cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t66c7
title: Data from: Invasion genetics of a human commensal rodent: the black rat Rattus rattus in Madagascar

description: Studies focusing on geographical genetic patterns of commensal species and
 on human history complement each other, and provide proxies to trace
 common colonisation events. On Madagascar, the unintentional introduction
 and spread of the commensal species Rattus rattus by people may have left
 a living clue of human colonization patterns and history. In this study,
 we addressed this question by characterising the genetic structure of
 natural populations of R. rattus using both microsatellites and
 mitochondrial sequences, on an extensive sampling across the island. Such
 datasets were analysed by a combination of methods using population
 genetics, phylogeography and Approximate Bayesian Computation. Our results
 indicated two different introduction events to Madagascar from the same
 ancestral source of R. rattus, one in the extreme north of the island and
 the other further south. The latter was the source of a large spatial
 expansion, which may have initially started from an original point located
 on the southern coast. The inferred timing of introduction events –
 several centuries ago - is temporally congruent with the Arabian trade
 network in the Indian Ocean, which was flourishing from the middle of the
 first millennium.
description: Microsatellite data (17
 loci) for 38 population samples of Malagasy Rattus
 rattusL1: title; L2-18: locus
 names; individual genotypes in a "Genepop" format. Population
 samples are separated by "pop" and labelled according the 4
 first letters of the individual code.Ratmadtotf.txtInput datafile for the main DIYABC analyses of the paper: microsatellite and D-loop data for two Madagascan population samplesL1: title; L2-18: locus names; individual genotypes (Genepop format) for two population samples of Madagascar: DIE (Diego Suarez), north Madagascar, and MAN (Mandena), south of MadagascarDieMan_dloop.txtCode for Diyabc analysesReference table associated with the file DieMan_Dloop.txt and containing the code for scenarios, chosen prior distributions and summary statisticsHeader_DieMan.txtAssembly_DloopD-loop final sequence assembly for the 36 haplotypes found in Malagasy R. rattusAssembly_1762bp1762 bp mitochondrial sequences of the 47 haplotypes found from R. rattus samples collected in the Western Indian Ocean area
DOI: 10.5061/dryad.4647d
title: Data from: Constraints on adaptation of Escherichia coli to mixed-resource environments increase over time

description: Can a population evolved in two resources reach the same fitness in both
 as specialist populations evolved in each of the individual resources?
 This question is central to theories of ecological specialization, the
 maintenance of genetic variation, and sympatric speciation, yet relatively
 few experiments have examined costs of generalism over long-term
 adaptation. We tested whether selection in environments containing two
 resources limits a population's ability to adapt to the individual
 resources by comparing the fitness of replicate Escherichia coli
 populations evolved for 6000 generations in the presence of glucose or
 lactose alone (specialists), or in varying presentations of glucose and
 lactose together (generalists). We found that all populations had
 significant fitness increases in both resources, though the magnitude and
 rate of these increases differed. For the first 4000 generations, most
 generalist populations increased in fitness as quickly in the individual
 resources as the corresponding specialist populations. From 5000
 generations, however, a widespread cost of adaptation affected all
 generalists, indicating a growing constraint on their abilities to adapt
 to two resources simultaneously. Our results indicate that costs of
 generalism are prevalent, but may influence evolutionary trajectories only
 after a period of cost-free adaptation.
description: SCevolution2015Includes raw data in .txt files (collected in the lab), R scripts used to create the figures and do statistics, and the figures themselves.
DOI: 10.5061/dryad.8jq98
title: Data from: Chewing on the trees: constraints and adaptation in the evolution of the primate mandible

description: Chewing on different food types is a demanding biological function. The
 classic assumption in studying the shape of feeding apparatuses is that
 animals are what they eat, meaning that adaptation to different food items
 accounts for most of their interspecific variation. Yet, a growing body of
 evidence points against this concept. We use the primate mandible as a
 model structure to investigate the complex interplay between shape, size,
 diet and phylogeny. We find a weak but significant impact of diet on
 mandible shape variation in primates as a whole but not in anthropoids and
 catarrhines as tested in isolation. These clades mainly exhibit allometric
 shape changes which are unrelated to diet. Diet is an important factor in
 the diversification of strepsirrhines and platyrrhines and a phylogenetic
 signal is detected in all primate clades. Peaks in morphological disparity
 occur during the Oligocene (between 37 and 25 Ma) supporting the notion
 that an adaptive radiation characterized the evolution of South American
 monkeys. In all primate clades, the evolution of mandible size is faster
 than its shape pointing to a strong effect of allometry on
 ecomorphological diversification in this group.
description: Meloro-et-al_Form_143Primates2D landmark Procustes coordinates and PC scores of primate mandibles belonging to 143 species. The procustes coordinates can be manipulated to make ".NTS" files suitable for tps series and for the R package geomorph.143_Primates_PhyloPhylogenetic tree in nexus format suitable for Mesquite describing evolutionary relationship for 143 primates. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.143_Primates_RPhylogenetic tree in nexus format suitable for R describing evolutionary relationship for 143 primates. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.AnthropoidsPhylogenetic tree in nexus format suitable for Mesquite describing evolutionary relationship for 114 anthropoids. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.CatarrhiniPhylogenetic tree in nexus format suitable for Mesquite describing evolutionary relationship for 82 catarrhines. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.PlatyrrhiniPhylogenetic tree in nexus format suitable for Mesquite describing evolutionary relationship for 32 platyrrhines. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.StrepsirrhiniPhylogenetic tree in nexus format suitable for Mesquite describing evolutionary relationship for 28 strepsirrhines. The topology and branch lenghts are based on on Springer et al 2012, PLoS One, 7:e49521.
DOI: 10.5061/dryad.gt0m3
title: Data from: In the presence of specialist root and shoot herbivory, invasive-range Brassica nigra populations have stronger competitive effects than native-range populations

description: 1. The evolution of increased competitive ability (EICA) hypothesis
 predicts that release from specialist herbivores enables invasive plants
 to evolve increased growth. The most powerful tests of EICA hypothesis are
 provided by approaches that simultaneously assess the effects of
 specialist herbivory and competitive interactions. However, such
 approaches are extremely rare, and hence how simultaneous release from
 root and shoot herbivory influence competitive ability of invasive plants
 remains little understood. 2. Here, we tested whether invasive-range
 Brassica nigra plants have evolved increased competitive ability, and
 whether expression of competitive ability depends on separate and
 simultaneous effects of specialist root and shoot herbivory. To do this,
 we grew B. nigra plants from eight invasive-range and eight native-range
 populations in the presence versus absence of competition with a community
 of native plant species, and in the absence versus presence of separate
 and simultaneous damage by a specialist root herbivore (Delia radicum) and
 a specialist shoot herbivore (Plutella xylostella). Brassica nigra
 performance was assessed by measuring biomass production and flowering of
 individual B. nigra plants. 3. In partial support of the EICA hypothesis,
 invasive-range B. nigra had greater flowering than native-range
 conspecifics in the absence of competition. However, contrary to a
 prediction of the EICA hypothesis, invasive-range B. nigra produced less
 aboveground biomass than native-range B.nigra in the absence of shoot
 herbivory and competition. Moreover, with simultaneous root and shoot
 herbivory, invasive-range B. nigra suppressed a competing community more
 strongly than native-range B. nigra did. 4. Synthesis: Our results suggest
 that invasiveness may be driven by mechanisms other than increased
 individual size. Simultaneous root and shoot herbivory in the invasive
 range may enhance suppressive effects of introduced plant species that
 have not completely escaped herbivore damage in the introduced range.
description: Brassica nigra and
 Community data
DOI: 10.5061/dryad.7cn23
title: Data from: Genetic differentiation and selection against migrants in evolutionarily replicated extreme environments

description: We investigated mechanisms of reproductive isolation in livebearing fishes
 (genus Poecilia) inhabiting sulfidic and nonsulfidic habitats in three
 replicate river drainages. Although sulfide spring fish convergently
 evolved divergent phenotypes, it was unclear if mechanisms of reproductive
 isolation also evolved convergently. Using microsatellites, we found
 strongly reduced gene flow between adjacent populations from different
 habitat types, suggesting that local adaptation to sulfidic habitats
 repeatedly caused the emergence of reproductive isolation. Reciprocal
 translocation experiments indicate strong selection against immigrants
 into sulfidic waters, but also variation among drainages in the strength
 of selection against immigrants into nonsulfidic waters. Mate choice
 experiments revealed the evolution of assortative mating preferences in
 females from nonsulfidic but not from sulfidic habitats. The inferred
 strength of sexual selection against immigrants (RIs) was negatively
 correlated with the strength of natural selection (RIm), a pattern that
 could be attributed to reinforcement, whereby natural selection
 strengthens behavioral isolation due to reduced hybrid fitness. Overall,
 reproductive isolation and genetic differentiation appear to be replicated
 and direct consequences of local adaptation to sulfide spring
 environments, but the relative contributions of different mechanisms of
 reproductive isolation vary across these evolutionarily independent
 replicates, highlighting both convergent and nonconvergent evolutionary
 trajectories of populations in each drainage.
description: Dryad DATA_Plath et
 al._2013_EVOLUTIONThe file comprises data
 on our translocation experiments, the mate choice experiments as well as
 microsatellites.
DOI: 10.5061/dryad.kc423
title: Data from: Intraspecific variability in the parasitoid wasp Trichogramma chilonis: can we predict the outcome of hybridization?

description: In the framework of biological control, the selection of effective natural
 enemies determines the final pest control. Thus, the genetic improvement
 of biocontrol agents could enhance the efficiency of biocontrol programs.
 Although promising, this approach has rarely been applied in this field.
 At the intraspecific level, hybridization between divergent populations of
 agents is expected to promote hybrid vigor (heterosis), but it is not
 clear to what extent. An even more difficult task is the ability to
 predict the fitness of hybrids from the biological characteristics of
 their parents. We investigated these general questions by crossing seven
 populations of the parasitoid wasp Trichogramma chilonis (Hymenoptera:
 Trichogrammatidae). Our results show different levels of mating
 compatibilities among populations, including asymmetric or almost complete
 reproductive isolation. Hybrids’ performance (fitness of the F1
 generation) ranges from inbreeding depression to heterosis. It was
 possible, to some extent, to predict hybrid fitness from pairwise genetic
 and phenotypic distances among parents, in accordance with the “dominance”
 hypothesis. This may provide general guidelines for the genetic
 improvement of biological control agents.
description: EVA-2012-039-OA.R1_dataset2_JmatingEVA-2012-039-OA.R1_dataset1_Hybridization
DOI: 10.5061/dryad.5m8p3
title: Data from: Towards a synthesis of frameworks in nutritional ecology: interacting effects of protein, carbohydrate, and phosphorus on field cricket fitness

description: Phosphorus has been identified as an important determinant of
 nutrition-related biological variation. The macronutrients protein (P) and
 carbohydrates (C), both alone and interactively, are known to affect
 animal performance. No study, however, has investigated the importance of
 phosphorus relative to dietary protein or carbohydrates, or the
 interactive effects of phosphorus with these macronutrients, on
 fitness-related traits in animals. We used a nutritional geometry
 framework to address this question in adult field crickets (Gryllus
 veletis). Our results showed that lifespan, weight gain, acoustic mate
 signalling and egg production were maximized on diets with different P : C
 ratios, that phosphorus did not positively affect any of these fitness
 traits, and that males and females had different optimal macronutrient
 intake ratios for reproductive performance. When given a choice, crickets
 selected diets that maximized both lifespan and reproductive performance
 by preferentially eating diets with low P : C ratios, and females selected
 diets with a higher P : C ratio than males. Conversely, phosphorus intake
 was not regulated. Overall, our findings highlight the importance of
 disentangling the influences of different nutrients, and of quantifying
 both their individual and interactive effects, on animal fitness traits,
 so as to gain a more integrative understanding of their nutritional
 ecology.
description: Gryllus veletis Diet
 Study- Raw Data- Harrison et al (2014)This file contains all
 raw data for experiments 1-3 for Harrison et al's (2014) study
 examining the effects of dietary protein, carbohydrates, and phosphorus on
 field cricket (Gryllus veletis) fitness traits and diet
 choice.Gryllus veletis Diet Study- Raw
 Data.xlsx
DOI: 10.5061/dryad.p5067
title: Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution

description: Natural selection acts on multiple traits simultaneously. How mechanisms
 underlying such traits enable or constrain their response to simultaneous
 selection is poorly understood. We show how antagonism and synergism among
 three traits at the developmental level enable or constrain evolutionary
 change in response to simultaneous selection on two focal traits at the
 phenotypic level. After 10 generations of 25% simultaneous directional
 selection on all four combinations of body size and development time in
 Manduca sexta (Sphingidae), the changes in the three developmental traits
 predict 93% of the response of development time and 100% of the response
 of body size. When the two focal traits were under synergistic selection,
 the response to simultaneous selection was enabled by juvenile hormone and
 ecdysteroids and constrained by growth rate. When the two focal traits
 were under antagonistic selection, the response to selection was due
 primarily to change in growth rate and constrained by the two hormonal
 traits. The approach used here reduces the complexity of the developmental
 and endocrine mechanisms to three proxy traits. This generates explicit
 predictions for the evolutionary response to selection that are based on
 biologically informed mechanisms. This approach has broad applicability to
 a diverse range of taxa, including algae, plants, amphibians, mammals, and
 insects.
description: Data for Fig F1
 directions of selectionDirections of selection-
 short and long development time and antagonistic and synergistic
 directions of selection, as in Figure F1.Data for Fig F2 PTTH and
 20ERelationship between
 timing of PTTH and ecdysone secretion as in Figure F2.dat for Fig F3
 JHERelationship between JHE
 titers and critical weight and body size, as in Figure
 F3.dat for Fig F4
 mortalityMortality data for each
 of the selected lines, as in Figure F4.All
 linesResponse to selection of
 all lines for body size, development time, critical weight, interval to
 cessation of growth and growth rate.Data for Figs 3 and
 4Response to ten
 generations of selection for body size and development time individually
 and their simultaneous response, as in Figures 3 and 4.data for Fig 6 observed
 vs predictedRelationship between the
 predicted and observed response to selection of body size and development
 time across all genetic lines, as in Figure 6.data for Fig 7 photogate
 and 20ETiming of photoperiodic
 gate for PTTH secretion and ecdysone secretion, as in Figure
 7.
DOI: 10.5281/zenodo.18382157
title: Algorithmic Textuality and Necroalgorithmization Dataset

description: This dataset documents the empirical test conducted on Google Images using the query “cabelo feio” (ugly hair). It includes the search context, date and time of access, and a documented list of observed results. The dataset supports the analysis presented in the article “Algorithmic Textuality and Necroalgorithmization” submitted to Cadernos de Linguística.
DOI: 10.5061/dryad.35vf4
title: Data from: Mind the gap: genetic manipulation of basicranial growth within synchondroses modulates calvarial and facial shape in mice through epigenetic interactions

description: Phenotypic integration patterns in the mammalian skull have long been a
 focus of intense interest as a result of their suspected influence on the
 trajectory of hominid evolution. Here we test the hypothesis that
 perturbation of cartilage growth, which directly affects only the
 chondrocranium during development, will produce coordinated shape changes
 in the adult calvarium and face regardless of mechanism. Using two murine
 models of cartilage undergrowth that target two very different mechanisms,
 we show that strong reduction in cartilage growth produces a short, wide,
 and more flexed cranial base. This in turn produces a short, wide face in
 both models. Cranial base and face are already correlated early in
 ontogeny, and the relationship between these modules gains structure
 through postnatal growth and development. These results provide further
 evidence that there exist physical interactions between developing parts
 of the phenotype that produce variation at a distance from the actual
 locus upon which a particular selective pressure is acting. Phenotypic
 changes observed over the course of evolution may not all require
 adaptationist explanations; rather, it is likely that a substantial
 portion of observed phenotypic variation over the history of a clade is
 not directly adaptive but rather a secondary consequence of some local
 response to selection.
description: Adult Skull Landmark
 DataThis file contains raw
 landmark coordinates for adult mouse skulls.Adult.csvNeonatal Skull Landmark DataThis file contains raw landmark coordinates for neonatal mouse skulls.Neonatal.csv
DOI: 10.5061/dryad.32610
title: Data from: Cross-cultural variation in men’s preference for sexual dimorphism in women’s faces

description: Both attractiveness judgements and mate preferences vary considerably
 cross-culturally. We investigated whether men's preference for
 femininity in women's faces varies between 28 countries with diverse
 health conditions by analysing responses of 1972 heterosexual
 participants. Although men in all countries preferred feminized over
 masculinized female faces, we found substantial differences between
 countries in the magnitude of men's preferences. Using an average
 femininity preference for each country, we found men's facial
 femininity preferences correlated positively with the health of the
 nation, which explained 50.4% of the variation among countries. The
 weakest preferences for femininity were found in Nepal and strongest in
 Japan. As high femininity in women is associated with lower success in
 competition for resources and lower dominance, it is possible that in
 harsher environments, men prefer cues to resource holding potential over
 high fecundity.
description: RawDataRaw data
DOI: 10.5061/dryad.hq48044
title: Data from: Cytokinin transfer by a free-living mirid to Nicotiana attenuata recapitulates a strategy of endophytic insects

description: Endophytic insects provide the textbook examples of herbivores that
 manipulate their host plant's physiology, putatively altering
 source/sink relationships by transferring cytokinins (CK) to create
 'green islands' that increase the nutritional value of infested
 tissues. However, unambiguous demonstrations of CK transfer are lacking.
 Here we show that feeding by the free-living herbivore Tupiocoris notatus
 on Nicotiana attenuata is characterized by stable nutrient levels,
 increased CK levels and alterations in CK-related transcript levels in
 attacked leaves, in striking similarity to endophytic insects. Using
 15N-isotope labeling, we demonstrate that the CK N6-isopentenyladenine
 (IP) is transferred from insects to plants via their oral secretions. In
 the field, T. notatus preferentially attacks leaves with transgenically
 increased CK levels; plants with abrogated CK-perception are less tolerant
 of T. notatus feeding damage. We infer that this free-living insect uses
 CKs to manipulate source/sink relationships to increase food quality and
 minimize the fitness consequences of its feeding.
description: Raw_data_FIGURE_1Raw_data_FIGURE_1_S1Raw_data_FIGURE_2Raw_data_FIGURE_2_S1Raw_data_FIGURE_2_S2Raw_data_FIGURE_2_S3Raw_data_FIGURE_3Raw_data_FIGURE_3_S1Raw_data_FIGURE_3_S2Raw_data_FIGURE_3_S3Raw_data_FIGURE_3_S4Raw_data_FIGURE_4Raw_data_FIGURE_4_S1Raw_data_FIGURE_4_S2Raw_data_FIGURE_4_S3Raw_data_FIGURE_6_S1Raw_data_FIGURE_6Raw_data_FIGURE_7