cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zpc866t92
title: Plant functional traits

description: The whole-plant economics spectrum (PES) refers to the trade-offs among
 the many plant functional traits that are commonly used as indicators of
 major adaptive strategies, thereby providing insights into plant
 distributions, ecosystem processes, and evolution. However, there are few
 studies of what may be called the whole-plant economic spectrum (PES) that
 integrates bark, wood, and leaf functional traits for different
 leaf-types and growth habits (evergreen versus deciduous species). To
 address this gap in our knowledge, 6 bark traits, 7 wood traits
 (including mechanical support and nutrient transport characteristics), and
 12 leaf traits (including chemical, structural, and physiological
 characteristics) of 59 representative subtropical woody species were
 examined using principal component analysis (PCA) to determine PES
 strategies. The economics spectra of bark (BES), wood (WES), and leaves
 (LES), and the entire PES indicated that major traits represent resource
 acquisition strategies and conservation strategies clustering on the
 opposite ends of the PCA axis. A significant correlation was observed
 among the 25 functional traits. The data indicated that N and P
 nutrient levels were at the hub of BES, WES,
 LES, and PES interrelationships. Evergreen and deciduous species had
 different WES and LES, and thus PES resource acquisition
 strategies. With the exception of the BES, evergreen species clustered on
 the conservative side, whereas deciduous species clustered on the
 acquisitive side. The PES presented here informs our
 understanding of whole-plant responses to environmental differences,
 particularly regarding the role of N and P traits
 at the whole-plant level. It also reveals and further
 supports the notion that evergreen and deciduous species respectively
 manifest conservative and acquisitive strategies, further informing our
 understanding of species biodiversity maintenance.
DOI: 10.25338/b8hk9d
title: Functional trade-offs asymmetrically promote phenotypic evolution

description: Trade-offs are thought to bias evolution and are core features of many
 anatomical systems. Therefore, trade-offs may have far-reaching
 macroevolutionary consequences, including patterns of morphological,
 functional, and ecological diversity. Jaws, like many complex anatomical
 systems, are comprised of elements involved in biomechanical trade-offs.
 We test the impact of a core mechanical trade-off, transmission of
 velocity versus force (i.e., mechanical advantage), on rates of jaw
 evolution in Neotropical cichlids. Across 130 species representing a wide
 array of feeding ecologies, we find that the velocity-force trade-off
 impacts evolution of the surrounding jaw system. Specifically, rates of
 jaw evolution are faster at functional extremes than in more functionally
 intermediate or unspecialized jaws. Yet, surprisingly, the effect on jaw
 evolution is uneven across the extremes of the velocity-force continuum.
 Rates of jaw evolution are 4 to 10-fold faster in velocity-modified jaws,
 whereas force-modified jaws are 7 to 18-fold faster, compared to
 unspecialized jaws, depending on the extent of specialization. Further, we
 find that a more extreme mechanical trade-off resulted in faster rates of
 jaw evolution. The velocity-force trade-off reflects a gradient from
 specialization on capture-intensive (e.g., evasive or buried) to
 processing-intensive prey (e.g., attached or shelled), respectively. The
 velocity extreme of the trade-off is characterized by large magnitudes of
 trait change leading to functionally divergent specialists and ecological
 stasis. By contrast, the force extreme of the trade-off is characterized
 by enhanced ecological lability made possible by phenotypes more readily
 co-opted for different feeding ecologies. This asymmetry of
 macroevolutionary outcomes along each extreme is likely result of an
 enhanced utility of the pharyngeal jaw system as force-modified oral jaws
 are adapted for prey that require intensive processing (e.g., algae,
 detritus, and molluscs). The velocity-force trade-off, a fundamental
 feature of many anatomical systems, promotes rapid phenotypic evolution of
 the surrounding jaw system in a canonical continental adaptive radiation.
 Considering that the velocity-force trade-off is an inherent feature of
 all jaw systems that involve a lower element that rotates at a joint,
 spanning the vast majority of vertebrates, our results may be widely
 applicable across the tree of life.
DOI: 10.21979/n9/ioskyx
title: Replication Data for: Quantum plasmonic nonreciprocity in parity-violating magnets

description: This dataset contains numerical data for the paper "Quantum Plasmonic Nonreciprocity in Parity-Violating Magnets"
DOI: 10.5061/dryad.83bk3j9s6
title: Data from: Evaluating the foraging performance of individual honey bees in different environments with automated field RFID systems

description: Measuring the individual foraging performances of pollinators is crucial
 to guide environmental policies that aim at enhancing pollinator health
 and pollination services. Automated systems have been developed to track
 the activity of individual honey bees, but their deployment is extremely
 challenging. This has limited the assessment of individual foraging
 performances in full-strength bee colonies in the field. Most studies
 available to date have been constrained to use downsized bee colonies
 located in urban and suburban areas. Environmental policy-making, on the
 other hand, needs a more comprehensive assessment of honey bee
 performances in a broader range of environments, including in remote
 agricultural and wild areas. Here we detail a new autonomous field method
 to record high quality data on the flight ontogeny and foraging
 performance of honey bees, using Radio-Frequency Identification (RFID). We
 separate bee traffic into returning and exiting tunnels to improve data
 quality, solving many previous limitations of RFID systems caused by
 traffic jams and the parasitic coupling of RFID antennae. With this
 method, we assembled a large RFID dataset made of control bee colonies
 from experiments conducted in different locations and seasons. We hope our
 results will be a starting point to understand how ontogenetic and
 environmental factors affect the individual performances of honey bees,
 and that our method will enable the large-scale replication of individual
 pollinator performance studies.
DOI: 10.5061/dryad.g79cnp5qj
title: Projected shifts in deadwood bryophytes in Sweden, data used for species distribution modelling and for climate and forest scenario analysis

description: Climate change and habitat loss are main threats to forest biodiversity.
 We fitted ensembles of single species distribution models for 23
 deadwood-living bryophyte species in Sweden, based on species records from
 the Swedish Lifewatch website. This data set comprises the
 species and environmental data used for species distribution modelling,
 and coefficients of the fitted single species distribution models (GLM,
 Poisson point-process, MaxEnt). Based on the fitted species distribution
 models, we conducted simulations of future species distributions
 given realistic climate and forest projection scenarios at the national
 scale of Sweden. The data used for the scenario analysis are stored here.
description: Bryophyte records were downloaded from the Swedish Lifewatch
 Website (www.analysisportal.se). The original data were presence-only, but we could also establish a presence-absence data set based on records from 12 professional bryologists using consistent methodology. Species data were aggregated to the 100m grid-cell resolution. Forest data were based on estimates which combine satellite images and ground truthing (http://skogskarta.slu.se). Gridded meteorological data were obtained from the EURO4M MESAN data set (http://esg-dn1.nsc.lui.se).  Forest and climate scenario data were produced as part of the Swedish Nationwide Forestry Scenario Analysis 2015.
DOI: 10.5061/dryad.nzs7h44sd
title: Seasonal and daily movement patterns of an alpine passerine suggest high flexibility in relation to environmental conditions

description: Mountains naturally offer variable habitat conditions, but their
 biodiversity is currently facing the extra challenge of adapting to rapid
 environmental shifts that are much more pronounced than in the lowlands.
 Among adaptive responses, intra- and inter-seasonal movements represent
 potentially important coping strategies for wildlife that remain largely
 unexplored. We investigated the seasonal and daily movements of the ring
 ouzel Turdus torquatus, a European mountain bird species that is declining
 in many parts of its distribution. We tracked individuals breeding in the
 Swiss Alps using light-level geolocators and multi-sensor loggers. Of the
 birds traced to their non-breeding grounds, two thirds reached the Atlas
 Mountains while one third stayed in Spain, a region potentially more
 significant for overwintering than previously thought. The birds remained
 mostly above 1000 m throughout the annual cycle, highlighting a strict
 association of ring ouzels with mountain habitats. We also evidenced
 flexible daily elevational movements, especially upon spring arrival on
 the breeding grounds in relation to date and snowfall occurrence,
 suggesting adaptive potential in response to environmental variation. This
 study shows how modern technology can deliver deeper and valuable insights
 into movements, behavioural patterns, and life-history strategies for
 relatively little-studied animal species. By doing so, it paves the way
 for refined assessments of species’ vulnerability to ongoing global change
 while providing basic conservation guidance.
description: Data from geolocators (GDL2 & GDL-uTag, Swiss
 Ornithological Institute) and multi-sensor loggers (GDL3-PAM, Swiss
 Ornithological Institute) fitted using leg-loop harnesses on Alpine Ring
 Ouzels (<em>Turdus torquatus alpestris</em>) breeding in the
 Swiss Alps. There is both raw data (light intensity,
 pressure, acceleration, magnetism) and data on classified twilight events
 and estimated migratory tracks (coordinates with uncertainty and fitted
 models).
description: See README.txt file
DOI: 10.5061/dryad.xd2547dhg
title: Plastic responses of survival and fertility following heat stress in pupal and adult Drosophila virilis

description: The impact of rising global temperatures on survival and reproduction is
 putting many species at risk of extinction. In particular, it has recently
 been shown that thermal effects on reproduction, particularly limits to
 male fertility, can underpin species distributions in insects. However,
 the physiological factors influencing fertility at high temperatures are
 poorly understood. Key factors that affect somatic thermal tolerance such
 as hardening, the ability to phenotypically increase thermal tolerance
 after a mild heat shock, and the differential impact of temperature on
 different life stages, are largely unexplored for thermal fertility
 tolerance. Here, we examine the impact of high temperatures on male
 fertility in the cosmopolitan fruit fly Drosophila virilis. We first
 determined whether temperature stress at either the pupal or adult
 life-history stage impacts fertility. We then tested the capacity for
 heat-hardening to mitigate heat-induced sterility. We found that thermal
 stress reduces fertility in different ways in pupae and adults. Pupal heat
 stress delays sexual maturity, whereas males heated as adults can
 reproduce initially following heat stress, but lose the ability to produce
 offspring. We also found evidence that while heat-hardening in D. virilis
 can improve high temperature survival, there is no significant protective
 impact of this same hardening treatment on fertility. These results
 suggest that males may be unable to prevent the costs of high temperature
 stress on fertility through heat-hardening which limits a species’ ability
 to quickly and effectively reduce fertility loss in the face of short-term
 high temperature events.
description: All statistical analyses in R.
DOI: 10.15468/dl.ut8t76
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Sea lamprey distribution and abundance in the River Spey: phases II and III, 2001/2002"
 ]
}

 The dataset includes 92 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002939-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mkkwh711b
title: Data from: Whole-genome phylogenetic reconstruction as a powerful tool to reveal homoplasy and ancient rapid radiation in waterflea evolution

description: The Supplementary Material (and text) to Van Damme et al., contains 10
 Supplementary Figures (Figs S1-S10), 5 Supplementary Tables (Tables
 S1-S5), Supplementary Materials and Methods (ST1), Supplementary
 Discussion (ST2) and a complete reference list to the manuscript and
 supplement (Supplementary References SR1). All Supplementary material and
 text have been peer-reviewed as part of the manuscript. The
 supplementary discussion provides an additional framework
 including the importance of the findings of the phylogenomic study for the
 interpretation of evolution in the Cladocera.
description: See main manuscript (Van Damme, Cornetti, Fields & Ebert
 in <em>Systematic Biology</em>) and additional materials and
 methods under Supplementary Material (ST1).
description: These are additional files including all supplementary figures,
 tables, and supplementary text to accompany the manuscript.
DOI: 10.5061/dryad.f4qrfj6wt
title: Woe is the loner: Female Treefrogs prefer clusters of displaying males over single “hotshot” males

description: Communal displays such as leks and choruses are puzzling phenomena, as it
 is not obvious why signalers or choosers should aggregate. It has been
 hypothesized that signalers enjoy higher per capita reproductive success
 because choosers prefer to sample among dense configurations (“clusters”)
 that are easier to compare. While female preferences as well as
 the signal features of attractive males are well characterized in many
 chorusing species, we know little about how mate sampling is influenced by
 the spatial dynamics within communal displays. Here we ask how
 female Eastern Gray Treefrogs (Hyla versicolor) respond
 to isolated and clustered call stimuli in a simple 1 vs.
 3 playback design. We explored i) whether females exhibit a
 general preference for call clusters, ii) whether spatial preference is
 robust to call-feature preference, and iii) how this affects the relative
 success of attractive and unattractive males in different spatial
 combinations. We found generalized spatial discrimination against lone
 callers but did observe fine-scale assessment of call features within
 clusters. The prominence of the spatial preference impacts the
 attractiveness of males, conferring particular advantage to attractive
 callers within clusters, while reducing attractiveness of isolated males
 regardless of their acoustic features. Our findings indicate that female
 frogs navigate complex choruses by initially orientating toward clusters
 of calling males, and then assess call-features within them. This
 study provides novel insight into the mate choice
 heuristics involved in animal choruses. 
description: The dataset contains the raw choice data (Recorded manually) as
 well as choice latencies (recorded with a stopwatch).
description: Blank cells indicate frogs that did not chose in a given
 experiment.
DOI: 10.5061/dryad.41ns1rnf4
title: A genetically based ecological trade-off contributes to setting a geographic range limit

description: Understanding the ecological factors that shape geographic range limits
 and the evolutionary constraints that prevent populations from adaptively
 evolving beyond these limits is an unresolved question. Here, we
 investigated why the euryhaline fish, Poecila reticulata, is confined to
 freshwater within its native range, despite being tolerant of brackish
 water. We hypothesized that competitive interactions with a close
 relative, Poecilia picta, in brackish water prevents P. reticulata from
 colonizing brackish water. Using a combination of field transplant, common
 garden breeding, and laboratory behavior experiments we find support for
 this hypothesis, as P. reticulata are behaviorally subordinate and have
 lower survival in brackish water with P. picta. We also found a negative
 genetic correlation between P. reticulata growth in brackish water versus
 freshwater in the presence of P. picta, suggesting a genetically based
 trade-off between salinity tolerance and competitive ability could
 constrain adaptive evolution at the range limit.
description: The methods surrounding the data can be found in the manuscript.
 The data presented here is the raw data needed to recreate the analyses in
 the manuscript.
description: We believe reading the methods and accessing this dataset will
 allow users to recreate analyses using their preferred statistical
 software. If users wish to see our R code, please email.
DOI: 10.5061/dryad.xgxd254hd
title: Reproductive effort and terminal investment in a multi-species assemblage of Amazon electric fish

description: The terminal investment hypothesis (TIH) predicts that individuals with
 favorable prospects for future reproduction (i.e., high residual
 reproductive value, RRV) should moderate current reproductive investment
 in favor of growth, survival, and future reproduction, whereas those with
 low RRV should ‘terminally invest’ by diverting somatic resources towards
 current reproduction at the expense of future reproduction. However,
 support for the TIH in wild animal populations is fragmentary, and the
 ecological contexts of terminal investment remain poorly known. We report
 a remarkable case of simultaneous terminal investment involving five
 sympatric species of the electric knifefish genus Brachyhypopomus, from
 Amazonian floodplain and terra firme stream habitats. We found that
 terminal investment is synchronized by seasonal breeding, in response to
 circannual environmental variation in mortality risk. Four species exhibit
 a uniseasonal iteroparous (annual) life history with complete
 post-reproductive mortality after a single breeding season. One species
 (B. beebei) exhibits a two-year multiseasonal iteroparous life history
 with breeding in two seasons and post-reproductive mortality after the
 second. In mature females and (most) males of the annual species, as well
 as in both mature female and male second-year (but not first-year) B.
 beebei, we documented an increase in two metrics of reproductive effort
 (size-adjusted gonad mass and electric signal amplitude) and a concomitant
 reduction in somatic condition (size-adjusted somatic mass) – all in
 response to proximity to the end of the common breeding season, when RRV
 approximates zero. In mature first-year B. beebei, we documented neither
 an increase in reproductive effort nor a decline in somatic condition,
 implying an alternative strategy of reproductive restraint. Our findings
 support Kirkwood’s disposable soma theory, which posits that death by
 reproductive exhaustion can be delayed if terminal investment is replaced
 by reproductive restraint, allowing individuals to survive and breed in a
 subsequent season. Deferral of the terminal investment response in annual
 species, and the origin of a gonadal regression-regeneration sequence, may
 open pathways for rapid evolutionary transitions to multiseasonal
 iteroparity. Excepting the age (year-group) dependency of terminal
 investment in B. beebei, we were unable to identify intrinsic cues or
 extrinsic environmental cues for the terminal investment response in
 Brachyhypopomus.
description: See manuscript: Waddell, J. C & Crampton, W.G.R.
 Reproductive effort and terminal investment in a multi-species assemblage
 of Amazon electric fish. Ecological Monographs
description: See README.txt file
DOI: 10.5061/dryad.31zcrjdmd
title: Green turtle ddRAD raw sequencing data

description: The occasional westward transport of warm water of the Agulhas Current,
 ‘Agulhas leakage’, around southern Africa has been suggested to facilitate
 tropical marine connectivity between the Atlantic and Indian oceans, but
 the ‘Agulhas leakage’ hypothesis doesn’t explain the signatures of
 eastward gene flow observed in many tropical marine fauna. We investigated
 an alternative hypothesis: the establishment of a warm-water corridor
 during comparatively warm interglacial periods. The ‘warm-water corridor’
 hypothesis was investigated by studying the population genomic structure
 of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035
 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD
 sequencing. Model-based and multivariate clustering suggested a
 hierarchical population structure with two main Atlantic and Southwest
 Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster
 nested within the Atlantic cluster. Coalescent-based model selection
 supported a model where Southwest Indian Ocean and Caribbean populations
 diverged from the East Atlantic population during the transition from the
 last interglacial period (130 – 115 thousand years ago; kya) to the last
 glacial period (115 – 90 kya). The onset of the last glaciation appeared
 to isolate Atlantic and Southwest Indian Ocean green turtles into three
 refugia, which subsequently came into secondary contact in the Caribbean
 and Southwest Indian Ocean when global temperatures increased after the
 Last Glacial Maximum. Our findings support the establishment of a
 warm-water corridor facilitating tropical marine connectivity between the
 Atlantic and Southwest Indian Ocean during warm interglacials.
description: The dataset consists of 16 gzipped FASTQ files containing raw
 ddRAD-seq Illumina sequencing data obtained from green turtles
 (<em>Chelonia mydas</em>). A zipped archive containing the
 Python and R scripts used to perform the simulation analysis is also
 provided, but can also be found on GitHub:
 https://github.com/jpvdz/green-turtle-sims.
description: Please see the published manuscript and accompanying
 supplementary material for a detailed description of the methods and steps
 required to analyze the raw data. Please see the README.md in the zipped
 archive containing the simulation scripts, or on GitHub
 (https://github.com/jpvdz/green-turtle-sims) for instructions on how to
 run the simulation analysis.