cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qn77s
title: Data from: Two different strategies of host manipulation allow parasites to persist in intermediate-definitive host systems

description: Trophically-transmitted parasites start their development in an
 intermediate host, before they finish the development in their definitive
 host when the definitive host preys on the intermediate host. In
 intermediate-definitive host systems, two strategies of host manipulation
 have been evolved: increasing the rate of transmission to the definitive
 host by increasing the chance that the definitive host will prey on the
 intermediate host, or increasing the lifespan of the parasite in the
 intermediate host by decreasing the predation chance when the intermediate
 host is not yet infectious. As the second strategy is less well studied
 than the first, it is unknown under what conditions each of these
 strategies are prevailed and evolved. We analysed the effect of both
 strategies on the presence of parasites in intermediate-definitive host
 systems with a structured population model. We show that the parasite can
 increase the parameter space where it can persist in the
 intermediate-definitive host system by using one of these two strategies
 of host manipulation. We found that when the intermediate host or the
 definitive host have life-history traits that allow the definitive host to
 reach large population densities, i.e. high reproduction rate of the
 intermediate host or high conversion efficiency of the definitive host
 (efficiency at which the uninfected definitive host converts caught
 intermediate hosts into offspring) respectively, evolving manipulation to
 decrease the predation chance of the intermediate host will be more
 beneficial than manipulation to increase the predation chance to enhance
 transmission. Furthermore, manipulation to decrease the predation chance
 of the intermediate host results in higher population densities of
 infected intermediate hosts than manipulation that increases the predation
 chance to enhance transmission. Our study shows that host manipulation in
 early stages of the parasite development to decrease predation might be a
 more frequently evolved way of host manipulation than is currently
 assumed.
description: Matlab script for
 manipulation of host by parasiteMatlab script for the
 model to explore under what conditions the two strategies of host
 manipulation allow trophically-transmitted parasites to persist in
 predator-prey systems: decreasing predation chance early in the
 development of the parasite, or increasing predation chance to increase
 the transmission rate of the parasites.ParasietHost_Script.mFunction used by the Matlab scriptFunction used by the Matlab script to model the effect of parasite presence on population dynamics of the intermediate and definitive hosts.ParasietHost_Model.m
DOI: 10.5061/dryad.jd1cq
title: Data from: Female house mice avoid fertilization by t haplotype incompatible males in a mate choice experiment

description: The t haplotype in house mice is a well-known selfish genetic element with
 detrimental, nonadditive fitness consequences to its carriers: recessive
 lethal mutations cause t/t homozygotes to perish in utero. Given the
 severe genetic incompatibility imposed by the t haplotype, we predict
 females to avoid fertilization by t haplotype incompatible males. Indeed,
 some of the strongest evidence for compatibility mate choice is related to
 the t haplotype in house mice. However, all previous evidence for
 compatibility mate choice in this system is based on olfactory preference.
 It is so far unknown how general these preferences are and whether they
 are relevant in an actual mating context. Here, we assess female
 compatibility mate choice related to t haplotypes in a setting that – for
 the first time – allowed females to directly interact and mate with males.
 This approach enabled us to analyse female behaviour during the testing
 period, and the resulting paternity success and fitness consequences of a
 given choice. We show that genetic incompatibilities arising from the t
 haplotype had severe indirect fitness consequences and t females avoided
 fertilization by t incompatible males. The results are inconclusive
 whether this avoidance of t fertilization by t females was caused by pre-
 or post-copulatory processes.
description: mate_choice_experiment_data
DOI: 10.5061/dryad.5qd0gd0
title: Data from: Geography of speciation affects rate of trait divergence in haemulid fishes

description: Speciation and the interactions between recently diverged species are
 thought to be major causes of ecological and morphological divergence in
 evolutionary radiations. We explored the role of these factors in the
 diversification of New World haemulid fishes, a major radiation of shore
 fishes in the tropical West Atlantic and East Pacific that are key members
 of coral reef ecosystems in this region. A time calibrated molecular
 phylogeny of this group reveals 21 sister species pairs, of which 8 are
 fully sympatric and 13 are allopatric. We find no difference between
 sympatric and allopatric pairs in the rate of divergence in color pattern,
 overall body shape or functional morphological traits associated with
 locomotion or feeding. However, sympatric pairs show a significant
 decrease in the rate of divergence in all of these traits with increasing
 time since their divergence, consistent with an elevated rate of
 divergence at the time of speciation, the effect of which attenuates as
 divergence time increases. Our results are consistent with an important
 role for speciation driving phenotypic divergence of haemulids, but the
 lack of difference in divergence between sympatric and allopatric pairs
 indicates that the interactions between closely related species are not
 dominant drivers of this divergence.
description: Size corrected
 phylogenetic independent contrastSize corrected
 phylogenetic independent contrast for every sister pair among New World
 gruntsPhySizCorPhyloPcaPairs2.csv
DOI: 10.5061/dryad.6k7gh
title: Data from: An evaluation of the hybrid speciation hypothesis for Xiphophorus clemenciae based on whole genome sequences

description: Once thought rare in animal taxa, hybridization has been increasingly
 recognized as an important and common force in animal evolution. In the
 past decade, a number of studies have suggested that hybridization has
 driven speciation in some animal groups. We investigate the signature of
 hybridization in the genome of a putative hybrid species, Xiphophorus
 clemenciae, through whole genome sequencing of this species and its
 hypothesized progenitors. Based on analysis of this data, we find that X.
 clemenciae is unlikely to have been derived from admixture between its
 proposed parental species. However, we find significant evidence for
 recent gene flow between Xiphophorus species. Though we detect genetic
 exchange in two pairs of species analyzed, the proportion of genomic
 regions that can be attributed to hybrid origin is small, suggesting that
 strong behavioral pre-mating isolation prevents frequent hybridization in
 Xiphophorus. The direction of gene flow between species supports a role
 for sexual selection in mediating hybridization.
description: msshellmigrationscript to simulate expected divergence under an allopatric speciation model with limited migration using the msHOT program. Usage: perl msshellmigration.plmsshelladmixscript to simulate expected divergence under a hybrid speciation model using the msHOT program. Usage: perl msshelladmix.plmsshell_largethetascript to simulate expected divergence under an allopatric speciation model with a large ancestral theta using the msHOT program. Usage: perl msshell_largetheta.plmspositionswindowsCompanion script to simulation scripts msshell_largetheta.pl msshelladmix.pl and msshellmigration.pl which takes the output of ms or msHOT and calculates divergence between simulated sequences.
DOI: 10.5061/dryad.7h3v1
title: Data from: Cytokine responses in birds challenged with the human food-borne pathogen Campylobacter jejuni implies a Th17 response

description: Development of process orientated understanding of cytokine interactions
 within the gastrointestinal tract during an immune response to pathogens
 requires experimentation and statistical modelling. The immune response
 against pathogen challenge depends on the specific threat to the host.
 Here, we show that broiler chickens mount a breed-dependent immune
 response to Campylobacter jejuni infection in the caeca by analysing
 experimental data using frequentist and Bayesian structural equation
 models (SEM). SEM provides a framework by which cytokine
 interdependencies, based on prior knowledge, can be tested. In both breeds
 important cytokines including pro-inflammatory interleukin (IL)-1β, ,
 IL-4, IL-17A, interferon (IFN)-γ and anti-inflammatory IL-10 and
 transforming growth factor (TGF)-β4 were expressed post-challenge. The SEM
 revealed a putative regulatory pathway illustrating a T helper (Th)17
 response and regulation of IL-10, which is breed-dependent. The prominence
 of the Th17 pathway indicates the cytokine response aims to limit the
 invasion or colonization of an extracellular bacterial pathogen but the
 time-dependent nature of the response differs between breeds.
description: reid_openscience_dataThese cytokine data are based on total RNA samples taken from caecal tissue of commercial broilers, which were held under laboratory conditions. The birds were challenged with the pathogen Campylobacter jejuni. The results are expressed as fold changes in corrected target gene expression in infected birds relative to controls.
DOI: 10.5061/dryad.kk4qn
title: Data from: Increased prenatal maternal investment reduces inbreeding depression in offspring

description: Inbreeding depression refers to the reduction of fitness that results from
 matings between relatives. Evidence for reduced fitness in inbred
 individuals is widespread, but the strength of inbreeding depression
 varies widely both within and among taxa. Environmental conditions can
 mediate this variation in the strength of inbreeding depression, with
 environmental stress exacerbating the negative consequences of inbreeding.
 Parents can modify the environment experienced by offspring, and have thus
 the potential to mitigate the negative consequences of inbreeding. While
 such parental effects have recently been demonstrated during the postnatal
 period, the role of prenatal parental effects in influencing the
 expression of inbreeding depression remains unexplored. To address this
 gap, we performed matings between full-sibs or unrelated individuals in
 replicated lines of Japanese quail (Coturnix japonica) experimentally
 selected for high and low maternal egg provisioning. We show that in the
 low maternal investment lines hatching success was strongly reduced when
 parents were related. In the high maternal investment lines, however, this
 negative effect of inbreeding on hatching success was absent,
 demonstrating that prenatal maternal provisioning can alleviate the
 negative fitness consequences of inbreeding.
description: Ihle_data
DOI: 10.5061/dryad.85mm7
title: Data from: Trace fossils of possible parasites inside the gut contents of a hadrosaurid dinosaur, Upper Cretaceous Judith River Formation, Montana

description: Tiny sinuous trace fossils have been found within probable gut contents of
 an exceptionally preserved specimen of a hadrosaurid dinosaur,
 Brachylophosaurus canadensis, from the Judith River Formation of Montana.
 Approximately 280 examples of the trace fossils were observed in 19
 samples of gut region material. The tubular structures typically are about
 0.3 mm across. Many have thin calcareous linings or layers, and some
 exhibit fine surficial striae. At least two dozen of these trace fossils
 share walls with adjacent tubular traces, and this association can extend
 for several millimeters. While the trace fossils share some
 characteristics with fine rhizoliths, these features are most consistent
 with tiny burrows, or possibly body impressions, of worms (vermiform
 organisms) of uncertain biologic affinity. Such trace fossils have not
 been reported previously, and herein described as Parvitubulites striatus
 n. gen. n. sp. Either autochthonous (parasites) or allochthonous
 (scavengers) worms may have created the trace fossils, but taphonomic
 factors suggest that autochthonous burrowers are more likely. Several
 lines of evidence, such as constant diameters and matching directional
 changes, suggest that the paired trace fossils were made by two
 individuals moving at the same time, which implies sustained intraspecific
 contact. Parvitubulites striatus provides a rare record of interactions
 between terrestrial, meiofaunal-sized, soft-bodied invertebrates and a
 dinosaur carcass. The evidence that the worms may have parasitized a
 living hadrosaur and subsequently left traces of intraspecific behavior
 between individual worms adds unique information to our understanding of
 Mesozoic trophic interactions.
description: Measurements of examples
 of Parvitubulites striatusIndividual burrow
 characteristics. For percentages, N=73. For average diameter, N=57.
 (*=these five burrows were omitted from diameter calculations because
 their very poor preservation made it difficult to determine diameter; some
 may have actually been pairs. Including these five burrows increases the
 average diameter to 0.4 mm.)tweet_etal_J_Paleo_supplement.csv
DOI: 10.5061/dryad.k49ht50
title: Data from: Separate block based parameter estimation method for Hammerstein systems

description: Different from the output-input representation based identification
 methods of two-block Hammerstein systems, this paper concerns a separate
 block based parameter estimation method for each block of a two-block
 Hammerstein CARMA system, without combining the parameters of two parts
 together. The idea is to consider each block as a subsystem and to
 estimate the parameters of the nonlinear block and the linear block
 separately (interactively), by using two least squares algorithms in one
 recursive step. The internal variable between the two blocks (the output
 of the nonlinear block, and also the input of the linear block) is
 replaced by different estimates: when estimating the parameters of the
 nonlinear part, the internal variable between the two blocks is computed
 by the linear function; when estimating the parameters of the linear part,
 the internal variable is computed by the nonlinear function. The proposed
 parameter estimation method possesses property of the higher computational
 efficiency compared with the previous over-parameterization method in
 which many redundant parameters need to be computed. The simulation
 results show the effectiveness of the proposed algorithm.
description: Code for separated
 estimation method for Hammerstein systems1. SepHCARMA.m is the
 program of separate block based estimation method for Hammerstein systems;
 2. integral.m is the program of evaluating of the integral of the rational
 function; 3. f_ls.m computes RLS estimates and error; 4. f_rn.m is the
 program of generate norm distributed random number.SeparatedBlockLS_HCARMAsystem.zip
DOI: 10.5061/dryad.b2207
title: Data from: Social media enhances languages differentiation: a mathematical description

description: Understanding and predicting the evolution of competing languages is a
 topic of high interest in a world with more than 6000 languages competing
 in a highly connected environment. We consider a reasonable mathematical
 model describing a situation of competition between two languages and
 analyse the effect of the speakers' connectivity (i.e. social
 networks). Surprisingly, instead of homogenizing the system, a high degree
 of connectivity helps to introduce differentiation for the appropriate
 parameters.
description: C codeZIP file containing C
 code that solves numerically the coupled differential equation system f,g
 described in the article.code.zip
DOI: 10.5061/dryad.01f0f
title: Data from: Evolutionary stability of jointly evolving traits in subdivided populations

description: The evolutionary stability of quantitative traits depends on whether a
 population can resist invasion by any mutant. While uninvadability is well
 understood in well-mixed populations, it is much less so in subdivided
 populations when multiple traits evolve jointly. Here, we investigate
 whether a spatially subdivided population at a monomorphic equilibrium for
 multiple traits can withstand invasion by any mutant or is subject to
 diversifying selection. Our model also explores the correlations among
 traits arising from diversifying selection and how they depend on
 relatedness due to limited dispersal. We find that selection tends to
 favor a positive (negative) correlation between two traits when the
 selective effects of one trait on relatedness is positively (negatively)
 correlated to the indirect fitness effects of the other trait. We study
 the evolution of traits for which this matters: dispersal that decreases
 relatedness and helping that has positive indirect fitness effects. We
 find that when dispersal cost is low and the benefits of helping
 accelerate faster than its costs, selection leads to the coexistence of
 mobile defectors and sessile helpers. Otherwise, the population evolves to
 a monomorphic state with intermediate helping and dispersal. Overall, our
 results highlight the effects of population subdivision for evolutionary
 stability and correlations among traits.
description: M-file for individually
 based simulationsMathematicaCode.m
DOI: 10.5061/dryad.3n977
title: Data from: The balanced-lethal system of crested newts: a ghost of sex chromosomes past?

description: Balanced lethal systems are more than biological curiosities: As theory
 predicts, they should quickly be eliminated through the joint forces of
 recombination and selection. That such systems might become fixed in
 natural populations poses a challenge to evolutionary theory. Here we
 address the case of a balanced lethal system fixed in crested newts and
 related species, which makes 50% of offspring die early in development.
 All adults are heteromorphic for chromosome pair 1. The two homologs (1A
 and 1B) have different recessive deleterious alleles fixed on a
 non-recombining segment, so that heterozygotes are viable, while
 homozygotes are lethal. Given such a strong segregation load, how could
 autosomes stop recombining? We propose a role for a sex-chromosome
 turnover from pair 1 (putative ancestral sex chromosome) to pair 4
 (currently active sex chromosome). Accordingly, 1A and 1B represent two
 variants (YA and YB) of the Y chromosome from an ancestral
 male-heterogametic system. We formalize a scenario where turnovers are
 driven by sex-ratio selection stemming from gene-environment interactions
 on sex determination. Individual-based simulations show that a
 balanced-lethal system can be fixed with significant likelihood, provided
 the masculinizing allele on chromosome 4 appears after the elimination of
 the feminizing allele on chromosome 1. Our study illustrates how
 strikingly maladaptive traits might evolve through natural selection.
description: InputFilesInput files for simulations run. See "ReadMe.txt" for more information
DOI: 10.5281/zenodo.18385779
title: DEKORATIV SAN'ATDA "KITOBSEVAR INSON" OBRAZINI YARATISHNING NAZARIY VA BADIIY-ESTETIK ASOSLARI.
DOI: 10.5281/zenodo.18385778
title: DEKORATIV SAN'ATDA "KITOBSEVAR INSON" OBRAZINI YARATISHNING NAZARIY VA BADIIY-ESTETIK ASOSLARI.
DOI: 10.5061/dryad.c112f
title: Data from: Control of parental investment changes plastically over time with residual reproductive value

description: Evolutionary conflict between parents and offspring over parental resource
 investment is a significant selective force on the traits of both parents
 and offspring. Empirical studies have shown that for some species, the
 amount of parental investment is controlled by the parents, whereas in
 other species, it is controlled by the offspring. The main difference
 between these two strategies is the residual reproductive value of the
 parents or opportunities for future reproduction. Therefore, this could
 explain the patterns of control of parental investment at the species
 level. However, the residual reproductive value of the parents will change
 during their lifetime; therefore, parental influence on the amount of
 investment can be expected to change plastically. Here, we investigated
 control of parental investment when parents were young and had a high
 residual reproductive value, compared to when they were old and had a low
 residual reproductive value using a cross-fostering experiment in the
 burying beetle Nicrophorus quadripunctatus. We found that parents exert
 greater control over parental investment when they are young, but parental
 control is weakened as the parents age. Our results demonstrate that
 control of parental investment is not fixed, but changes plastically
 during the parent's lifetime.
description: Supporting data for
 "Control of parental investment changes plastically over time with
 residual reproductive value"Data were collected in
 the laboratory. The data file was created by Microsoft Excel for Mac 2011
 Version 14.5.1. Explanation for column headings;
 "ID_of_larval_genetic_parent" is an ID of female parents who
 produced the larva. "thoracic_width_of_female_parent" is a
 thoracic width of female parents who cared for the larva.
 "experimental group" is names of experimental group (group A:
 young parents cared for their natal offspring, B: young parents cared for
 foster offspring, C: old parents cared for their natal offspring, D: old
 parents cared for foster offspring). "parent_age" is an age of
 female parents used in this experiment. "relationship" is
 genetic relationship between parent and offspring ("related"
 means parents cared for natal offspring, "unrelated" means
 parents cared for foster offspring). "body_weight_at_120h" is a
 body weight of larvae at 120 h age in the first breeding attempt.
 "body_weight_at_120h_2" is a body weight of larvae at 120 h age
 in the second breeding attempt.Data_for_Dryad.csv
DOI: 10.5061/dryad.688jj72
title: Data from: Thermal niche evolution across replicated Anolis lizard adaptive radiations

description: Elucidating how ecological and evolutionary mechanisms interact to produce
 and maintain biodiversity is a fundamental problem in evolutionary
 ecology. We investigate this issue by focusing on how physiological
 evolution affects performance and species coexistence along the thermal
 niche axis in replicated radiations of Anolis lizards, groups best known
 for resource partitioning based on morphological divergence. We find
 repeated divergence in thermal physiology within these radiations, and
 that this divergence significantly affects performance within natural
 thermal environments. Morphologically similar species that co-occur
 invariably differ in their thermal physiology, providing evidence that
 physiological divergence facilitates species co-existence within anole
 communities. Despite repeated divergence in traits of demonstrable
 ecological importance, phylogenetic comparative analyses indicate that
 physiological traits have evolved more slowly than key morphological
 traits related to the structural niche. Phylogenetic analyses also reveal
 that physiological divergence is correlated with divergence in broad-scale
 habitat climatic features commonly used to estimate thermal niche
 evolution, but that the latter incompletely predicts variation in the
 former. We provide comprehensive evidence for repeated adaptive evolution
 of physiological divergence within Anolis adaptive radiations, including
 the complementary roles of physiological and morphological divergence in
 promoting community-level diversity. We recommend greater integration of
 performance-based traits into analyses of climatic niche evolution, as
 they facilitate a more complete understanding of the phenotypic and
 ecological consequences of climatic divergence.
description: Topt data
 PRSLBOptimal temperature
 datapr jamaica ctmax
 PRSLBCTmax (heat tolerance)
 data