cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9tb07
title: Data from: The evolutionary origins of modularity

description: A central biological question is how natural organisms are so evolvable
 (capable of quickly adapting to new environments). A key driver of
 evolvability is the widespread modularity of biological networks--their
 organization as functional, sparsely connected subunits--but there is no
 consensus regarding why modularity itself evolved. While most hypotheses
 assume indirect selection for evolvability, here we demonstrate that the
 ubiquitous, direct selection pressure to reduce the cost of connections
 between network nodes causes the emergence of modular networks.
 Computational evolution experiments with selection pressures to maximize
 network performance and minimize connection costs yield networks that are
 significantly more modular and more evolvable than control experiments
 that only select for performance. These results will catalyze research in
 numerous disciplines, including neuroscience, genetics and harnessing
 evolution for engineering purposes.
description: Data and script files
 for each figure of the paper Data generated using
 simulations with our software. See: https://members.loria.fr/jbmouret/src/modularity/sferes2_modularity.tgz   Video of networks from each treatment evolving across generations Illustration of the change across evolutionary time for both the PA and P&CC treatments. modularity.mp4
DOI: 10.5061/dryad.f9j15
title: Data from: The number of markers and samples needed for detecting bottlenecks under realistic scenarios, with and without recovery: a simulation-based study

description: Detecting bottlenecks is a common task in molecular ecology. While several
 bottleneck detection methods exist, evaluations of their power have
 focused only on severe bottlenecks (e.g. to Ne ~10). As a component of a
 recent review, Peery et al. () analysed the power of two approaches, the
 M-ratio and heterozygote excess tests, to detect moderate bottlenecks
 (e.g. to Ne ~100), which is realistic for many conservation situations. In
 this Comment, we address three important points relevant to but not
 considered in Peery et al. Under moderate bottleneck scenarios, we test
 the (i) relative advantage of sampling more markers vs. more individuals,
 (ii) potential power to detect the bottleneck when utilizing dozens of
 microsatellites (a realistic possibility for contemporary studies) and
 (iii) reduction in power when postbottleneck recovery has occurred. For
 the realistic situations examined, we show that (i) doubling the number of
 loci shows equal or better power than tripling the number of individuals,
 (ii) increasing the number of markers (up to 100) results in continued
 additive gains in power, and (iii) recovery after a moderate amount of
 time or gradual change in size reduces power, by up to one-half. Our
 results provide a practical supplement to Peery et al. and encourage the
 continued use of bottleneck detection methods in the genomic age, but also
 emphasize that the power under different sampling schemes should be
 estimated, using simulation modelling, as a routine component of molecular
 ecology studies.
description: Zip file containing
 parameter files, analysis scripts, and example output
 filesThis zip files contains
 4 parameter files for running in Simcoal, 4 example data files in Arlequin
 format, 2 analysis scripts written in java, a readme file, and 2 example
 output files which contain final results in terms of power at M-ratio and
 heterozygote excess test. These files, and how to run analysis, are
 described in the readme text file, which can be opened in
 notepad.Hoban_et_al_MolEcol_param_data_files.zip
DOI: 10.15468/dl.6dz7qs
title: Occurrence Download

description: A dataset containing 104 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-80.05053 -3.07221,-78.88087 -2.73031,-78.71892 -1.02081,-78.25106 0.09487,-78.01712 1.46247,-79.54668 1.53445,-80.96826 -0.40899,-81.23818 -2.29843,-80.35644 -3.03622,-80.05053 -3.07221))",
 "TaxonKey is Panthera onca"
 ]
}

 The dataset includes 104 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001591-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.2d5m8
title: Data from: Thermal sensitivity of immune function: evidence against a generalist-specialist tradeoff among endothermic and ectothermic vertebrates

description: Animal body temperature (T_body) varies over daily and annual cycles,
 affecting multiple aspects of biological performance in both endothermic
 and ectothermic animals. Yet a comprehensive comparison of thermal
 performance among animals varying in T_body (mean and variance) and heat
 production is lacking. Thus, we examined the thermal sensitivity of immune
 function (a crucial fitness determinant) in Vertebrata, a group
 encompassing species of varying thermal biology. Specifically, we
 investigated temperature-related variation in two innate immune
 performance metrics, hemagglutination and hemolysis, for 13 species across
 all seven major vertebrate clades. Agglutination and lysis were
 temperature dependent and were more strongly related to the thermal
 biology of species (e.g., mean T_body) than to the phylogenetic
 relatedness of species, although these relationships were complex and
 frequently surprising (e.g., heterotherms did not exhibit broader thermal
 performance curves than homeotherms). Agglutination and lysis performance
 were positively correlated within species, except in taxa that produce
 squalamine, a steroidal antibiotic that does not lyse red blood cells.
 Interestingly, we found the antithesis of a generalist-specialist
 trade-off: species with broader temperature ranges of immune performance
 also had higher peak performance levels. In sum, we have uncovered thermal
 sensitivity of immune performance in both endotherms and ectotherms,
 highlighting the role that temperature and life history play in immune
 function across Vertebrata.
description: Agglutination and lysis
 scores for all samplesThese are the scores
 that MWB and ZRS calculated for each sample at all
 temperatures.DryadData.xls
DOI: 10.5061/dryad.s6997
title: Data from: Structure and evolution of the sea star egg receptor for sperm bindin

description: Selection on coevolving sperm- and egg-recognition molecules is a potent
 engine of population divergence leading to reproductive isolation and
 speciation. The study of receptor–ligand pairs can reveal co-evolution of
 male- and female-expressed genes or differences between their evolution in
 response to selective factors such as sperm competition and sexual
 conflict. Phylogeographical studies of these patterns have been limited by
 targeted gene methods that favour short protein-coding sequences
 amplifiable by PCR. Here, I use high-throughput transcriptomic methods to
 characterize the structure and divergence of full-length coding sequences
 for the gene encoding the protein component of a large complex egg surface
 glycopeptide receptor for the sperm acrosomal protein bindin from the sea
 star Patiria miniata. I used a simple but effective method for resolving
 nucleotide polymorphisms into haplotypes for phylogeny-based analyses of
 selection. The protein domain organization of sea star egg bindin receptor
 (EBR1) was similar to sea urchins and included a pair of
 protein-recognition domains plus a series of tandem repeat domains of two
 types. Two populations separated by a well-characterized phylogeographical
 break included lineages of EBR1 alleles under positive selection at
 several codons (similar to selection on sperm bindin in the same
 populations). However, these populations shared the same alleles that were
 under selection for amino acid differences at multiple codons (unlike the
 pattern of selection for population divergence in sperm bindin). The
 significance of positively selected EBR1 domains and alleles could be
 tested in functional analyses of fertilization rates associated with EBR1
 (and bindin) polymorphisms.
description: Ovary contig assemblies
 from RNASeq (transcriptomes)Patiria_miniata_ovary_transcriptomes.zip
DOI: 10.5061/dryad.9gf10
title: Data from: A genomic island linked to ecotype divergence in Atlantic cod

description: The genomic architecture underlying ecological divergence and ecological
 speciation with gene flow is still largely unknown for most organisms. One
 central question is whether divergence is genome-wide or localized in
 “genomic mosaics” during early stages when gene flow is still pronounced.
 Empirical work has so far been limited, and the relative impacts of gene
 flow and natural selection on genomic patterns have not been fully
 explored. Here, we use ecotypes of Atlantic cod to investigate genomic
 patterns of diversity and population differentiation in a natural system
 characterized by high gene flow and large effective population sizes,
 properties which theoretically could restrict divergence in local genomic
 regions. We identify a genomic region of strong population
 differentiation, extending over approximately 20 cM, between pairs of
 migratory and stationary ecotypes examined at two different localities.
 Furthermore, the region is characterized by markedly reduced levels of
 genetic diversity in migratory ecotype samples. The results highlight the
 genomic region, or “genomic island”, as potentially associated with
 ecological divergence and suggest a selective sweep involved in ecological
 divergence. Finally, we also confirm earlier findings of localized genomic
 differentiation in three other linkage groups associated with divergence
 among eastern Atlantic populations. Thus, although underlying mechanisms
 are still unknown, the results suggest that “genomic mosaics” of
 differentiation may even be found under high levels of gene flow, and that
 marine fishes may provide insightful model systems for studying and
 identifying initial targets of selection during ecological divergence.
description: Individual genotype
 dataTab-separated matrix of
 individual genotypes with individuals in rows and loci in columns. Each
 individual is coded as “population_year_individual”. NA: missing
 data.Atlantic_cod_genotypes.txt
DOI: 10.5061/dryad.0hv88
title: Data from: Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets

description: DNA barcoding-type studies assemble single-locus data from large samples
 of individuals and species, and have provided new kinds of data for
 evolutionary surveys of diversity. An important goal of many such studies
 is to delimit evolutionarily significant species units, especially in
 biodiversity surveys from environmental DNA samples. The Generalized Mixed
 Yule Coalescent (GMYC) method is a likelihood method for delimiting
 species by fitting within- and between-species branching models to
 reconstructed gene trees. Although the method has been widely used, it has
 not previously been described in detail or evaluated fully against
 simulations of alternative scenarios of true patterns of population
 variation and divergence between species. Here, we present important
 reformulations to the GMYC method as originally specified, and demonstrate
 its robustness to a range of departures from its simplifying assumptions.
 The main factor affecting the accuracy of delimitation is the mean
 population size of species relative to divergence times between them.
 Other departures from the model assumptions, such as varying population
 sizes among species, alternative scenarios for speciation and extinction,
 and population growth or subdivision within species, have relatively
 smaller effects. Our simulations demonstrate that support measures derived
 from the likelihood function provide a robust indication of when the model
 performs well and when it leads to inaccurate delimitations. Finally, the
 so-called single-threshold version of the method outperforms the
 multiple-threshold version of the method on simulated data: we argue that
 this might represent a fundamental limit due to the nature of evidence
 used to delimit species in this approach. Together with other studies
 comparing its performance relative to other methods, our findings support
 the robustness of GMYC as a tool for delimiting species when only
 single-locus information is available.
description: Fujisawa.SupplementaryTable&FiguresSupplementary table and figures for Fujisawa and Barraclough 2013Fujisawa.RcodeZipped file containing the R code for simulations and analyses reported in Fujisawa and Barraclough 2013tigerbeetle_treesTiger beetle trees from Pons et al. 2006 and 2011 used as examples in Fujisawa and Barraclough 2013Fujisawa.SimulationAtoH.outputsSimulated trees used in Fujisawa and Barraclough 2013
DOI: 10.5061/dryad.fn50c
title: Data from: Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in Campanulid angiosperms

description: The growth of phylogenetic trees in scope and in size is promising from
 the standpoint of understanding a wide variety of evolutionary patterns
 and processes. With trees comprised of larger, older, and globally
 distributed clades, it is likely that the lability of a binary character
 will differ significantly among lineages, which could lead to errors in
 estimating transition rates and the associated inference of ancestral
 states. Here we develop and implement a new method for identifying
 different rates of evolution in a binary character along different
 branches of a phylogeny. We illustrate this approach by exploring the
 evolution of growth habit in Campanulidae, a flowering plant clade
 containing some 35,000 species. The distribution of woody versus
 herbaceous species calls into question the use of traditional models of
 binary character evolution. The recognition and accommodation of changes
 in the rate of growth form evolution in different lineages demonstrates,
 for the first time, a robust picture of growth form evolution across a
 very large, very old, and very widespread flowering plant clade.
description: USYS-2012-190.tarAlignment and a snapshot version of our corHMM software package for R
DOI: 10.5061/dryad.rp187
title: Data from: Functional genomic and phenotypic responses to desiccation in natural populations of a desert drosophilid

description: We used whole transcriptome microarrays to assess changes in gene
 expression and monitored mortality rates and epicuticular hydrocarbons
 (CHCs) in response to desiccation stress in four natural populations of
 Drosophila mojavensis from Baja California and mainland Mexico.
 Desiccation had the greatest effect on gene expression, followed by
 biogeographical variation at regional and population levels. Genes
 involved in environmental sensing and cuticular structure were
 up-regulated in dry conditions, while genes involved in transcription
 itself were down-regulated. Flies from Baja California had higher
 expression of reproductive and mitochondrial genes, suggesting that these
 populations have greater fecundity and higher metabolic rates. Host plant
 differences had a surprisingly minor effect on the transcriptome. In most
 cases, desiccation-caused mortality was greater in flies reared on
 fermenting cactus tissues than laboratory media. Water content of adult
 females and males was significantly different, and was lower in Baja
 California males. Different groups of CHCs simultaneously increased and
 decreased in amounts due to desiccation exposure of 9 and 18 hr and were
 population-specific and dependent on larval rearing substrates. Overall,
 we observed that changes in gene expression involved a coordinated
 response of metabolic, behavioral, and cuticular genes. Together with
 differential expression of cuticular hydrocarbons, this study revealed
 some of the mechanisms that have allowed D. mojavensis to exploit its
 harsh desert conditions. Certainly, for D. mojavensis that uses different
 host plants, population-level understanding of responses to stressors
 associated with future climate change in desert regions must be evaluated
 across geographical and local ecological scales.
description: Body_mass_data ME
 2013Changes in body mass in
 D. mojavensis after oven drying at 50 CCHC data ME
 2013Cuticular hydrocarbon
 amounts for D. mojavensis after 0, 9, and 18 hoiurs of
 desiccationMortality Data ME
 2013Mortality of adult D.
 mojavensis during 0, 9, and 18 hours of desiccationViability data ME
 2013Egg to adult viability
 for cactus-reared populations of D. mojavensis
DOI: 10.18715/ipgp.2025.m7ok4rfm
title: Swarm Bravo ASM-V data version 06XX

description: This dataset consists of version 06XX 1 Hz (bandwidth 0-0.4 Hz) self-calibrated experimental vector data acquired by the ASM magnetometer on board satellite Bravo of the ESA Swarm mission. These data are produced by IPGP when the ASM instrument is set in its “vector mode”, which is the mode in which this instrument has been operated for the most part of the mission, except at times (typically during one week sessions per month) when the instruments are set in their alternative "scalar burst mode". The dataset is organized in annual zipped folders (one per year since 2013), each folder containing all available daily files for the year of interest. The dataset also comes with a SW-ASMV-DD-IPGP-0007_ASMV_Experimental_L1B_Product_Definition Revision 1A file, providing details of the data definition and format of the daily files.
DOI: 10.5061/dryad.04q24
title: Data from: The evolution of mammal body sizes: responses to Cenozoic climate change in North American mammals

description: Explanations for the evolution of body size in mammals have remained
 surprisingly elusive despite the central importance of body size in
 evolutionary biology. Here, we present a model which argues that the body
 sizes of Nearctic mammals were moulded by Cenozoic climate and vegetation
 changes. Following the early Eocene Climate Optimum, forests retreated and
 gave way to open woodland and savannah landscapes, followed later by
 grasslands. Many herbivores that radiated in these new landscapes
 underwent a switch from browsing to grazing associated with increased
 unguligrade cursoriality and body size, the latter driven by the
 energetics and constraints of cellulose digestion (fermentation).
 Carnivores also increased in size and digitigrade, cursorial capacity to
 occupy a size distribution allowing the capture of prey of the widest
 range of body sizes. With the emergence of larger, faster carnivores,
 plantigrade mammals were constrained from evolving to large body sizes and
 most remained smaller than 1 kg throughout the middle Cenozoic. We find no
 consistent support for either Cope's Rule or Bergmann's Rule in
 plantigrade mammals, the largest locomotor guild (n = 1186, 59% of species
 in the database). Some cold-specialist plantigrade mammals, such as
 beavers and marmots, showed dramatic increases in body mass following the
 Miocene Climate Optimum which may, however, be partially explained by
 Bergmann's rule. This study reemphasizes the necessity of considering
 the evolutionary history and resultant form and function of mammalian
 morphotypes when attempting to understand contemporary mammalian body size
 distributions.
description: Body size JEB
 Supplementary electronic information rev 2
DOI: 10.5061/dryad.h3t86
title: Data from: Evolution of resistance to a multiple-herbavore community: genetic correlations, diffuse coevolution, and constraints on the plant's response to selection

description: Although plants are generally attacked by a community of several species
 of herbivores, relatively little is known about the strength of natural
 selection for resistance in multiple-herbivore communities—particularly
 how the strength of selection differs among herbivores that feed on
 different plant organs or how strongly genetic correlations in resistance
 affect the evolutionary responses of the plant. Here, we report on a field
 study measuring natural selection for resistance in a diverse community of
 herbivores of Solanum carolinense. Using linear phenotypic-selection
 analyses, we found that directional selection acted to increase resistance
 to seven species. Selection was strongest to increase resistance to fruit
 feeders, followed by flower feeders, then leaf feeders. Selection favored
 a decrease in resistance to a stem borer. Bootstrapping analyses showed
 that the plant population contained significant genetic variation for each
 of 14 measured resistance traits and significant covariances in one-third
 of the pairwise combinations of resistance traits. These genetic
 covariances reduced the plant's overall predicted evolutionary
 response for resistance against the herbivore community by about 60%.
 Diffuse (co)evolution was widespread in this community, and the diffuse
 interactions had an overwhelmingly constraining (rather than facilitative)
 effect on the plant's evolution of resistance.
description: Resistance and Damage
 MeasurementsThis is an Excel file
 with resistance/damage measurements for herbivores and fitness estimates
 for host plants. The data were used for selection
 analyses.Phenotypes - no missing
 data.xls
DOI: 10.5061/dryad.t8q3k
title: Data from: Adaptation of diploid and tetraploid Chamerion angustifolium to elevation but not local environment

description: Polyploid organisms often have different geographic ranges than their
 diploid relatives. However, it is unclear whether this divergence is
 maintained by adaptation or results from historical differences in
 colonization. Here we conducted a reciprocal transplant experiment with
 diploid and autotetraploid Chamerion angustifolium to test for adaptation
 at the ploidy and population level. In the Rocky Mountains, pure diploid
 populations occur at high elevations and pure autotetraploid populations
 occur at low elevations with mixed-ploidy populations between. We planted
 3134 seedlings in 2004 and 3890 juveniles (bolting) in 2005 among nine
 plots, three in each of the diploid, mixed-ploidy and tetraploid zones,
 and monitored survival until 2008. For both seedlings and juvenile plants,
 elevation significantly influenced survival. The juvenile plants also
 showed a significant ploidy by elevation interaction, indicating that
 diploids and tetraploids survived best at their native elevations. In
 contrast, we found no evidence of local adaptation to plot within
 elevation. This suggests that the current distribution of diploids and
 tetraploids across elevations is the result of adaptation and that genome
 duplication may have facilitated the invasion of lower elevation habitats
 by limiting the movement of maladapted alleles from diploid populations at
 higher elevations.
description: Martin and Husband
 Diameter Height DataThis file contains
 diameter measurements for seedlings of Chamerion angustifolium, grown from
 field collected seed, reared in the green house and planted into 9 plots
 in the Canadian Rocky Mountains. (See paper for details.) Read me on first
 sheet of work book.Martin and Husband
 Survival DataThis data represents
 information on the survival of Chamerion angustifolium seedlings (2004)
 and juveniles (2005) transplanted in to 9 plots in the Canadian Rocky
 Mountains. See paper for details. Read mes included in
 workbook.Martin and Husband
 Vegetation SurveyData collected during
 vegetation survey conducted in 2005 at the 9 plots involved in the
 experiment in the Canadian Rocky Mountains. (Read me
 included.)Martin and Husband
 Weather DataThis file contains daily
 meteorological data downloaded from Environment Canada
 (http://climate.weatheroffice.ec.gc.ca/climateData/canada_e.html) as csvs
 covering 1 year of data each and amalgamated. Specifically, the available
 data was downloaded for 9 stations in the Canadian Rocky Mountains for the
 period from 1997 to 2007. Station information and read me included in the
 data file.