cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qc3m7
title: Data from: Impacts of ocean acidification on sea urchin growth across the juvenile to mature adult life-stage transition is mitigated by warming

description: Understanding how growth trajectories of calcifying invertebrates are
 affected by changing climate requires acclimation experiments that follow
 development across life history transitions. In a long-term acclimation
 study, the effects of increased acidification and temperature on survival
 and growth of the tropical sea urchin Tripneustes gratilla from the early
 juvenile (5 mm test diameter- TD) through the developmental transition to
 the mature adult (60 mm TD) were investigated. Juveniles were reared in a
 combination of three temperature and three pH/pCO2 treatments, including
 treatments commensurate with global change projections. Elevated
 temperature and pCO2/pH both affected growth, but there was no interaction
 between these factors. The urchins grew more slowly at pH 7.6, but not at
 pH 7.8. Slow growth may be influenced by the inability to compensate
 coelomic fluid acid-base balance at pH 7.6. Growth was faster at +3 and +6
 °C compared to that in ambient temperature. Acidification and warming had
 strong and interactive effects on reproductive potential. Warming
 increased the gonad index, but acidification decreased it. At pH 7.6 there
 were virtually no gonads in any urchins regardless of temperature. The T.
 gratilla were larger at maturity under combined near-future warming and
 acidification scenarios (+3 °C/pH 7.8). Although the juveniles grew and
 survived in near-future warming and acidification conditions, chronic
 exposure to these stressors from an early stage altered allocation to
 somatic and gonad growth. In the absence of phenotypic adjustment, the
 interactive effects of warming and acidification on the benthic life
 phases of sea urchins may compromise reproductive fitness and population
 maintenance as global climatic change unfolds.
description: final data summary for
 dryadThis is the summary data
 for the paper contact the authors for explanation of the treatments
 codes.
DOI: 10.5061/dryad.50rb3
title: Data from: Predator experience overrides learned aversion to heterospecifics in stickleback species pairs

description: Predation risk can alter female mating decisions because the costs of mate
 searching and selecting attractive mates increase when predators are
 present. In response to predators, females have been found to plastically
 adjust mate preference within species, but little is known about how
 predators alter sexual isolation and hybridization among species. We
 tested the effects of predator exposure on sexual isolation between
 benthic and limnetic threespine sticklebacks (Gasterosteus spp.). Female
 discrimination against heterospecific mates was measured before and after
 females experienced a simulated attack by a trout predator or a control
 exposure to a harmless object. In the absence of predators, females showed
 increased aversion to heterospecifics over time. We found that predator
 exposure made females less discriminating and precluded this learned
 aversion to heterospecifics. Benthic and limnetic males differ in
 coloration, and predator exposure also affected sexual isolation by
 weakening female preferences for colourful males. Predator effects on
 sexual selection were also tested but predators had few effects on female
 choosiness among conspecific mates. Our results suggest that predation
 risk may disrupt the cognitive processes associated with mate choice and
 lead to fluctuations in the strength of sexual isolation between species.
description: Stickleback Female
 Preference DataEach row represents a
 single behavioral trial and the preference measures associated with that
 trial. Each female was tested twice so there are two rows per female. See
 Readme file for column descriptions.predmcLBallhetDryad.txt
DOI: 10.5061/dryad.gr060
title: Data from: Sida pradeepiana sp. nov. (Malvaceae) from India

description: The new species Sida pradeepiana is described from the Idukki district of
 Kerala state, India. It resembles S. alnifolia and S. rhomboidea, but
 differs by its concolorous-rhomboid leaves, unarticulated pedicels,
 mericarp apex beaked with a single muticous process and stellate pubescent
 mericarps and hilum of the seeds.
description: Comparative
 study
DOI: 10.5061/dryad.4407g
title: Data from: Maternal telomere length inheritance in the king penguin

description: Telomeres are emerging as a biomarker for ageing and survival, and are
 likely important in shaping life-history trade-offs. In particular,
 telomere length with which one starts in life has been linked to lifelong
 survival, suggesting that early telomere dynamics are somehow related to
 life-history trajectories. This result highlights the importance of
 determining the extent to which telomere length is inherited, as a crucial
 factor determining early life telomere length. Given the scarcity of
 species for which telomere length inheritance has been studied, it is
 pressing to assess the generality of telomere length inheritance patterns.
 Further, information on how this pattern changes over the course of growth
 in individuals living under natural conditions should provide some insight
 on the extent to which environmental constraints also shape telomere
 dynamics. To fill this gap partly, we followed telomere inheritance in a
 population of king penguins (Aptenodytes patagonicus). We tested for
 paternal and maternal influence on chick initial telomere length (10 days
 old after hatching), and how these relationships changed with chick age
 (at 70, 200 and 300 days old). Based on a correlative approach, offspring
 telomere length was positively associated with maternal telomere length
 early in life (at 10 days old). However, this relationship was not
 significant at older ages. These data suggest that telomere length in
 birds is maternally inherited. Nonetheless, the influence of environmental
 conditions during growth remained an important factor shaping telomere
 length, as the maternal link disappeared with chicks’ age.
description: Telomere length
 dataThis data includes
 telomere length for chicks at different ages (10, 70, 200 and 300
 days-old) and telomere lengths of their parents.This study was conducted
 on king penguins (Aptenodytes patagonicus), in the colony of “La Grande
 Manchotière” (20 000 breeding pairs) Possession island, Crozet archipelago
 (Terres Australes Antarctiques Françaises) located 46° 25’S; 51° 52’E.
 Data were collected during two consecutive field seasons (2009 and
 2010).data
 heredity S Reichert.xlsx
DOI: 10.5061/dryad.vf896
title: Data from: Replaying evolution to test the cause of extinction of one ecotype in an experimentally evolved population

description: In a long-term evolution experiment with Escherichia coli, bacteria in one
 of twelve populations evolved the ability to consume citrate, a previously
 unexploited resource in a glucose-limited medium. This innovation led to
 the frequency-dependent coexistence of citrate-consuming (Cit+) and
 non-consuming (Cit–) ecotypes, with Cit−bacteria persisting on the
 exogenously supplied glucose as well as other carbon molecules released by
 the Cit+ bacteria. After more than 10,000 generations of coexistence,
 however, the Cit−lineage went extinct; cells with the Cit−phenotype
 dropped to levels below detection, and the Cit−clade could not be detected
 by molecular assays based on its unique genotype. We hypothesized that
 this extinction was a deterministic outcome of evolutionary change within
 the population, specifically the appearance of a more-fit Cit+ ecotype
 that competitively excluded the Cit−ecotype. We tested this hypothesis by
 re-evolving the population from a frozen population sample taken within
 500 generations of the extinction and from another sample taken several
 thousand generations earlier, in each case for 500 generations and with
 20-fold replication. To our surprise, the Cit−type did not go extinct in
 any of these replays, and Cit−cells also persisted in a single replicate
 that was propagated for 2,500 generations. Even more unexpectedly, we
 showed that the Cit−ecotype could reinvade the Cit+ population after its
 extinction. Taken together, these results indicate that the extinction of
 the Cit−ecotype was not a deterministic outcome driven by competitive
 exclusion by the Cit+ ecotype. The extinction also cannot be explained by
 demographic stochasticity alone, as the population size of the Cit−ecotype
 should have been many thousands of cells even during the daily transfer
 events. Instead, we infer that the extinction must have been caused by a
 rare chance event in which some aspect of the experimental conditions was
 inadvertently perturbed.
description: Figure1-CitMinusExtinctionThis file contains the data documenting the extinction of the Cit- ecotypeFigure2-CitMinusReinvasionThis file contains the data on the ability of a Cit- clone to reinvade Cit+ clones and populations.Strain ListList of ID numbers of all clones and populationsStrainList.csv
DOI: 10.5061/dryad.pb3tr
title: Data from: Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata

description: Topographic changes during the Pleistocene glacial/interglacial cycles
 affected the distribution of coastline mangroves and influenced their
 population genetic structure. The submergence of the continental shelf off
 southeast China during the postglacial age caused coastline expansions and
 resulted in the colonization of mangroves. Here, we performed multilocus
 genome scans using amplified fragment-length polymorphisms to explore the
 effects of topography and natural selection in structuring Kandelia
 obovata populations. Long-term isolation by the Taiwan Strait since the
 end of the last glacial maximum, which obstructed gene flow,
 differentiated the Taiwanese and Chinese populations. Founders that
 colonized from both outlets of the Taiwan Strait were sourced from the
 northern South China Sea and the Ryukyus, thereby creating a melting pot
 in the Taiwan Strait. Inner-strait currents played roles as vectors for
 propagule dispersal among populations. Upon examination of the
 allele-frequency distributions of outlier loci, most negative outliers
 reflected the widespread polymorphisms shared by common ancestors.
 Furthermore, significant differentiation in the genetic components of
 positive outliers between this and other populations and the negative
 correlation with geographic distance suggested the presence of geography-
 or latitude-independent population divergence. Restored populations were
 compared with their sources and revealed biased sampling of nursery
 seedlings, which caused within-population substructures and reduced
 effective population sizes. This study indicated that multiple factors
 affect the population structure of the mangroves off southeast China.
description: AFLP
 lociThe zip file contains
 three sheets of AFLP loci of Kandelia obovata, the neutral loci, the
 negative-outlier loci, and the positive outlier loci.AFLP
 Data.zip
DOI: 10.5061/dryad.kk241
title: Data from: Testing the effects of ant invasions on non-ant arthropods with high-resolution taxonomic data

description: Invasions give rise to a wide range of ecological effects. Many invasions
 proceed without noticeable impacts on the resident biota, whereas others
 shift species composition and even alter ecosystem function. Ant invasions
 generate a broad spectrum of ecological effects, but controversy surrounds
 the extent of these impacts, especially with regard to how other
 arthropods are affected. This uncertainty in part results from the
 widespread use of low-resolution taxonomic data, which can mask the
 presence of other introduced species and make it difficult to isolate the
 effects of ant invasions on native species. Here, we use high-resolution
 taxonomic data to examine the effects of Argentine ant invasions on
 arthropods on Santa Cruz Island, California. We sampled arthropods in
 eight pairs of invaded and uninvaded plots and then collaborated with
 taxonomic experts to identify taxa in four focal groups: spiders, bark
 lice, beetles, and ants. Spiders, bark lice, and beetles made up ~40% of
 the 9868 non-ant arthropod individuals sampled; the majority of focal
 group arthropods were putatively native taxa. Although our results
 indicate strong negative effects of the Argentine ant on native ants, as
 is well documented, invaded and uninvaded plots did not differ with
 respect to the richness, abundance, or species composition of spiders,
 bark lice, and beetles. One common, introduced species of bark louse was
 more common in uninvaded plots than in invaded plots, and including this
 species into our analyses changed the relationship between bark louse
 richness vs. L. humile abundance from no relationship to a significant
 negative relationship. This case illustrates how failure to differentiate
 native and introduced taxa can lead to erroneous conclusions about the
 effects of ant invasions. Our results caution against unqualified
 assertions about the effects of ant invasions on non-ant arthropods, and
 more generally demonstrate that accurate assessments of invasion impacts
 depend on adequate information about species identity.
description: Fig1Data_HannaetalFig2Data_HannaetalFig3Data_Hannaetal
DOI: 10.5061/dryad.6s7p8
title: Data from: Description of two new species of Indo-Pacific Thylacoplethus and a new record of Thompsonia japonica (Rhizocephala: Akentrogonida: Thompsoniidae) from hermit, porcelain and mud crabs (Decapoda) based on morphological and molecular data

description: Rhizocephalans of the order Akentrogonida are parasitic barnacles that
 infest decapods, stomatopods, peracarids, and other cirripedes. Within
 this order, Thompsoniidae is found in decapods and stomatopods, and is a
 family comprised of species characterized by having multiple globular
 reproductive bodies (externae) erupting from the host’s extremities and
 abdominal surface, and connected internally by a root-like system. Two of
 the four genera currently accepted within Thompsoniidae, Thompsonia and
 Thylacoplethus, contain perhaps the most morphologically derived species
 within Akentrogonida. Herein we describe two new species of
 Thylacoplethus, T. porcellanus and T. umanguvatus, from the porcellanid
 and hermit crabs Petrolisthes scabriculus (Dana, 1852) and Calcinus
 morgani Rahayu and Forest, 1999, respectively. We also redescribe
 Thompsonia japonica Häfele, 1911 from a xanthid brachyuran crab based on
 morphological characters and DNA sequences of the nuclear 18S rDNA gene.
 The new species from the porcellanid crab comprises the first record of an
 akentrogonid rhizocephalan parasitizing a species of Porcellanidae. We
 reconstruct a molecular phylogeny of Akentrogonida using new and published
 DNA sequences, and we discuss our findings within an evolutionary context
 of host speciation. All species in the four thompsoniid genera are briefly
 reviewed, and a replacement name is proposed for the preoccupied Pottsia
 Høeg and Lützen, 1993.
description: Hiller_et_al_Rhizocephala_NEXUS.nexNexus file with 18S rDNA sequencesHiller_et_al_Rhizocephala_BayesTree.conBayesian tree obtained using the Nexus file also submitted
DOI: 10.5061/dryad.pp6k7
title: Data from: Inbreeding removes sex differences in lifespan in a population of Drosophila melanogaster

description: Sex differences in ageing rates and lifespan are common in nature, and an
 enduring puzzle for evolutionary biology. One possibility is that
 sex-specific mortality rates may result from recessive deleterious alleles
 in ‘unguarded’ heterogametic X or Z sex chromosomes (the unguarded X
 hypothesis). Empirical evidence for this is, however, limited. Here, we
 test a fundamental prediction of the unguarded X hypothesis in Drosophila
 melanogaster, namely that inbreeding shortens lifespan more in females
 (the homogametic sex in Drosophila) than in males. To test for additional
 sex-specific social effects, we studied the lifespan of males and females
 kept in isolation, in related same-sex groups, and in unrelated same-sex
 groups. As expected, outbred females outlived outbred males and inbreeding
 shortened lifespan. However, inbreeding-mediated reductions in lifespan
 were stronger for females, such that lifespan was similar in inbred
 females and males. We also show that the social environment, independent
 of inbreeding, affected male, but not female lifespan. In conjunction with
 recent studies, the present results suggest that asymmetric inheritance
 mechanisms may play an important role in the evolution of sex-specific
 lifespan and that social effects must be considered explicitly when
 studying these fundamental patterns.
description: Lifespan
 dataLifespan data for ms
 published in Biology Letters "Inbreeding removes sex differences in
 lifespan in a population of Drosophila melanogaster." This is a .csv
 file with the following variables (see ms for details): Set, Inbreeding
 treatment, Sex, Lifespan (in days), Social environment treatment, and
 whether the individual had to be censored (Censor = 0; in which case
 lifespan = day in which this happened) or not (Censor =
 1).data.csv
DOI: 10.5061/dryad.303hh
title: Data from: Optimizing mating encounters by sexually dimorphic movements

description: All organisms with sexual reproduction undergo a process of mating, which
 essentially involves the encounter of two individuals belonging to
 different sexes. During mate search, both sexes should mutually optimize
 their encounters, thus raising a question of how they achieve this. Here,
 we show that a population with sexually dimorphic movement patterns
 achieves the highest individual mating success under a limited lifespan.
 Extensive simulations found and analytical approximations corroborated the
 existence of conditions under which sexual dimorphism in the movement
 patterns (i.e. how diffusively they move) is advantageous over sexual
 monomorphism. Mutual searchers with limited lifespans need to balance the
 speed and accuracy of finding their mates, and dimorphic movements can
 solve this trade-off. We further demonstrate that the sexual dimorphism
 can evolve from an initial sexually monomorphic population. Our results
 emphasize the importance of considering mutual optimization in problems of
 random search.
description: simulation
 codesSimulation codes written
 in C++. These are used for creating data shown in the
 manuscript.
DOI: 10.5061/dryad.22sf7
title: Data from: Ecophysiological variation across a forest-ecotone gradient produces divergent climate change vulnerability within species

description: Climate change related risks and impacts on ectotherms will be mediated by
 habitats and their influence on local thermal environments. While many
 studies have documented morphological and genetic aspects of niche
 divergence across habitats, few have examined thermal performance across
 such gradients and directly linked this variation to contemporary climate
 change impacts. In this study, we quantified variation in thermal
 performance across a gradient from forest to gallery forest-savanna mosaic
 in Cameroon for a skink species (Trachylepis affinis) known to be
 diverging genetically and morphologically across that habitat gradient.
 Based on these results, we then applied a mechanistic modelling approach
 (NicheMapR) to project changes in potential activity, as constrained by
 thermal performance, in response to climate change. As a complimentary
 approach, we also compared mechanistic projections with climate-driven
 changes in habitat suitability based on species distribution models of
 forest and ecotone skinks. We found that ecotone skinks may benefit from
 warming and experience increased activity while forest skinks will likely
 face a drastic decrease in thermal suitability across the forest zone.
 Species distribution models projected that thermal suitability for forest
 skinks in coastal forests would decline but in other parts of the forest
 zone skinks are projected to experience increased thermal suitability. The
 results here highlight the utility of mechanistic approaches in revealing
 and understanding patterns of climate change vulnerability which may not
 be detected with species distribution models alone. This study also
 emphasizes the importance of intra-specific physiological variation, and
 habitat-specific thermal performance relationships in particular, in
 determining warming responses.
description: Trachylepis affinis
 forest and ecotone thermal toleranceCritical thermal minimum
 and maximum values measured for all individuals collected in the ecotone
 (n=7) and forest sites (n=29) from June 2015 to April
 2016.affinisctlimits.csvTrachylepis affinis locality points in CameroonList of coordinate points for sites in Cameroon where T. affinis has been found during the period of 2001 to 2005.affinislocalitynoduplicates.csvTrachylepis affinis raw maximum running speed dataMaximum running speed values (in m/s) measured at seven different body temperatures for individuals collected from ecotone (n=7) and forest sites (n=29) from June 2015 to April 2016.affinisspeeds.csvTrachylepis affinis thermal performance valuesRange of thermal physiological metrics for each individual collected in the ecotone (n=7) and forest sites (n=29) from June 2015 to April 2016. These values were extracted from the "double exponential" model fit to the raw maximum running speed data (Appendix 1, Table A1).affinisperformancedoubleexponential.csv
DOI: 10.5061/dryad.67kq8346
title: Data from: Different diversification rates between sexual and asexual organisms

description: Patterns of diversity reflect the balance between speciation and
 extinction over time. Here we estimate net diversification rates for
 samples of sexual and asexual rotifers using phylogenetic reconstructions
 from sequence data of one mtDNA locus, cytochrome oxidase c subunit I. All
 four clades of bdelloid rotifers, obligate asexuals, had higher number of
 species per clade and significantly higher accumulation of diversification
 events towards the root of the trees than the four clades of their sexual
 relatives, the monogonont rotifers. Such differences were robust to
 confounding effects of number of analysed sequences, haplotype diversity,
 overall genetic divergence or age of the clades. Our results support the
 idea that differences in diversification rates could thus be ascribed to
 different mechanisms of speciation, with ecological speciation as the most
 plausible mechanism for asexual organisms.
description: Adineta_65phylogenetic tree of the genus AdinetaBrachionus_calyciflorus_12phylogenetic tree of the species complex Brachionus calyciflorusBrachionus_plicatilis_36phylogenetic tree of the species complex Brachionus plicatilisPhilodina_73phylogenetic tree of the genus PhilodinaRotaria_rotatoria_78phylogenetic tree of the species complex Rotaria rotatoriaRotaria_sordida_19phylogenetic tree of the species complex Rotaria sordidaSynchaeta_15phylogenetic tree of the genus SynchaetaTestudinella_11phylogenetic tree of the genus Testudinella
DOI: 10.5061/dryad.2k11f
title: Data from: Aging parasites produce offspring with poor fitness prospects

description: Senescing individuals have poor survival prospects and low fecundity. They
 can also produce offspring with reduced survival and reproductive success.
 We tested the effect of parental age on the performance of descendants in
 the nematode Heligmosomoides polygyrus, an intestinal parasite of rodents.
 We found that offspring of senescing worms had reduced within-host
 survival and reduced egg shedding over the first month post-infection
 compared with offspring produced by young parents. These results suggest
 that declining offspring quality is a component of senescence in parasitic
 nematodes and might have evolutionary consequences for the optimal
 schedule of age-dependent investment into reproductive effort.
description: dryad_data