cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f54v6
title: Data from: Catchment zoning for freshwater conservation: refining plans to enhance action on the ground

description: 1. Recent advances in freshwater conservation planning allow addressing
 some of the specific needs of these systems. These include spatial
 connectivity or propagation of threats along stream networks, essential to
 ensure the maintenance of ecosystem processes and the biodiversity they
 sustain. However, these peculiarities make conservation recommendations
 difficult to implement as they often require considering large areas that
 cannot be managed under conventional conservation schemes (e.g. strict
 protection). 2. To facilitate the implementation of conservation in
 freshwater systems, a multizoning approach with different management zones
 subject to different management regimes was proposed. So far, this
 approach has only been used in post hoc exercises where zones were
 allocated using expert criteria. This might undermine the
 cost-effectiveness of conservation recommendations, because both the
 allocation and extent of these zones have never been optimized using the
 principles of systematic planning. 3. Here, we demonstrate how to create a
 catchment multizone plan by using a commonly applied tool in marine and
 terrestrial realms. We first test the capability of Marxan with Zones to
 address problems in rivers by using a simulated example and then apply the
 findings to a real case in the Daly River catchment, northern Australia.
 We also demonstrate how to address common conservation planning issues,
 such as accounting for threats or species-specific connectivity needs in
 this multizone framework, and evaluate their effects on the spatial
 distribution and extent of different zones. 4. We found that by
 prioritizing the allocation of zones subject to different management
 regimes, we could minimize the total area in need of strict conservation
 by a twofold factor. This reduction can be further reduced (threefold)
 when considering species’ connectivity needs. The integration of threats
 helped reduce the average threats of areas selected by a twofold factor.
 5. Synthesis and applications. Catchment zoning can help refine
 conservation recommendations and enhance cost-effectiveness by prescribing
 different management regimes informed by ecological needs or distribution
 of threats. Reliable information on these factors is a key to ensure
 soundness of planning. Freely available software can be used to implement
 the approach we demonstrate here.
description: Species and threat
 distributions in the Daly River catchmentThis file contains, for
 each of the 864 subcatchments delineated in the Daly River catchment, the
 spatial distribution of the 45 freshwater fish species and the proportion
 of each subcatchment covered by grazing (used as estimate of threat in
 this study). The file also contains the latitude and longitude of the
 centroid of each subcatchment, so the information can be spatially
 explored.Hermoso et al. (2015)_Species
 and threats distribution Daly River
 catchment.xlsx
DOI: 10.5061/dryad.1q0s4gf
title: Data from: Untargeted metabolic profiling reveals geography as the strongest predictor of metabolic phenotypes of a cosmopolitan weed

description: Plants produce a multitude of metabolites that contribute to their fitness
 and survival, and play a role in local adaptation to environmental
 conditions. The effects of environmental variation is particularly well
 studied within the genus Plantago, however, previous studies have largely
 focused on targeting specific metabolites. Studies exploring metabolome
 wide changes are lacking, and the effects of natural environmental
 variation and herbivory on the metabolomes of plants growing in situ
 remain unknown. An untargeted metabolomic approach using ultra-high
 performance liquid chromatography-mass spectrometry, coupled with
 variation partitioning, general linear mixed modelling, and network
 analysis was used to detect differences in metabolic phenotypes of
 Plantago major in fifteen natural populations across Denmark. Geographic
 region, distance, habitat type, phenological stage, soil parameters, light
 levels, and leaf area, were investigated for their relative contributions
 to explaining differences in foliar metabolomes. Herbivory effects were
 further investigated by comparing metabolomes from damaged and undamaged
 leaves from each plant. Geographic region explained the greatest number of
 significant metabolic differences. Soil pH had the second largest effect,
 followed by habitat and leaf area, whilst phenological stage had no
 effect. No evidence of the induction of metabolic features was found
 between leaves damaged by herbivores compared to undamaged leaves on the
 same plant. Differences in metabolic phenotypes explained by geographic
 factors are attributed to genotypic variation and/or unmeasured
 environmental factors that differ at the regional level in Denmark. A
 small number of specialised features in the metabolome may be involved in
 facilitating the success of a widespread species such as Plantago major
 into such wide range of environmental conditions, though overall
 resilience in the metabolome was found in response to environmental
 parameters tested. Untargeted metabolomic approaches have great potential
 to improve our understanding of how specialised plant metabolites respond
 to environmental change and assist in adaptation to local conditions.
description: PlantagoMetabolomics_EnviroData_finalData from UPLC-Qtof-MS for damaged and undamaged leaves from the weed Plantago major. Includes meta data collected in the field and used for analyses. Metabolomic data is untargeted and each potential metabolite is denoted by RetentionTIme_mass.
DOI: 10.5061/dryad.8q3p913p
title: Data from: Two distinct genomic regions, harbouring the period and fruitless genes, affect male courtship song in Drosophila montana

description: Acoustic signals often play a significant role in pair formation and in
 species recognition. Determining the genetic basis of signal divergence
 will help to understand signal evolution by sexual selection and its role
 in the speciation process. An earlier study investigated QTL for male
 courtship song carrier frequency in Drosophila montana using
 microsatellite markers. We refined this study by adding to the linkage map
 markers for ten candidate genes known to affect song production in D.
 melanogaster. We also extended the analyses to additional song characters
 (pulse train length, pulse number, interpulse interval, pulse length and
 cycle number). Our results indicate that loci in two different regions of
 the genome control distinct features of the courtship song. Pulse train
 traits (pulse train length and pulse number) mapped to the X chromosome,
 showing significant linkage with the period gene. In contrast, characters
 related to song pulse properties (pulse length, cycle number and carrier
 frequency) mapped to the region of chromosome 2 near the candidate gene
 fruitless, identifying these genes as suitable loci for further
 investigations. In previous studies, the pulse train traits have been
 found to vary substantially between Drosophila species, and so are
 potential species recognition signals, while the pulse traits may be more
 important in intra-specific mate choice.
description: Song_dataThis dataset contains measurements of song traits (means from 3 measurements per individual) for 3 generations of experimental crosses.QTL_dataThis dataset contains information on song traits and genotypes at microsatellite and candidate gene markers for males from F3 generation of experimental crossess.
DOI: 10.5061/dryad.74s05
title: Data from: Sexual fidelity trade-offs promote regulatory variation in the prairie vole brain

description: Individual variation in social behavior seems ubiquitous, but we know
 little about how it relates to brain diversity. Among monogamous prairie
 voles, levels of vasopressin receptor (encoded by the gene avpr1a) in
 brain regions related to spatial memory predict male space use and sexual
 fidelity in the field. We find that trade-offs between the benefits of
 male fidelity and infidelity are reflected in patterns of territorial
 intrusion, offspring paternity, avpr1a expression, and the evolutionary
 fitness of alternative avpr1a alleles. DNA variation at the avpr1a locus
 includes polymorphisms that reliably predict the epigenetic status and
 neural expression of avpr1a, and patterns of DNA diversity demonstrate
 that avpr1a regulatory variation has been favored by selection. In prairie
 voles, trade-offs in the fitness consequences of social behaviors seem to
 promote neuronal and molecular diversity.
description: Data from Okhovat et al.
 2015This file contains
 various data that was used to perform analyses and construct figures in
 Okhovat et al. 2015.Okhovat_et_al_DryadData.zip
DOI: 10.5061/dryad.tg3d788k
title: Data from: Limited usefulness of microsatellite markers from the malaria vector Anopheles gambiae when applied to the closely related species Anopheles melas

description: Anopheles melas is a brackish water mosquito found in coastal West Africa
 where it is a dominant malaria vector locally. In order to facilitate
 genetic studies of this species, 45 microsatellite loci originally
 developed for Anopheles gambiae were sequenced in An . melas. Those that
 were suitable based on repeat number and flanking regions were examined in
 2 natural populations from Equatorial Guinea. Only 15 loci were eventually
 deemed suitable as polymorphic markers in An . melas populations. These
 loci were screened in 4 populations from a wider geographic range.
 Heterozygosity estimates ranged from 0.18 to 0.79, and 2.5–15 average
 alleles were observed per locus, yielding 13 highly polymorphic markers
 and 2 loci with lower variability. To examine the usefulness of
 microsatellite markers when applied in a sibling species, the original An
 . gambiae specific markers were used to amplify 5 loci in An . melas. Null
 alleles were found for 1 An . gambiae marker. We discuss the pitfalls of
 using microsatellite loci across closely related species and conclude that
 in addition to the problem of null alleles associated with this practice,
 many loci may prove to be of very limited use as polymorphic markers even
 when used in a sibling species.
description: Deitz et al Suppl.
 TablesDeitz et al Data
 file
DOI: 10.5061/dryad.j8n68
title: Data from: Effect of juvenile hormone on senescence in males with terminal investment

description: Senescence, a decline in survival and reproductive prospects with age, is
 controlled by hormones. In insects, juvenile hormone (JH) is involved in
 senescence with captive individuals, but its effect under natural
 conditions is unknown. We have addressed this gap by increasing JH levels
 in young and old wild males of the damselfly Hetaerina americana. We
 assessed survival in males that were treated with a JH analogue
 (methoprene), which is known to promote sexual activity, and an immune
 challenge, which is known to promote terminal investment in reproduction
 in the studied species. We replicated the same procedure in captivity (to
 control for environmental variation), where males were deprived of any
 activity or food. We expected old males to show the lowest survival after
 being treated with JH and immune-challenged, because the effect of
 terminal investment on senescence would be exacerbated by JH. However,
 this should be the case for wild animals, but not for captive animals, as
 the effects of JH and immune challenge should lead to an increase in high
 energetic-demanding activities only occurring in the wild. Old animals
 died sooner compared with young animals in both the wild and captivity,
 confirming that males are subject to senescence. In wild but not captive
 animals, JH decreased survival in young males and increased it in old
 males, confirming that JH is sensitive to the environment when shaping
 animal senescence. Immune challenge had no effect on survival, suggesting
 no effect of terminal investment on senescence. Additionally, contrary to
 the expected effects of terminal investment, with an immune challenge,
 recapture rates increased in young males and decreased in old males. Our
 results show that male senescence in the wild is mediated by JH and that
 terminal investment does not cause senescence. One explanation is that
 animals undergoing senescence and terminal investment modify their feeding
 behaviour to compensate for their physiological state.
description: Inv Term Met
 CautiverioSurvival in
 captivityInv Term
 MetoprenoSurvival under natural
 conditions
DOI: 10.5061/dryad.vc94d
title: Data from: Directional mitochondrial introgression and character displacement due to reproductive interference in two closely related Pterostichus ground beetle species

description: Reproductive interference due to interspecific hybridization can lead to
 character displacement among related species with overlapping ranges.
 However, no studies have examined which reproductive traits are most
 important in reducing reproductive interference. We conducted molecular
 analyses of two nuclear genes (28S and Wingless) and a mitochondrial gene
 (COI) from two closely related ground beetle species, Pterostichus
 thunbergi and P. habui (Coleoptera: Carabidae), with overlapping
 distributions. In addition, we examined four reproductive traits (body
 size, organ morphologies of intromittent and non-intromittent male genital
 organs, and female reproductive period) in sympatric and allopatric
 habitats. We compared male genital morphology using geometric morphometric
 analysis. The species determined by morphology were classified into
 separate groups based on the phylogenetic tree constructed by the nuclear
 gene (Wingless). However, according to the mitochondrial genes examined,
 P. thunbergi was not monophyletic, while at the sympatric sites these
 species formed a monophyletic clade. This incongruence suggests that
 interspecific hybridization and subsequent mitochondrial introgression
 from P. habui to P. thunbergi have occurred. Concerning genital
 morphology, both of the intromittent and non-intromittent organs of P.
 thunbergi differed more from P. habui at the sympatric sites than between
 allopatric sites, suggesting directional reproductive character
 displacement. Pterostichus thunbergi, which likely arrived in P. habui
 habitat in small numbers, would have experienced stronger selection
 pressures than P. habui.
description: Raw coordinates for
 aedeagusaedeagus.ntsRaw coordinates for paramereparamere.ntsCapture rates of Pterostichus thunbergi and P. habui at the sympatric site (site D)headlength
DOI: 10.5061/dryad.s4cc3
title: Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?

description: In the African buffalo (Syncerus caffer) population of the Kruger National
 Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio
 suppressor have been shown to occur on the Y chromosome. A subsequent
 autosomal microsatellite study indicated that two types of deleterious
 alleles with a negative effect on male body condition, but a positive
 effect on relative fitness when averaged across sexes and generations,
 occur genome-wide and at high frequencies in the same population. One type
 negatively affects body condition of both sexes, while the other acts
 antagonistically: it negatively affects male but positively affects female
 body condition. Here we show that high frequencies of male-deleterious
 alleles are attributable to Y-chromosomal distorter-suppressor pair
 activity and that these alleles are suppressed in individuals born after
 three dry pre-birth years, likely through epigenetic modification.
 Epigenetic suppression was indicated by statistical interactions between
 pre-birth rainfall, a proxy for parental body condition, and the
 phenotypic effect of homozygosity/heterozygosity status of microsatellites
 linked to male-deleterious alleles, while a role for the Y-chromosomal
 distorter-suppressor pair was indicated by between-sex genetic differences
 among pre-dispersal calves. We argue that suppression of male-deleterious
 alleles results in negative frequency-dependent selection of the Y
 distorter and suppressor; a prerequisite for a stable polymorphism of the
 Y distorter-suppressor pair. The Y distorter seems to be responsible for
 positive selection of male-deleterious alleles during resource-rich
 periods and the Y suppressor for positive selection of these alleles
 during resource-poor periods. Male-deleterious alleles were also
 associated with susceptibility to bovine tuberculosis, indicating that
 Kruger buffalo are sensitive to stressors such as diseases and droughts.
 We anticipate that future genetic studies on African buffalo will provide
 important new insights into gene fitness and epigenetic modification in
 the context of sex-ratio distortion and infectious disease dynamics.
description: Genetic
 dataIndividual
 microsatellite data of African buffalo sampled in Kruger National Park in
 1998.geneticdata.csvRainfall dataRainfall data for Kruger National Park, from 19 rainfall stations in the period 1975-1999.rainfalldata.csv
DOI: 10.5061/dryad.34kt1
title: Data from: Do community-weighted mean functional traits reflect optimal strategies?

description: The notion that relationships between community-weighted mean (CWM) traits
 (i.e. plot-level trait values weighted by species abundances) and
 environmental conditions reflect selection towards locally optimal
 phenotypes is challenged by the large amount of interspecific trait
 variation typically found within ecological communities. Reconciling these
 contrasting patterns is a key to advancing predictive theories of
 functional community ecology. We combined data on geographical
 distributions and three traits (wood density, leaf mass per area and
 maximum height) of 173 tree species in Puerto Rico. We tested the
 hypothesis that species are more likely to occur where their trait values
 are more similar to the local CWM trait values (the ‘CWM-optimality’
 hypothesis) by comparing species occurrence patterns (as a proxy for
 fitness) with the functional composition of forest plots across a
 precipitation gradient. While 70% of the species supported CWM-optimality
 for at least one trait, nearly 25% significantly opposed it for at least
 one trait, thereby contributing to local functional diversity. The
 majority (85%) of species that opposed CWM-optimality did so only for one
 trait and few species opposed CWM-optimality in multivariate trait space.
 Our study suggests that constraints to local functional variation act more
 strongly on multivariate phenotypes than on univariate traits.
description: Muscarella_and_Uriarte_ProcBData to conduct analyses included in Muscarella & Uriarte, "Do community-weighted mean functional traits reflect optimal strategies?" Please see metadata file for more details.Data_for_Dryad_2.27.16.RDS
DOI: 10.5061/dryad.v20gh
title: Data from: Adult plasticity in African Cichlids: rapid changes in opsin expression in response to environmental light differences

description: Phenotypic plasticity allows organisms to adapt quickly to local
 environmental conditions and could facilitate adaptive radiations.
 Cichlids have recently undergone an adaptive radiation in Lake Malawi
 where they inhabit diverse light environments and tune their visual
 sensitivity through differences in cone opsin expression. While cichlid
 opsin expression is known to be plastic over development, whether adults
 remain plastic is unknown. Adult plasticity in visual tuning could play a
 role in cichlid radiations by enabling survival in changing environments
 and facilitating invasion into novel environments. Here we examine the
 existence of and temporal changes in adult visual plasticity of two
 closely related species. In complementary experiments, wild adult
 Metriaclima mbenji from Lake Malawi were moved to the lab under
 UV-deficient fluorescent lighting; while lab raised M. benetos were placed
 under UV-rich lighting designed to mimic light conditions in the wild.
 Surprisingly, adult cichlids in both experiments showed significant
 changes in the expression of the UV-sensitive single cone opsin, SWS1, in
 only three days. Modeling quantum catches in the light environments
 revealed a possible link between the light available to the SWS1 visual
 pigment and SWS1 expression. We conclude that adult cichlids can undergo
 rapid and significant changes in opsin expression in response to
 environmental light shifts that are relevant to their habitat and
 evolutionary history in Lake Malawi. This could have contributed to the
 rapid divergence characteristic of these fantastic fishes.
description: Opsin expression data
 for Natural to Narrow experimentExpression values of all
 opsins normalized to cone type (single /double cones) and housekeeping
 gene (GNAT2).Natural-to-Narrow.xlsxOpsin expression data for Narrow to Broad experimentExpression values for all opsins normalized to cone type (single/double cone) and housekeeping gene (GNAT2).Narrow-to-Broad.xlsxRelative SWS1 cone opsin expression for Figure 6.Expression values for SWS1 opsin relative to single cones for all species shown in Figure 6.Figure6.xlsx
DOI: 10.5061/dryad.7kk62
title: Data from: Despite introgressive hybridization, North American birches (Betula spp.) maintain strong differentiation at nuclear microsatellite loci

description: Extensive chloroplast introgression has been documented in polyploid
 Betula species of eastern North America. However, the extent to which the
 nuclear genomes of these species are differentiated is unknown. Therefore,
 we evaluated genetic differentiation among largely sympatric Betula
 papyrifera, B. alleghaniensis, and B. lenta using nuclear microsatellite
 markers. Principal components analysis (PCA) and analysis of molecular
 variation (AMOVA) were used to evaluate genetic differentiation. Bayesian
 model-based clustering was used to identify putatively admixed
 individuals. Despite a high incidence of allele sharing, all of the
 species were significantly differentiated even within zones of sympatry. A
 number of individuals were identified as possibly admixed between B.
 papyrifera and B. alleghaniensis and between B. alleghaniensis and B.
 lenta. Admixture estimates between B. alleghaniensis and B. papyrifera
 increased significantly moving northward into the sympatric zone,
 suggesting the occurrence of hybridization in previously glaciated
 habitats. In contrast, admixture proportions of B. papyrifera and B.
 alleghaniensis did not show a significant geographic trend, which points
 to recent ancestry as the likely cause of allele sharing between these two
 species. We suggest that allele sharing of B. papyrifera and B.
 alleghaniensis results from a combination of ongoing gene flow and
 historic introgression via pollen swamping during northward colonization
 into post-glacial environments.
description: Nuclear microsatellite
 genotypes for eastern North American BetulaThe file contains
 genotypes at six nuclear microsatellite loci for three species of Betula
 native to eastern North America: Betula papyrifera, B. alleghaniensis, and
 B. lenta. Samples were collected in the field and whole genomic DNA was
 extracted from dried leaf tissue.Betula_nSSR_Genotypes.csv