issue by addressing the non-trivial case
 of insect cuticles tessellated with polygonal microcells with iridescent
 colors due to the twisted cholesteric organization of chitin fibers. By
 using hyperspectral imaging within a common methodology, we compare, at
 several length scales, the textural, structural and spectral properties of
 the microcells found in the two-band cuticle of the scarab beetle Chrysina
 gloriosa with those of the polygonal texture formed in flat films of
 cholesteric liquid crystal oligomers. The hyperspectral imaging technique
 offers a unique opportunity to reveal the common features and differences
 in the spectral-spatial signatures of biological and synthetic samples at
 a 6-nm spectral resolution over 400 nm-1000 nm and a spatial resolution of
 150 nm. The biomimetic design of chiral tessellations is relevant to the
 field of non-specular properties such as deflection and lensing in
 geometric phase planar optics.
description: <b>Scarab beetle.</b> A male specimen of <i><sub>C. gloriosa </sub></i>was collected in Saltillo (Coahuila, Mexico) in July 2009. <b>Oligomers.</b> CLC oligomers from Wacker Chemie GmbH were used.<sup> </sup> <b>Optical setup. </b>In the current experiment, we made use of a formerly described reflective hyperspectral microscope, relying on nematic liquid-crystal-based Fourier spectrometry<sup> </sup>[A. Jullien et al., OPTICA 2017, 4, 400]<sup> </sup>The lamp source was a tungsten halogen lamp with a stable spectrum. The spatial resolution was fixed by the microscope and was 150 nm. The field of view was 16 µm by 64 µm. <b>Analysis.</b> The principle of the Fourier algorithm is described in [A. Jullien et al., OPTICA 2017, 4, 400].<sup> </sup>However, we proposed to implement independent component analysis (ICA) to decrease the noise level and significantly reduce the analysis time.