cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wh70rxwr9
title: Breeding system data for populations of T. perfoliata

description: Both intrinsic and extrinsic forces work together to shape connectivity
 and genetic variation in populations across the landscape. Here we
 explored how geography, breeding system traits, and environmental factors
 influence the population genetic patterns of Triodanis perfoliata, a
 widespread mix-mating annual plant in the contiguous US. By integrating
 population genomic data with spatial analyses and modeling the
 relationship between breeding system and genetic diversity, we illustrate
 the complex ways in which these forces shape genetic variation.
 Specifically, we used 4,705 single nucleotide polymorphisms to assess
 genetic diversity, structure, and evolutionary history among 18
 populations. Populations with more obligately selfing flowers harbored
 less genetic diversity (π: R2 = 0.63, P = 0.01, n = 9 populations), and we
 found significant population structuring (FST = 0.48). Both geographic
 isolation and environmental factors played significant roles in predicting
 the observed genetic diversity: we found that corridors of suitable
 environment appear to facilitate gene flow between populations, and that
 environmental resistance is correlated with increased genetic distance
 between populations. Last, we integrated our genetic results with species
 distribution modeling to assess likely patterns of connectivity among our
 study populations. Our landscape and evolutionary genetic results suggest
 that T. perfoliata experienced a complex demographic and evolutionary
 history, particularly in the center of its distribution. As such, there is
 no singular mechanism driving this species’ evolution. Together, our
 analyses support the hypothesis that breeding system, geography, and
 environmental variables shape the patterns of diversity and connectivity
 of T. perfoliata in the US.
description: Following methods in Ansaldi et
 al., 2018, we quantified the
 breeding system (i.e., extent of cleistogamy) in a subset of populations
 included in our genetic analyses. Because these analyses aimed to estimate
 the total floral input of each flower type in a population (total CH and
 CL), we used only individuals with fully mature stems (flowering completed), and populations for which we had access to
 N&gt;20 vouchered individuals. Breeding system data for the OCN population (Otter
 Creek North Carolina) were derived from Ansaldi et al.
 2018. The total average
 production of each flower type in each population was estimated by
 collecting whole individual, fully mature plants (range = 20–50; 33 = mean
 individuals per population). For each population we assessed the average
 number of CH flowers, number of CL flowers, total flower number and the
 proportion of flowers that were CH out of the total flower number
 (pCH)
DOI: 10.5061/dryad.0cfxpnw5z
title: Data from: Choice of prioritization method impacts recommendations for climate-informed bird conservation in the United States

description: Climate-informed spatial planning is urgently needed to guide initiatives
 aimed at both conserving biodiversity as a whole (e.g., protection of 30%
 of lands and waters by 2030) and recovering North American avifauna in
 particular. Various methods for prioritizing conservation areas exist, yet
 alternative methods may direct managers to different lands for protection
 and thus varying recommendations for meeting area-based targets. Here, we
 used bird species distribution models and landcover projections to
 systematically evaluate two widely-used methods for prioritizing areas
 most likely to facilitate the persistence of multiple species under
 climate change: (1) in situ macrorefugia, identified as areas of high
 predicted species retention; and (2) complementarity-based optimizations,
 identified using the Zonation conservation planning software. For 17
 biogeographical groups in the continental United States, we compared
 priority areas for bird conservation derived from these two alternatives
 with respect to their spatial distributions and consensus (i.e., overlap),
 expected conservation outcomes (e.g., species and functional diversity),
 predicted climate change exposure, habitat characteristics, landscape
 configurations, and degree of formal protection. Spatial distributions of
 priority areas differed by biogeographical group and method, with 40.5%
 consensus on average across groups. Consensus was extensive within
 mountainous and coastal regions and limited at high latitudes (e.g.,
 Alaska) and in flat, interior regions (e.g., grasslands). As expected,
 complementarity-based optimizations more efficiently represented species
 than retention-based in situ macrorefugia, especially for forest groups,
 and had greater overall biodiversity value and better habitat condition.
 Conversely, in situ macrorefugia encompassed higher elevations and larger
 contiguous patches and were expected to experience less winter-season
 warming. Formal protection averaged &lt;50% across biogeographical
 groups, regardless of prioritization method. Our findings illustrate the
 value of complementarity-based optimizations for bird conservation under
 climate change. More broadly, comparing approaches for prioritizing areas
 for long-term species persistence can reveal critical tradeoffs in
 recommendations for climate-informed protected area planning.
DOI: 10.5061/dryad.3ffbg79n6
title: Geomorphology shapes relationships between animal communities and ecosystem function in large rivers

description: Understanding how the Earth's surface (i.e., ‘nature’s stage’)
 influences connections between biodiversity and ecosystem function (BEF)
 is a central objective in ecology. Despite recent calls to examine these
 connections at multiple trophic levels and at more complex and realistic
 scales, little is known about how landscape structure shapes BEF
 relationships among animal communities in nature. We coupled
 high-resolution habitat mapping with extensive field sampling to quantify
 connections among the geophysical habitat templet, invertebrate
 assemblages, and secondary production in two large North American
 riverscapes. Patterns of sediment size governed invertebrate assemblage
 structure, with particularly strong effects on composition, richness, and
 taxonomic and functional diversity. These relationships propagated to
 drive positive relationships between biodiversity and secondary production
 that were modified by scale, context-dependencies, and anthropogenic
 modification. Finally, leveraging spatially explicit descriptions of
 geophysical and biological properties, we uncovered distinct and nested
 spatial scales of biodiversity and secondary production, and suggest that
 multiple geophysical processes simultaneously influence these patterns at
 different scales. Together, our findings advance our understanding of
 relationships between the physical templet and patterns of BEF, and help
 to predict how perturbations to the Earth’s surface may propagate to
 influence biodiversity and energy flux through food webs.
description: This dataset contains habitat information from the Missouri and
 Yellowstone Rivers that was collected in 2013-2014 via side scan sonar,
 geoprocessed in ArcMap, and organized and analyzed in Microsoft Excel and
 R. Additionally, 25-30 invertebrate samples were collected from 6 reaches
 in the Missouri and Yellowstone Rivers throughout the year from a wide
 variety of habitats in 2014-2015. More specifically, the methods used to
 quantitatively sample invertebrate communities were as follows:
 main-channel sand habitat: a Ponar dredge sampler (0.052 m²) attached to a
 sounding reel on a boat; cobble/gravel: a Hess sampler (0.086 m²); wood:
 250 μm mesh bags and scrubbed; depositional off-channels: a stovepipe core
 (0.031 m²); and large boulders: scrubbed in buckets while a D-frame dip
 net was held downstream. Samples were preserved with buffered formalin and
 rinsed onto nested sieves (1 mm and 250 um) in the laboratory.
 Invertebrates were enumerated and measured to the nearest mm to estimate
 abundance, biomass, and secondary production.
description: All results and figures can be recreated with Microsoft Excel and
 R.
DOI: 10.5061/dryad.fj6q573z8
title: Data from: A first draft of the core fungal microbiome of Schedonorus arundinaceus with and without its fungal mutualist Epichloë coenophiala

description: Tall fescue (Schedonorus arundinaceus) is a cool-season grass that is
 commonly infected with the fungal endophyte Epichloë coenophiala. Although
 the relationship between tall fescue and E. coenophiala is well-studied,
 less is known about its broader fungal communities. We used
 next-generation sequencing of the ITS2 region to describe the complete
 foliar fungal microbiomes in a set of field-grown tall fescue plants over
 two years, and whether these fungal communities were affected by the
 presence of Epichloë. We used the Georgia 5 cultivar of tall fescue, grown
 in the field for six years prior to sampling. Plants were either
 uninfected with E. coenophiala, or they were infected with one of two E.
 coenophiala strains: the common toxic strain or the AR542 strain (sold
 commercially as MaxQ). We observed 3,487 amplicon sequence variants (ASVs)
 across all plants and identified 43 ASVs that may make up a potential core
 microbiome. Fungal communities did not differ strongly between Epichloë
 treatments but did show a great deal of variation between the two years.
 Plant fitness also changed over time but was not influenced by E.
 coenophiala infection.
DOI: 10.5061/dryad.p8cz8w9tg
title: Data From: Females alter their mate preferences depending on hybridization risk

description: Mating with another species is often maladaptive because it generally
 results in no or low-fitness offspring. When hybridization is sufficiently
 costly, individuals should avoid mating with heterospecifics even if it
 reduces their ability to mate with high-quality conspecifics that resemble
 heterospecifics. Here, we used spadefoot toads, Spea multiplicata, to
 evaluate whether females alter their preferences for conspecific male
 sexual signals (call rate) depending on heterospecific presence. When
 presented with conspecific signals against a background including both
 conspecific and heterospecific signals, females preferred male traits that
 were most dissimilar to heterospecifics—even though these signals are
 potentially associated with lower-quality mates. However, when these same
 females were presented with a background that included only conspecific
 signals, some females switched their preferences, choosing conspecific
 signals that were exaggerated and indicative of high-quality conspecific
 mates. Because only some females switched their preferences between these
 two chorus treatments, there was no population-level preference for
 exaggerated male signals in the absence of heterospecifics. Thus,
 hybridization risk can impact mate choice and thereby alter patterns of
 sexual selection. These results also emphasize that reproductive barriers
 between species (such as mate choice) can be context-dependent, with
 important implications for the origins and maintenance of species
 boundaries.
description: Female <em>S. mulitplicata </em>mate preferences were
 measured via two-choice phonotaxis experiments in the laboratory at
 University of North Carolina-Chapel Hill.  Detailed data collection
 methods can be found in the manuscript and associated supplementary
 methods file.
description: The analysis code files can be opened using R (open source).  All
 analyses were conducted using R version 3.6.1.  The data files can be
 opened using excel, R (open source), or any software capable of reading
 .csv files.
DOI: 10.5061/dryad.djh9w0w3k
title: Temporal variation in translocated Isle Royale wolf diet

description: Wolves (Canis lupus) can exert top-down pressure and shape ecological
 communities through predation of ungulates and beavers (Castor spp.).
 Therefore, understanding wolf foraging is critical to estimating their
 ecosystem-level effects. Specifically, if wolves are consumers that
 optimize tradeoffs between costs and benefits of prey acquisition, changes
 in these factors may lead to prey switching or negative-density dependent
 selection with potential consequences for community stability. For wolves,
 factors affecting cost and benefits include prey vulnerability, risk,
 reward, and availability which can vary temporally. We described wolf diet
 by frequency of occurrence and percent biomass and characterized diet
 using prey remains found in wolf scats on Isle Royale National Park,
 Michigan, USA during May–October 2019 and 2020. We used logistic
 regression to estimate prey consumption over time. We predicted prey with
 temporal variation in cost (availability and/or vulnerability) such as
 adult moose (Alces alces), calf moose, and beaver (Castor canadensis) to
 vary in wolf diets. We analyzed 206 scats and identified 62% of remains as
 beaver, 26% as moose, and 12% as other species (birds, smaller mammals,
 and wolves). Adult moose were more likely to occur in wolf scats in May,
 when moose are in poor condition following winter. The occurrence of moose
 calves peaked during June–mid July following birth but before calf
 vulnerability declined as they matured. In contrast, beaver occurrence in
 wolf scat did not change over time, reflecting the importance of
 low-handling cost prey items for recently introduced lone or paired
 wolves. Our results demonstrate that wolf diet is responsive to temporal
 changes in prey costs. Temporal fluctuation in diet may influence wolves’
 ecological role if prey respond to increased predation risk by altering
 foraging or breeding behavior.
description: From 5 May–5 October 2019 and 13 June–22 September 2020 , we
 collected all wolf scats encountered during fieldwork in IRNP. We
 collected fresh scats (e.g., strong smell, moist, tracks present) at wolf
 radio-collar GPS location clusters (Svoboda et al., 2013) and on
 established hiking trails (Fig. 1). We placed each scat in a plastic bag,
 recorded the date and location (NAD83, UTM Zone 16N), and froze them for
 later processing. We considered the collection date as the date of
 deposit, although scats may have been up to 11 days old (Sanchez et al.,
 2004). <br><br>We processed and identified scat contents
 following Chenaux–Ibrahim (2015). We placed frozen scats into nylon
 stockings, washed them in a washing machine to remove digestible material
 and then dried the contents in an oven. We spread the contents on a 21.5cm
 x 28cm plate, overlaid a 25-point grid, and randomly selected one hair
 from each point for microscopic identification (Ciucci et al., 2004). We
 could determine moose age class (adult or calf) until 15 September, when
 the first molt occurs (Muller, 2006). After 15 September, we identified
 all moose hair as adult.
DOI: 10.5061/dryad.1c59zw3zk
title: Combining sampling gear to optimally inventory species highlights the efficiency of eDNA metabarcoding

description: Biodiversity surveys may require the use of multiple types of sampling
 gear to maximize the efficiency of species detections, yet few studies
 have investigated how to optimally distribute effort among gear. In this
 study, we conducted eDNA metabarcoding and capture-based sampling surveys
 (electrofishing, fyke netting, gillnetting, and seining) to sample fish
 species richness in a large northern temperate lake. We evaluated the
 success of the sampling methods individually and in combination to
 determine the allocation of effort and cost across sampling gear that
 provides the optimal approach for lake-wide species inventories. We found
 that eDNA metabarcoding detected more species than any other sampling
 method, including 11 species that were not detected with any capture-based
 approach. Optimal gear combination analyses revealed that detected species
 richness is maximized when most of the effort or budget is allocated to
 eDNA metabarcoding, with smaller allocations to seining and fyke netting.
 eDNA metabarcoding and capture sampling gear showed similar patterns of
 spatial heterogeneity in the fish community across habitat types, with
 pelagic samples forming a group that was distinct from nearshore samples.
 Our results indicate that eDNA metabarcoding is a rapid and cost-efficient
 tool for biodiversity monitoring and that assessing the complementarity of
 multiple sampling types can inform the development of optimal approaches
 for measuring fish species richness.
description: See manuscript for a complete description of methods.
description: All scripts used for bioinformatics,
 taxonomic assignments, and statistical analyses are available on GitHub:
 https://github.com/karaandres/Oneida_metabarcoding
DOI: 10.5061/dryad.1zcrjdfvw
title: Data for: Modeling climate-driven range shifts in populations of two bird species limited by habitat independent of climate

description: Ranges of species around the world are expected to contract in response to
 climate change. Species distribution models (SDMs) are a powerful tool for
 predicting changes in habitat availability, but the variables selected to
 create SDMs influence their performance. In addition to climate, habitat
 characteristics and species traits can play a role in predicted species
 distribution. In this paper, we consider how variable selection influences
 the accuracy of SDMs when applied to isolated subpopulations of two widely
 distributed bird species: the great gray owl (Strix nebulosa) and the
 willow flycatcher (Empidonax traillii). In the Sierra Nevada of
 California, these species are restricted largely to discrete patches of
 meadow habitat within a forest matrix, providing the potential to identify
 specific locations to target conservation efforts. We contrast predictions
 made by SDMs that consider climatic variables alone with those that
 incorporate both climate and geophysical variables. Adding geophysical
 variables resulted in differing model predictions. For willow flycatchers,
 adding geophysical variables improved predictive performance. In the case
 of great gray owls, models with and without geophysical variables had
 nearly identical performance under historical conditions but differed
 starkly in their predictions. The full model (climatic and geophysical
 variables) predicted habitat availability to decrease moderately, whereas
 the climate-only model predicted nearly complete loss of favorable habitat
 by 2099. The climate-only model is consistent with expectations based on
 previous SDMs of birds across North America, but previous studies also
 assume homogeneity in species traits and range-wide habitat requirements.
 The full model appears more consistent with recent trends in great gray
 owl numbers in the Sierra Nevada specifically, where the population has
 remained relatively stable over recent decades. Given contradictions in
 our model predictions, care should be taken when trying to apply similar
 SDM models to other systems.
DOI: 10.15468/dl.m2qr9v
title: Occurrence Download

description: A dataset containing 9376 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)) isea3hcellcode,
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000)), "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.countrycode = 'DK'
 AND occurrence.occurrencestatus = 'PRESENT'
 AND GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '52', TRUE)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL AND occurrence.hascoordinate = TRUE)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year",
 GBIF_ISEA3HCODE(4, decimallatitude, decimallongitude, COALESCE(coordinateuncertaintyinmeters, 1000))

 The dataset's 9376 records were derived from 124 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003233-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.