cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70rxwdbvq
title: Becoming creatures of habit: among- and within-individual variation in nesting behavior shifts with age

description: The quantification of repeatability has enabled behavioral and
 evolutionary ecologists to assess the heritable potential of traits. For
 behavioral traits that vary across life, age-related variation should be
 accounted for to prevent biasing the microevolutionary estimate of
 interest. Moreover, to gain a mechanistic understanding of ontogenetic
 variation in behavior, among- and within-individual variance should be
 quantified across life. We leveraged a 30-year study of painted turtles
 (Chrysemys picta) to assess how age contributes to variation in the
 repeatability of nesting behaviors. We found that four components of
 nesting behavior were repeatable, and that accounting for age increased
 the repeatability estimate for maternal choice of canopy cover over nests.
 We detected canalization (diminished within-individual variance with age)
 of canopy cover choice in a reduced dataset despite no shift in
 repeatability. Additionally, random regression analysis revealed that
 females became more divergent from each other in their choice of canopy
 cover with age. Thus, properly modeling age-related variance should more
 precisely estimate heritable potential, and assessing among- and
 within-individual variance components in addition to repeatability will
 offer a more mechanistic understanding of behavioral variation across age.
description: We collected data on the nesting ecology of <i>C.
 picta</i> from 1989–2018 at the Thomson Causeway Recreation Area
 along the Mississippi River in northwest Illinois. We created separate
 datasets for each dependent variable so that females that remained in each
 dataset had &gt;1 observation for that variable for analysis. Please
 see the Methods section in the manuscript for more details.  
description: Date = date of the observation Year = year of
 the observation YearNestNumber = year + nest number,
 which is a unique identifier for each nest ID = female
 identification code for field ID Nest = nest ID which
 restarts at one each year PL = plastron
 length SoilType = 0 represents nests that were entirely
 loam; 1 represents nests that contained some gravel
 TrueID = female identification code that has been cleaned back on
 campus (used for analysis over ID) Observed = 1 for
 every time a female was observed Frequency = the number
 of observations a female laid a nest and that dependent variable was
 recorded Age = age of the female at the time of that
 observation ConvertedCanopyOpen = overstory canopy
 cover from hemiphotos and converted densiometer measures 
 CanopyOpenness = overstory canopy cover from hemiphotos
 only DTW = distance to water
DOI: 10.5061/dryad.37pvmcvhg
title: Parasite intensity and the evolution of migratory behavior

description: Migration can allow individuals to escape parasite infection, which can
 lead to a lower infection probability (prevalence) in a population and/or
 fewer parasites per individual (intensity). Since individuals with more
 parasites often have lower survival and/or fecundity, infection intensity
 shapes the life-history tradeoffs determining when migration is favored as
 a strategy to escape infection. Yet, most theory relies on
 susceptible-infected (SI) modeling frameworks, defining individuals as
 either healthy or infected, ignoring details of infection intensity. Here
 we develop a novel modeling approach that captures infection intensity as
 a spectrum, and ask under what conditions migration evolves as function of
 how infection intensity changes over time. We show that the relative
 timescales of migration and infection accumulation determine when
 migration is favored. We also find that population-level heterogeneity in
 infection intensity can lead to partial migration, where less-infected
 individuals migrate while more infected individuals remain resident. Our
 model is one of the first to consider how infection intensity can lead to
 migration. Our results frame migratory escape in light of infection
 intensity, rather than prevalence, thus demonstrating that decreased
 infection intensity should be considered a benefit of migration, alongside
 other typical drivers of migration.
description: README.txt: This text file contains readme and notes for all
 files.<br>
DOI: 10.5061/dryad.kprr4xh2z
title: Divergent evolution of mutation rates and biases in the long-term evolution experiment with Escherichia coli

description: Abstract All organisms encode enzymes that replicate, maintain, pack,
 recombine, and repair their genetic material. For this reason, mutation
 rates and biases also evolve by mutation, variation, and natural
 selection. By examining metagenomic time series of the Lenski long-term
 evolution experiment (LTEE) with Escherichia coli (Good, et al. 2017), we
 find that local mutation rate variation has evolved during the LTEE. Each
 LTEE population has evolved idiosyncratic differences in their rates of
 point mutations, indels, and mobile element insertions, due to the
 fixation of various hypermutator and antimutator alleles. One LTEE
 population, called Ara+3, shows a strong, symmetric wave pattern in its
 density of point mutations, radiating from the origin of replication. This
 pattern is largely missing from the other LTEE populations, most of which
 evolved missense, indel, or structural mutations in topA, fis, and dusB—
 loci that all affect DNA topology. The distribution of mutations in those
 genes over time suggests epistasis and historical contingency in the
 evolution of DNA topology, which may have in turn affected local mutation
 rates. Overall, the replicate populations of the LTEE have largely
 diverged in their mutation rates and biases, even though they have adapted
 to identical abiotic conditions.
DOI: 10.5061/dryad.c59zw3r58
title: Ecological resilience and resistance to extreme weather events - review data

description: Extreme weather events (EWEs) are expected to increase in stochasticity,
 frequency, and intensity due to climate change. Documented effects of
 EWEs, such as droughts, hurricanes, and temperature extremes, range from
 shifting community stable states to species extirpations. To date, little
 attention has been paid to how populations resist and/or recover from EWEs
 through compensatory (behavioural, demographic or physiological)
 mechanisms; limiting the capacity to predict species responses to future
 changes in EWEs. Here, we systematically reviewed the global variation in
 species’ demographic responses, resistance to, and recovery from EWEs
 across weather types, species, and biogeographic regions. Through a
 literature review and meta-analysis, we tested the prediction that
 population abundance and probability of persistence will decrease in
 populations after an EWE and how compensation affects that probability.
 Across 524 species population responses to EWEs reviewed (27 articles), we
 noted large variation in responses, such that, on average, the effect of
 EWEs on population demographics was not negative as predicted. The
 majority of species populations (80.4%) demonstrated compensatory
 mechanisms during events to reduce their deleterious effects. However, for
 populations that were negatively impacted, the demographic consequences
 were severe. Nearly 20% of the populations monitored experienced declines
 of over 50% after an EWE, and 6.8% of populations were extirpated.
 Population declines were reflected in a reduction in survival. Further,
 resilience was not common, as 80.0% of populations that declined did not
 recover to before EWE levels while monitored. However, average monitoring
 time was only two years with over a quarter of studies tracking recovery
 for less than the study species generation time. We conclude that EWEs
 have positive and negative impacts on species demography, and this varies
 by taxa. Species population recovery over short time intervals is rare,
 but long-term studies are required to accurately assess species resilience
 to current and future events.
description: We queried the Web of Science on
 October 16, 2017 using the search terms “extreme weather event” and
 “species” and on January 21, 2018 for search terms “extreme weather event”
 and “populations”. Additionally, we queried Scopus on January 21, 2018
 using the same search terms. Whereas we did not conduct an exhaustive
 search, we consider our search terms to be unbiased and representative of
 the literature. These searches resulted in 336 peer-reviewed, scientific
 articles between 1992 and 2017.
description: The 'Abund_add' file is a subset of the main data,
 subset to those records with EWE ~abundance effects then joined to body
 size and female age of maturity metrics.
DOI: 10.5061/dryad.fn2z34trv
title: Data from: Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models

description: Ensembling combines the predictions made by individual component base
 models with the goal of achieving a predictive accuracy that is better
 than that of any one of the constituent member models. Diversity
 among the base models in terms of predictions is a crucial criterion in
 ensembling. However, there are practical instances when the
 available base models produce highly correlated predictions, because they
 may have been developed within the same research group or may have been
 built from the same underlying algorithm. We investigated, via a
 case study on Fusarium head blight (FHB) on wheat in the U.S., whether
 ensembles of simple yet highly correlated models for predicting the risk
 of FHB epidemics, all generated from logistic regression, provided any
 benefit to predictive performance, despite relatively low levels of base
 model diversity.  Three ensembling methods were explored: soft
 voting, weighted averaging of smaller subsets of the base models, and
 penalized regression as a stacking algorithm. Soft voting and
 weighted model averages were generally better at classification than the
 base models, though not universally so. The performances of
 stacked regression were superior to those of the other two ensembling
 methods we analyzed in this study. Ensembling simple yet
 correlated models is computationally feasible and is therefore worth
 pursuing for models of epidemic risk.
DOI: 10.5061/dryad.g1jwstqpb
title: Invasive earthworms reduce chemical defense and increase herbivory and pathogen infection in native trees

description: Recent research shows that earthworms can alter defense traits of plants
 against herbivores and pathogens by affecting soil biochemistry. Yet, the
 effects of invasive earthworms on defense traits of native plants from
 previously earthworm-free ecosystems as well as the consequences for
 multitrophic interactions are virtually unknown. Here we use a combination
 of an observational study and a complementary experimental study to
 investigate the effects of invasive earthworms on leaf defense traits,
 herbivore damage, and pathogen infection in two poplar tree species
 (Populus balsamifera and Populus tremuloides) native to North American
 boreal forests. Our observational study showed that earthworm invasion was
 associated with enhanced leaf herbivory in saplings of both tree species.
 However, we only detected significant shifts in the concentration of
 chemical defense compounds in response to earthworm invasion for P.
 balsamifera. Specifically, leaf phenolic concentrations, including
 salicinoids and catechin, were lower in P. balsamifera from
 earthworm-invaded sites. Our experimental study confirmed an
 earthworm-induced reduction in leaf defense levels in P. balsamifera for
 one of the defense compounds, tremulacin. The experimental study
 additionally showed that invasive earthworms reduced leaf dry matter
 content, potentially increasing leaf palatability, and enhanced
 susceptibility of trees to infection by a fungal pathogen, but not to
 aphids, in the same tree species. Synthesis. Our results show that
 invasive earthworms can decrease the concentrations of some chemical
 defense compounds in P. balsamifera, which could make them susceptible to
 leaf-chewing insects. Such potential impacts of invasive earthworms are
 likely to have implications for tree survival and competition, native tree
 biodiversity, and ecosystem functioning.
DOI: 10.5061/dryad.2bvq83bnp
title: Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks

description: Pollinator sharing can have negative consequences for plant fitness with
 the arrival of foreign (i.e. heterospecific) pollen, yet responses are
 often variable among species.  Plant traits and relatedness of
 donor and recipient species have been suggested to drive the variations in
 plant fitness, but how they shape the structure of pollen competition
 networks has been overlooked at the community level. To understand the
 importance of reproductive traits and relatedness on the impacts of
 heterospecific pollen we conducted a controlled glasshouse experiment with
 an artificial co-flowering community. We performed 1800 reciprocal crosses
 by experimentally transferring 50% and 100% foreign pollen among 10
 species belonging to three different plant families. We found a
 significant reduction in seed set with 50% foreign pollen for 67% of the
 crosses driven largely by recipient traits and the interaction between
 recipient-donor traits under specific circumstances of trait-matching. In
 general, species with shorter styles, smaller stigmas and lower
 pollen:ovule ratios were more impacted by foreign pollen. These traits and
 their differences among species led to a hierarchical (or transitive)
 structure of pollen competition with clear winners and losers. However,
 phylogenetic distance among recipient and donor species did not explain
 the effects. Synthesis: Our study shows that specific traits and trait
 combinations between donor and recipient species are important in
 determining fitness outcomes with heterospecific pollen deposition.
 Moreover, the differences in traits between species lead to a competitive
 structure with clear “winners” or “losers” species. The results of this
 study indicate the need to shift from pairwise to community level
 interactions to elucidate the mechanisms underlying foreign pollen impacts
 upon plant reproductive fitness.
DOI: 10.5061/dryad.bvq83bk6r
title: Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis

description: Information on demographic, genetic, and environmental parameters of wild
 and captive animal populations has proven to be crucial to conservation
 programs and strategies. Genetic approaches in conservation programs of
 Brazilian snakes remain scarce despite their importance for critically
 endangered species, such as Bothrops insularis, the golden lancehead,
 which is endemic to Ilha da Queimada Grande, coast of São Paulo State,
 Brazil. This study aims to (i) characterize the genetic diversity of
 ex-situ and in-situ populations of B. insularis using heterologous
 microsatellites; (ii) investigate genetic structure among and within these
 populations; and (iii) provide data for the conservation program of the
 species. Twelve informative microsatellites obtained from three species of
 the B. neuwiedi group were used to access genetic diversity indexes of
 ex-situ and in-situ populations. Low-to-medium genetic diversity
 parameters were found. Both populations showed low — albeit significant —
 values of system of mating inbreeding coefficient, whereas only the
 in-situ population showed a significant value of pedigree inbreeding
 coefficient. Significant values of genetic differentiation indexes suggest
 a small differentiation between the two populations. Discriminant analysis
 of principal components (DAPC) recovered five clusters. No geographic
 relationship was found in the island, suggesting the occurrence of gene
 flow. Also, our data allowed the establishment of six preferential
 breeding couples, aiming to minimize inbreeding and elucidate uncertain
 parental relationships in the captive population. In a conservation
 perspective, continuous monitoring of both populations is demanded: it
 involves the incorporation of new individuals from the island into the
 captive population to avoid inbreeding and to achieve the recommended
 allelic similarity between the two populations. At last, we recommend that
 the genetic data support researches as a base to maintain a viable and
 healthy captive population, highly genetically similar to the in-situ one,
 which is crucial for considering a reintroduction process into the island.
description: Dataset description and
 information: (i)
 Geographic information of the samplings: Supplementary Material
 1;  (ii) List of the 33 microsatellites
 tested: Supplementary Material 2; 
 (iii) R-script used in the
 analysis: Supplementary Material 3; 
 (iv) Simplified scheme of the
 methodology: Supplementary Material 4; 
 (v) Genotype data obtained from PCR
 amplification of the 12 loci for the 80 representative samples used
 herein: Supplementary Material 5; 
 (vi) Table of the kinship value
 obtained for each pair of individuals that was alive (<i>n</i>
 = 34): Supplementary Material 6;  (vii)
 Pedigree from the <i>ex-situ</i> population of <i>B.
 insularis </i>housed at the Laboratório de Ecologia e Evolução,
 Instituto Butantan, São Paulo state, Brazil: Supplementary Material
 7.
DOI: 10.5061/dryad.4tmpg4f7k
title: Parallel responses of species diversity and functional diversity to changes in patch size are driven by distinct processes

description: 1. Do species and functional trait diversity respond similarly to
 deterministic and random processes? Theory predicts that the contributions
 of random and deterministic processes to species diversity depend on patch
 size. Smaller patches are more strongly influenced by random sampling
 effects, by having fewer individuals, as well as ecological drift, which
 propagates the effects of small samples through stochastic birth and death
 processes. These random processes decrease species richness and increase
 compositional differences among small patches. Larger patches are
 predicted to be more deterministically assembled, with greater species
 richness and greater predictability of composition for a particular
 environment. The consequences of patch size for the diversity of
 functional traits, however, are poorly understood. Species diversity may
 be a poor proxy for functional diversity due to trait redundancies among
 species, making it unclear how random and deterministic processes alter
 functional diversity within patches of differing size, and how these
 differences scale up to determine among-patch functional diversity. 2. We
 report a novel experimental study of species and functional diversity
 across spatial scales. We manipulated patch area in an experimental plant
 metacommunity and used a nested sampling design to distinguish the effects
 of deterministic processes, ecological drift, and sampling effects on
 species and functional trait diversity. 3. Our study revealed a pervasive
 influence of ecological drift and sampling effects on diversity, with
 distinct influences on functional traits and species composition within
 and among patches. Overall, drift and sampling effects caused a 2- to
 3-fold decrease in the importance of deterministic processes in small
 fragments. Species and functional diversity showed similar patterns with
 patch size: larger patches had greater within-patch (alpha) diversity and
 lower among-patch (beta) diversity, consistent with theory. However, our
 nested sampling design revealed that sampling effects (i.e. the size of
 the sample area) largely determined alpha species diversity and beta
 functional diversity, while ecological drift had a stronger influence on
 alpha functional diversity and beta species diversity. 4. Synthesis. The
 compositions of species and functional diversity in a community are
 influenced by distinct processes, resulting in divergent spatial scaling
 of species and their traits within patches and across landscapes.
DOI: 10.5281/zenodo.18395849
title: 3D U-Net training dataset samples
DOI: 10.5281/zenodo.18395850
title: 3D U-Net training dataset samples
DOI: 10.5061/dryad.x0k6djhgz
title: Community level phylogenetic diversity does not differ between rare and common lineages across tallgrass prairies in northern Great Plains

description: In some cases, rare lineages provide resistance to invasions, serve as
 keystone species, and contribute unique functional or phylogenetic
 diversity to their communities. In other cases, rare species may be
 functionally redundant with common species and do not significantly
 contribute to phylogenetic diversity. How rare and common species coexist
 and contribute to local species pools may depend upon attributes of their
 communities and remains an open question in ecology. Niche differentiation
 has served as an explanation for species coexistence, and phylogenetic
 relatedness provides a means to approximate how ecologically similar
 species are to each other. To explore the contribution of rare species to
 community phylogenetic diversity, we sampled twenty-one plant
 communities  across the Prairie Coteau ecoregion, home
 of the largest tracts of untilled northern tallgrass prairie and of high
 conservation concern. We used breakpoint analysis through iterative
 addition of less abundant species to the phylogenetic tree for each
 community. We also assessed the phylogenetic signal of abundance classes
 using Blomberg’s K statistic and calculated the phylogenetic similarity
 between rare and common species using a phylogenetic beta diversity metric
 (Dnn). To estimate the phylogenetic structuring of these prairie
 communities, we calculated two common metrics that capture evolutionary
 relatedness between species (MPD, and MNTD) and examine the correlation
 between these metrics and species richness. Overall, we found rare species
 do not contribute higher levels of phylogenetic diversity than more common
 species in the Prairie Coteau ecoregion. Eight of 21 communities had
 significant breakpoints, where the addition of a less common species
 resulted in a shift in phylogenetic diversity, with only four communities
 having an increasing trend for the rarest species. Phylogenetic signal for
 abundance was low and unsignificant across 18 communities, while four
 sites did show significant low phylogenetic signal. We additionally found
 our communities had lower phylogenetic diversity than expected from the
 regional species pool. Finally, we found weak to no correlation when using
 MPD and MNTD. Our results indicate niche differentiation does not explain
 rare species persistence in tallgrass prairies. We found species were more
 closely related than expected from random community assembly, suggesting
 high functional redundancy within this system. This is promising for the
 long term viability of this ecosystem, but only insofar as enough species
 remain in the system to create redundancy. With ongoing biodiversity loss,
 it is essential we understand the role rare species play in their
 communities. Phylogenetic diversity could be an important tool for
 researchers and managers to utilize for conservation of critically
 threatened systems such as tallgrass prairies.
description: R is required to use code.