cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qb6h8
title: Data from: Investigating evolutionary lag using the species-pairs evolutionary lag test (SPELT)

description: For traits showing correlated evolution, one trait may evolve more slowly
 than the other, producing evolutionary lag. The species-pairs evolutionary
 lag test (SPELT) uses an independent contrasts based approach to detect
 evolutionary lag on a phylogeny. We investigated the statistical
 performance of SPELT in relation to degree of lag, sample size (species
 pairs), and strength of association between traits. We simulated trait
 evolution under two models: one in which trait X changes during speciation
 and the lagging trait Y catches up as a function of time since speciation;
 and another in which trait X evolves in a random walk and the lagging
 trait Y is a function of X at a previous time period. Type I error rates
 under “no lag” were close to the expected level of 5%, indicating that the
 method is not prone to false-positives. Simulation results suggest that
 reasonable statistical power (80%) is reached with around 140 species
 pairs, although the degree of lag and trait associations had additional
 influences on power. We applied the method to two datasets and discuss how
 estimation of a branch length scaling parameter (κ) can be used with SPELT
 to detect lag.
description: Endocranial volume
 female Isler et al. 2008Data used to assess
 evolutionary lag in primate endocranial volume, from Isler, K., E.
 Christopher Kirk, J. Miller, G. A. Albrecht, B. R. Gelvin, and R. D.
 Martin. 2008. Endocranial volumes of primate species: scaling analyses
 using a comprehensive and reliable data set. Journal of Human Evolution
 55:967-978.data_female_b.csvPrimate Males and Females.csvData on number of males and number of females, from Lindenfors, P., L. Froberg, and C. L. Nunn. 2004. Females drive primate social evolution. Proceedings of the Royal Society of London Series B-Biological Sciences 271:S101-S103.Lindenfors_et_al_2004_Data_FINAL.csvLag Method 1 Threshold Based LagR code for Lag Method 1 described in paper.Lag Method 2 Increment Based LagR code for Lag Method 2 described in paper.
DOI: 10.5061/dryad.8f251
title: Data from: The body beyond the body: expectation of a sensory event is enough to induce ownership over a fake hand

description: More than 100 papers have been published on the rubber hand illusion since
 its discovery 14 years ago. The illusion has been proposed as a
 demonstration that the body is distinguished from other objects by its
 participation in specific forms of intermodal perceptual correlation.
 Here, we radically challenge this view by claiming that perceptual
 correlation is not necessary to produce the experience of this body as
 mine. Each of 15 participants was seated with his/her right arm resting
 upon a table just below another smaller table. Thus, the real hand was
 hidden from the participant's view and a life-sized rubber model of a
 right hand was placed on the small table in front of the participant. The
 participant observed the experimenter's hand while
 approaching—without touching—the rubber hand. Phenomenology of the
 illusion was measured by means of skin conductance response and
 questionnaire. Both measures indicated that participants experienced the
 illusion that the experimenter's hand was about to touch their hidden
 hand rather than the rubber hand, as if the latter replaced their own
 hand. This did not occur when the rubber hand was rotated by 180° or
 replaced by a piece of wood. This illusion indicates that our brain does
 not build a sense of self in a merely reactive way, via perceptual
 correlations; rather it generates predictions on what may or may not
 belong to itself.
description: dataRHI
DOI: 10.5061/dryad.sg4hb67
title: Data from: Biochemical evolution in response to intensive harvesting in algae: evolution of quality and quantity

description: Evolutionary responses to indirect selection pressures imposed by
 intensive harvesting are increasingly common. While artificial selection
 has shown that biochemical components can show rapid and dramatic
 evolution, it remains unclear as to whether intensive harvesting can
 inadvertently induce changes in the biochemistry of harvested populations.
 For applications such as algal culture, many of the desirable bioproducts
 could evolve in response to harvesting, reducing cost-effectiveness, but
 experimental tests are lacking. We used an experimental evolution approach
 where we imposed heavy and light harvesting regimes on multiple lines of
 an alga of commercial interest for twelve cycles of harvesting and then
 placed all lines in a common garden regime for four cycles. We have
 previously shown that lines in a heavy harvesting regimes evolve a ‘live
 fast’ phenotype with higher growth rates relative to light harvesting
 regimes. Here, we show that algal biochemistry also differs between
 regimes, though they were temporarily masked by differences in density
 under those different regimes. Heavy harvesting regimes, evolved lower
 productivity of desirable bioproducts, particularly fatty acids relative
 to light harvesting regimes. We suggest that commercial operators wishing
 to maximise productivity of desirable bioproducts should maintain mother
 cultures, kept at higher densities (which tend to select for desirable
 phenotypes), and periodically restart their intensively harvested cultures
 to minimise the negative consequences of biochemical evolution. Our study
 shows that the burgeoning algal culture industry should pay careful
 attention to the role of evolution in intensively harvested crops as these
 effects are nontrivial if subtle.
description: Biochemistry
 databiochemical data from
 the experimental evolution experimentsBiochem combined data
 correct.xlsx
DOI: 10.5061/dryad.16vk4
title: Data from: Sex allocation adjustment to mating group size in a simultaneous hermaphrodite

description: Sex allocation theory is considered as a touchstone of evolutionary
 biology, providing some of the best supported examples for Darwinian
 adaptation. In particular, Hamilton’s local mate competition theory has
 been shown to generate precise predictions for extraordinary sex ratios
 observed in many separate-sexed organisms. In analogy to local mate
 competition, Charnov’s mating group size model predicts how sex allocation
 in simultaneous hermaphrodites is affected by the mating group size (i.e.,
 the number of mating partners plus one). Until now studies have not
 directly explored the relationship between mating group size and sex
 allocation, which we here achieve in the simultaneously hermaphroditic
 flatworm Macrostomum lignano. Using transgenic focal worms with ubiquitous
 expression of green-fluorescent protein (GFP), we assessed the number of
 wild-type mating partners carrying GFP-positive sperm from these focal
 worms when raised in different social group sizes. This allowed us to test
 directly how mating group size was related to the sex allocation of focal
 worms. We find that the proportion of male investment initially increases
 with increasing mating group size, but then saturates as predicted by
 theory. To our knowledge, this is the first direct test of the mating
 group size model in a simultaneously hermaphroditic animal.
description: DATA_Janicke_et_al_SexAlloAdj_EvolutionEstimates of mating group size, body size and sex allocation assessed for different social group sizes. Data file contains three data sheets: (1) mean values, (2) individual values and (3) legend of column headings for (1) and (2).
DOI: 10.5061/dryad.mk59gk0
title: Data from: Lactation and resource limitation affect stress responses, thyroid hormones, immune function and antioxidant capacity of sea otters (Enhydra lutris)

description: 1. Lactation is the most energetically demanding stage of reproduction in
 female mammals. Increased energetic allocation toward current reproduction
 may result in fitness costs, though the mechanisms underlying these
 trade-offs are not well understood. Trade-offs during lactation may
 include reduced energetic allocation to cellular maintenance, immune
 response and survival, and may be influenced by resource limitation. 2. As
 the smallest marine mammal, sea otters (Enhydra lutris) have the highest
 mass-specific metabolic rate necessitating substantial energetic
 requirements for survival. To provide the increased energy needed for
 lactation, female sea otters significantly increase foraging effort,
 especially during late-lactation. Caloric insufficiency during lactation
 is reflected in the high numbers of maternal deaths due to End-Lactation
 Syndrome in the California subpopulation. 3. We investigated the effects
 of lactation and resource limitation on maternal stress responses,
 metabolic regulation, immune function and antioxidant capacity in two
 subspecies of wild sea otters (northern: E. l. nereis and southern: E. l.
 kenyoni) within the California, Washington and Alaska subpopulations. 4.
 Lactation and resource limitation were associated with reduced
 glucocorticoid responses to acute capture stress. Corticosterone release
 was lower in lactating otters. Cortisol release was lower under resource
 limitation and suppression during lactation was only evident under
 resource limitation. Lactation and resource limitation were associated
 with alterations in thyroid hormones. Immune responses and total
 antioxidant capacity were not reduced by lactation or resource limitation.
 Southern sea otters exhibited higher concentrations of antioxidants,
 immunoglobulins and thyroid hormones than northern sea otters. 5. These
 data provide evidence for allocation trade-offs during reproduction and in
 response to nutrient limitation but suggest self-maintenance of immune
 function and antioxidant defenses despite energetic constraints.
 Income-breeding strategists may be especially vulnerable to the
 consequences of stress and modulation of thyroid function when food
 resources are insufficient to support successful reproduction and may come
 at a cost to survival, and thereby influence population trends.
description: CHINN.et.al_SeaOtter_DryadThese are original data from Chinn et al. 2018. This .csv file has data for measured concentrations of Total Antioxidant, Cortisol, Corticosterone, IgM, IgG, Total T4, Total T3, Reverse T3 analytes measured in northern and southern sea otters from California, Washington, and Alaska, USA.
DOI: 10.5061/dryad.c6f97
title: Data from: Plant sex alters Allee effects in aggregating plant parasites

description: Species interactions are central to our understanding of population
 dynamics. While density typically strengthens competition, reducing
 absolute fitness, Allee effects can reverse this pattern, increasing
 fitness with density. Allee effects emerge in host-parasite systems when
 higher parasite densities dilute immune responses or increase
 resource-mobilization. The optimal density of individuals in these systems
 should be influenced by how host quality alters the rates at which
 facilitative and competitive effects change across densities. We tested
 these ideas using sumac (Rhus typhina) and a gall-forming parasite
 (Melaphis rhois) that attacks sumac leaves. Fitness peaked at intermediate
 densities , indicating an Allee effect, but the fitness peak depended on
 host sex. Patterns of abundance mirrored fitness patterns, with galls
 clustered on leaves and female hosts supporting greater numbers of galls.
 Within leaves, galls near the stem were more fit, and gall-makers
 preferentially oviposited near to the stem. The patterns of fitness and
 abundance are consistent with Allee effects caused by increased resource
 mobilization at higher gall-maker densities rather than diluted immune
 responses. Our results suggest that Allee effects in parasites can be
 described as the summative effects of competitive and facilitative
 processes and, because both are common, Allee effects are likely common in
 host-parasite systems.
description: dryad
 files
DOI: 10.5281/zenodo.18384828
title: Data for PRB publication "Andreev bound state spectroscopy of a quantum-dot-based Aharonov-Bohm     interferometer with superconducting terminals"
DOI: 10.5061/dryad.bk175
title: Data from: Natural selection on floral morphology depends on climate

description: Climate has the potential to influence evolution, but how it influences
 the strength or direction of natural selection is largely unknown. We
 quantified the strength of selection on four floral traits of the
 subalpine herb Ipomopsis sp. in 10 years that differed in precipitation,
 causing extreme temporal variation in the date of snowmelt in the Colorado
 Rocky Mountains. The chosen floral traits were under selection by
 hummingbird and hawkmoth pollinators, with hawkmoth abundance highly
 variable across years. Selection for flower length showed environmental
 sensitivity, with stronger selection in years with later snowmelt, as
 higher water resources can allow translation of pollination success into
 fitness based on seed production. Selection on corolla width also varied
 across years, favouring narrower corolla tubes in two unusual years with
 hawkmoths, and wider corollas in another late snowmelt year. Our results
 illustrate how changes in climate could alter natural selection even when
 the primary selective agent is not directly influenced.
description: Selection on floral
 traitsCollected at two common
 garden field sites in Poverty Gulch, Gunnsion County, CO. Corollalength
 and corollawidth are in mm. NPR24 is in uL/24 hr. RminusG is proportion of
 petal reflectance in red compared to in green. Seeds is total seeds
 produced by the plant, and flowers is total flowers.Campbell and Powers 2015
 data.xlsx
DOI: 10.5281/zenodo.18384827
title: Data for PRB publication "Andreev bound state spectroscopy of a quantum-dot-based Aharonov-Bohm     interferometer with superconducting terminals"
DOI: 10.5061/dryad.gd489
title: Data from: Invasive pathogen drives host population collapse: effects of a travelling wave of sarcoptic mange on bare-nosed wombats

description: 1.Emerging and invasive pathogens can have long-lasting impacts on
 susceptible wildlife populations, including localised collapse and
 extirpation. Management of threatening disease is of widespread interest
 and requires knowledge of spatiotemporal patterns of pathogen spread.
 2.Theory suggests disease spread often occurs via two patterns: homogenous
 mixing and travelling waves. However, high resolution empirical data
 demonstrating localised (within population) disease spread patterns are
 rare. 3.This study examined the spread of sarcoptic mange (aetiological
 agent Sarcoptes scabiei) in a population of bare-nosed wombats (Vombatus
 ursinus), and investigated whether pathogen spread occurred by homogenous
 mixing or a travelling wave. 4.Using seven years of population surveys and
 four years of disease severity surveys, we show that mange was first
 detected in the east of a wombat population in northern Tasmania, and
 progressed westward as a travelling wave. Wombat mortality rates reached
 100% behind the wave, with a 94% decline in overall wombat abundance
 within the park. 5.Synthesis and applications. Globally distributed
 pathogens may have severe impacts on susceptible host species. This is the
 first study to quantify population level impacts of sarcoptic mange upon
 bare-nosed wombats, showing a wave of mange disease which resulted in a
 dramatic population decline. Successful management of the spread of this
 and similar pathogens may hinge on the capacity to establish transmission
 barriers at local or between-population scales.
description: Wombat abundance and
 mange severity dataThis file contains
 average wombat abundance across different sections of the park over time
 (tab labelled "Presence Data") and mange severity scores from
 mange surveys (tab labelled "Mange Data")Martin et al _
 Data.xlsx
DOI: 10.5061/dryad.86642
title: Data from: Overyielding in young tree plantations is driven by local complementarity and selection effects related to shade tolerance

description: 1. Overyielding in mixed-species forests has been demonstrated in a vast
 body of literature, and the focus of functional biodiversity research is
 now shifting towards a mechanistic understanding of these observations. 2.
 We explored diversity-productivity relationships (DPRs) at two sites of a
 large-scale tree diversity experiment, with benign (Zed) and harsh (Ged)
 environmental conditions for plantation establishment. Additive
 partitioning methodologies were adopted to detect phenomenological
 patterns in the productivity data, and the trait structure of mixed
 communities was used to advance insights into compositional effects. 3.
 After six years of plantation development, biomass productivity was
 significantly higher in mixtures compared to the monocultures of component
 species. We observed that processes operated through direct tree-tree
 interactions, since the diversity signal disappeared where trees in mixed
 stands were surrounded by conspecific neighbors only. This result is
 particularly relevant for mixed-species planation systems, as trees are
 commonly planted in monospecific patches to simplify the management.
 Partitioning unveiled strong selection effects at both plantation sites.
 However, at the Ged-site this was caused by competitive dominance of
 species with fast young growth whereas at the Zed-site, species with slow
 young growth improved their performances but not at the expense of others
 (i.e. trait-dependent complementarity). Species tolerance to shading is an
 influential trait to predict biodiversity effects, with community-weighted
 means in shade tolerance mediating dominance effects (Ged) and functional
 diversity in shade tolerance mediating (trait-dependent) complementarity
 effects (Zed). 4. Synthesis. This study highlights that biodiversity
 effects in young tree plantations could be explained by the functional
 composition of mixed communities, with a key role for species levels of
 shade tolerance. As contrasting results between plantation sites were
 observed, future research should target the context-dependency of DPRs.
description: Data
 productivityData from FORBIO
 biodiversity experiment (Belgium) including six-years proudctivity data.
 Please consider the main manuscript and supporting information for more
 details about data collection and processing.Analyses 6y
 DRYAD.xlsx
DOI: 10.5061/dryad.vv150
title: Data from: A quantitative framework for investigating risk of deadly collisions between marine wildlife and boats

description: Speed regulations of watercraft in protected areas are designed to reduce
 lethal collisions with wildlife but can have economic consequences. We
 present a quantitative framework for investigating the risk of deadly
 collisions between boats and wildlife. We apply encounter rate theory to
 demonstrate how marine mammal-boat encounter rate can be used to predict
 the expected number of deaths associated with management scenarios. We
 illustrate our approach with management scenarios for two endangered
 species: the Florida manatee Trichechus manatus latirostris and the North
 Atlantic right whale Eubalaena glacialis. We used a Monte Carlo simulation
 approach to demonstrate the uncertainty that is associated with our
 estimate of relative mortality. We show that encounter rate increased with
 vessel speed but that the expected number of encounters varies depending
 on the boating activities considered. For instance, in a scenario
 involving manatees and boating activities such as water skiing, the
 expected number of encounters in a given area (in a fixed time interval)
 increased with vessel speed. In another scenario in which a vessel made a
 transit of fixed length the expected number of encounters decreases
 slightly with boat speed. In both cases the expected number of encounters
 increased with distanced travelled by the boat. For whales, we found a
 slight reduction (~0.1%) in the number of encounters under a scenario
 where speed is unregulated; this reduction, however, is negligible, and
 overall expected relative mortality was ~30% lower under the scenario with
 speed regulation. The probability of avoidance by the animal or vessel was
 set to 0 because of lack of data, but we explored the importance of this
 parameter on the model predictions. In fact, expected relative mortality
 under speed regulations decreases even further when the probability of
 avoidance is a decreasing function of vessel speed. By applying encounter
 rate theory to the case of boat collisions with marine mammals, we gained
 new insights about encounter processes between wildlife and watercraft.
 Our work emphasizes the importance of considering uncertainty when
 estimating wildlife mortality. Finally, our findings are relevant to other
 systems and ecological processes involving the encounter between moving
 agents.
description: Encounter_Rate_Expected_Mortality.txtThis file includes R scripts to estimate encounter rates and expected mortality. It includes input information to reproduce results presented in the main text of the paper and in Appendix S4.Correlated_Random_Walk_SimulationsThis file includes R scripts to estimate encounter rates based on a simulation approach. It includes input information to reproduce results presented in the main text of the paper.Monte_Carlo_Simulations.txtThis file includes R scripts to implement Monte Carlo simulations. It includes input information to reproduce results presented in the main text of the paper.
DOI: 10.5061/dryad.2jv17
title: Data from: Permutation tests for phylogenetic comparative analyses of high-dimensional shape data: what you shuffle matters

description: Evaluating statistical trends in high-dimensional phenotypes poses
 challenges for comparative biologists, because the high-dimensionality of
 the trait data relative to the number of species can prohibit parametric
 tests from being computed. Recently, two comparative methods were proposed
 to circumvent this difficulty. One obtains phylogenetic independent
 contrasts for all variables, and statistically evaluates the linear model
 by permuting the PICs of the response data. The other uses a
 distance-based approach to obtain coefficients for generalized least
 squares models (D-PGLS), and subsequently permutes the original data to
 evaluate the model effects. Here we show that permuting PICs is not
 equivalent to permuting the data prior to the analyses as in D-PGLS. We
 further explain why PICs are not the correct exchangeable units under the
 null hypothesis, and demonstrate that this mis-specification of permutable
 units leads to inflated type I error rates of statistical tests. We then
 show that simply shuffling the original data and re-calculating the
 independent contrasts with each iteration yields significance levels that
 correspond to those found using D-PGLS. Thus, while summary statistics
 from methods based on PICs and PGLS are the same, permuting PICs can lead
 to strikingly different inferential outcomes with respect to statistical
 and biological inferences.
description: PlethHead-SVL-DataHead shape and body size data (species means) for 42 species of Plethodon salamanderPlethodon PhylogenyPlethodon phylogeny (from Wiens et al. 2006)plethred.treType I Error Simulation ScriptR script for simulating data to evaluate Type I error rates of two multivariate phylogenetic comparative method approachesPICRand-TypeIError.rSimulation support scriptsSupport scripts for Type I error simulationsprocD.pic.r