cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.dbrv15f4v
title: Code and data for: Nitrogen-induced hysteresis in grassland biodiversity: A theoretical test of litter-mediated mechanisms

description: The global rise in anthropogenic reactive nitrogen (N) and the negative
 impacts of N deposition on terrestrial plant diversity are
 well-documented. The R* theory of resource competition predicts reversible
 decreases in plant diversity in response to N loading. However, empirical
 evidence for the reversibility of N-induced biodiversity loss is mixed. In
 a long-term N-enrichment experiment in Minnesota, a low-diversity state
 that emerged during N addition has persisted for decades after additions
 ceased. Hypothesized mechanisms preventing recovery of biodiversity
 include nutrient recycling, insufficient external seed supply, and litter
 inhibition of plant growth. Here we present an ODE model that unifies
 these mechanisms, produces bistability at intermediate N inputs, and
 qualitatively matches the observed hysteresis at Cedar Creek. Key features
 of the model, including native species' growth advantage in low-N
 conditions and limitation by litter accumulation, generalize from Cedar
 Creek to North American grasslands. Our results suggest that effective
 biodiversity restoration in these systems may require management beyond
 reducing N inputs, such as burning, grazing, haying, and seed additions.
 By coupling resource competition with an additional inter-specific
 inhibitory process, the model also illustrates a general mechanism for
 bistability and hysteresis that may occur in multiple ecosystem
 types. 
description: The MATLAB and Mathematica codes used to visualize and simulate
 the model were developed by Katherine Meyer and James Broda.
 The data used to estimate parameters come from public datasets
 obtained from the BioCON experiment (e141) at Cedar Creek Ecosystem
 Science Reserve and the Total Deposition Maps collection prepared by the
 National Atmospheric Deposition Program (NADP) and US Environmental
 Protection Agency. The README.md file provides further details on the
 sources and processing of data.
description: MATLAB (open-source alternative Octave)
 Mathematica R/RStudio
DOI: 10.5061/dryad.xwdbrv1hc
title: On the predictability of phenotypic divergence in geographic isolation

description: Do related populations that are separated by barriers predictably evolve
 differences from one another over time, or is such divergence
 idiosyncratic and unpredictable? We test these alternatives by
 investigating patterns of trait evolution for 54 sister pairs of Andean
 forest birds that live in similar environments on either side of the arid
 Marañón Gap, a strong dispersal barrier for humid montane species. We
 measured divergence in both sexual (song and plumage) and ecological (beak
 size and beak shape) traits. Sexual traits evolve in a clock-like fashion,
 with trait divergence positively correlated with genetic distance (r = 0.6
 to 0.7). In contrast, divergence in ecological traits is uncorrelated or
 only loosely correlated with genetic distance (r = 0.0 to 0.3). Thus, for
 geographically isolated Andean montane forest birds that live in similar
 environments, divergence is predictable in sexual traits, but not for
 ecological traits. This means that sexual trait divergence occurs
 independently of adaptive ecological divergence within the mega-diverse
 tropical Andean avifauna. Last, we show that variation in genetic
 divergence across a biogeographic barrier is associated with traits that
 are proxies for species’ opportunities for dispersal (low elevation limit
 and elevational niche breadth), but not with traits that are proxies for
 species’ dispersal abilities (hand-wing index and foraging strata).
DOI: 10.5061/dryad.6t1g1jx2w
title: Data for: Phylogenetic placement and taxonomic revision of the enigmatic Brazilian genus Monochilus Fisch. & C. A. Mey. (Lamiaceae)

description: Monochilus (Lamiaceae) is an enigmatic genus endemic to Brazil with two
 rarely collected species currently recognized. Based on morphological
 features Monochilus is hypothesized to be closely related to Amasonia
 within subfamily Ajugoideae. However, Monochilus is one of the few genera
 within Lamiaceae never to be represented in a published molecular
 phylogenetic study and thus has an uncertain placement with the subfamily.
 During recent herbarium exploration in association with the Flora of
 Brasil 2020 project, new specimens of Monochilus gloxinifolius and M.
 obovatus were uncovered. Based on this material, a new phylogeny of
 Ajugoideae was constructed based on nuclear ribosomal ITS and the
 chloroplast markers matK and trnL-trnF. Monochilus, as previously
 hypothesized, is closely related to Amasonia and placed within Ajugoideae.
 We discuss the phylogenetic placement of the genus and provide a taxonomic
 revision with a description, distribution maps, an identification key,
 preliminary conservation assessments, photographic plates and comments on
 both the taxonomy and ecology of these two species. Additionally, we
 provide a lecotypification for M. gloxinifolius.
DOI: 10.5061/dryad.t76hdr84c
title: Survival and mass data of King penguin Aptenodytes patagonicus chicks throughout the winter

description: From 2002 to 2022, yearly King Penguin Aptenodytes patagonicus chick
 mortality and mass data was collected in April, just before the winter
 fast. The same chicks were relocated after the winter to assess mortality.
 The data was collected on Kerguelen Island, located in the Southern
 Ocean. 
description: All data was collected at Ratmanoff’s colony in the Kerguelen
 archipelago (-49° 14′ 33″, 70° 33′ 40″), which hosts approximately 80
 000-90 000 breeding pairs of king penguins (Barbraud et al. 2020). Chick
 mass and survival was assessed yearly from 2002-2022, apart from 2007
 (i.e. 20 studied years). Randomly selected chicks were weighed and marked
 with fish tags (FloyTags, Seattle, USA) in April before the winter fast,
 except for 2009, where weighing occurred in May due to fieldwork
 constraints. The number of chicks marked annually varied from 28-55, with
 most years (14) having n = 40 chicks. The colony was again visited in
 spring (October-November) to relocate the marked chicks and assess winter
 mortality.
DOI: 10.5061/dryad.bnzs7h4fc
title: Does experimental seaweed cultivation affect benthic communities and shorebirds? Applications for extensive aquaculture

description: Extensive seaweed aquaculture is a growing industry expected to expand
 globally due to its relatively low impact and benefits in the form of
 ecosystem services. However, seaweeds are ecosystem engineers that may
 alter coastal environments by creating complex habitats on previously bare
 mudflats. These changes may scale up to top-consumers, particularly
 migratory shorebirds, species of conservation concern that regulate
 trophic webs at these habitats. Understanding how habitats are transformed
 and how this affects different species is critical to direct ecological
 applications for commercial seaweed management. We experimentally assessed
 through a Before-After Control-Impact (BACI) design the potential changes
 exerted by Gracilaria chilensis farming on bare mudflats on the abundance,
 biomass, and assemblage structure of benthic macroinvertebrates, and their
 scaled-up effects on shorebirds’ habitat use and prey consumption.
 Experimental cultivation of G. chilensis significantly affects different
 components of biodiversity that scale-up from lower to upper trophic
 levels. The total biomass of benthic macroinvertebrates increased with
 seaweed cultivation and remained high for at least two months after
 harvest, boosted by an increase in the median size of polychaetes,
 particularly Nereids. Tactile-foraging shorebirds tracked these changes at
 the patch level increasing their abundance and spending more time foraging
 at seaweed cultivated plots. These results suggest that seaweed farming
 has the potential to impact shorebird populations by favouring
 tactile-foraging species which could lead to a competitive disadvantage to
 species that rely on visual cues. Therefore, the establishment of new
 seaweed farms in bare mudflats at key sites for shorebirds must be planned
 warranting habitat heterogeneity (i.e., cultivated and non-cultivated
 areas) at the landscape level and based on an experimental approach to
 account for local characteristics. Fostering properly designed extensive
 seaweed farming over other aquaculture industries with greater negative
 environmental impacts would provide benefits for human well-being and for
 ecosystem functions.
DOI: 10.5061/dryad.j6q573nj3
title: An invasive seagrass drives its own success in two invaded seas by both negatively affecting native seagrasses and benefiting from those costs

description: The nature and strength of interactions between native and invasive
 species can determine invasion success. Species interactions can drive,
 prevent or facilitate invasion, making understanding the nature and
 outcome of these interactions critical. We conducted mesocosm experiments
 to test the outcome of interactions between Halophila stipulacea, a
 seagrass that invaded the Mediterranean and Caribbean Seas, and native
 seagrasses (Cymodocea nodosa and Syringodium filiforme, respectively) to
 elucidate mechanisms explaining the successful invasions. Mesocosms
 contained intact cores with species grown either mixed or alone. Overall,
 in both locations, there was a pattern of the invasive growing faster with
 the native than when alone, while also negatively affecting the native,
 with similar patterns for shoot density, aboveground and belowground
 biomass. In the Caribbean, H. stipulacea increased by 5.6 ± 1.0 SE shoots
 in 6 weeks when grown with the native while, when alone, there was a net
 loss of −0.8 ± 1.6 SE shoots. The opposite pattern occurred for S.
 filiforme, although these differences were not significant. While the
 pattern in the Mediterranean was the same as the Caribbean, with the
 invasive grown with the native increasing shoots more than when it grew
 alone, these differences for shoots were not significant. However, when
 measured as aboveground biomass, H. stipulacea had negative effects on the
 native C. nodosa. Our results suggest that a seagrass that invaded two
 seas may drive its own success by both negatively affecting native
 seagrasses and benefiting from that negative interaction. This is a novel
 example of a native seagrass species facilitating the success of an
 invasive at its own cost, providing one possible mechanism for the
 widespread success of this invasive species.
DOI: 10.5061/dryad.cnp5hqc84
title: Data from: Eastern Whip-poor-wills have larger nonbreeding home ranges in areas with more agriculture and forest fragmentation

description: Migratory bird populations can be limited by events in disparate parts of
 the world. Birds in tropical regions are facing rapid habitat loss,
 climate change, and intensive agricultural regimes, potentially
 contributing to population declines. However, an understanding of basic
 non-breeding ecology of species, such as habitat and space use, is
 critical for determining if this is the case. Populations of the
 nocturnal/crepuscular Eastern Whip-poor-will (Antrostomus vociferus) have
 declined by 70% since the 1960’s, yet data on the species are sparse
 outside of the breeding season. We extracted data from 41 archival GPS
 tags deployed on whip-poor-wills and estimated non-breeding home ranges
 and land covers used. We used satellite imagery and stable carbon and
 nitrogen isotope values from claws grown during the non-breeding season to
 analyze how land cover and habitat moisture impacted home range size and
 relative trophic level. Forest was by far the most prevalent land cover
 used by whip-poor-wills, occurring in all home ranges and accounting for
 &gt;80% of diurnal roosting points. We found that less forest, the
 presence of agriculture, and more edge (irrespective of land cover) were
 associated with larger home ranges. Stable isotope values differed by
 broadscale ecoregion but not local land cover characteristics in our
 study, indicating that regional idiosyncrasies or broadscale processes can
 be more important in determining stable isotope ratios. Our findings
 suggest that the loss, fragmentation, and replacement of forest by
 agriculture in the core of the whip-poor-will’s non-breeding range may
 represent a threat to the species, as they rely heavily upon forest, and
 appear to alter space use in response to changes in forest cover.
description: See README file and associated manuscript (including the
 supporting information).
description: Please cite both the data repository and the original article if
 using this data. See README file and the associated manuscript (including
 the supporting information) for additional
 information.<br><br>The full article can be cited
 as: <br>Skinner, A. A., S. N. Matthews, M. P. Ward, I. Souza-Cole,
 J. R. Wright, F. R. Thompson III, T. J. Benson, and C. M. Tonra (2022).
 Eastern Whip-poor-wills have larger nonbreeding home ranges in areas with
 more agriculture and forest fragmentation. Ornithological Applications
 125:duac050. https://doi.org/10.1093/ornithapp/duac050
DOI: 10.6078/d1c135
title: Nexus file for: Molecular diversification of hummingbirds

description: The tempo of species diversification in large clades can reveal
 fundamental evolutionary mechanisms that operate on large temporal and
 spatial scales. Hummingbirds have radiated into a diverse assemblage of
 specialized nectarivores comprising 338 species, but their evolutionary
 history has not, until now, been comprehensively explored. We studied
 hummingbird diversification by estimating a time-calibrated phylogeny for
 284 hummingbird species, demonstrating that hummingbirds invaded South
 America by ~22 million years ago, and subsequently diversified into nine
 principal clades. Using ancestral state reconstruction and diversification
 analyses, we (1) estimate the age of the crown-group hummingbird
 assemblage, (2) investigate the timing and patterns of lineage
 accumulation for hummingbirds overall and regionally, and (3) evaluate the
 role of Andean uplift in hummingbird speciation. Detailed analyses reveal
 disparate clade-specific processes that allowed for ongoing species
 diversification. One factor was significant variation among clades in
 diversification rates. For example, the nine principal clades of
 hummingbirds exhibit ~15-fold variation in net diversification rates, with
 evidence for accelerated speciation of a clade that includes the Bee,
 Emerald, and Mountain Gem groups of hummingbirds. A second factor was
 colonization of key geographic regions, which opened up new ecological
 niches. For example, some clades diversified in the context of the uplift
 of the Andes Mountains, whereas others were affected by the formation of
 the Panamanian land bridge. Finally, although species accumulation is
 slowing in all groups of hummingbirds, several major clades maintain rapid
 rates of diversification on par with classical examples of rapid adaptive
 radiation.
description: DNA sequences representing six genes (four nuclear and two
 mitochondrial) were obtained for 451 individual birds, including 436
 hummingbirds representing 284 species. Our sampling includes 101 of 105
 currently recognized trochilid genera (lacking only three monotypic
 genera, <em>Anopetia</em>, <em>Hylonympha</em>,
 and <em>Sternoclyta</em>, as well as the bitypic genus
 <em>Augastes</em>). We included 15 outgroup species spanning
 four avian orders.
description: Our preferred time-calibrated Bayesian phylogenetic analyses were
 performed using BEAST v1.7.1.
DOI: 10.7291/d13h47
title: Data for: Urban form and its impacts on air pollution and access to green space: A global analysis of 462 cities

description: A better understanding of urban form metrics and their environmental
 outcomes can help urban policymakers determine which policies will lead to
 more sustainable growth. In this study, we have examined five urban form
 metrics – weighted density, density gradient slope, density gradient
 intercept, compactness, and street connectivity – for 462 metropolitan
 areas worldwide. We compared urban form metrics and examined their
 correlations with each other across geographic regions and socioeconomic
 characteristics such as income. Using the K-Means clustering algorithm, we
 then developed a typology of urban forms worldwide. Furthermore, we
 assessed the associations between urban form metrics and two important
 environmental outcomes: green space access and air pollution. Our results
 demonstrate that while higher density is often emphasized as the way to
 reduce driving and thus PM2.5 emissions, it comes with a downside – less
 green space access and more exposure to PM2.5. Moreover, street
 connectivity has a stronger association with reduced PM2.5 emissions from
 the transportation sector. We further show that it is not appropriate to
 generalize urban form characteristics and impacts from one income group or
 geographical region to another, since the correlations between urban form
 metrics are context specific. Our conclusions indicate that density is not
 the only proxy for different aspects of urban form and multiple indicators
 such as street connectivity are needed. Our findings provide the
 foundation for future work to understand urban processes and identify
 effective policy responses.
description: The dataset
 includes the raw data required to calculate the urban form metrics used in
 the article including weighted density, street connectivity, density
 gradient slope, density gradient intercept, and compactness. We merged it
 with the GHSL statistics data (open-source data
 available here) for the analysis. The street connectivity metric was calculated using the approach proposed by Barrington-Leigh and Millard-Ball (2020). The metric was calculated based on OpenStreetMap. Other metrics were calculated using the expressions and methods explained in the paper. The data source for the process was the Global Human Settlement Layer (GHSL) 2015. Please see the README document for more information. 
description: The data is in the .csv format which can be opened and read with Google Sheets, Microsoft Excel, R, Python, and several other programs.
DOI: 10.15468/dl.ec76pu
title: Occurrence Download

description: A dataset containing 17040 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Cyperus rotundus",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2026"
 ]
}

 The dataset includes 17040 records from 595 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003361-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9w0vt4bk7
title: Data for: Ectoparasite population dynamics affected by host body size but not host density or water temperature in a 32-year long time series

description: Host density, host body size, and ambient temperature have all been
 positively associated with increases in parasite infection. However, the
 relative importance of these factors in shaping long-term parasite
 population dynamics in wild host populations is unknown due to the absence
 of long-term studies. Here, we examine long-term drivers of gill lice
 (Copepoda) infections in Arctic charr (Salmonidae) over 32 years. We
 predicted that host density and body size and water temperature would all
 positively affect parasite population size and population growth rate. Our
 results show that fish size was the main driver of gill lice infections in
 Arctic charr. In addition, Arctic charr became infected at smaller sizes
 and with more parasites in years of higher brown trout population size.
 Negative intraguild interactions between brown trout and Arctic charr
 appear to drive smaller Arctic charr to seek refuge in deeper areas of the
 lake, thus increasing infection risk. There was no effect of host density
 on the force of infection, and the relationship between Arctic charr
 density and parasite mean abundance was negative, possibly due to an
 encounter-dilution effect. The population densities of host and parasite
 fluctuated independently of one another. Water temperature had negligible
 effects on the temporal dynamics of the gill lice population.
 Understanding long-term drivers of parasite population dynamics is key for
 research and management. In fish farms, artificially high densities of
 hosts lead to vast increases in the transmission of parasitic copepods.
 However, in wild fish populations fluctuating at natural densities, the
 surface area available for copepodid attachment might be more important
 than the density of available hosts.
description: A total of 6893 Arctic charr were checked macroscopically for
 <em>S. edwardsii</em> on the gills and branchial cavity
 shortly after capture, and the total number of adult female copepods were
 counted. Arctic charr were sampled annually during the ice-free season
 from 1980 to 2018, except in 1998, but fish sampled from Takvatn prior to
 1987 were not checked for <em>S. edwardsii</em> infection.
 Multimesh gillnets were placed in the littoral (&lt;15 m depth),
 profundal (25–40 m depth) and pelagic (offshore, &gt;30 m depth)
 habitats of the lake, and fished overnight for approximately 12 hours.
 Each fish was wet-weighed (±0.1 g), had its fork length measured (±0.1 cm)
 and its sex determined.
description: Any program that can open .csv files, such as Excel or R.
DOI: 10.5061/dryad.ksn02v782
title: Data from: Competitive behavior in house mice

description: Background: House mice are commensal animals with a nearly global
 distribution, structured into well-differentiated local populations.
 Besides genetic differences between the populations, they have also
 diverged behaviorally over time, whereby it remains open how fast general
 behavioral characteristics can change. Here we study the competitive
 potential of two very recently separated populations of the Western house
 mouse (Mus musculus domesticus) by using two different approaches – one
 under controlled cage conditions, the other under more natural conditions
 in enclosures mimicking a secondary encounter condition. Results: We
 observe a clear bias in the competitive ability towards one of the
 populations for both tests. The measured behavioral bias is also reflected
 in the number of hybrid offspring produced in the enclosures. Conclusion:
 Our data suggest that key behavioral characteristics with a direct
 influence on relative fitness can quickly change during the evolution of
 populations. It seems possible that the colonization situation in Western
 Europe, with a rapid spread of the mice after their arrival, would have
 favored more competitive populations on the expansion front. The study
 shows the possible impact of behavioral changes on the evolution of
 populations.
description: 1. Data from Dyad experiments. This excel sheet contains two
 spreadsheets. The first contains information about all behaviors to be
 observed during the Dyad Experiments. The second spreadsheet contains the
 metadata (age, weight, population origin, Dyad Number) of all mice used in
 in the Dyad Experiment, as well as the number of occurrences of each
 behavior. 2. Data from the Enclosure Experiment. This
 excel sheet contains three spreadsheets. "legend" contains all
 information about all columns in the other two spreadsheets. Spreadsheet
 "room113" and "room114" contains all information about
 all mice in the enclosure experiment in the respective room.