cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.863c8sk
title: Data from: Reproductive losses due to climate change-induced earlier flowering are not the primary threat to plant population viability in a perennial herb

description: 1. Despite a global footprint of shifts in flowering phenology in response
 to climate change, the reproductive consequences of these shifts are
 poorly understood. Furthermore, it is unknown whether altered flowering
 times affect plant population viability. 2. We examine whether climate
 change-induced earlier flowering has consequences for population
 persistence by incorporating reproductive losses from frost damage (a risk
 of early flowering) in population models of a subalpine sunflower
 (Helianthella quinquenervis). Using long-term demographic data for three
 populations that span the species’ elevation range (8–15 years, depending
 on the population), we first examine how snowmelt date affects plant vital
 rates. To verify vital rate responses to snowmelt date experimentally, we
 manipulate snowmelt date with a snow removal experiment at one population.
 Finally, we construct stochastic population projection models and Life
 Table Response Experiments for each population. 3. We find that
 populations decline (λs &lt; 1) as snowmelt dates become earlier.
 Frost damage to flower buds, a consequence of climate change-induced
 earlier flowering, does not contribute strongly to population declines.
 Instead, we find evidence that negative effects on survival, likely due to
 increased drought risk during longer growing seasons, drive projected
 population declines under earlier snowmelt dates. 4. Synthesis. Shifts in
 flowering phenology are a conspicuous and important aspect of biological
 responses to climate change, but here we show that the phenology of
 reproductive events can be unreliable measures of threats to population
 persistence, even when earlier flowering is associated with substantial
 reproductive losses. Evidence for shifts in reproductive phenology, along
 with scarcer evidence that these shifts actually influence reproductive
 success, are valuable but can paint an incomplete and even misleading
 picture of plant population responses to climate change.
description: HEQU_demography
 dataLong-term demographic
 vital rates for Helianthella quinquenervis, across three study
 populations. The csv file was made in Excel. See README.txt file for
 detailed description of all variables.snowmeltData on first day of bare ground (snowmelt date, shown as day of year; 1 Jan = 1) from a long-term snow monitoring plot monitored by billy barr, near the mid-elevation study population described in the paper (The Rocky Mountain Biological Laboratory). snowmeltT1 refers to the date of melt in year t+1 and snowmeltTm1 refers to the date of melt in year t-1.snow.removal.experimentVital responses to experimental snow removal at one study population. The csv file was made in Excel. Variables are described in the associated README.txt file.
DOI: 10.5061/dryad.fn38f87
title: Data from: Postglacial colonization routes coincide with a life history breakpoint along a latitudinal gradient

description: While adaptive divergence along environmental gradients has repeatedly
 been demonstrated, the role of postglacial colonization routes in
 determining phenotypic variation along gradients has received little
 attention. Here we used a hierarchical QST-FST approach to separate the
 roles of adaptive and neutral processes in shaping phenotypic variation in
 moor frog (Rana arvalis) larval life-histories along a 1700 km latitudinal
 gradient across northern Europe. This species has colonized Scandinavia
 via two routes with a contact zone in northern Sweden. By using neutral
 SNP and common garden phenotypic data from 13 populations at two
 temperatures, we showed that most of the variation along the gradient
 occurred between the two colonizing lineages. We found little phenotypic
 divergence within the lineages, however, all phenotypic traits were
 strongly diverged between the southern and northern colonization routes,
 with higher growth and development rates and larger body size in the
 north. The QST estimates between the colonization routes were four times
 higher than FST, indicating a prominent role for natural selection. QST
 within the colonization routes did not generally differ from FST, but we
 found temperature-dependent adaptive divergence close to the contact zone.
 These results indicate that lineage-specific variation can account for
 much of the adaptive divergence along a latitudinal gradient.
description: Phenotypic data from
 common-garden experimentrawdata-arvalis2014.txtNeutral SNP from 13 populations of Rana arvalisinput_neutralFst_13populations.dat
DOI: 10.5061/dryad.jn365c2
title: Data from: Polyandry and polygyny in a social rodent: an integrative perspective based on social organization, copulations, and genetics

description: Animal mating systems have fascinated biologists for thousands of years.
 Ways to describe amating systeminclude determining social organization,
 observing copulations, or using genetics to assign parentage. Social
 organization can be difficult to quantify, however, documentation of
 copulations is often challenging, many copulations do not produce
 offspring, and genetic variation is sometimes minimal. Here we use data
 from a 7-year study of wild white-tailed prairie dogs (WTPDs, Cynomys
 leucurus) living in Colorado USA to estimate the frequencies of polyandry
 (i.e., copulation with ≥2 males) and polygyny (i.e., copulation with ≥2
 females) from three independent approaches: (1) determination of the
 number of males and females living in the same territory (social
 organization); (2) observations of copulations; and (3) genetic
 assignments of paternity from seven polymorphic microsatellites. We
 predicted that our three approaches would yield similar estimates of
 polyandry and polygyny. Because a WTPD female’s period of sexual
 receptivity each spring is limited to several hours on a single day, we
 also predicted that frequencies of polyandry and polygyny would be lower
 for WTPDs than for animals with longer periods of receptivity. Our results
 did not support these predictions. For polyandry, observations of
 copulations and genetics indicated similar overall percentages (27%), but
 social organization indicated a much lower percentage (2%). For polygyny,
 observations of copulations indicated the highest overall percentage
 (84%), then social organization (59%), then genetics (46%). All three
 approaches showed striking annual variation in the frequencies of WTPD
 polyandry and polygyny. Long-term studies that integrate behavioral and
 genetic insights can provide a detailed view of a mating system, but
 feasibility will depend on ease of capture, visibility of copulations,
 length of mating season, research objectives, and genetic variation.
description: PrairieDog_msatgenotypes_010516_parentageanalysis_Allrev010516_summary_forRPaternity assignment results for Cervus for White-tailed Prairie Dogs. Significance evaluated at 95% (strict) and 80% (relaxed).WTPD_Litter_Parentage_Info_Allrev010516Maternity and candidate paternity for each offspring (grouped by litter) for White-tailed Prairie Dogs.PrairieDog_msatgenotypes_041913_forCervusMicrosatellite genotypes for 7 loci genotyped for 801 White-tailed Prairie Dogs analyzed for paternity analysis.
DOI: 10.5061/dryad.2mm56k2
title: Data from: Differences in combinatorial calls among the 3 elephant species cannot be explained by phylogeny

description: Understanding why related species combine calls in different ways could
 provide insight into the selection pressures on the evolution of
 combinatorial communication. African savannah elephants (Loxodonta
 africana), African forest elephants (Loxodonta cyclotis), and Asian
 elephants (Elephas maximus) all combine broadband calls (roars, barks, and
 cries) and low-frequency calls (rumbles) into single utterances known as
 “combination calls.” We investigated whether the structure of such calls
 differs among species and whether any differences are better explained by
 phylogenetic relationships or by socio-ecological factors. Here, we
 demonstrate for the first time that the species differ significantly in
 the frequency with which they produce different call combinations using
 data from multiple study sites. E. maximus and L. africana mostly produced
 roar-rumble combinations, while L. cyclotis produced a more even
 distribution of roar-rumble, rumble-roar and rumble-roar-rumble
 combinations. There were also significant differences in favored structure
 among populations of the same species. Moreover, certain call orders were
 disproportionately likely to be given in particular behavioral contexts.
 In L. africana, rumble-roar-rumble combinations were significantly more
 likely than expected by chance to be produced by individuals separated
 from the group. In E. maximus, there was a marginally non-significant
 trend for rumble-roar-rumbles to be given more often than expected by
 chance in response to a disturbance. Site-specific socio-ecological
 conditions appear more influential for call combination structure than
 phylogenetic history.
description: Raw data for elephant
 combination call studyThis file contains the
 raw data for a comparative study of combination calls across the three
 elephant species. Data includes species, population from which the call
 was recorded, call type, call order (if a combination call), sex, age
 class, and individual identity of the caller (if known), and the
 behavioral context of the call if known20190125_data_for_dryad.csv
DOI: 10.5061/dryad.774c492
title: Data from: Modes of berm and beachface recovery following storm reset: observations using a continuously scanning lidar

description: Following the rapid and destructive impacts of storm erosion, beach
 recovery is a key natural process of restoration, returning eroded
 sediment to the subaerial beach and rebuilding coastal morphology. While
 the effects of storm erosion have commonly been investigated, detailed
 studies into post-storm recovery are currently lacking. This study
 investigates wave-driven recovery processes of the berm and beachface on a
 microtidal, swash-aligned sandy beach. Following complete removal of the
 berm by a significant storm event, the entire 76-day rebuilding of a swash
 berm is analysed at the timescale of every semi-diurnal tidal cycle,
 utilising high resolution (5 Hz) swash and subaerial beach profile
 measurements from a continuously scanning fixed lidar. Tide-by-tide rates
 of subaerial volume change during berm recovery were most frequently
 observed between 1 - 2 m3/m/day, including losses and gains on the order
 of several m3/m/day, substantially larger in magnitude than the more
 gradual rate of net gain (0.7 m3/m/day) observed for the entire recovery
 period. Patterns of berm crest formation and vertical growth were found to
 be primarily governed by the neap-spring tide variations in total water
 levels. Tide-by-tide beachface and berm volume changes were used to
 classify four principal behavioural modes of subaerial profile variability
 during recovery. Using decision tree classification, modes were
 differentiated according to nearshore dimensionless fall velocity, swash
 exceedance of the berm crest and ocean water levels. The findings provide
 novel behavioural and parametric insight into the tide-by-tide rebuilding
 of the beachface and berm by swash throughout a complete post-storm
 recovery period.
description: Fixed lidar beach
 monitoring - beach profiles, berm crests, swash exceedance and total water
 levelsFixed lidar beach
 monitoring data for beach recovery period 22 April to 7 July 2015.
 Included are low tide beach profiles, berm crest positions, swash
 exceedance statistics of the berm crest and total water levels. Please
 refer to read me documents for more information.Datasets.zip
DOI: 10.5061/dryad.cb690j5
title: Data from: Thermodynamic constraints and the evolution of parental provisioning in vertebrates

description: Why is post-natal parental provisioning so rare in ectothermic vertebrates
 while prolonged parental care is almost ubiquitous in endotherms? We argue
 that the scarcity of post-natal parental care is a result of ectothermy
 itself. While almost all endothermic young require prolonged post-natal
 care due to thermal constraints, ectothermic physiology does not pose the
 same constraint. Most ectothermic young are thus independent from birth.
 Ectothermic mothers are better off investing in future reproductive events
 than to continue investing into independent young, because the costs of
 feeding young does not outweigh the benefits. Ectothermy further releases
 the constraint on offspring size resulting in offspring of ectothermic
 vertebrates often being much smaller than their parents. When parents and
 offspring differ greatly in size, both tend to specialise on different
 diets, making the feeding of young by much larger individuals not
 impossible, but less likely. Additionally, when the size difference
 between parents and offspring is significant, both are likely to live in
 different habitats. Such spatial segregation is also less conducive to the
 evolution of parental care. In those species where parents and offspring
 are not spatially separated and parental care does occur, it is mainly
 restricted to the guarding of eggs or juveniles; parents of very few
 species provide their offspring with food. We conclude that parental care
 beyond the guarding of eggs or young is much less likely to evolve in
 ectothermic vertebrates compared with endothermic vertebrates, unless
 there are exceptional circumstances that strongly select for parents to
 provide for their offspring.
description: Offspring are cheap for
 ectothermsData to test hypotheses
 that (i) energy investment into eggs differs between egg-laying
 vertebrates, with birds (endotherms) investing significantly more than
 reptiles, amphibians, and fish (ectotherms) and that (ii) such investment
 depends on species body size. Source: Add-my-Pet database
 [PLoS Comput Biol
 14(5): e1006100].Beekman_et_al-Data.ods
DOI: 10.5061/dryad.68q4hf7
title: Data from: Mathematical modelling of the vitamin C clock reaction

description: Chemical clock reactions are characterised by a relatively long induction
 period followed by a rapid `switchover' during which the
 concentration of a \emph{clock chemical} rises rapidly. In addition to
 their interest in chemistry education, these reactions are relevant to
 industrial and biochemical applications. A substrate-depletive,
 non-autocatalytic clock reaction involving household chemicals (vitamin C,
 iodine, hydrogen peroxide and starch) is modelled mathematically via a
 system of nonlinear ordinary differential equations. Following dimensional
 analysis the model is analysed in the phase plane and via matched
 asymptotic expansions. Asymptotic approximations are found to agree
 closely with numerical solutions in the appropriate time regions.
 Asymptotic analysis also yields an approximate formula for the dependence
 of switchover time on initial concentrations and the rate of the slow
 reaction. This formula is tested via `kitchen sink chemistry'
 experiments, and is found to enable a good fit to experimental series
 varying in initial concentrations of both iodine and vitamin C. The
 vitamin C clock reaction provides an accessible model system for
 mathematical chemistry.
description: data_and_codeMatlab code to plot phase planes and solutions, and to carry out parameter fitting. Excel sheets with experimental results and concentration calculations.
DOI: 10.5061/dryad.8qq1607
title: Data from: Geographic variation in thermal sensitivity of early life traits in a widespread reptile

description: Taxa with large geographic distributions generally encompass diverse
 macroclimatic conditions, potentially requiring local adaptation and/or
 phenotypic plasticity to match their phenotypes to differing environments.
 These eco-evolutionary processes are of particular interest in organisms
 with traits that are directly affected by temperature, such as embryonic
 development in oviparous ectotherms. Here we examine the spatial
 distribution of fitness-related early-life phenotypes across the range of
 a widespread vertebrate, the painted turtle (Chrysemys picta). We
 quantified embryonic and hatchling traits from 7 locations (in Idaho,
 Minnesota, Oregon, Illinois, Nebraska, Kansas, and New Mexico) after
 incubating eggs under constant conditions across a series of
 environmentally relevant temperatures. Thermal reaction norms for
 incubation duration and hatchling mass varied among locations under this
 common-garden experiment, indicating genetic differentiation or
 pre-ovulatory maternal effects. However, latitude, a commonly-used proxy
 for geographic variation, was not a strong predictor of these geographic
 differences. Our findings suggest that this macroclimatic proxy may be an
 unreliable surrogate for microclimatic conditions experienced locally in
 nests. Instead, complex interactions between abiotic and biotic factors
 likely drive among-population phenotypic variation in this system.
 Understanding spatial variation in key life-history traits provides an
 important perspective on adaptation to contemporary and future climatic
 conditions.
description: GeographicVariationLabIncubationLat = Latitude Temp= Incubation temperature ID= individual identifier Clutch= Clutch/Maternal identifier CL= Carapace length CW= Carapace Width PL= Plastron length Abnorm= shell/tail abnormalities IncDur= Incubation duration State= location of turtle population Surv= Survivalgeographic variation lab incubation dryad.csv
DOI: 10.5061/dryad.fd0s01b
title: Data from: Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes.

description: Genetic architecture fundamentally affects the way that traits evolve.
 However, the mapping of genotype to phenotype includes complex
 interactions with the environment or even the sex of an organism that can
 modulate the expressed phenotype. Line cross analysis is a powerful
 quantitative genetics method to infer genetic architecture by analyzing
 the mean phenotype value of two diverged strains and a series of
 subsequent crosses and backcrosses. However, it has been difficult to
 account for complex interactions with the environment or sex within this
 framework. We have developed extensions to line cross analysis that allow
 for gene by environment and gene by sex interactions. Using extensive
 simulations studies and reanalysis of empirical data, we show that our
 approach can account for both unintended environmental variation when
 crosses cannot be reared in a common garden and can be used to test for
 the presence of gene by environment or gene by sex interactions. In
 analyses that fail to account for environmental variation between crosses
 we find that line cross analysis has low power and high false positive
 rates. However, we illustrate that accounting for environmental variation
 allows for the inference of adaptive divergence, and that accounting for
 sex differences in phenotypes allows practitioners to infer the genetic
 architecture of sexual dimorphism.
description: suppThis compressed file
 contains all files and script described in the original
 manuscript.
DOI: 10.5061/dryad.gt81779
title: Data from: Assessing combinability of phylogenomic data using Bayes Factors

description: With the rapid reduction in sequencing costs of high-throughput genomic
 data, it has become commonplace to use hundreds of genes to infer
 phylogeny of any study system. While sampling a large number of genes has
 given us a tremendous opportunity to uncover previously unknown
 relationships and improve phylogenetic resolution, it also presents us
 with new challenges when the phylogenetic signal is confused by
 differences in the evolutionary histories of sampled genes. Given the
 incorporation of accurate marginal likelihood estimation methods into
 popular Bayesian software programs, it is natural to consider using the
 Bayes Factor (BF) to compare different partition models in which genes
 within any given partition subset share both tree topology and edge
 lengths. We explore using marginal likelihood to assess data subset
 combinability when data subsets have varying levels of phylogenetic
 discordance due to deep coalescence events among genes (simulated within a
 species tree), and compare the results with our recently-described
 phylogenetic informational dissonance index (D) estimated for each data
 set. BF effectively detects phylogenetic incongruence, and provides a way
 to assess the statistical significance of D values. We use BFs to assess
 data combinability using an empirical data set comprising 56 plastid genes
 from the green algal order Volvocales. We also discuss the potential need
 for calibrating BFs and demonstrate that BFs used in this study are
 correctly calibrated.
description: Sys_Bio_Suppl_Feb25_2019Supplementary material
DOI: 10.5061/dryad.282bm46
title: Data from: Developing allometric models to predict the individual aboveground biomass of shrubs worldwide

description: Aim Existing global models to predict standing woody biomass are based on
 trees characterized by a single principal stem, well-developed in height.
 However, their use in open woodlands and shrublands, characterized by
 multistemmed species with substantial crown development, generates a high
 level of uncertainty in biomass estimates. This limitation led us to i)
 develop global predictive models of shrub individual aboveground biomass
 based on simple allometric variables; ii) to compare the fit of these
 models with existing global biomass models; and iii) to assess whether
 models fit change when bioclimatic variables are considered. Location
 Global. Time period Present. Major taxa studied 118 species. Methods We
 compile a database of 3243 individuals across 49 sites distributed
 worldwide. Including basal diameter, height and crown diameter as
 predictor variables, we built potential models and compared their fit
 using generalized least squares. We used mixed effects models to determine
 if bioclimatic variables improved the accuracy of biomass models. Results
 Although the most important variable in terms of predictive capacity was
 stem basal diameter, crown diameter significantly improved the models fit,
 followed by height. Four models were finally chosen, with the best model
 combining all these variables in the same equation (R2 = 0.930, RMSE =
 0.476). Selected models performed as well as established global biomass
 models. Including the individual bioform significantly improved the models
 fit. Main conclusions Basal diameter, crown diameter and height measures
 could be combined to provide robust AGB estimates of individual shrub
 species. Our study supplements well-established models developed for
 trees, allowing more accurate biomass estimation of multistemmed woody
 individuals. We further provide tools for a methodological standardization
 of individual biomass quantification in these species. We expect these
 results contribute to improve the quality of biomass estimates across
 ecosystems, but also to generate methodological consensus on field biomass
 assessments in shrubs.
description: Conti_ShrubAllometricDatabaseDatabase of individual allometric data (stem diameter, height, crown diameter) and aboveground ground biomass of shrub species compiled from existing literature. More details in the Metadata and Readme sheet in the file.