cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4g1t4ht
title: Data from: Controlling invasive rodents via synthetic gene drive and the role of polyandry

description: House mice are a major ecosystem pest, particularly threatening island
 ecosystems as a non-native invasive species. Rapid advances in synthetic
 biology offer new avenues to control pest species for biodiversity
 conservation. Recently, a synthetic sperm killing gene drive construct
 called t-Sry has been proposed as a means to eradicate target mouse
 populations due to a lack of females. A factor that has received little
 attention in the discussion surrounding such drive applications is
 polyandry. Previous research has demonstrated that sperm killing drivers
 are extremely damaging to a male's sperm competitive ability. Here we
 examine the importance of this effect on the t-Sry system using a
 theoretical model. We find that polyandry substantially hampers the spread
 of t-Sry such that release efforts have to be increased 3- to 6-fold for
 successful eradication. We discuss the implications of our finding for
 pest potential control programs, the risk of drive spread beyond the
 target population, and the emergence of drive resistance. Our work
 highlights that a solid understanding of the forces that determine drive
 dynamics in a natural setting are key for successful drive application,
 and that exploring the natural diversity of gene drives may inform
 effective gene drive design.
description: R Source Code of the
 ModelThis file contains the R
 Source Code of the most complex model (as described in Supplementary Text
 S4) investigating the ecology and evolution of the tSry gene when released
 into a population.tSryPolyandry.RMaple Code for Analytical ApproximationsContains the Maple file (.mw) that calculates critical release thresholds using plausible approximations as described in Supplementary Text S3.tSryPolyandry.mwMaple Code for Analytical Approximations (.txt)Contains the Maple code that calculates critical release thresholds using plausible approximations as described in Supplementary Text S3, in this version in a plain text (.txt).tSryPolyandry.txt
DOI: 10.5061/dryad.k69gf52
title: Data from: How phenotypic convergence arises in experimental evolution

description: Evolutionary convergence is a core issue in the study of adaptive
 evolution, as well as a highly debated topic at present. Few studies have
 analyzed this issue using a “real-time” or evolutionary trajectory
 approach. Do populations that are initially differentiated converge to a
 similar adaptive state when experiencing a common novel environment?
 Drosophila subobscura populations founded from different locations and
 years showed initial differences and variation in evolutionary rates in
 several traits during short-term (~20 generations) laboratory adaptation.
 Here we extend that analysis to 40 more generations to analyze (1) how
 differences in evolutionary dynamics between populations change between
 shorter and longer time spans, and (2) whether evolutionary convergence
 occurs after sixty generations of evolution in a common environment. We
 found substantial variation in longer-term evolutionary trajectories and
 differences between short and longer-term evolutionary dynamics. Though we
 observed pervasive patterns of convergence towards the character values of
 long-established populations, populations still remain differentiated for
 several traits at the final generations analyzed. This pattern might
 involve transient divergence, as we report in some cases, indicating that
 more generations should lead to final convergence. These findings
 highlight the importance of longer-term studies for understanding
 convergent evolution.
description: Database_ID
 19-0168.R1File with the raw data
 (excel format).
DOI: 10.5061/dryad.0k3fv2j
title: Data from: Early evolution of the ossicular chain in Cetacea: into the middle ear gears of a semi-aquatic protocetid whale

description: Modifications of the morphology and acoustic properties of the ossicular
 chain are among the major changes that accompanied the adaptation of
 Cetacea to the aquatic environment. Thus, data on the middle ear ossicles
 of early whales are crucial clues to understand the first steps of the
 emblematic terrestrial/aquatic transition that occurred in that group.
 Yet, the delicate nature and very small size of these bones make their
 preservation in the fossil record extremely rare. Due to the scarcity of
 available data, major questions remain concerning the sound transmission
 pathways in early non-fully aquatic whales. Virtual reconstruction of a
 partially complete ossicular chain of an Eocene protocetid whale documents
 for the first time the three ossicles of a semi-aquatic archaeocete.
 Contrary to previous hypotheses, these ossicles present different
 evolutionary patterns, showing that the ossicular chain does not act as a
 single morphological module. Functional analyses of the different middle
 ear units highlight a mosaic pattern of terrestrial and aquatic
 signatures. This integrative anatomical and functional study brings strong
 evidence that protocetids were adapted to their dual acoustic environment
 with efficient hearing in both air and water.
description: Mourlam &
 Orliac_Ossicles Protocetid_ESM_Table S1Table S1. Measurements
 of the middle ear hearing parametersMourlam &
 Orliac_Ossicles Protocetid_ESM_Document S1Content Text S1.
 Incudomallear complex orientation; Text S2. Chorda tympani hypothetical
 pathway; Figure S1. Spatial “incudomallear-centred” referential; Figure
 S2. Bone thickness maps of UM-KPG-M 73; Figure S3. Tympanic membrane area
 estimation; Figure S4. Stapes - Comparative plate; Figure S5. Incus -
 Comparative plate; Figure S6. Malleus reconstruction and comparison;
 Figure S7. Chorda tympani location; Figure S8. Malleus - Comparative
 plate; Figure S9. Middle ear’s functional profile
 comparison.
DOI: 10.5061/dryad.8778hh9
title: Data from: When the "selfish herd" becomes the "frozen herd": spatial dynamics and population persistence in a colonial seabird

description: Aggregations are common in ecological systems at a range of scales and may
 be driven by exogenous constraints such as environmental heterogeneity and
 resource availability or by 'self-organizing' interactions among
 individuals. One mechanism leading to self-organized animal aggregations
 is captured by Hamilton's ‘selfish herd’ hypothesis, which suggests
 that aggregations may be driven by an individual's effort to minimize
 their risk of predation by surrounding themselves with conspecifics. We
 demonstrate that aggregations observed in Adélie penguin (Pygoscelis
 adeliae) colonies are a convolution of both self-organized dynamics and
 external forcing arising from landscape terrain. In fluid, highly mobile
 aggregations, individuals are constantly moving in response to changing
 environmental conditions, the locations of predators, or the movements of
 conspecifics. However, when the ability to rearrange is limited and
 spatial reconfiguration occurs on slower time scales than changes in
 population size, systems may become trapped in sub-optimal arrangements.
 We use simulated annealing to demonstrate that Adélie penguin colonies are
 frozen in sub-optimal spatial arrangements, and employ an individual-based
 modelling approach to demonstrate that this sub-optimal spatial
 configuration is driven by a convolution of nest site fidelity and
 stochastic events at the level of individual nests. The resulting spatial
 dynamics are responsible for a hysteretic response to long-term changes in
 abundance. We find that declining abundance leads to fragmentation even in
 a homogeneous environment, which has population-level consequences for
 reproductive success because predation is biased towards colony edges.
 Strong edge effects from heterogeneous predation coupled with
 fragmentation in response to population declines creates a positive
 feedback cycle that can accelerate population decline. This work provides
 a mechanistic understanding of complex spatial structuring in penguin
 colonies, provides a link between current spatial patterning and past
 dynamics, and suggests the possibility of critical collapse in seabird
 populations.
description: McDowall and Lynch
 Supplementary DataShapefile containing all
 1,893,597 hexagonal cells, along with information on each cell's
 elevation, slope, cost-weighted distance to shore, flow accumulation,
 occupancy status (occupied vs unoccupied), and number of first-order
 neighbors. See Appendix S1 for further details.
DOI: 10.5061/dryad.27257r3
title: Data from: Climate change amplifies plant invasion hotspots in Nepal

description: Aim Climate change has increased the risk of biological invasions,
 particularly by increasing the climatically suitable regions for invasive
 alien species. The distribution of many native and invasive species has
 been predicted to change under future climate. We performed species
 distribution modelling of invasive alien plants (IAPs) to identify
 hotspots under current and future climate scenarios in Nepal, a country
 ranked among the most vulnerable countries to biological invasions and
 climate change in the world. Location Nepal Methods We predicted
 climatically suitable niches of 24 out of the total 26 reported IAPs in
 Nepal under current and future climate (2050 for RCP 6.0) using an
 ensemble of species distribution models. We also conducted hotspot
 analysis to highlight the geographic hotspots for IAPs in different
 climatic zones, land cover, ecoregions, physiography, and federal states.
 Results Under future climate, climatically suitable regions for 75% of
 IAPs will expand in contrast to a contraction of the climatically suitable
 regions for the remaining 25% of the IAPs. A high proportion of the
 modelled suitable niches of IAPs occurred on agricultural lands followed
 by forests. In aggregation, both extent and intensity (invasion hotspots)
 of the climatically suitable regions for IAPs will increase in Nepal under
 future climate scenarios. The invasion hotspots will expand towards the
 high-elevation mountainous regions. In these regions, land use is rapidly
 transforming due to the development of infrastructure and expansion of
 tourism and trade. Main conclusions Negative impacts on livelihood,
 biodiversity, and ecosystem services, as well as economic loss caused by
 IAPs in the future, may be amplified if preventive and control measures
 are not immediately initiated. Therefore, the management of IAPs in Nepal
 should account for the vulnerability of climate change-induced biological
 invasions into new areas, primarily in the mountains.
description: Occurence (survey) data
 of invasive alien plants in NepalOut of 26 invasive alien
 plant species reported from Nepal, this data has occurrence locations of
 24 species in Nepal. The data occurrence locations were recorded roadside
 survey and vegetation sampling between 2012 and 2018.Occurence (survey) data of
 invasive plants in Nepal.xlsx
DOI: 10.5061/dryad.2jg0d2m
title: Data from: Can competitive asymmetries maintain offspring size variation? A manipulative field test

description: Offspring sizes vary within populations but the reasons are unclear.
 Game-theoretic models predict that selection will maintain offspring-size
 variation when large offspring are superior competitors (i.e. competition
 is asymmetric), but small offspring are superior colonisers. Empirical
 tests are equivocal, however, and typically rely on interspecific
 comparisons, while explicit intraspecific tests are rare. In a field
 study, we test whether offspring size affects competitive asymmetries
 using the sessile marine invertebrate, Bugula neritina. Surprisingly, we
 show that offspring size determines whether interactions are competitive
 or facilitative – large neighbours strongly facilitated small offspring,
 but also strongly competed with large offspring. These findings contradict
 the assumptions of classic theory – that is, large offspring were not
 superior competitors. Instead, smaller offspring actually benefit from
 interactions with large offspring – suggesting that asymmetric
 facilitation, rather than asymmetric competition, operates in our system.
 We argue that facilitation of small offspring may be more widespread than
 currently appreciated, and may maintain variation in offspring size via
 negative frequency-dependent selection. Offspring size theory has
 classically viewed offspring interactions through the lens of competition
 alone, yet our results and those of others, suggest that theory should
 accommodate positive interactions in explorations of offspring-size
 variation.
description: Offspring size-mediated
 performance at 11 weeksThe empirical data from
 our field experiment that investigated the effects of size differences
 among offspring on the outcomes of pairwise
 interactions.
DOI: 10.5061/dryad.cr90637
title: Data from: Where to forage when afraid: Does perceived risk impair use of the foodscape?

description: The availability and quality of forage on the landscape constitute the
 foodscape within which animals make behavioral decisions to acquire food.
 Novel changes to the foodscape, such as human disturbance, can alter
 behavioral decisions that favor avoidance of perceived risk over food
 acquisition. Although behavioral changes and population declines often
 coincide with the introduction of human disturbance, the link(s) between
 behavior and population trajectory are difficult to elucidate. To identify
 a pathway by which human disturbance may affect ungulate populations, we
 tested the Behaviorally Mediated Forage-Loss Hypothesis, wherein
 behavioral avoidance is predicted to reduce use of available forage
 adjacent to disturbance. We used GPS-collar data collected from migratory
 mule deer (Odocoileus hemionus) to evaluate habitat selection, movement
 patterns, and time-budgeting behavior in response to varying levels of
 forage availability and human disturbance in three different populations
 exposed to a gradient of energy development. Subsequently, we linked
 animal behavior with measured use of forage relative to human disturbance,
 forage availability, and quality. Mule deer avoided human disturbance at
 both home range and winter range scales, but showed negligible differences
 in vigilance rates at the site level. Use of the primary winter forage,
 sagebrush (Artemisia tridentata), increased as production of new annual
 growth increased but use decreased with proximity to disturbance.
 Consequently, avoidance of human disturbance prompted loss of otherwise
 available forage, resulting in indirect habitat loss that was 4.6-times
 greater than direct habitat loss from roads, well pads, and other
 infrastructure. The multiplicative effects of indirect habitat loss, as
 mediated by behavior, impaired use of the foodscape by reducing the amount
 of available forage for mule deer—a consequence of which may be winter
 ranges that support fewer animals than they did before development.
description: GPS_dataGPS location data from mule deer in western Wyoming, 2013-2015.ForageUseProduction and use of sagebrush (Artemisia tridentata) sampled from 150 transects in western Wyoming, 2013-2015. Included are measurements of quality and quantity of sagebrush, including crude protein, digestibility, available biomass, and concentrations of plant secondary metabolites.BehavioralObsBehavioral observations of time-budgeting behavior of mule deer (Odocoileus hemionus) in western Wyoming 2013-2014. Behaviors recorded include seconds animals spent vigilant, feeding, moving, and bedded.
DOI: 10.5061/dryad.bm8458m
title: Data from: Conservation of old individual trees and small populations is integral to maintain species’ genetic diversity of a historically fragmented woody perennial

description: Historically fragmented and specialised habitats such as granite outcrops
 are understudied globally unique hotspots of plant evolution. In contrast
 to predictions based on mainstream population genetics theory, some
 granite outcrop plants appear to have persisted as very small populations
 despite prolonged geographic and genetic isolation. Eucalyptus caesia
 Benth. is a long-lived lignotuberous tree endemic with a naturally
 fragmented distribution on granite outcrops in south-western Australia. To
 quantify population to landscape level genetic structure we employed
 microsatellite genotyping at 14 loci of all plants in 18 stands of E.
 caesia. Sampled stands were characterised by low levels of genetic
 diversity, small absolute population sizes, localised clonality and strong
 fine-scale genetic sub-division. There was no significant relationship
 between population size and levels of heterozygosity. At the landscape
 scale, high levels of population genetic differentiation were most
 pronounced among representatives of the two subspecies in E. caesia as
 originally circumscribed. Past genetic interconnection was evident between
 some geographical neighbours separated by up to 20 kilometres.
 Paradoxically, other pairs of neighbouring stands as little as 7
 kilometres apart were genetically distinct. There was no consistent
 pattern of isolation by distance across the 280 km range of E. caesia. Low
 levels of gene flow, together with strong drift within stands, provides
 some explanation of the patterns of genetic differentiation we observed.
 Individual genet longevity via the ability to repeatedly re-sprout and
 expand from a lignotuber may enhance the persistence of some woody
 perennial endemic plants despite small population size, minimal genetic
 interconnection and low heterozygosity.
description: Eucalyptus caesia
 genotypesThe data file contains
 microsatellite genotypes and GPS coordinates (UTM easting and northing)
 for individuals of Eucalyptus caesia.Bezemer et al.
 genotypes.xlsx
DOI: 10.5061/dryad.gv2qr76
title: Data from: Positive plant-soil feedbacks trigger tannin evolution by niche construction: a spatial stoichiometric model

description: 1. Among plant traits, plant secondary metabolites such as tannins mediate
 plant herbivore interactions but also have after-life effects on litter
 decomposition and nutrient cycling. We propose that niche construction
 mechanisms based on positive plant-soil feedbacks (PSF) could influence
 the evolution of tannin production. 2. By modeling the flow of nitrogen
 (N) and carbon (C) through plants and soil in a spatially explicit
 context, we explored the relative contribution of herbivory and positive
 PSF as drivers of tannin evolution. We assumed soil N to be contained in
 labile and recalcitrant compartments, the latter made of tannin-protein
 complexes from which plants can absorb nutrients via associations with
 mycorrhizal fungi. 3. In infertile environments and for plants with low
 biomass turnover rates, we show that when tannins modify soil properties
 locally, positive PSF alone can drive their evolution. We further predict
 the existence of positive coevolutionary feedbacks between associations
 with mycorrhizal fungi with a decaying ability and tannins, possibly
 triggered by the evolution of the latter as protection against herbivores.
 In line with our theoretical results, empirical evidence suggest that
 tannins are mostly present in plants with low tissue turnover, associated
 with mycorrhizal fungi able to decay organic matter and inhabiting
 infertile environments. 4. Synthesis. Our model proposes that the
 evolution of tannin production can be triggered by positive PSF, provided
 that tannins promote the local N retention and that mycorrhizal fungi
 associated with plants are able to absorb N from tannin-protein complexes.
 In our model, tannin production evolves only in infertile ecosystems, in
 agreement with field observations. Our findings highlight that the
 strength of niche construction depends on the ecological context, hence
 that global ecological properties constrain local eco-evolutionary
 dynamics.
description: spatial
 implicitPython 2 code to
 reproduce Fig. 3. The prediction for tannin evolution in the spatial
 implicit approach, as a function of turnover rate and soil
 fertility.cellular_automatonPython 2 code of the cellular automaton, used to generate Fig. 2 and Fig. 4.coevolutionPython 2 code to smile;ulate the coevolutionary dynamics of symbiotic capacity and tannin production.
DOI: 10.5061/dryad.t384224
title: Data from: Genetic admixture accelerates invasion via provisioning rapid adaptive evolution

description: Genetic admixture, the intraspecific hybridization among divergent
 introduced sources, can immediately facilitate colonization via hybrid
 vigor and profoundly enhance invasion via contributing novel genetic
 variation to adaption. As hybrid vigor is short-lived, provisioning
 adaptation is anticipated to be the dominant and long-term profit of
 genetic admixture, but the evidence for this is rare. We employed the 30
 years’ geographic-scale invasion of the salt marsh grass, Spartina
 alterniflora, as an evolutionary experiment and evaluated the consequences
 of genetic admixture by combining the reciprocal transplant experiment
 with quantitative and population genetic surveys. Consistent with the
 documentation, we found that the invasive populations in China had
 multiple origins from the southern Atlantic coast and the Gulf of Mexico
 in the US. Interbreeding among these multiple sources generated a “hybrid
 swarm” that spread throughout the coast of China. In the northern and
 mid-latitude China, natural selection greatly enhanced fecundity, plant
 height and shoot regeneration compared to the native populations.
 Furthermore, genetic admixture appeared to have broken the negative
 correlation between plant height and shoot regeneration, which was
 genetically-based in the native range, and have facilitated the evolution
 of super competitive genotypes in the invasive range. In contrast to the
 evolved northern and mid-latitude populations, the southern invasive
 populations showed slight increase of plant height and shoot regeneration
 compared to the native populations, possibly reflecting the heterotic
 effect of the intraspecific hybridization. Therefore, our study suggests a
 critical role of genetic admixture in accelerating the geographic invasion
 via provisioning rapid adaptive evolution.
description: 20190618 SSR &
 Greenhouse & Gardens & climate datas
DOI: 10.5061/dryad.78tp3m2
title: Data from: Greater growth stability of trees in marginal habitats suggests a patchy pattern of population loss and retention in response to increased drought at the rear edge

description: Species rear range-edges are predicted to retract as climate warms, yet
 evidence of population persistence is accumulating. Accounting for this
 disparity is essential to enable prediction and planning for species’
 range retractions. At the Mediterranean edge of European beech-dominated
 temperate forest, we tested the hypothesis that individual performance
 should decline at the limit of the species’ ecological tolerance in
 response to increased drought. We sampled 40 populations in a crossed
 factor design of geographical and ecological marginality and assessed tree
 growth resilience and decline in response to recent drought. Drought
 impacts occurred across the rear edge, but tree growth stability was
 unexpectedly high in geographically isolated marginal habitat and lower
 than anticipated in the species’ continuous range and better-quality
 habitat. Our findings demonstrate that, at the rear edge, range shifts
 will be highly uneven and characterised by reduction in population density
 with local population retention rather than abrupt range retractions.
description: Diameter at breast
 height (dbh, cm) of sampled treesdbh_trees.csvBasal area increment (mm2) of sampled treesbai.csvLocation of sampling sites. See supplementary material for details on population selectionsites.csv
DOI: 10.5281/zenodo.18379720
title: Data: Simple Box-Cox probabilistic models for hourly streamflow predictions
DOI: 10.5281/zenodo.18379721
title: Data: Simple Box-Cox probabilistic models for hourly streamflow predictions