cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4ps8k
title: Data from: Reproductive isolation among allopatric Drosophila montana populations

description: An outstanding goal in speciation research is to trace the mode and tempo
 of the evolution of barriers to gene flow. Such research benefits from
 studying incipient speciation, in which speciation between populations has
 not yet occurred but where multiple potential mechanisms of reproductive
 isolation (RI: i.e. premating, postmating-prezygotic (PMPZ), and
 postzygotic barriers) may act. We used such a system to investigate these
 barriers among allopatric populations of Drosophila montana. In all
 heteropopulation crosses we found premating (sexual) isolation which was
 either symmetric or asymmetric depending on the population pair compared.
 Postmating isolation was particularly strong in crosses involving males
 from one of the study populations, and while sperm were successfully
 transferred, stored and motile, we experimentally demonstrated that the
 majority of eggs produced were unfertilized. Thus, we identified the
 nature of a PMPZ incompatibility. There was no evidence of intrinsic
 postzygotic effects. Measures of absolute and relative strengths of pre-
 and post-mating barriers showed that populations differed in the mode and
 magnitude of RI barriers. Our results indicate that incipient RI among
 populations can be driven by different contributions of both premating and
 PMPZ barriers occurring between different population pairs and without the
 evolution of postzygotic barriers.
description: Jennings et al 2014
 associated DATA DRYAD deposit in Tab delimited formatThis data file consists
 of the data used for analysis and subsequent display. For each
 table/figure generated, the spreadsheet indicates the data that were used.
 The ReadMe file describes the data for each set of columns corresponding
 to display items in the paper. Read me text is listed for rows and columns
 when imported into Excel as a comma delimited file.Jennings et al 2014 Dryad
 text.txt
DOI: 10.5061/dryad.rb5hr
title: Data from: Chronic exposure to low-dose radiation at Chernobyl favours adaptation to oxidative stress in birds

description: 1. Ionizing radiation produces oxidative stress, but organisms can adapt
 to their exposure with physiological adaptive responses. However, the role
 of radioadaptive responses in wild populations remains poorly known. 2. At
 Chernobyl, studies of birds and other taxa including humans show that
 chronic exposure to radiation depletes antioxidants and increases
 oxidative damage. Here we present analyses of levels of the most important
 intracellular antioxidant (i.e., glutathione, GSH), its redox status, DNA
 damage and body condition in 16 species of birds exposed to radiation at
 Chernobyl. We use an approach that allows considering the individual bird
 as the sampling unit while controlling for phylogenetic effects, thus
 increasing the statistical power by avoiding the use of species means as
 done for most previous comparative studies. 3. As a consequence, we found
 a pattern radically different from previous studies in wild populations,
 showing that GSH levels and body condition increased, and oxidative stress
 and DNA damage decreased, with increasing background radiation. Thus, when
 several species are considered, the overall pattern indicates that birds
 are not negatively affected by chronic exposure to radiation and may even
 obtain beneficial hormetic effects following an adaptive response.
 Analysis of the phylogenetic signal supports the existence of adaptation
 in the studied traits, particularly in GSH levels and DNA damage. 4. We
 also show that, under equal levels of radiation, the birds that produce
 larger amounts of the pigment pheomelanin and lower amounts of eumelanin
 pay a cost in terms of decreased GSH levels, increased oxidative stress
 and DNA damage, and poorer body condition. Radiation, however, diminished
 another potential cost of pheomelanin, namely its tendency to produce free
 radicals when exposed to radiation, because it induced a change toward the
 production of less pro-oxidant forms of pheomelanin with higher
 benzothiazole-to-benzothiazine ratios, which may have facilitated the
 acclimation of birds to radiation exposure. 5. Our findings represent the
 first evidence of adaptation to ionizing radiation in wild animals, and
 confirm that pheomelanin synthesis represents an evolutionary constraint
 under stressful environmental conditions because it requires GSH
 consumption.
description: Chernobyl2010_Dryad
DOI: 10.5061/dryad.61rq8
title: Data from: Parental exposure modulates the effects of UV-B on offspring in guppies

description: 1.The environment experienced by parents can alter offspring phenotypes.
 Such developmental plasticity is beneficial when it optimises offspring
 responses to their prevailing environment. Plasticity may be detrimental,
 however, if there is a mismatch between parental and offspring
 environments, although reversible acclimation within individuals could
 counteract a developmental mismatch. 2.UV-B radiation damages cells
 directly and by increasing reactive oxygen species (ROS) formation. There
 are indications that the developmental environment can influence ROS
 defences, which could enhance performance and fitness. Additionally,
 animals exposed to UV-B can acclimate to increase their antioxidant
 defences and thereby reduce ROS-induced damage. Our aim was to test
 experimentally whether there are transgenerational effects of UV-B
 exposure. We tested the hypothesis that parental exposure to UV-B
 modulates offspring ROS defence mechanisms to reduce the negative effects
 of UV-B in offspring. 3.In a fully factorial experiment, we show that
 exposing guppies (Poecilia reticulata) to UV-B increased the resilience of
 their offspring to the negative effects of UV-B. When exposed to UV-B,
 offspring from parents also exposed to UV-B had significantly greater
 sustained swimming performance compared to controls. Higher swimming
 performance was paralleled by increased catalase activity and glutathione
 concentrations, and reduced ROS-induced damage to membranes and proteins.
 There was no effect of parental exposure to UV-B on offspring superoxide
 dismutase activity, resting and active metabolic rates, or offspring size.
 However, parental exposure to UV-B increased damage to proteins and
 infection rates by white spot fungus in control (no UV-B) offspring. 4.Our
 results showed that UV-B acts as a signal that can induce developmental
 modification of phenotypes. Transgenerational matching of offspring
 phenotypes is likely to have a fitness advantage in environments exposed
 to UV-B. However, the trade-off between the beneficial effects of parental
 UV-B exposure on offspring performance when exposed to UV-B, and the
 increased susceptibility to infection and protein damage when offspring
 are not exposed to UV-B can be important in determining the resilience of
 populations in variable and modified environments.
description: Data associated with
 Ghanizadeh-Kazeroni et alExcel file containing
 all data used in the publication. Different experimental responses are
 presented on separate sheets in the Excel file, and the first sheet
 (Metadata) provides explanations for each entry.Ghanizadeh-Kazeroni et
 al_data.xlsx
DOI: 10.5061/dryad.8vg83db
title: Data from: Odor is linked to adrenocortical function and male ornament size in a colonial seabird

description: Crested auklets (Aethia cristatella), colonial seabirds of Alaska and
 Siberia, emit a citrus-like odorant from wick-like feathers. We examined
 whether the odorant emission is linked to adrenocortical function and
 correlated with size of the crest feather ornament. Conventional signals
 like the size of crest ornament are inexpensive to produce and thus may be
 prone to deception. However, assessment signals such as the odorant could
 be more reliable if they impose costs and more proximate since they are
 continually produced. This may be the case for the crested auklet’s
 volatile aldehyde odorant. The signal is composed of highly volatile
 chemicals that appear to be products of fatty acid metabolism.
 Adrenocortical function helps to mobilize endogenous resources for
 metabolism. Elevation of corticosterone may be needed to sustain a
 reliable chemical signal, but there are physiological costs for prolonged
 elevation of circulating corticosterone. We predicted that higher odorant
 emissions would be correlated with larger crest ornaments. Furthermore, we
 predicted that odorant emissions would be linked to adrenocortical
 response. Octanal, the most abundant compound in the citrus-like odorant,
 was positively correlated with crest size in males, and adrenocortical
 response explained 42% of the variation in octanal emissions, after
 controlling for stage of the breeding period. Adrenocortical response was
 positively correlated with octanal emissions (rs = 0.57) in females. We
 conclude that dominant individuals with greater capacity to mount a more
 robust stress response may have greater capacity to sustain odorant
 secretions.
description: DouglasEtAlCrestedAukletMaleOdorCortBigKoniuji2002Annotated open office spreadsheet with data for male crested aukletsDouglasEtAlCrestedAukletFemaleOdorCortBigKoniuji2002Annotated open office spreadsheet with data for female Crested Auklets from Big Koniuji Island, Alaska 2002
DOI: 10.5061/dryad.cn4d8bv4
title: Data from: Sex roles and mutual mate choice matters during mate sampling

description: The roles of females and males in mating competition and mate choice have
 lately proven more variable, between and within species, than previously
 thought. In nature, mating competition occurs during mate search, and is
 expected to be regulated by the numbers of potential mates and same-sex
 competitors. Here, we present the first study to test how a temporal
 change in sex roles affects mating competition and mate choice during mate
 sampling. Our model system (the marine fish Gobiusculus flavescens) is
 uniquely suitable because of its change in sex roles, from conventional to
 reversed, over the breeding season. As predicted from sex role theory,
 courtship was typically initiated by males and terminated by females early
 in the breeding season. The opposite pattern was observed late in the
 season, at which time several females often simultaneously courted the
 same male. Mate-searching females visited more males early than late in
 the breeding season. Our study shows that mutual mate choice and mating
 competition can have profound effects on female and male behavior. Future
 work needs to consider the dynamical nature of mating competition and mate
 choice if we aim to fully understand sexual selection in the wild.
description: MS-dataFile contains summarized data (per female) about mate sampling events during observations of focal female two-spotted gobies (Gobiusculus flavescens)encounterFile contains data from each encounter with a male two-spotted goby (Gobiusculus flavescens)that included courtship
DOI: 10.5061/dryad.r139p
title: Data from: Demographic and population-genetic tests provide mixed support for the abundant center hypothesis in the endemic plant Leavenworthia stylosa

description: The abundant centre hypothesis (ACH) assumes that population abundance,
 population size, density and per-capita reproductive output should peak at
 the centre of a species' geographic range and decline towards the
 periphery. Increased isolation among and decreased reproductive output
 within edge populations should reduce within-population genetic diversity
 and increase genetic differentiation among edge relative to central
 populations. The ACH also predicts asymmetrical gene flow, with net
 movement of migrants from the centre to edges. We evaluated these
 ecological assumptions and population-genetic predictions in the endemic
 flowering plant Leavenworthia stylosa. Although populations were more
 spatially isolated near range edges, the geographic centre was surrounded
 by and not coincident with areas of peak population abundance, and plant
 density increased towards range edges. Per-capita seed number was not
 associated with distance to the range centre, but seed number/m2 increased
 near range edges. In support of ACH predictions, allelic diversity at 12
 microsatellite loci declined with distance from the range centre, and
 pairwise FST values were higher between edge populations than between
 central populations. Coalescent analyses confirmed that gene flow was most
 infrequent between edge populations, but there was not an asymmetric
 pattern of gene flow predicted by the ACH. This study shows that
 among-population demographic variability largely did not support the ACH,
 while patterns of genetic diversity, differentiation and gene flow were
 generally consistent with its predictions. Such mixed support has
 frequently been observed in tests of the ACH and raises concerns regarding
 the generality of this hypothesis for species range limits.
description: Microsatellite alleles
 for Leavenworthia stylosa in genepop formatAlleles for 12
 microsatellite loci scored at Washington State University by AL Dixon.
 Data file is in GENEPOP format.Dryad-genepop.xlsxPopulation locations for Leavenworthia stylosa and field and genetic population meansLatitude and longitude for 68 extant Leavenworthia stylosa populations. Population means for density, coefficient of variation for plant density, flower number, fruit number, fruit set, and average seed number per flower. All population means were collected in the field by AL Dixon, CR Herlihy, and JW Busch. Expected heterozygosity and allelic diversity were calculated using GENEPOP and HP-RARE, respectively from 12 microsatellite loci scored by AL Dixon at Washington State University.Dryad.xlsx
DOI: 10.5061/dryad.p281g
title: Data from: The importance of crown dimensions to improve tropical tree biomass estimates

description: Tropical forests play a vital role in the global carbon cycle, but the
 amount of carbon they contain and its spatial distribution remain
 uncertain. Recent studies suggest that once tree height is accounted for
 in biomass calculations, in addition to diameter and wood density, carbon
 stock estimates are reduced in many areas. However, it is possible that
 larger crown sizes might offset the reduction in biomass estimates in some
 forests where tree heights are lower because even comparatively short
 trees develop large, well-lit crowns in or above the forest canopy. While
 current allometric models and theory focus on diameter, wood density, and
 height, the influence of crown size and structure has not been well
 studied. To test the extent to which accounting for crown parameters can
 improve biomass estimates, we harvested and weighed 51 trees (11-169 cm
 diameter) in southwestern Amazonia where no direct biomass measurements
 have been made. The trees in our study had nearly half of total
 aboveground biomass in the branches (44 ± 2 %), demonstrating the
 importance of accounting for tree crowns. Consistent with our predictions,
 key pantropical equations that include height, but do not account for
 crown dimensions, underestimated the sum total biomass of all 51 trees by
 11 to 14 %, primarily due to severe underestimates of many of the largest
 trees. In our models, including crown radius greatly improves performance
 and reduces error, especially for the largest trees. In addition, over the
 full dataset, crown radius marginally explained more variation in
 aboveground biomass (10.5 %) than height (6.0 %). Crown form is also
 important: trees with a monopodial architectural type are estimated to
 have 21-44 % less mass than trees with other growth patterns. Our analysis
 suggests that accounting for crown allometry would substantially improve
 the accuracy of tropical estimates of tree biomass and its distribution in
 primary and degraded forests.
description: Tree Biomass Data from
 Madre de Dios, PeruDirectly-measured tree
 biomass data from Madre de Dios, Peru. Fifty-one trees were weighed, with
 diameters ranging from 10 to 169 cm. Twelve trees have diameters exceeding
 100 cm. Dataset includes diameter, total height, height of the first
 branch, wood density, crown radius, crown area, an architectural
 classification (monopodial or not), wood density, stem mass, crown mass,
 and total aboveground biomass.Goodman et al 2013_Madre de
 Dios Tree Biomass Data.xlsx
DOI: 10.5061/dryad.136bm
title: Data from: A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes

description: Technological and methodological advances have facilitated the use of
 genetic data to infer census population size (Nc) in natural populations,
 particularly where traditional mark-and-recapture is challenging. The
 effective number of breeders (Nb) describes how many adults effectively
 contribute to a cohort and is often correlated with Nc. Predicting Nc from
 Nb or vice-versa in species with overlapping generations has important
 implications for conservation by permitting (i) estimation of the more
 difficult to quantify variable and (ii) inferences of Nb/Nc relationships
 in related species lacking data. We quantitatively synthesized Nb/Nc
 relationships in three salmonid fishes where sufficient data has recently
 accumulated. Mixed-effects models were analyzed in which each variable was
 included as a dependent variable or predictor term (Nb from Nc and vice
 versa). Species-dependent Nb/Nc slope estimates were significantly
 positive in two of three species; variation in species slopes were likely
 due to varying life histories and reinforce caution when inferring Nb/Nc
 from taxonomically-related species. Models provided maximum probable
 estimates for Nb and Nc for two species. However, study, population, and
 year effects explained substantial amounts of variation (39-57%).
 Consequently, prediction intervals were wide and included or were close to
 zero for all population sizes and species; model predictive utility was
 limited. Cost-benefit trade-offs when estimating Nb and/or Nc were also
 discussed using a real-world system example. Our findings based on
 salmonids suggest that no short-cuts currently exist when estimating
 population size; researchers should focus on quantifying the variable of
 interest or be aware of caveats when inferring the desired variable
 because of cost or logistics. We caution that the salmonid species
 examined share life-history traits that may obscure relationships between
 Nb and Nc. Sufficient data on other taxa were unavailable; additional
 research examining Nb/Nc relationships in species with potentially
 relevant life-history trait differences (e.g. differing survival curves)
 are needed.
description: Yates_et_al_2016_datasetData associated with quantitative synthesis examining Nb/Nc relationships among three salmonid fishes
DOI: 10.5061/dryad.190kg
title: Data from: Multi-trophic guilds respond differently to changing elevation in a subtropical forest

description: Negative relationships between species richness and elevation are common
 and attributed to changes in single environmental properties associated to
 elevation, such as temperature and habitat area. However, research has
 lacked taxonomic breadth and comprehensive elevation studies that consider
 multiple groups from different trophic levels are rare. We thus analysed
 24 groups of plants, arthropods, and microorganisms grouped into six
 trophic guilds (predators, detritivores, herbivores, plants, bacteria and
 fungi) along a relatively short elevational gradient (~600 m) in a
 subtropical forest in south-east China. The total species richness of all
 organisms was not related to elevation, nor was the richness of plants,
 herbivores or microorganisms. However, species richness and abundance in
 two major trophic guilds of arthropods changed with elevation, which was
 mediated by changes in elevation-associated habitat properties.
 Specifically, deadwood mass increased with elevation, which increased
 detritivore richness indirectly via detritivore abundance, thus supporting
 the ‘more individuals hypothesis’. In contrast, lower predator richness at
 higher elevations was directly related to lower mean temperatures, which
 had no effect on abundance. Our study demonstrates that even along
 relatively short gradients, elevation can have strong direct and
 abundance-mediated effects on species richness, but with effects varying
 from positive to negative signs depending on local resource availability
 and the characteristics of groups or trophic guilds. If elevation
 positively influences local environmental properties that benefit a given
 group, richness can increase towards higher elevations. Thus, the effect
 of global change in mountainous regions should be evaluated within the
 local environmental context using multi-taxon approaches.
description: Dataset for Binkenstein
 et al., Multi-trophic guilds respond differently to changing elevation in
 a subtropical forestThe data set is
 described in detail in the associated README file.
DOI: 10.5061/dryad.j11s7
title: Data from: Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent

description: Currently, the effects of chronic, continuous low dose environmental
 irradiation on the mitochondrial genome of resident small mammals are
 unknown. Using the bank vole (Myodes glareolus) as a model system, we
 tested the hypothesis that approximately 50 generations of exposure to the
 Chernobyl environment has significantly altered genetic diversity of the
 mitochondrial genome. Using deep sequencing, we compared mitochondrial
 genomes from 131 individuals from reference sites with radioactive
 contamination comparable to that present in Northern Ukraine before the
 April 26, 1986 meltdown, to populations where substantial fallout was
 deposited following the nuclear accident. Population genetic variables
 revealed significant differences among populations from contaminated and
 uncontaminated localities. Therefore, we rejected the null hypothesis of
 no significant genetic effect from 50 generations of exposure to the
 environment created by the Chernobyl meltdown. Samples from contaminated
 localities exhibited significantly higher numbers of haplotypes and
 polymorphic loci, elevated genetic diversity, and a significantly higher
 average number of substitutions-per-site across mitochondrial gene
 regions. Observed genetic variation was dominated by synonymous mutations,
 which may indicate a history of purify selection against nonsynonymous or
 insertion/deletion mutations. These significant differences were not
 attributable to sample size artifacts. The observed increase in
 mitochondrial genomic diversity in voles from radioactive sites is
 consistent with the possibility that chronic, continuous irradiation
 resulting from the Chernobyl disaster has produced an accelerated mutation
 rate in this species over the last 25 years. Our results, being the first
 to demonstrate this phenomenon in a wild mammalian species, are important
 for understanding genetic consequences of exposure to low-dose radiation
 sources.
description: mtDNA gene
 alignmentsA zipped folder
 containing alignments of mtDNA genes.All
 samples.zip