cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jq869
title: Data from: Quantifying temporal isolation: a modelling approach assessing the effect of flowering time differences on crop-to-weed pollen flow in sunflower

description: Flowering time divergence can be a crucial component of reproductive
 isolation between sympatric populations but few studies have quantified
 its actual contribution to the reduction of gene flow. In this study, we
 aimed at estimating pollen-mediated gene flow between cultivated sunflower
 and a weedy conspecific sunflower population growing in the same field,
 and at quantifying how it is affected by the weeds’ flowering time. For
 that purpose, we extended an existing mating model by including a temporal
 distance (i.e. flowering time difference between potential parents) effect
 on mating probabilities. Using phenological and genotypic data gathered on
 the crop and on a sample of the weedy population and its offspring, we
 estimated an average hybridization rate of approximately 10%. This rate
 varied strongly from 30% on average for weeds flowering at the crop
 flowering peak to 0% when the crop finished flowering, and was affected by
 the local density of weeds. Our result also suggested the occurrence of
 other factors limiting crop-to-weed gene flow. This level of gene flow and
 its dependence on flowering time might influence the evolutionary fate of
 weedy sunflower populations sympatric to their crop relative.
description: Genetic_dataGenotypic data for 13 microsatellites for the cultivated variety, a sample of the weedy population and its offspring; missing data coded as NAPhenotypic_dataThe excel file has both the data (one worksheet for the weedy population, one worksheet for phenological data of cultivated fields), and a worksheet explaining each of the columns/fields.
DOI: 10.5061/dryad.7tp7f
title: Data from: The impact of phylogenetic dating method on interpreting trait evolution: a case study of Cretaceous–Palaeogene eutherian body-size evolution

description: The fossil record of the earliest Cenozoic contains the first large-bodied
 placental mammals. Several evolutionary models have been invoked to
 explain the transition from small to large body sizes, but methods for
 determining evolutionary mode of trait change depend on input from tree
 topology and divergence dates. Different dating methods may therefore
 affect inference of evolutionary model. Here, we fit models of body mass
 evolution onto dated phylogenies of Cretaceous and Palaeogene mammals,
 comparing the effect of dating method on interpretation of evolutionary
 model. Among traditional palaeontological dating approaches, an
 Ornstein–Uhlenbeck model with high alpha parameters is recovered as
 best-fitting when minimum-age dating is used, while branch-sharing methods
 are highly sensitive to topology. Release or release–radiate models are
 preferred when Bayesian fossilized birth–death method is used, but when
 using stochastic cal3 dating of trees, a model of increased evolutionary
 rate without a release in constraint at the Cretaceous–Palaeogene boundary
 has highest support. These results demonstrate unambiguously that choice
 of dating method is critical for interpretation of continuous trait
 evolution, and that care must therefore be taken to consider these effects
 in macroevolutionary studies.
description: File S1 - Mass
 dataEstimated body masses
 for 177 genera of eutherian mammal, and sources of that
 data.File
 S1.xlsxSI
 MethodsAdditional description
 of methods used in Halliday and Goswami (2016), particularly with respect
 to model parameters.SI Bayes
 FileFile for submission to
 MrBayes including character matrix and MrBayes commands and
 parameters.File S5 -
 WeightsAkaike weights for all
 models for each tree for each set of constrained
 topologies.File
 S5.xlsxSI Dating
 ScriptScript used for dating
 phylogeny using cal3.
DOI: 10.5061/dryad.bg04r
title: Data from: The effect of terrain and female density on survival of neonatal white-tailed deer and mule deer fawns

description: Juvenile survival is a highly variable life-history trait that is critical
 to population growth. Antipredator tactics, including an animal's use
 of its physical and social environment, are critical to juvenile survival.
 Here, we tested the hypothesis that habitat and social characteristics
 influence coyote (Canis latrans) predation on white-tailed deer
 (Odocoileus virginianus) and mule deer (O. hemionus) fawns in similar ways
 during the neonatal period. This would contrast to winter when the habitat
 and social characteristics that provide the most safety for each species
 differ. We monitored seven cohorts of white-tailed deer and mule deer
 fawns at a grassland study site in Alberta, Canada. We used logistic
 regression and a model selection procedure to determine how habitat
 characteristics, climatic conditions, and female density influenced fawn
 survival during the first 8 weeks of life. Fawn survival improved after
 springs with productive vegetation (high integrated Normalized Difference
 Vegetation Index values). Fawns that used steeper terrain were more likely
 to survive. Fawns of both species had improved survival in years with
 higher densities of mule deer females, but not with higher densities of
 white-tailed deer females, as predicted if they benefit from protection by
 mule deer. Our results suggest that topographical variation is a critical
 resource for neonates of many ungulate species, even species like
 white-tailed deer that use more gentle terrain when older. Further, our
 results raise the possibility that neonatal white-tailed fawns may benefit
 from associating with mule deer females, which may contribute to the
 expansion of white-tailed deer into areas occupied by mule deer.
description: Lingle_Bonar_DryadDataDescriptionThis Microsoft Word file describes data columns used in two data files: File 1 filename = Fawn_Sightings_Raw_Data which has data for individual sightings of deer fawns. File 2 = Fawn_Summary_Data.xlsx has a summary row for each fawn.Fawn_Sightings_Raw_DataThis file has data from individual sightings of mule deer and white-tailed deer fawns. Data columns include identifying characteristics for fawns (species), habitat characteristics obtained using GIS, and climatic variables. Information about individual data columns is in the accompanying Microsoft Word file "Lingle_Bonar_DryadData Description.docx".Fawn_Summary_DataThis file has summary data for mule deer and white-tailed deer fawns. We used data from individual sightings (see data file "Fawn_Sightings_Raw_Data.xlsx") to obtain an average value for several habitat traits. This file also includes climatic data and data on female density. Information about individual data columns is in the accompanying Microsoft Word file "Lingle_Bonar_DryadData Description.docx".
DOI: 10.5061/dryad.nb259
title: Data from: Shifting fitness landscapes in response to altered environments

description: The role of adaptation in molecular evolution has been contentious for
 decades. Here, we shed light on the adaptive potential in Saccharomyces
 cerevisiae by presenting systematic fitness measurements for all possible
 point mutations in a region of Hsp90 under four environmental conditions.
 Under elevated salinity, we observe numerous beneficial mutations with
 growth advantages up to 7% relative to the wild type. All of these
 beneficial mutations were observed to be associated with high costs of
 adaptation. We thus demonstrate that an essential protein can harbor
 adaptive potential upon an environmental challenge, and report a
 remarkable fit of the data to a version of Fisher's geometric model
 that focuses on the fitness trade-offs between mutations in different
 environments.
description: Sequence Counts in
 30C-Salt30C-S.xlsxSequence Counts in 30C+salt30C+S.xlsxSequence Counts in 36C-Salt36C-S.xlsxSequence Counts in 36C+Salt36C+S.xlsx
DOI: 10.5061/dryad.bd6vs
title: Data from: A quantitative genetic approach to assess the evolutionary potential of a coastal marine fish to ocean acidification

description: Assessing the potential of marine organisms to adapt genetically to
 increasing oceanic CO2 levels requires proxies such as heritability of
 fitness-related traits under ocean acidification (OA). We applied a
 quantitative genetic method to derive the first heritability estimate of
 survival under elevated CO2 conditions in a metazoan. Specifically, we
 reared offspring, selected from a wild coastal fish population (Atlantic
 silverside, Menidia menidia), at high CO2 conditions (~2,300 μatm) from
 fertilization to 15 days post hatch, which significantly reduced survival
 compared to controls. Perished and surviving offspring were quantitatively
 sampled and genotyped along with their parents, using 8 polymorphic
 microsatellite loci, to reconstruct a parent-offspring pedigree and
 estimate variance components. Genetically related individuals were
 phenotypically more similar (i.e., survived similarly long at elevated CO2
 conditions) than unrelated individuals, which translated into a
 significantly non-zero heritability (0.20 ± 0.07). The contribution of
 maternal effects was surprisingly small (0.05 ± 0.04) and non-significant.
 Survival among replicates was positively correlated with genetic
 diversity, particularly with observed heterozygosity. We conclude that
 early life survival of M. menidia under high CO2 levels has a significant
 additive genetic component that could elicit an evolutionary response to
 OA, depending on the strength and direction of future selection.
description: Malvezzi etal EVA2015
 source data
DOI: 10.5061/dryad.d37p59vg
title: Data from: Late Paleozoic fusulinoidean gigantism driven by atmospheric hyperoxia

description: Atmospheric hyperoxia, with pO2 in excess of 30%, has long been
 hypothesized to account for late Paleozoic (360-250 million years ago)
 gigantism in numerous higher taxa. However, this hypothesis has not been
 evaluated statistically because comprehensive size data have not been
 compiled previously at sufficient temporal resolution to permit
 quantitative analysis. In this study, we test the hyperoxia-gigantism
 hypothesis by examining the fossil record of fusulinoidean foraminifers, a
 dramatic example of protistan gigantism with some individuals exceeding 10
 cm in length and exceeding their relatives by six orders of magnitude in
 biovolume. We assembled and examined comprehensive regional and global,
 species-level datasets containing 270 and 1823 species, respectively. A
 statistical model of size evolution forced by atmospheric pO2 is
 conclusively favored over alternative models based on random walks or a
 constant tendency toward size increase. Moreover, the ratios of volume to
 surface area in the largest fusulinoideans are consistent in magnitude and
 trend with a mathematical model based on oxygen transport limitation. We
 further validate the hyperoxia-gigantism model through an examination of
 modern foraminiferal species living along a measured gradient in oxygen
 concentration. These findings provide the first quantitative confirmation
 of a direct connection between Paleozoic gigantism and atmospheric
 hyperoxia.
description: payne_database_S1payne_database_S2payne_database_S3payne_database_S4
DOI: 10.5061/dryad.1gm13
title: Data from: Deflating trees: improving Bayesian branch-length estimates using informed priors

description: Prior distributions can have a strong effect on the results of Bayesian
 analyses. However, no general consensus exists for how priors should be
 set in all circumstances. Branch-length priors are of particular interest
 for phylogenetics, because they affect many parameters and biologically
 relevant inferences have been shown to be sensitive to the chosen prior
 distribution. Here, we explore the use of outside information to set
 informed branch-length priors and compare inferences from these informed
 analyses to those using default settings. For both the commonly used
 exponential and the newly proposed compound Dirichlet prior distributions,
 the incorporation of relevant outside information improves inferences for
 datasets that have produced problematic branch- and tree-length estimates
 under default settings. We suggest that informed priors are worthy of
 further exploration for phylogenetics.
description: EmpPrior.0.1.1_Dryad
DOI: 10.5061/dryad.052ng
title: Data from: The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae)

description: Background: Aciliini presently includes 69 species of medium-sized water
 beetles distributed on all continents except Antarctica. The pattern of
 distribution with several genera confined to different continents of the
 Southern Hemisphere raises the yet untested hypothesis of a Gondwana
 vicariance origin. The monophyly of Aciliini has been questioned with
 regard to Eretini, and there are competing hypotheses about the
 intergeneric relationship in the tribe. This study is the first
 comprehensive phylogenetic analysis focused on the tribe Aciliini and it
 is based on eight gene fragments. The aims of the present study are: 1) to
 test the monophyly of Aciliini and clarify the position of the tribe
 Eretini and to resolve the relationship among genera within Aciliini, 2)
 to calibrate the divergence times within Aciliini and test different
 biogeographical scenarios, especially if a Gondwana vicariance origin is
 plausible, and3) to evaluate the utility of the gene CAD (rudimentary) for
 phylogenetic analysis in Dytiscidae. Results: Our analyses confirm
 Aciliini as monophyletic and Eretini as the sister group, with high
 support. All six genera with multiple species are also supported as
 monophyletic. The origin of the tribe is firmly based on the Southern
 Hemisphere with the arrangement of Neotropical and Afrotropical taxa as
 the most basal clades suggesting a Gondwana vicariance origin. However,
 the uncertainty as to whether a fossil can be used as a stem- or
 crowngroup calibration point for Acilius influenced the result: as
 crowngroup calibration, the 95% HPD interval for the basal nodes included
 the geological age estimate for the Gondwana break-up, but as a stem group
 calibration the basal nodes were too young. Our study suggests CAD to be
 the most informative marker between 15 and 50 Ma. Notably, the 2000 bp CAD
 fragment analyzed alone fully resolved the tree with high support on all
 basal branches as well as for all genera as monophyletic. Conclusions: 1)
 Molecular data confirmed Aciliini as a monophyletic group. 2) Bayesian
 optimizations of the biogeographical history are consistent with an
 influence of Gondwana break-up history, but were dependent on the
 calibration method. 3) The evaluation using a method of phylogenetic
 signal, suggested Wnt and CAD as the most informative of our sampled genes
 per base pair.
description: Acillini_datasetnexus fileSpecimen data and NCBI accession numbersTable1.pdfTable 2. Primers. Primers used for amplification and sequencing were derived from several sourcesTable 2.pdfTable 3. Summary of the partitions and models. The best-fit partitioning scheme and model according to PartitionFinder.Table 3.pdf
DOI: 10.5061/dryad.70sr1
title: Data from: Speciation and the latitudinal diversity gradient: insights from the global distribution of endemic fish

description: The nearly universal pattern that species richness increases from the
 poles to the equator (the latitudinal diversity gradient [LDG]) has been
 of intense interest since its discovery by early natural-history
 explorers. Among the many hypotheses proposed to explain the LDG,
 latitudinal variation in (1) productivity, (2) time and area available for
 diversification, and (3) speciation and/or extinction rates have recently
 received the most attention. Because tropical regions are older and were
 formerly more widespread, these factors are often intertwined, hampering
 efforts to distinguish their relative contributions to the LDG. Here we
 examine the global distribution of endemic lake fishes to determine how
 lake age, area, and latitude each affect the probability of speciation and
 the extent of diversification occurring within a lake. We analyzed the
 distribution of endemic fishes worldwide (1,933 species and subspecies
 from 47 families in 2,746 lakes) and find that the probability of a lake
 containing an endemic species and the total number of endemics per lake
 increase with lake age and area and decrease with latitude. Moreover, the
 geographic locations of endemics in 34 of 41 families are found at lower
 latitudes than those of nonendemics. We propose that the greater
 diversification of fish at low latitudes may be driven in part by
 ecological opportunities promoted by tropical climates and by the
 coevolution of species interactions.
description: Global Lake Endemic Fish
 DataGlobal data on the
 single-lake endemic fish in lakes with surface areas greater than 50
 square kilometers. Included are geographic, physical, chemical information
 on each lake as well as the richness of endemic fish in each lake. The
 latitudinal centers of both endemic and non-endemic native fish in the
 lake data set are reported. References specific to each lake are
 associated with the unique ID number for each lake.AmNat 57165
 Data.xlsx
DOI: 10.5061/dryad.r18b12m
title: Data from: Functional capacity of kangaroo rat hindlimbs: adaptations for locomotor performance

description: Many cursorial and large hopping species are extremely efficient
 locomotors with various morphological adaptations believed to reduce
 mechanical demand and improve movement efficiency, including elongated
 distal limb segments. However, despite having elongated limbs, small
 hoppers such as desert kangaroo rats (Dipodomys deserti) are less
 efficient locomotors than their larger counterparts, which may be in part
 due to avoiding predators through explosive jumping movements. Despite
 potentially conflicting mechanical demands between the two movements,
 kangaroo rats are both excellent jumpers and attain high hopping speeds,
 likely due to a specialized hindlimb musculoskeletal morphology. This
 study combined experimental dissection data with a static analysis of
 muscle moment generating capacities using a newly developed
 musculoskeletal model to characterize kangaroo rat hindlimb
 musculoskeletal architecture and investigate how morphology has evolved to
 meet hopping and jumping mechanical demands. Hindlimb morphology appears
 biased towards generating constant moment arms over large joint ranges of
 motion in this species, which may balance competing requirements by
 reducing the need for posture and movement specific excitation patterns.
 The ankle extensors are a major exception to the strong positive
 relationship exhibited by most muscles between muscle architecture
 parameters (e.g. Lfibre) and joint moment arms. These muscles appear
 suited to meeting the high moments required for jumping: the biarticular
 nature of the ankle extensors is leveraged to reduce MTU strain and create
 a four-bar linkage that facilitates proximal force transfer. The kangaroo
 rat hindlimb provides an interesting case study for understanding how
 morphology balances the sometimes competing demands of hopping and
 jumping.
description: Kangaroo Rat
 Musculoskeletal Model (One Hindlimb)This zip file contains
 all of the data files required to view the kangaroo rat musculoskeletal
 model in SIMM (Musculographics, Inc).KratModel.zipJumping and Hopping Motion FilesThese files contain the joint angle histories for a hopping and jumping motion of a desert kangaroo rat. The files are meant to be used and viewed with the musculoskeletal model included in this data set.KRat_Motion_Files.zipMuscle Architecture DataThis is a Microsoft Excel file containing the muscle architecture data underlying the information presented in Table 2 of the paper.Compiled_Muscle_Architecture_Data.xlsx
DOI: 10.5061/dryad.vk26r
title: Data from: February precipitation in the wintering grounds of the lesser whitethroat, Sylvia curruca: is it a cue for migration onset?

description: Numerous studies report shifts in bird migration phenology, presumably
 owing to global warming. However, most studies focus on migration patterns
 in the Northern Hemisphere. In this study, we investigated associations
 between weather conditions in African wintering grounds of the lesser
 whitethroat, Sylvia curruca, and spring arrival time in Eilat, Israel.
 Using multivariate regression models, we analysed a 30-year dataset in
 order to examine correlations between median springtime arrival and 46
 climate variables of the wintering quarters. The model obtained exhibited
 a highly statistical fit, involving mean precipitation in February and
 March with negative effects and number of wet days during
 November–February. February precipitation levels were also the major
 factor associated with the interquartile range of arrival time.
 Interestingly and contrary to published results, annual or seasonal
 precipitation showed no correlation with spring arrival time, nor did
 temperature. Moreover, winter in this region falls into dry season with
 negligible rainfall quantities. Hence, it is unlikely that precipitation
 effect on habitat productivity is a driving force of migration, as
 suggested by other studies. Instead, we propose that precipitation in
 February acts as a cue for the birds, indicating the approach of spring
 and migration time.
description: SYLCUR data for
 manuscriptSpring arrival
 dataSylcur
 data for manuscript.xlsx
DOI: 10.5061/dryad.34v57
title: Data from: The influence of range-wide plant genetic variation on soil invertebrate communities

description: Plant genetic variation can have far-reaching effects on associated
 communities and ecosystems. Heritable variation in ecologically relevant
 plant traits is often non-randomly distributed across a species’ range and
 can exhibit geographic clines. In the event of range expansions and
 migration, previously unfamiliar genotypes may have large impacts on
 resident communities and ecosystems due to the introduction of novel and
 heritable phenotypic variation. Here we test the hypothesis that
 geographic origin of a focal plant genotype has effects on belowground
 invertebrate communities using a common garden field experiment. We
 sampled soil invertebrates from 103 Oenothera biennis genotypes, which
 were collected from across the species’ range and planted into a common
 garden field experiment at the northern range limit. We enumerated 24,000
 individuals from 190 morphospecies and found that the diversity,
 abundance, and composition of soil invertebrate communities varied greatly
 among plant genotypes. Despite strong effects of plant genotype, we found
 few genetic correlations between plant traits and soil invertebrate
 community variables. However, herbivore damage was strongly related to
 variation in the soil invertebrate community. Geographic origin of plant
 genotypes had at most a weak effect on belowground communities. We
 speculate that predicting the extended effects of population movement on
 associated communities will require detailed knowledge of the trait
 variation occurring within focal species across particular environmental
 gradients.
description: morphospecies_tableCounts of individual morphospecies in each soil invertebrate sample. Columns represent individual morphospecies and rows represent individual samples.genotype_traitsPhenotypic traits and geographic origin of each Oenothera biennis genotype.