cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tv8ph
title: Data from: Phylogentic analysis of serine proteases from Russell’s viper (Daboia russelli siamensis) and Agkistrodon piscivorus leucostoma venom

description: Serine proteases are widely found in snake venoms. They have variety of
 functions including contributions to hemostasis. In this study, five
 serine protease were cloned and characterized from two different cDNA
 libraries. Factor V activator (RVV-V), alpha fibrinogenase (RVAF) and beta
 fibrinogenase (RVBF) from Russell’s viper (Daboia russelli siamensis), and
 plasminogen activator (APL-PA) and protein C activator (APL-C) from
 Agkistrodon piscivorus leucostoma. The snake venom serine proteases were
 clustered in phylogenetic tree according to their functions. KA/KS values
 suggested that accelerated evolution has occurred in the mature
 protein-coding regions in cDNAs of snake venom serine proteases.
description: SPNT2011SPAA2011
DOI: 10.5061/dryad.s1989
title: Data from: The influence of organic material and temperature on the burial tolerance of the blue mussel, Mytilus edulis: considerations for the management of marine aggregate dredging

description: Rationale and Experimental Approach: Aggregate dredging is a growing
 source of anthropogenic disturbance in coastal UK waters and has the
 potential to impact marine systems through the smothering of benthic fauna
 with organically loaded screening discards. This study investigates the
 tolerance of the blue mussel, Mytilus edulis to such episodic smothering
 events using a multi-factorial design, including organic matter
 concentration, temperature, sediment fraction size and duration of burial
 as important predictor variables. Results and Discussion: Mussel mortality
 was significantly higher in organically loaded burials when compared to
 control sediments after just 2 days. Particularly, M. edulis specimens
 under burial in fine sediment with high (1%) concentrations of organic
 matter experienced a significantly higher mortality rate (p&lt;0.01)
 than those under coarse control aggregates. Additionally, mussels exposed
 to the summer maximum temperature treatment (20°C) exhibited significantly
 increased mortality (p&lt;0.01) compared to those in the ambient
 treatment group (15°C). Total Oxygen Uptake rates of experimental
 aggregates were greatest (112.7 mmol m-2 day-1) with 1% organic loadings
 in coarse sediment at 20°C. Elevated oxygen flux rates in porous coarse
 sediments are likely to be a function of increased vertical migration of
 anaerobically liberated sulphides to the sediment-water interface.
 However, survival of M. edulis under bacterial mats of Beggiatoa spp.
 indicates the species’ resilience to sulphides and so we propose that the
 presence of reactive organic matter within the burial medium may
 facilitate bacterial growth and increase mortality through pathogenic
 infection. This may be exacerbated under the stable interstitial
 conditions in fine sediment and increased bacterial metabolism under high
 temperatures. Furthermore, increased temperature may impose metabolic
 demands upon the mussel that cannot be met during burial-induced
 anaerobiosis. Summary: Lack of consideration for the role of organic
 matter and temperature during sedimentation events may lead to an
 overestimation of the tolerance of benthic species to smothering from
 dredged material.
description: Mortality data from
 Burial ExperimentsBurialdata.xlsxSediment Total Oxygen Uptake DataTOUdata.xlsxSediment Analysis dataSedimentdata.xlsxMonitored abiotic variables from experimental VORTsVORTdata.xlsx
DOI: 10.15468/dl.bge9eb
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Exodeconus prostratus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 42 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000912-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6s0s8
title: Data from: Social familiarity affects Diana monkey (Cercopithecus diana diana) alarm call responses in habitat-specific ways

description: Male Diana monkeys produce loud and acoustically distinct alarm calls to
 leopards and eagles that propagate over long distances, much beyond the
 immediate group. Calling is often contagious, with neighbouring males
 responding to each other’s calls, indicating that harem males communicate
 both to local group members and distant competitors. Here, we tested
 whether male Diana monkeys responding to each other’s alarm calls
 discriminated familiar from unfamiliar callers in two populations in Taï
 Forest (Ivory Coast) and on Tiwai Island (Sierra Leone). At both sites, we
 found specific acoustic markers in male alarm call responses that
 discriminated familiar from unfamiliar callers, but response patterns were
 site-specific. On Tiwai Island, males responded to familiar males’ eagle
 alarms with ‘standard’ eagle alarm calls, whereas unfamiliar males
 triggered acoustically atypical eagle alarms. The opposite was found in
 Taï Forest where males responded to unfamiliar males’ eagle alarm calls
 with ‘standard’ eagle alarms, and with atypical eagle alarms to familiar
 males’ calls. Moreover, only Taï, but not Tiwai, males also marked
 familiarity with the caller in their leopard-induced alarms. We concluded
 that male Diana monkeys encode not only predator type but also signaller
 familiarity in their alarm calls, although in population-specific ways. We
 explain these inter-site differences in vocal behaviour in terms of
 differences in predation pressure and population density. We discuss the
 adaptive function and implications of this behaviour for the origins of
 acoustic flexibility in primate communication.
description: latency of
 responseslatency.txtTai_varFeatures of vocal responses from TaiTiwai_varFeatures of vocal responses from Tiwai
DOI: 10.6084/m9.figshare.30971629
title: <b>High-quality chromosome-level genomes of </b><b><i>Leymus chinensis</i></b>

description: We improved the <i>L. chinensis</i> assembly and generated full-length transcriptomes of the elite breeding line Lc6 to refine gene models.Note: *.combined* files is gene structure annotations with isoforms.*.primary* files is gene structure annotations with longest isoforms preserved only.
DOI: 10.6084/m9.figshare.30971629.v1
title: <b>High-quality chromosome-level genomes of </b><b><i>Leymus chinensis</i></b>

description: We improved the <i>L. chinensis</i> assembly and generated full-length transcriptomes of the elite breeding line Lc6 to refine gene models.Note: *.combined* files is gene structure annotations with isoforms.*.primary* files is gene structure annotations with longest isoforms preserved only.
DOI: 10.5061/dryad.9907j
title: Data from: Phenotypic integration between anti-predator behaviour and camouflage pattern in juvenile sticklebacks

description: Predation is a strong selective force that promotes the evolution of
 anti-predator behaviours and camouflage in prey animals. However, the
 independent evolution of single traits cannot explain how observed
 phenotypic variations of these traits are maintained within populations.
 We studied genetic and phenotypic correlations between anti-predator
 behaviours (shoaling and risk-taking) and morphology traits (pigmentation
 and size) in juvenile three-spined sticklebacks by using pedigree-based
 quantitative genetic analysis to test phenotypic integration (or complex
 phenotype) as an evolutionary response to predation risk. Individuals with
 strongly melanised (i.e. camouflaged) phenotype and genotype were less
 sociable to conspecifics but bolder during foraging under predation risk.
 Individuals with faster growing phenotype and genotype were bolder, and
 those with lager eyes were more fearful. These phenotypic integrations
 were not confounded with correlated plastic responses to predation risk
 because the phenotypes were measured in naïve fish born in the laboratory
 but originated from a natural population with predation pressure.
 Consistent selection for particular combinations of traits under predation
 pressure or pleiotropic genes might influence the maintenance of the
 genetic (co)variations and polymorphism in melanin colour, growth
 trajectory and behaviour patterns.
description: Kim_Velando_dataData on behaviours, melanin colouration and size of sticklebacks
DOI: 10.5061/dryad.3nr84
title: Data from: Reproductive isolation and cryptic introgression in a sky island enclave of Appalachian birds

description: Reproductive isolation is central to the speciation process, and cases
 where the strength of reproductive isolation varies geographically can
 inform our understanding of speciation mechanisms. Although generally
 treated as separate species, Black-capped chickadees (Poecile
 atricapillus) and Carolina chickadees (P. carolinensis) hybridize and
 undergo genetic introgression in many areas where they come into contact
 across the eastern United States and in the northern Appalachian
 Mountains. The Great Smoky Mountains harbor the last large breeding
 population of atricapillus in the southern Appalachians, isolated from the
 species’ main range by nearly 200 km. This population is believed to be
 reproductively isolated from local carolinensis due to an unusual,
 behaviorally mediated elevational range gap, which forms during the
 breeding season and may function as an incipient reproductive isolating
 mechanism. We examined the effectiveness of this putative isolating
 mechanism by looking for genetic introgression from carolinensis in Great
 Smoky Mountain atricapillus. We characterized this population and parental
 controls genetically using hundreds of amplified fragment length
 polymorphism (AFLP) loci as well as mitochondrial DNA (mtDNA) sequence
 data from cytochrome-b. Great Smoky Mountain atricapillus have experienced
 nuclear genetic introgression from carolinensis, but at much lower levels
 than other populations near the hybrid zone to the north. No mitochondrial
 introgression was detected, in contrast to northern contact areas. Thus,
 the seasonal elevational range gap appears to have been effective in
 reducing gene flow between these closely related taxa.
description: aflp full data set tab
 delimited for dryadTab delimited AFLP
 dataset. Taxa names in column A. Species in Column B. AFLP loci in
 subsequent colums, with marker presence denoted by '1', absence
 denoted by '0', and missing data denoted by
 '-9'.
DOI: 10.5061/dryad.m64qc
title: Data from: Predators modify the evolutionary response of prey to temperature change

description: As climate regimes shift in many ecosystems worldwide, evolution may be a
 critical process allowing persistence in rapidly changing environments.
 Organisms regularly interact with other species, yet whether
 climate-mediated evolution can occur in the context of species
 interactions is not well understood. We tested whether a species
 interaction could modify evolutionary responses to temperature. We
 demonstrate that predation pressure by Dipteran larvae (Chaoborus
 americanus) modified the evolutionary response of a freshwater crustacean
 (Daphnia pulex) to its thermal environment over approximately seven
 generations in laboratory conditions. Daphnia kept at 21°C evolved higher
 population growth rates than those kept at 18°C, but only in those
 populations that were also reared with predators. Furthermore,
 predator-mediated selection resulted in the evolution of elevated Daphnia
 thermal plasticity. This laboratory natural selection experiment
 demonstrates that biotic interactions can modify evolutionary adaptation
 to temperature. Understanding the interplay between multiple selective
 forces can improve predictions of ecological and evolutionary responses of
 organisms to rapid environmental change.
description: tseng-oconnor-rawdata_fordryadexcel data file, 3 data sheets, 1 sheet with file and experiment description
DOI: 10.5061/dryad.4jp16
title: Data from: Applying community ecological theory to maximize productivity of cultivated biocrusts

description: Degraded rangelands around the world may benefit from the reestablishment
 of lost biological soil crusts (biocrusts, soil surface
 cryptogamic-microbial communities). Cultivation of biocrust organisms is
 the first step in this process, and may benefit from harnessing species
 interactions. Species interactions are a dominant force structuring
 ecological communities. One key element of community structure, species
 richness, is itself important because it can promote the productivity of
 the entire community. Here, we use biological soil crusts as a model to
 test the effects of species interactions on production of biocrust
 materials for use in ecosystem rehabilitation. We screened eight different
 moss and lichen species from semi-arid rangelands of Montana, USA, for
 growth potential under two watering regimes. Mosses generally grew well,
 but we were unable to cultivate the selected lichen species. We produced a
 &gt;400% increase in the biomass of one species (Ceratodon purpureus).
 We tested whether a parasite-host relationship between two lichens could
 be used to enhance productivity of the parasite species, but this also
 resulted in no net gain of lichen productivity. Finally, we constructed
 all possible community combinations from a pool of five moss species to
 test for overyielding (community productivity exceeding that expected from
 the growth of community members in monoculture), and to determine both if,
 and the mode in which, species richness increases productivity.
 Polycultures yielded more than would be expected based upon the production
 of community constituents in monoculture. Using structural equation models
 we determined that there was a modest effect of species richness on
 community productivity (r = 0.24-0.25), which was independent of a
 stronger effect of the identity of species in the community (r =
 0.41-0.50). These results will contribute to the optimization of biocrust
 cultivation, promoting the development of this emerging ecological
 rehabilitation technology.
description: Greenhouse monitoring
 dataCover through time of
 added biocrust species in three greenhouse experiments. File also includes
 derived data such as overyield and productivity as defined in
 text.
DOI: 10.5061/dryad.84c78
title: Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

description: Climate change, fisheries pressure on penguin prey, and direct human
 disturbance of wildlife have all been implicated in causing large shifts
 in the abundance and distribution of penguins in the Southern Ocean.
 Without mark-recapture studies, understanding how colonies form and, by
 extension, how ranges shift is challenging. Genetic studies, particularly
 focused on newly established colonies, provide a snapshot of colonisation
 and can reveal the extent to which shifts in abundance and occupancy
 result from changes in demographic rates (e.g., reproduction and survival)
 or migration among suitable patches of habitat. Here we describe the
 population structure of a colonial seabird breeding across a large
 latitudinal range in the Southern Ocean. Using multilocus microsatellite
 genotype data from 510 Gentoo penguin (Pygoscelis papua) individuals from
 14 colonies along the Scotia Arc and Antarctic Peninsula, together with
 mitochondrial DNA data, we find strong genetic differentiation between
 colonies north and south of the Polar Front, that coincides geographically
 with the taxonomic boundary separating the subspecies P. p. papua and P.
 p. ellsworthii. Using a discrete Bayesian phylogeographic approach, we
 show that southern Gentoos expanded from a possible glacial refuge in the
 centre of their current range, colonising regions to the north and south
 through rare, long-distance dispersal. Our findings show that this
 dispersal is important for new colony foundation and range expansion in a
 seabird species that ordinarily exhibits high levels of natal philopatry,
 but persistent oceanographic features serve as barriers to movement.
description: GPS_Coordinates_ColoniesThis file contains the GPS coordinates (Longitude West and Latitude South) and UTM coordinates for the 14 colonies where samples were obtained.Microsatellite_genotypes_Arlequin_formatThis file contains the microsatellite genotypes for each individual penguin, set by colony, in a format that can be used directly in Arlequin. The 8 microsatellite loci are labelled at the top in a comment.Microsatellite_genotypes_txtThis file contains the microsatellite genotypes for each individual penguin, set by colony, in a format that can be used directly in Arlequin (presented here in a .txt file). The 8 microsatellite loci are labelled at the top in a comment.
DOI: 10.5061/dryad.rk64m4c
title: Data from: The fluctuating world of a tundra predator guild: bottom-up constraints overrule top-down species interactions in winter

description: Global warming is predicted to change ecosystem functioning and structure
 in Arctic ecosystems by strengthening top-down species interactions, i.e.
 predation pressure on small herbivores and interference between predators.
 Yet, previous research is biased towards the summer season. Due to greater
 abiotic constraints, Arctic ecosystem characteristics might be more
 pronounced in winter. Here we test the hypothesis that top-down species
 interactions prevail over bottom-up effects in Scandinavian mountain
 tundra (Northern Sweden) where effects of climate warming have been
 observed and top-down interactions are expected to strengthen. But we test
 this a-priori hypothesis in winter and throughout the 3-4 year rodent
 cycle, which imposes additional pulsed resource constraints. We used
 snowtracking data recorded in 12 winters (2004-2015) to analyse the
 spatial patterns of a tundra predator guild (arctic fox Vulpes lagopus,
 red fox Vulpes vulpes, wolverine Gulo gulo) and small prey (ptarmigan,
 Lagopus spp). The a-priori top-down hypothesis was then tested through
 structural equation modelling, for each phase of the rodent cycle. There
 was weak support for this hypothesis, with top-down effects only discerned
 on arctic fox (weakly, by wolverine) and ptarmigan (by arctic fox) at
 intermediate and high rodent availability respectively. Overall, bottom-up
 constraints appeared more influential on the winter community structure.
 Cold specialist predators (arctic fox and wolverine) showed variable
 landscape associations, while the boreal predator (red fox) appeared
 strongly dependent on productive habitats and ptarmigan abundance. Thus,
 we suggest that the unpredictability of food resources determines the
 winter ecology of the cold specialist predators, while the boreal predator
 relies on resource rich habitats. The constraints imposed by winters and
 temporary resource lows should therefore counteract productivity-driven
 ecosystem change and have a stabilizing effect on community structure.
 Hence, the interplay between summer and winter conditions should determine
 the rate of Arctic ecosystem change in the context of global warming.
description: Snowtrack abundance
 index of an arctic predator guild and their main prey in Vindelfjällen,
 2004-2015Excel file containing
 three sheets: Abundance_index_2004_2015 ; Environmental_data ;
 Phase_of_rodent_cycleTriangle_data_2004_2015.xlsx
DOI: 10.5061/dryad.n541d0t
title: Data from: Biological interactions mediate context and species-specific sensitivities to salinity

description: Toxicants have both sub-lethal and lethal effects on aquatic biota,
 influencing organism fitness and community composition. However, toxicant
 effects within ecosystems may be altered by interactions with abiotic and
 biotic ecosystem components, including biological interactions.
 Collectively, this generates the potential for toxicant sensitivity to be
 highly context dependent, with significantly different outcomes in
 ecosystems than laboratory toxicity tests predict. We experimentally
 manipulated stream macroinvertebrate communities in 32 mesocosms to
 examine how communities from a low-salinity site were influenced by
 interactions with those from a high-salinity site along a gradient of
 salinity. Relative to those from the low-salinity site, organisms from the
 high-salinity site were expected to have greater tolerance and fitness at
 higher salinities. This created the potential for both salinity and
 tolerant-sensitive organism interactions to influence communities. We
 found that community composition was influenced by both direct toxicity
 and tolerant-sensitive organism interactions. Taxon and context-dependent
 responses included: (i) direct toxicity effects, irrespective of biotic
 interactions; (ii) effects that were owing to the addition of tolerant
 taxa, irrespective of salinity; (iii) toxicity dependent on
 sensitive-tolerant taxa interactions; and (iv) toxic effects that were
 increased by interactions. Our results reinforce that ecological processes
 require consideration when examining toxicant effects within ecosystems.
description: Cotter01_densitiesEstimated densities of organisms from the Cotter River. These data have had all taxa common to Cunningham and Cotter or Cunningham only removed.Environmental data.Corresponding environmental data.env5.csv
DOI: 10.5061/dryad.618fv
title: Data from: Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms

description: Selfing is assumed to reduce selection efficacy, especially purifying
 selection. This can be tested using molecular data, for example by
 comparing the Dn/Ds ratio between selfing and outcrossing lineages. So
 far, little evidence of relaxed selection against weakly deleterious
 mutations (as inferred by a higher Dn/Ds ratio) in selfers as compared to
 outcrossers has been found, contrary to the pattern often observed between
 asexual and sexual lineages. However, few groups have been studied to
 date. To further test this hypothesis, we compiled and analysed
 chloroplastic sequence data sets in several plant groups. We found a
 general trend towards relaxed selection in selfers in our data sets but
 with weak statistical support. Simulations suggested that the results were
 compatible with weak-to-moderate Dn/Ds ratio differences in selfing
 lineages. Simple theoretical predictions also showed that the ability to
 detect relaxed selection in selfers could strongly depend on the
 distribution of the effects of deleterious mutations on fitness. Our
 results are compatible with a recent origin of selfing lineages whereby
 deleterious mutations potentially have a strong impact on population
 extinction or with a more ancient origin but without a marked effect of
 deleterious mutations on the extinction dynamics.
description: AlignmentsThis folder contain all the clean alignments used for PAML analyses. The name of the files are of the form TaxonomicGroup_Gene.phy.Alignements.zipTreesThis text file contains all the trees used for the PAML analyses in newick format. As mentioned in the file, the PAML annotation (#1) was used to annotate SELF branches.