cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.559cs
title: Data from: Biodiversity in perennial and intermittent rivers: a meta-analysis

description: Comprehensive knowledge of the effects of disturbances on biodiversity is
 crucial for conservation and management, not least because ecosystems with
 low biodiversity may be the most vulnerable. In rivers, the role of
 disturbance in shaping aquatic biodiversity has mainly focused on floods.
 Perennial rivers (PRs) often flood, whereas intermittent rivers (IRs)
 flood, stop flowing and dry. Despite the recent and significant increase
 in research on IRs, controversy remains about whether they are more or
 less biodiverse than PRs. Our aim was to determine (Q1) if PRs and IRs
 differ in biodiversity and (Q2) if the direction and magnitude of the
 differences (effect sizes) are related to environmental (climate, season,
 habitat, longitudinal zonation and anthropogenic disturbance) and/or
 biological factors (taxonomic group). We conducted a meta-analysis on 44
 published studies of PR and IR biodiversity that had replicated data. We
 applied random effects models to the data to obtain weighted mean effect
 sizes for differences between PRs and IRs, and their confidence intervals,
 by first considering all studies and then by splitting studies into groups
 on the basis of the above factors. We found that biodiversity was
 significantly higher in PRs than in IRs (Q1). We also detected significant
 differences (PRs&gt;IRs) in studies of macroinvertebrates, in those
 conducted within arid and temperate climates, dry and wet sampling
 seasons, headwaters, and regions subject to different levels of
 anthropogenic disturbance (Q2). Our meta-analysis suggests that the
 expected increase in the prevalence of IRs in certain regions of the world
 due to global change could result in a decrease in freshwater
 biodiversity. To better manage and preserve aquatic biodiversity under
 future global change scenarios and to avoid potential ecosystem
 consequences of biodiversity loss, conservation efforts should be targeted
 towards those environmental conditions or taxonomic groups with
 significant differences (PRs&gt;IRs).
description: Meta-analysis_PRs_IRsPublished studies that recorded biodiversity of PRs and IRs. For each replicated study (i.e. with n &gt; 1): • We extracted means (i.e. P_M and Int_M), SDs (i.e. P_SD and Int_SD), and number of sites (i.e. P_N and Int_N). • We obtained information on site. In particular, we considered the following 6 factors, each with several levels within: climate, sampling season, habitat, longitudinal zonation, level of anthropogenic disturbance, and taxonomic group (see Table 1 and Appendix S3).
DOI: 10.5061/dryad.6sk0g
title: Data from: Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland

description: 1. The rapid loss of global biodiversity can greatly affect the
 functioning of above-ground components of ecosystems. However, how such
 biodiversity losses affect below-ground communities and linkages to soil
 carbon (C) sequestration is unclear. Here we describe how losses in plant
 functional groups (PFGs) affect soil microbial and nematode communities
 and net ecosystem exchange (NEE) in a 4-year removal experiment conducted
 on the Mongolian plateau, the world's largest remaining natural
 grassland. 2. Our results demonstrated that the biomasses or abundances of
 most components of the two below-ground communities (microbes and
 nematodes) were negatively affected by PFG loss and were positively
 related to above-ground plant biomass. The removal of dominant PFGs
 (perennial bunchgrasses and perennial rhizomatous grasses) reduced the
 biomass or abundance of below-ground community components while removal of
 less dominant PFGs (perennial forbs and annuals/biennials) did not change
 or increased the biomass or abundance of below-ground community
 components. 3. The biomass-based ratio of fungal to bacterial microbes and
 the number-based ratio of fungal-feeding to bacterial-feeding nematodes
 decreased with increasing PFG losses. Variation partitioning analyses
 showed that the identity of PFGs together with above-ground plant biomass
 explained most of the total variation in soil microbes and that the
 identity of PFGs and above-ground plant biomass together with nematode
 food resources explained most of the total variation in soil nematodes.
 The increase in NEE with PFG loss was mainly explained by decreases in
 above-ground plant biomass and the ratio of fungi to bacteria. 4.
 Synthesis. The shift of below-ground communities from a fungal-based to a
 bacterial-based energy channel as PFG richness decreases indicates that
 less diverse grassland ecosystems will have lower nutrient retention and
 hence be more sensitive to land use or climate change. The dominant
 effects of above-ground plant biomass and below-ground communities on NEE
 indicate that PFG loss resulting from land use or climate change has the
 potential to reduce C sequestration in semi-arid grassland soils. These
 findings suggest that predictive models may need to consider the
 composition of above-ground and below-ground communities in order to
 accurately simulate the dynamics of CO2 fluxes in terrestrial ecosystems.
description: BEF_data
DOI: 10.5061/dryad.fq22f
title: Data from: Effects of prior contest experience and contest outcome on female reproductive decisions and offspring fitness

description: Winning or losing a prior contest can influence the outcome of future
 contests, but it might also alter subsequent reproductive decisions. For
 example, losers may increase their investment in the current breeding
 attempt if losing a contest indicates limited prospects for future
 breeding. Using the burying beetle Nicrophorus vespilloides, we tested
 whether females adjust their prehatching and posthatching reproductive
 effort after winning or losing a contest with a same-sex conspecific.
 Burying beetles breed on carcasses of small vertebrates for which there is
 fierce intrasexual competition. We found no evidence that winning or
 losing a contest influenced reproductive investment decisions in this
 species. Instead, we show that a female's prior contest experience
 (regardless of its outcome) influenced the amount of posthatching care
 provided, with downstream consequences for the female's reproductive
 output; both winners and losers spent more time provisioning food to their
 offspring and produced larger broods than females with no contest
 experience. We discuss the wider implications of our findings and present
 a conceptual model linking contest-mediated adjustments in parental
 investment to population-level processes. We propose that the frequency of
 intraspecific contests could both influence and be influenced by
 population dynamics in species where contest experience influences the
 size and/or number of offspring produced.
description: PilakoutaHalfordRaczSmisethAMNAT2016Raw data on the effects of contest experience and contest outcome on female reproductive investment and offspring fitness in the burying beetle Nicrophorus vespilloides.
DOI: 10.5061/dryad.pr498
title: Data from: Macromtrium longipapillosum sp. nov. (Bryophyta, Orthotrichaceae) from Japan, with comments on M. comatum

description: The new species Macromtrium longipapillosum D. D. Li, J. Yu, T. Cao
 & S. L. Guo from Japan is described and illustrated by line
 drawings and photographs. The new species can be distinguished from all
 congeners by the combination of the following features: 1) lanceolate to
 oblong-lanceolate leaves with obtuse, acute to broadly acuminate apices;
 2) upper and median laminal cells with thin and inflated walls, with a
 single, large, occasionally forked papilla, 7–14 μm, occasionally up to 18
 μm, 3) basal cells near costae forming a ‘cancellina region’, 4) inner
 perichaetial leaves ovate lanceolate, abruptly narrowed to a long
 acuminate upper part; 5) short and left-twisted seta; and 6) obloid
 capsules with well-developed exostome teeth. We also revise the
 circumscription of Macromitrium comatum Mitt. and discuss the
 relationships of M. comatum with M. longipapillosum and other relevant
 species.
description: Data
 （2017-9-23）Papilla number and
 length in 14 specimens of Macromitrium longipapillosum and M. comatum,
 showing a discontinuous papilla variation pattern between the two
 speciesData_2017-9-23.docx
DOI: 10.5061/dryad.1m4gc
title: Data from: Reduced fitness in progeny from old parents in a natural population

description: A nongenetic, transgenerational effect of parental age on offspring
 fitness has been described in many taxa in the laboratory. Such a
 transgenerational fitness effect will have important influences on
 population dynamics, population age structure, and the evolution of aging
 and lifespan. However, effects of parental age on offspring lifetime
 fitness have never been demonstrated in a natural population. We show that
 parental age has sex-specific negative effects on lifetime fitness, using
 data from a pedigreed insular population of wild house sparrows. Birds
 whose parents were older produced fewer recruits annually than birds with
 younger parents, and the reduced number of recruits translated into a
 lifetime fitness difference. Using a long-term cross-fostering experiment,
 we demonstrate that this parental age effect is unlikely to be the result
 of changes in the environment but that it potentially is epigenetically
 inherited. Our study reveals the hidden consequences of late-life
 reproduction that persist into the next generation.
description: DataForMainAnalysisSchroederetal.2015PNASDataForMainAnalysisSchroederetal.2015PNAS.txt This file contains data on lifetime reproductive success of Lundy island house sparrows, and the age of their parents when the birds were born.ScriptForMainAnalysisSchroederetal.2015PNASR script of the main analysis
DOI: 10.5061/dryad.1b1d8
title: Data from: Dietary niche constriction when invaders meet natives: evidence from freshwater decapods

description: 1. Invasive species are a key driver of global environmental change, with
 frequently strong negative consequences for native biodiversity and
 ecosystem processes. Understanding competitive interactions between
 invaders and functionally similar native species provides an important
 benchmark for predicting the consequences of invasion. However, even
 though having a broad dietary niche is widely considered a key factor
 determining invasion success, little is known about the effects of
 competition with functionally similar native competitors on the dietary
 niche breadths of invasive species. 2. We used a combination of field
 experiments and field surveys to examine the impacts of competition with a
 functionally similar native crab species on the population densities,
 growth rates and diet of the globally widespread invasive red swamp
 crayfish in an African river ecosystem. 3. The presence of native crabs
 triggered significant dietary niche constriction within the invasive
 crayfish population. Further, growth rates of both species were reduced
 significantly, and by a similar extent, in the presence of one another. In
 spite of this, crayfish maintained positive growth rates in the presence
 of crabs, whereas crabs lost mass in the presence of crayfish.
 Consequently, over the three year duration of the study, crab abundance
 declined at those sites invaded by the crayfish, becoming locally extinct
 at one. 4. The invasive crayfish had a dramatic effect on ecosystem
 structure and functioning, halving benthic invertebrate densities and
 increasing decomposition rates four-fold compared to the crabs. This
 indicates that replacement of native crabs by invasive crayfish likely
 alters the structure and functioning of African river ecosystems
 significantly. 5. This study provides a novel example of the constriction
 of the dietary niche of a successful invasive population in the presence
 of competition from a functionally similar native species. This finding
 highlights the importance of considering both environmental and ecological
 contexts in order to predict and manage the impacts of invasive species on
 ecosystems.
description: Stable isotope
 dataStable isotope data for
 invasive crayfish (P. clarkii) and native crabs (P. loveni) from a in situ
 experiment (in 2010) and a field survey (2008, 2009, 2010) in the River
 Malewa in Kenya.SIA
 data_Malewa.xlsx
DOI: 10.5061/dryad.5gb67
title: Data from: Predator-driven brain size evolution in natural populations of Trinidadian killifish (Rivulus hartii)

description: Vertebrates exhibit extensive variation in relative brain size. It has
 long been assumed that this variation is the product of ecologically
 driven natural selection. Yet, despite more than 100 years of research,
 the ecological conditions that select for changes in brain size are
 unclear. Recent laboratory selection experiments showed that selection for
 larger brains is associated with increased survival in risky environments.
 Such results lead to the prediction that increased predation should favour
 increased brain size. Work on natural populations, however, foreshadows
 the opposite trajectory of evolution; increased predation favours
 increased boldness, slower learning, and may thereby select for a smaller
 brain. We tested the influence of predator-induced mortality on brain size
 evolution by quantifying brain size variation in a Trinidadian killifish,
 Rivulus hartii, from communities that differ in predation intensity. We
 observed strong genetic differences in male (but not female) brain size
 between fish communities; second generation laboratory-reared males from
 sites with predators exhibited smaller brains than Rivulus from sites in
 which they are the only fish present. Such trends oppose the results of
 recent laboratory selection experiments and are not explained by
 trade-offs with other components of fitness. Our results suggest that
 increased male brain size is favoured in less risky environments because
 of the fitness benefits associated with faster rates of learning and
 problem-solving behaviour.
description: Brain_size_raw
DOI: 10.5061/dryad.7rt02
title: Data from: Body size affects the evolution of hidden colour signals in moths

description: Many cryptic prey have also evolved hidden contrasting colour signals
 which are displayed to would-be predators. Given that these hidden
 contrasting signals may confer additional survival benefits to the prey by
 startling/intimidating predators, it is unclear why they have evolved in
 some species, but not in others. Here, we have conducted a comparative
 phylogenetic analysis of the evolution of colour traits in the family
 Erebidae (Lepidoptera), and found that the hidden contrasting colour
 signals are more likely to be found in larger species. To understand why
 this relationship occurs, we present a general mathematical model,
 demonstrating that selection for a secondary defence such as deimatic
 display will be stronger in large species when (i) the primary defence
 (crypsis) is likely to fail as its body size increases and/or (ii) the
 secondary defence is more effective in large prey. To test the model
 assumptions, we conducted behavioural experiments using a robotic moth
 which revealed that survivorship advantages were higher against wild birds
 when the moth has contrasting hindwings and large size. Collectively, our
 results suggest that the evolutionary association between large size and
 hidden contrasting signals has been driven by a combination of the need
 for a back-up defence and its efficacy.
description: Behavioral Experiment
 DataBehavioralExpData.xlsx
DOI: 10.5061/dryad.4cs45
title: Data from: Natural history constrains the macroevolution of foot morphology in European plethodontid salamanders

description: The natural history of organisms can have major effects on the tempo and
 mode of evolution, but few examples show how unique natural histories
 affect rates of evolution at macroevolutionary scales. European
 plethodontid salamanders (Plethodontidae: Hydromantes) display a
 particular natural history relative to other members of the family.
 Hydromantes commonly occupy caves and small crevices, where they cling to
 the walls and ceilings. On the basis of this unique and strongly selected
 behavior, we test the prediction that rates of phenotypic evolution will
 be lower in traits associated with climbing. We find that, within
 Hydromantes, foot morphological traits evolve at significantly lower rates
 than do other phenotypic traits. Additionally, Hydromantes displays a
 lower rate of foot morphology evolution than does a nonclimbing genus,
 Plethodon. Our findings suggest that macroevolutionary trends of
 phenotypic diversification can be mediated by the unique behavioral
 responses in taxa related to particular attributes of their natural
 history.
description: Hydromantes.dataMeasurement data for Hydromantes salamandersRcodeR script for running analyses
DOI: 10.5061/dryad.1v8kj
title: Data from: Nocturnality in Synapsids predates the origin of mammals by over 100 million years

description: Nocturnality is widespread among extant mammals and often considered the
 ancestral behavioural pattern for all mammals. However, mammals are nested
 within a larger clade, Synapsida, and non-mammalian synapsids comprise a
 rich phylogenetic, morphological and ecological diversity. Even though
 non-mammalian synapsids potentially could elucidate the early evolution of
 diel activity patterns and enrich the understanding of synapsid
 palaeobiology, data on their diel activity are currently unavailable.
 Using scleral ring and orbit dimensions, we demonstrate that nocturnal
 activity was not an innovation unique to mammals but a character that
 appeared much earlier in synapsid history, possibly several times
 independently. The 24 Carboniferous to Jurassic non-mammalian synapsid
 species in our sample featured eye morphologies consistent with all major
 diel activity patterns, with examples of nocturnality as old as the Late
 Carboniferous (ca 300 Ma). Carnivores such as Sphenacodon ferox and
 Dimetrodon milleri, but also the herbivorous cynodont Tritylodon longaevus
 were likely nocturnal, whereas most of the anomodont herbivores are
 reconstructed as diurnal. Recognizing the complexity of diel activity
 patterns in non-mammalian synapsids is an important step towards a more
 nuanced picture of the evolutionary history of behaviour in the synapsid
 clade.
description: Scleral ring and orbit
 morphologyThis table contains
 linear measurements of scleral rings and orbit morphology of avians,
 squamates, and fossil synapsids. All measurements are in mm. Columns refer
 to taxon names (taxon), orbit length (ol), maximum external scleral ring
 diameter (ext), maximum internal scleral ring diameter (int), the
 geometric mean of ol, ext, and int (geomm), the optical ratio (opt), and
 diel activity pattern (groups).scleral.rings.csvPhylogenyNewick tree file, matching the scleral ring and orbit morphology dataset.amniotes.phylo.nex
DOI: 10.5061/dryad.d6396sd
title: Data from: Genetic diagnosis of a rare myrmecochorous species, Plagiorhegma dubium (Berberidaceae): historical genetic bottlenecks and strong spatial structures among populations

description: Distribution of genetic variation over time and space is relevant to
 demographic histories, and tightly linked to ecological disturbances as
 well as evolutionary potential of an organism. Therefore, understanding
 the pattern of genetic diversity is a primary step in conservation and
 management projects for rare and threatened plant species. We used 8
 microsatellite markers to examine the level of genetic diversity, spatial
 structure and demographic history of Plagiorhegma dubium, a rare
 myrmecochorous herb, populations sampled across northeast Asia and
 Siberia. We found low within-population genetic variation associated with
 historical bottlenecks. Although pairwise FST values were not much higher
 than the ones found in similar life form species, STRUCTURE and PCoA
 revealed a clear broad-scale spatial pattern of genetic structure.
 Bayesian clustering (best K=6) and PCoA identified three populations that
 are distinctive from neighboring populations in the Korean peninsula,
 which suggests potential units for conservation and management plans in
 Korea. MIGRATE-N and BAYESASS showed that both contemporary (0.003-0.045)
 and historical migration rates (2e-5-4.6e-4) were low. Our findings
 provide a good example, where genetic considerations should be integrated
 for conservation and management plans of rare and threatened species.
description: Plagiorhegma ssr
 genotype
DOI: 10.5061/dryad.181qq
title: Data from: State-space modeling to support management of brucellosis in the Yellowstone bison population

description: The Yellowstone bison (Bison bison) exemplifies the challenge of
 conserving large mammals that migrate across the boundaries of
 conservation areas. Bison in Yellowstone are infected with brucellosis
 (Brucella abortus). Their seasonal movements can expose livestock to
 infection. We developed a Bayesian state-space model to reveal the
 influence of brucellosis on the dynamics of the Yellowstone bison
 population and to inform decisions on bison management. A model of
 frequency dependent transmission was superior to a density dependent model
 in its ability to predict out-of-sample observations of the probability of
 horizontal transmission (mean square prediction error frequency model =
 0.78, density dependent model = 0.91). Conditional on the frequency
 dependent model, the median transmission rate of brucellosis was 1.86
 year-1 (95% equal-tailed credible interval, BCI = 1.5, 2.2). The median of
 the posterior distribution of the basic reproductive ratio (R0) was 1.76
 (BCI = 1.47, 2.36). Seroprevalence of adult females varied around 60%
 during the last two decades; however only 13 of 100 adult females were
 infectious (BCI = 0.1, 0.15). Estimation of population growth rate (_) in
 the presence of brucellosis reflected the depressing effect of the disease
 on recruitment; _ for an infected population averaged 1.07 (BCI = 1.03,
 1.11) and for a healthy population _ = 1.12 (BCI = 1.07, 1.16). We used
 forecasting with a five year horizon to evaluate the ability of different
 actions to meet goals for management relative to a no action alternative.
 Annually removing 200 seropositive female bison increased the probability
 of reducing seroprevalence below 40% by 30-fold relative to no action and
 increased the probability of achieving a 50% reduction in transmission
 probability by a factor of 110 relative to no action. Annually vaccinating
 200 seronegative animals increased the probability of achieving a 50%
 reduction transmission probability by five fold over no action. Forecasts
 of the future state of the population became increasingly uncertain with
 increases in the forecast horizon. Our findings emphasize the necessity of
 iterative, adaptive management with a relatively short term commitment to
 action, a commitment that must be reevaluated frequently in response to
 new data and model forecasts.
description: Hobbs_et_al_Ecological_MonographThese data were collected by Yellowstone National Park. Details of data collection are given in the paper.Data files were created using R. Details on the data files are given in the text file Description of Data files.text