cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0k0mt
title: Data from: Down syndrome cell adhesion molecule 1: testing for a role in insect immunity, behaviour and reproduction

description: Down syndrome cell adhesion molecule 1 (Dscam1) has wide-reaching and
 vital neuronal functions although the role it plays in insect and
 crustacean immunity is less well understood. In this study, we combine
 different approaches to understand the roles that Dscam1 plays in
 fitness-related contexts in two model insect species. Contrary to our
 expectations, we found no short-term modulation of Dscam1 gene expression
 after haemocoelic or oral bacterial exposure in Tribolium castaneum, or
 after haemocoelic bacterial exposure in Drosophila melanogaster.
 Furthermore, RNAi-mediated Dscam1 knockdown and subsequent bacterial
 exposure did not reduce T. castaneum survival. However, Dscam1 knockdown
 in larvae resulted in adult locomotion defects, as well as dramatically
 reduced fecundity in males and females. We suggest that Dscam1 does not
 always play a straightforward role in immunity, but strongly influences
 behaviour and fecundity. This study takes a step towards understanding
 more about the role of this intriguing gene from different phenotypic
 perspectives.
description: Raw
 dataPeuß
 Dryad raw data.xlsx
DOI: 10.5061/dryad.qq601
title: Data from: Initiators, leaders and recruitment mechanisms in the collective movements of damselfish

description: Explaining how individual behavior and social interactions give rise to
 group-level outcomes and affect issues such as leadership is fundamental
 to the understanding of collective behavior. Here we examined individual
 and collective behavioral dynamics in groups of humbug damselfish both
 before and during a collective movement. During the predeparture phase,
 group activity increased until the collective movement occurred. Although
 such movements were precipitated by one individual, the success or failure
 of any attempt to instigate a collective movement was not solely dependent
 on this initiator’s behavior but on the behavior of the group as a whole.
 Specifically, groups were more active and less cohesive before a
 successful initiation attempt than before a failed attempt. Individuals
 who made the most attempts to initiate a collective movement during each
 trial were ultimately most likely to lead the collective movement.
 Leadership was not related to dominance but was consistent between trials.
 The probability of fish recruiting to a group movement initiative was an
 approximately linear function of the number of fish already recruited.
 Overall, these results are consistent with nonselective local mimetism,
 with the decision to leave based on a group’s, rather than any particular
 individual’s, readiness to leave.
description: Damsel Data for Am
 Nat
DOI: 10.5061/dryad.2d504
title: Data from: Restoration as mitigation: analysis of stream mitigation for coal mining impacts in southern Appalachia

description: Compensatory mitigation is commonly used to replace aquatic natural
 resources being lost or degraded but little is known about the success of
 stream mitigation. This article presents a synthesis of information about
 434 stream mitigation projects from 117 permits for surface mining in
 Appalachia. Data from annual monitoring reports indicate that the ratio of
 lengths of stream impacted to lengths of stream mitigation projects were
 &lt; 1 for many projects, and most mitigation was implemented on
 perennial streams while most impacts were to ephemeral and intermittent
 streams. Regulatory requirements for assessing project outcome were
 minimal; visual assessments were the most common and 97% of the projects
 reported suboptimal or marginal habitat even after 5 years of monitoring.
 Less than a third of the projects provided biotic or chemical data; most
 of these were impaired with biotic indices below state standards and
 stream conductivity exceeding federal water quality criteria. Levels of
 selenium known to impair aquatic life were reported in 7 of the 11
 projects that provided Se data. Overall, the data show that mitigation
 efforts being implemented in southern Appalachia for coal mining are not
 meeting the objectives of the Clean Water Act to replace lost or degraded
 streams ecosystems and their functions.
description: Compensatory mitigation
 stream restoration monitoring dataHabitat scores,
 biological indices, and water quality monitoring data for constructed
 mitigation projects compensating for mining impacts in Appalachian coal
 region. Data were derived from mitigation monitoring reports submitted to
 the Army Corps of Engineers for approval. Mitigation projects include
 stream creation, stream restoration, and stream
 enhancement.Palmer_EST_mitigation
 data.zipMitigation
 locationsLocations of mitigation
 sites used in analysis.Palmer_EST_mitigation_locations.kml
DOI: 10.5061/dryad.p36kh
title: Data from: Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs

description: Animals from different clades but subject to similar environments often
 evolve similar body shapes and physiological adaptations due to convergent
 evolution, but this has been rarely tested at the transcontinental level
 and across entire classes of animal. Australia's biome diversity,
 isolation and aridification history provide excellent opportunities for
 comparative analyses on broad-scale macroevolutionary patterns. We
 collected morphological and environmental data on eighty-four (98%)
 Australian hylid frog species and categorized them into ecotypes. Using a
 phylogenetic framework, we tested the hypothesis that frogs from the same
 ecotype display similar body shape patterns: (i) across all the Australian
 hylids, and (ii) through comparison with a similar previous study on 127
 (97%) Australian myobatrachid species. Body size and shape variation did
 not follow a strong phylogenetic pattern and was not tightly correlated
 with environment, but there was a stronger association between morphotype
 and ecotype. Both arboreal and aquatic frogs had long limbs, whereas limbs
 of fossorial species were shorter. Other terrestrial species were
 convergent on the more typical frog body shape. We quantified the strength
 of morphological convergence at two levels: (i) between fossorial
 myobatrachid and hylid frogs, and (ii) in each ecomorph within the hylids.
 We found strong convergence within ecotypes, especially in fossorial
 species. Ecotypes were also reflected in physiological adaptations: both
 arboreal and cocooned fossorial frogs tend to have higher rates of
 evaporative water loss. Our results illustrate how adaptation to different
 ecological niches plays a crucial role in morphological evolution,
 boosting phenotypic diversity within a clade. Despite phylogenetic
 conservatism, morphological adaptation to repeatedly emerging new
 environments can erase the signature of ancestral morphotypes, resulting
 in phenotypic diversification and convergence both within and between
 diverse clades.
description: Morphological
 measurements of all specimensMorphological_data.xlsx
DOI: 10.5061/dryad.g6jm6
title: Data from: Contrasting effects of landscape features on genetic structure in different geographical regions in the ornate dragon lizard, Ctenophorus ornatus

description: Habitat fragmentation can have profound effects on the distribution of
 genetic variation within and between populations. Previously, we showed
 that in the ornate dragon lizard, Ctenophorus ornatus, lizards residing on
 outcrops that are separated by cleared agricultural land are significantly
 more isolated and hold less genetic variation than lizards residing on
 neighbouring outcrops connected by undisturbed native vegetation. Here, we
 extend that fine-scale study to examine the pattern of genetic variation
 and population structure across the species’ range. Using a landscape
 genetics approach, we test whether land clearing for agricultural purposes
 has affected the population structure of the ornate dragon lizard. We
 found significant genetic differentiation between outcrop populations (FST
 = 0.12), as well as isolation-by-distance within each geographic region.
 In support of our previous study, land clearing was associated with higher
 genetic divergences between outcrops and lower genetic variation within
 outcrops, but only in the region that had been exposed to intense
 agriculture for the longest period of time. No other landscape features
 influenced population structure in any geographic region. These results
 show that the effects of landscape features can vary across species’
 ranges and suggest there may be a temporal-lag in the response to
 contemporary changes in land use. These findings therefore highlight the
 need for caution when assessing the impact of contemporary land use
 practices on genetic variation and population structure.
description: C. ornatus
 dataIndividuals: This data
 file provides all the raw molecular data for each individual. The first
 column gives the outcrop from which each individual was taken. The second
 column the individual’s ID, a unique number across all outcrops. The
 remaining columns give the allele sizes for each individual at each locus
 (listed in the first row). Each locus has 2 columns, one for each allele.
 Missing data are left as empty cells. Outcrops: This file provides all the
 outcrop level information used in the analyses. The first column gives the
 outcrop name, the second gives the region where the outcrop is located.
 The third and fourth columns give the geographical location of the outcrop
 as latitude and longitude. The fifth column gives the number of outcrops
 within a 2km radius of the sampled outcrop and the sixth the percentage
 cover of granite within a 2km radius of the sampled outcrop. The seventh
 column indicates whether the outcrop is found in a cleared (CL) or
 uncleared (U) landscape and the final column provides the mean annual
 rainfall for the outcrop.
DOI: 10.5061/dryad.jc86t
title: Data from: Protection first then facilitation: a manipulative parasite modulates the vulnerability to predation of its intermediate host according to its own developmental stage

description: Many trophically-transmitted parasites with complex life cycles manipulate
 their intermediate host behavior in ways facilitating their transmission
 to final host by predation. This facilitation generally results from
 lowering host’s anti-predatory defences when the parasite is infective to
 the final host. However, a recent theoretical model predicts that an
 optimal parasitic strategy would be to protect the intermediate host from
 predation when non-infective, before switching to facilitation when the
 infective stage is reached. We tested this hypothesis in the fish
 acanthocephalan parasite Pomphorhynchus laevis using the amphipod Gammarus
 pulex as intermediate host. Gammarids parasitized by non-infective stage
 of P. laevis (acanthella) hid significantly more under refuges than
 uninfected ones. In addition, acanthella-infected gammarids were less
 predated upon by trout than uninfected ones. As predicted, a switch
 towards decreased anti-predatory behavior of G. pulex and enhanced
 vulnerability to predation was found when P. laevis reached the stage
 infective to its final host. The parasites appear to be able to exploit
 plasticity in host anti-predatory responses, and shift the host optimal
 response towards their own optimal balance.
description: Dianne_et_al_Refuge_use_experimentsDianne_et_al_Predation_tests
DOI: 10.5061/dryad.g61d1
title: Data from: Little evidence for morphological change in a resilient endemic species following the introduction of a novel predator

description: Human activities, such as species introductions, are dramatically and
 rapidly altering natural ecological processes, and often result in novel
 selection regimes. To date, we still have a limited understanding of the
 extent to which such anthropogenic selection may be driving contemporary
 phenotypic change in natural populations. Here we test whether the
 introduction of the piscivorous Nile perch, Lates niloticus, into East
 Africa's Lake Victoria and nearby lakes coincided with morphological
 change in one resilient native prey species, the cyprinid fish
 Rastrineobola argentea. Drawing on prior eco-morphological research, we
 predicted that this novel predator would select for increased allocation
 to the caudal region in R. argentea to enhance burst-swimming performance,
 and hence escape ability. To test this prediction, we compared body
 morphology of R. argentea across space (nine Ugandan lakes differing in
 Nile perch invasion history) and through time (before and after
 establishment of Nile perch in Lake Victoria). Spatial comparisons of
 contemporary populations only partially supported our predictions, with R.
 argentea from some invaded lakes having larger caudal regions and smaller
 heads compared to R. argentea from uninvaded lakes. There was no clear
 evidence of predator-associated change in body shape over time in Lake
 Victoria. We conclude that R. argentea have not responded to the presence
 of Nile perch with consistent morphological changes, and that other
 factors are driving observed patterns of body shape variation in R.
 argentea.
description: Shape variation across
 lakesThis file contains basic
 biometric data (length, weight, sex, maturity) and raw shape data (partial
 warps, uniform components, and relative warps) for R. argentea collected
 from Ugandan lakes in 2010.Sharpe_mukene shape across
 lakes_Dryad.csvShape variation across
 timeThis file contains basic
 biometric data (length) and raw shape data (partial warps, uniform
 components, and relative warps) for R. argentea collected from Lake
 Victoria from 1966 to 2010.Sharpe_mukene shape across
 time_Dryad.csv
DOI: 10.5061/dryad.hr768
title: Data from: Hybridisation increases invasive knotweed success

description: Hybridization is one of the fundamental mechanisms by which rapid
 evolution can occur in exotic species. If hybrids show increased vigour,
 this could significantly contribute to invasion success. Here, we compared
 the success of the two invasive knotweeds, Fallopia japonica and F.
 sachalinensis, and their hybrid, F. × bohemica, in competing against
 experimental communities of native plants. Using plant material from
 multiple clones of each taxon collected across a latitudinal gradient in
 Central Europe, we found that knotweed hybrids performed significantly
 better in competition with a native community, and that they more strongly
 reduced the growth of the native plants. One of the parental species, F.
 sachalinensis, regenerated significantly less well from rhizomes, and this
 difference disappeared if activated carbon was added to the substrate,
 which suggests allelopathic inhibition of F. sachalinensis regeneration by
 native plants. We found substantial within-taxon variation in competitive
 success in all knotweed taxa, but variation was generally greatest in the
 hybrid. Interestingly, there was also significant variation within the
 genetically uniform F. japonica, possibly reflecting epigenetic
 differences. Our study shows that invasive knotweed hybrids are indeed
 more competitive than their parents, and that hybridisation increased the
 invasiveness of the exotic knotweed complex.
description: KnotweedHybridisation
DOI: 10.5061/dryad.420h7
title: Data from: Coalescent species delimitation in milksnakes (genus Lampropeltis) and impacts on phylogenetic comparative analyses

description: Both gene-tree discordance and unrecognized diversity are sources of error
 for accurate estimation of species trees, and can affect downstream
 diversification analyses by obscuring the correct number of nodes, their
 density, and the lengths of the branches subtending them. While the
 theoretical impact of gene-tree discordance on evolutionary analyses has
 been examined previously, the effect of unsampled and cryptic diversity
 has not. Here, we examine how delimitation of previously unrecognized
 diversity in the milksnake (Lampropeltis triangulum) and use of a
 species-tree approach affects both estimation of the Lampropeltis
 phylogeny and comparative analyses with respect to the timing of
 diversification. Coalescent species delimitation indicates that L.
 triangulum is not monophyletic and that there are multiple species of
 milksnake, which increases the known species diversity in the genus
 Lampropeltis by 40%. Both genealogical and temporal discordance occurs
 between gene trees and the species tree, with evidence that mtDNA
 introgression is a main factor. This discordance is further manifested in
 the preferred models of diversification, where the concatenated gene tree
 strongly supports an early burst of speciation during the Miocene, in
 contrast to species-tree estimates where diversification follows a
 birth-death model and speciation occurs mostly in the Pliocene and
 Pleistocene. This study highlights the crucial interaction among
 coalescent-based phylogeography and species delimitation, systematics, and
 species diversification analyses.
description: Online Appendix
 2This
 is online Appendix 2 that includes all GenBank numbers for all samples
 with data already available on GenBank.DATASET_LampropeltisThis is the dataset consisting of phased sequences in nexus format. It includes a full cytb dataset (329 taxa) and a smaller cytb dataset that only includes samples that were also used for the nuclear datasets (124 taxa).Lamp_Data.zipOnline Appendix 1This appendix includes all information for the samples used in the study.
DOI: 10.15468/dl.z5kqnj
title: Occurrence Download

description: A dataset containing 5439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "TaxonKey is Hormaphis hamamelidis"
 ]
}

 The dataset includes 5439 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000725-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m06s2
title: Data from: Intralocus sexual conflict and environmental stress

description: Intralocus sexual conflict (ISC) occurs when selection at a given locus
 favors different alleles in males and females, placing a fundamental
 constraint on adaptation. However, the relative impact of ISC on
 adaptation may become reduced in stressful environments that expose
 conditionally deleterious mutations to selection. The genetic correlation
 for fitness between males and females (rMF) provides a quantification of
 ISC across the genome. We compared ISC at a benign (29˚C) and a stressful
 (36˚C) temperature by estimating rMFs in two natural populations of the
 seed beetle Callosobruchus maculatus using isofemale lines. In one
 population, we found substantial ISC under benign conditions signified by
 a negative rMF (-0.51) and, as predicted, a significant reduction of ISC
 under stress signified by a reversed and positive rMF (0.21). The other
 population displayed low ISC at both temperatures (rMF: 0.38; 0.40). In
 both populations, isofemale lines harboring alleles beneficial to males
 but detrimental to females at benign conditions tended to show overall low
 fitness under stress. These results offer support for low ISC under stress
 and suggest that environmentally sensitive and conditionally deleterious
 alleles that are sexually selected in males mediate changes in ISC. We
 discuss implications for adaptive evolution in sexually reproducing
 populations.
description: Fitness
 dataGives the lLife Time
 Reproductive success (LRS = number of offspring) of males and females of
 73 isofemale lines belonging to two populations (Lome and Ofuya). LRS was
 measured at 29C and 36C, in 5 different temporal blocks. LRS is given in
 raw format (number of offspring) and in relative terms (number
 offspring/mean) per sex:temperature:population.DRYADdata.txt
DOI: 10.5061/dryad.665
title: Data from: mtDNA Ribosomal Gene Phylogeny of Sea Hares in the Genus Aplysia (Gastropoda, Opisthobranchia, Anaspidea): Implications for Comparative Neurobiology

description: Sea hares within the genus Aplysia are important neurobiological model
 organisms, and as studies based on different Aplysia species appear in the
 literature, a phylogenetic framework has become essential. We present a
 phylogenetic hypothesis for this genus, based on portions of two
 mitochondrial genes (12S and 16S). In addition, we reconstruct the
 evolution of several behavioral characters of interest to neurobiologists
 in order to illustrate the potential benefits of a phylogeny for the genus
 Aplysia. These benefits include the determination of ancestral traits, the
 direction and timing of evolution of characters, prediction of the
 distribution of traits, and identification of cases of independent
 acquisition of traits within lineages. This last benefit may prove
 especially useful in understanding the linkage between behaviors and their
 underlying neurological basis.
description: Medina et al Data Set
 1Medina.nexusMedina et al Data Set 2Medina.txt
DOI: 10.5061/dryad.b74d0
title: Data from: Marginal predation: do encounter or confusion effects explain the targeting of prey group edges?

description: Marginal predation, also known as the edge effect, occurs when
 aggregations of prey are preferentially targeted on their periphery by
 predators and has long been established in many taxa. Two main processes
 have been used to explain this phenomenon, the confusion effect and the
 encounter rate between predators and prey group edges. However, it is
 unknown at what size a prey group needs to be before marginal predation is
 detectable and to what extent each mechanism drives the effect. We
 conducted 2 experiments using groups of virtual prey being preyed upon by
 3-spined sticklebacks (Gasterosteus aculeatus) to address these questions.
 In Experiment 1, we show that group sizes do not need to be large for
 marginal predation to occur, with this being detectable in groups of 16 or
 more. In Experiment 2, we find that encounter rate is a more likely
 explanation for marginal predation than the confusion effect in this
 system. We find that while confusion does affect predatory behaviors
 (whether or not predators make an attack), it does not affect marginal
 predation. Our results suggest that marginal predation is a more common
 phenomenon than originally thought as it also applies to relatively small
 groups. Similarly, as marginal predation does not need the confusion
 effect to occur, it may occur in a wider range of predator–prey species
 pairings, for example those where the predators search for prey using
 nonvisual sensory modalities.
description: Group Size Plotted
 Points DataPlotted points of the
 fish and prey locations at the point of attack during group size
 trialsGroup Density Plotted
 Points DataPlotted points of the
 fish and prey locations at the point of attack during group density
 trialsGroup size attack and
 trial dataData on trials
 environmental factors and attacks for group size trialsGroup density attack and
 trial dataData on trials
 environmental factors and attacks for group density
 trials