cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4jj8r
title: Data from: Fine-scale genetic analysis of species-specific female preference in Drosophila simulans

description: Behavioral differences are thought to be the first components to
 contribute to species isolation, yet the precise genetic basis of
 behavioral isolation remains poorly understood. Here, we used a
 combination of behavior assays and genetic mapping to provide the first
 refined map locating candidate genes for interspecific female preference
 isolating Drosophila simulans from D. melanogaster. First, we tested
 whether two genes identified as affecting D. melanogaster female
 intraspecific mate choice also affect interspecific mate choice; neither
 of these genes was found to contribute to species-specific female
 preference. Next, we used deficiency mapping to locate genes on the right
 arm of the third chromosome for species-specific female preference and
 identified five small significant regions that contain candidate genes
 contributing to behavioral isolation. All five regions were located in
 areas that would have low interspecific recombination, which mirrors the
 results of other behavioral isolation studies that used quantitative trait
 locus (QTL) mapping, but without the potential concern of bias towards
 regions of low recombination that QTL mapping may have. Since this model
 system may be refined to the individual gene level using the same
 methodology, this initial map we provide may potentially serve as a ready
 template for the identification and characterization of the first
 behavioral isolation genes.
description: Supplementary Table
 2The
 courtship values and statistics for the four genotypes tested
 (simulans/deficiency, simulans/ Balancer, melanogaster/Deficiency,
 melanogaster/Balancer).Supplementary Table
 3The
 average effects of the balancer on mating for simulans/Balancer genotypes
 tested.Supplementary Table
 4Candidate genes within
 each significant region identified through deficiency mapping as
 contributing to female interspecific mate choice.
DOI: 10.5061/dryad.qr8v5f4v
title: Data from: Migratory behavior of birds affects their coevolutionary relationship with blood parasites

description: Host traits, such as migratory behavior, could facilitate the dispersal of
 disease causing parasites, potentially leading to the transfer of
 infections both across geographic areas and between host species. There is
 however, little quantitative information on whether variation in such host
 attributes do indeed affect the evolutionary outcome of host-parasite
 associations. Here, we employ Leucocytozoon blood parasites of birds, a
 group of parasites closely related to avian malaria, to study
 host-parasite coevolution in relation to host behavior using a
 phylogenetic comparative approach. We reconstruct the molecular
 phylogenies of both the hosts and parasites and use cophylogenetic tools
 to assess whether each host-parasite association contributes significantly
 to the overall congruence between the two phylogenies. We find evidence
 for a significant fit between host and parasite phylogenies in this
 system, but show that this is due only to associations between non-migrant
 parasites and their hosts. We also show that migrant bird species harbor a
 greater genetic diversity of parasites compared with non-migrant species.
 Taken together, these results suggest that the migratory habits of birds
 could influence their coevolutionary relationship with their parasites,
 and that consideration of host traits is important in predicting the
 outcome of coevolutionary interactions.
description: cytb_cospecavian cytochrome b sequencescoi_cospecCO1 sequence data (bird)nd2_cospecND2 bird sequence datand3_cospecND3 sequence dataall_leuco2Leucocytozoon spp sequence data
DOI: 10.5061/dryad.7h7h3
title: Data from: Female remating decisions and a shorter inter-mating interval diminish last-male sperm precedence

description: Highly variable within and across species, patterns of sperm use not only
 are often driven by post-copulatory sexual selection but can also be
 impacted by experimental design. In investigations of paternity bias using
 competitive double matings, the inter-mating interval is a temporal factor
 that can affect sperm use patterns if the first male’s sperm is used or
 lost at an appreciable rate between matings or if its viability or
 relative competitiveness is influenced by the time since ejaculation.
 Rapid loss of first-male sperm within the female after mating has been
 established in the seed beetle (Callosobruchus maculatus), a model system
 in sperm competition studies. However, our understanding of sperm
 precedence in this species, which disproportionately favors the last
 (second) male to mate, is based on long inter-mating intervals. Here, I
 determine the effect of a shortened inter-mating interval on second-male
 paternity (P2) and, importantly, the extent to which females in this
 species are willing to remate immediately. I find that P2 is significantly
 reduced when females remate immediately than when they remate 24 or 48 h
 after the first mating and that immediate remating is common, indicating
 that there is a substantial potential for female remating decisions to
 influence the intensity of sperm competition within species. To understand
 the variation in inter-mating intervals from a female perspective, I
 further identify key differences between females that did and did not
 remate at three inter-mating intervals (0, 24, and 48 h after the initial
 mating) and discuss potential mechanisms for the observed variation in
 female refractoriness.
description: SB1CSperm Precedence
 DataRematingFemale remating propensity data (all females)Remate0Data for analyses if IMI 0 - for all females in experimentRemate24Data for analysis of IMI 24 - for all females in experiment that didn't remate at IMI 0Remate48Data for analysis of IMI 48 - for all females in experiment that didn't remate at IMI 0Correction Factors for Sterile Male TechniqueSupplementary Materials Data: Correction Factors for Sterile Male TechniqueR CodeR Code to run analyses in manuscript
DOI: 10.5061/dryad.jj110
title: Data from: Deciphering the associations between soil microbial diversity and ecosystem multifunctionality driven by long-term fertilization management

description: 1.An increasing number of studies indicate that microbial diversity plays
 a crucial role in the mediation of ecosystem multifunctionality (EMF) in
 natural ecosystems. However, this point remains mostly overlooked in
 managed ecosystems, especially in agriculture. 2.Here, we compiled
 promising strategies for the targeted exploitation of the associations
 between microbial diversity and EMF of agricultural soils using samples
 from two long-term (more than 30 years) experimental field sites in
 southern China. The two sites experienced a similar subtropical monsoon
 climate and fertilization management practices. We used high-throughput
 amplicon sequencing, structural equation modeling (SEM), and random forest
 analysis, to analyze our data and validate our hypotheses. 3.We found that
 soil physiochemical properties and the C-, N-, P- and S-cycle enzyme
 activities were increased with the increase of microbial diversity.
 Specifically, a positive linear relationship was observed between
 microbial diversity and EMF, which was mediated by long-term fertilization
 management via changes in soil microbial communities and physiochemical
 properties. Random forest analysis and SEM showed that the important role
 of microbial diversity on EMF was maintained even when simultaneously
 taking multiple multifunctionality drivers (soil physiochemical
 properties, soil aggregation and enzymatic patterns) into account. In
 addition, microbial diversity, C-cycle enzyme activity and pH value are
 feasible predictors of EMF; these factors were shown to be the main
 drivers of EMF of arable soils. 4. Our findings suggest that there may be
 a limited degree of multifunctional redundancy in arable soils. The
 relationship we observed between microbial diversity and EMF suggests that
 management practices that foster more diverse soil microbial communities
 may have the potential to improve the functioning of agroecosystems.
description: Raw
 datasetThere are seven excel
 files in this dataset. The spreadsheets "OTU table (bacteria;
 Anhui)”, “OTU table (fungi; Jiangxi)”, “OTU table(bacteria; Jiangxi)”,“OTU
 table(fungi; Anhui)”,“Enzyme activity”,“Phylogenetic diversity”and
 “Physicochemical properties” contain the raw data used in this paper,
 where a description of all the variables and units can be
 found.
DOI: 10.5061/dryad.g1hm0
title: Data from: Fungal adaptation to contemporary fungicide applications: the case of Botrytis cinerea populations from Champagne vineyards (France)

description: In addition to being one of the most acute problems impeding chemical
 control of fungal diseases, the evolution of fungicide resistance is an
 emblematic case of local adaptation to spatially heterogeneous and
 temporally variable selection pressures. Here we dissected the adaptation
 of Botrytis cinerea (the causal agent of grey mould) populations on grapes
 to several fungicides. We carried out a 2-year survey (four collection
 dates) on three treated/untreated pairs of plots from vineyards in
 Champagne (France) and monitored the frequency of four resistant
 phenotypes that are unambiguously associated with four distinct genotypes.
 For two loci under selection by currently used fungicides (MDR1 and MDR2),
 the frequencies of resistant mutations at vintage were greater in treated
 plots compared to untreated plots, showing that the effect of selection is
 detectable even at the plot scale. This effect was not detectable for two
 other loci under selection by previously used fungicides (BenR1 and
 ImiR1). We also found that treatment with currently used fungicides
 reduced B. cinerea effective population size, leading to a significant
 decrease in genic diversity and allelic richness in treated vs. untreated
 plots. We further highlight that even under ample drift and migration,
 fungal populations can present an efficient response to selection.
 Finally, for the four studied loci, the costs of fungicide resistance were
 estimated by modelling the decrease in the frequency of resistant
 mutations in the absence of treatment. We discuss the importance of these
 estimates for defining strategies for limiting or counteracting the local
 adaptation of pests to fungicides.
description: Data
 DryadExcel file
 containing:(1) identification of Botrytis cinerea strains (columns A to
 H), (2) microsatellite profile for 8 SSRs (colums I to P), (3) status of
 resistance for 7 loci (columns Q to W)
DOI: 10.5061/dryad.9bq5n41
title: Data from: Post-Cretaceous bursts of evolution along the benthic-pelagic axis in marine fishes

description: Ecological opportunity arising in the aftermath of mass extinction events
 is thought to be a powerful driver of evolutionary radiations. Here, we
 assessed how the wake of the Cretaceous-Paleogene (K-Pg) mass extinction
 shaped diversification dynamics in a clade of mostly marine fishes
 (Carangaria), which comprises a disparate array of benthic and pelagic
 dwellers including some of the most astonishing fish forms (e.g.,
 flatfishes, billfishes, remoras, archerfishes). Analyses of lineage
 diversification show time-heterogeneous rates of lineage diversification
 in carangarians, with highest rates reached during the Paleocene.
 Likewise, a remarkable proportion of Carangaria’s morphological variation
 originated early in the history of the group and in tandem with a marked
 incidence of habitat shifts. Taken together, these results suggest that
 all major lineages and body plans in Carangaria originated in an early
 burst shortly after the K-Pg mass extinction, which ultimately allowed the
 occupation of newly released niches along the benthic-pelagic habitat
 axis.
description: Carangaria-MCCMaximum Clade Credibility (MCC) tree obtained with BEAST.Harrington4545-taxa tree (from Harrington et al. 2016)Rabosky415405-taxa supermatrix tree (from Rabosky et al. 2018)Rabosky508508-taxa grafted tree obtained by adding two well-sampled carangarian subclades (carangoids and flatfishes]) into the Rabosky et al. 2018 backbone tree.Rabosky10061006-taxa imputed tree from Rabosky et al. 2018, which was populated with simulated taxa in place of missing tipsRabosky1057.treTESS-CoMETR script to calculate CoMET function in TESS.ChangesTTR script to calculate discrete changes through time.TESS-Model-FitR script to calculate relative fit of alternative models of lineage diversification using TESS.MVMORPHR script to calculate relative fit of alternative models of morphological evolution using MvMORPH.Calculate_Ancestral_StatesR script to calculate morphological ancestral states (CHRIS COONEY - 2017)
DOI: 10.5061/dryad.vv5347p
title: Data from: Incorporating non-equilibrium dynamics into demographic history inferences of a migratory marine species

description: Understanding how dispersal and gene flow link geographically separated
 populations over evolutionary history is challenging, particularly in
 migratory marine species. In southern right whales (SRWs, Eubalaena
 australis), patterns of genetic diversity are likely influenced by the
 glacial climate cycle and recent history of whaling. Here we use a dataset
 of mitochondrial DNA (mtDNA) sequences (n=1,327) and nuclear markers (17
 microsatellite loci, n=222) from major wintering grounds to investigate
 circumpolar population structure, historical demography, and effective
 population size. Analyses of nuclear genetic variation identify two
 population clusters that correspond to the South Atlantic and Indo-Pacific
 ocean basins that have similar effective breeder estimates. In contrast,
 all wintering grounds show significant differentiation for mtDNA, but no
 sex-biased dispersal was detected using the microsatellite genotypes. An
 approximate Bayesian computation (ABC) approac h with microsatellite
 markers compared scenarios with gene flow through time, or isolation and
 secondary contact between ocean basins, while modeling declines in
 abundance linked to whaling. Secondary-contact scenarios yield the highest
 posterior probabilities, implying that populations in different ocean
 basins were largely isolated and came into secondary contact within the
 last 25,000 years, but the role of whaling in changes in genetic diversity
 and gene flow over recent generations could not be resolved. We
 hypothesise that these findings are driven by factors that promote
 isolation, such as female philopatry, and factors that could promote
 dispersal, such oceanographic changes. These findings highlight the
 application of ABC approaches to infer connectivity in mobile species with
 complex population histories and currently low levels of differentiation.
description: Genotype data for
 Carroll et alMicrosatellite genotype
 data for southern right whales in Carroll et al 2018Carroll_et_al_2018_Genotypes.xlsx
DOI: 10.5061/dryad.4dn793t6
title: Data from: Massive phytoplankton blooms under Arctic sea ice

description: Phytoplankton blooms over Arctic Ocean continental shelves are thought to
 be restricted to waters free of sea ice. Here, we document a massive
 phytoplankton bloom beneath fully consolidated pack ice far from the ice
 edge in the Chukchi Sea, where light transmission has increased in recent
 decades because of thinning ice cover and proliferation of melt ponds. The
 bloom was characterized by high diatom biomass and rates of growth and
 primary production. Evidence suggests that under-ice phytoplankton blooms
 may be more widespread over nutrient-rich Arctic continental shelves and
 that satellite-based estimates of annual primary production in these
 waters may be underestimated by up to 10-fold.
description: arrigo_under_ice_blooms_scienceCTD bottle file of stations covering transects from open water into the pack ice and back (Cruise: HLY1101, stations 46-71)
DOI: 10.5061/dryad.fd986
title: Data from: Functional traits reveal the expansion and packing of ecological niche space underlying an elevational diversity gradient in passerine birds

description: Variation in species richness across environmental gradients may be
 associated with an expanded volume or increased packing of ecological
 niche space. However, the relative importance of these alternative
 scenarios remains unknown, largely because standardised information on
 functional traits and their ecological relevance is lacking for major
 diversity gradients. Here we combine data on morphological and ecological
 traits for 523 species of passerine birds distributed across an
 Andes-to-Amazon elevation gradient. We show that morphological traits
 capture substantial variation in species dietary (75%) and foraging niches
 (60%) when multiple independent trait dimensions are considered. Having
 established these relationships, we show that the 14-fold increase in
 species richness towards the lowlands is associated with both an increased
 volume and density of functional trait space. However, we find that
 increases in volume contribute little to changes in richness, with most
 (78%) lowland species occurring within the range of trait space occupied
 at high elevations. Taken together, our results suggest that high species
 richness is mainly associated with a denser occupation of functional trait
 space, implying an increased specialisation or overlap of ecological
 niches, and supporting the view that niche packing is the dominant trend
 underlying gradients of increasing biodiversity towards the lowland
 tropics.
description: Database
 S1This file contains mean
 (log-transformed) species trait measurements and ecological guild scores
 for 524 Passerines within Manu National park with associated elevation
 range limits (from Walker et al 2006).
DOI: 10.5061/dryad.gh90f5f
title: Data from: Field-scale experiments reveal persistent yield gaps in low-input and organic cropping systems

description: Knowledge of production-system performance is largely based on
 observations at the experimental plot scale. Although yield gaps between
 plot-scale and field-scale research are widely acknowledged, their extent
 and persistence have not been experimentally examined in a systematic
 manner. At a site in southwest Michigan, we conducted a 6-y experiment to
 test the accuracy with which plot-scale crop-yield results can inform
 field-scale conclusions. We compared conventional versus alternative, that
 is, reduced-input and biologically based–organic, management practices for
 a corn–soybean–wheat rotation in a randomized complete block-design
 experiment, using 27 commercial-size agricultural fields. Nearby
 plot-scale experiments (0.02-ha to 1.0-ha plots) provided a comparison of
 plot versus field performance. We found that plot-scale yields well
 matched field-scale yields for conventional management but not for
 alternative systems. For all three crops, at the plot scale, reduced-input
 and conventional managements produced similar yields; at the field scale,
 reduced-input yields were lower than conventional. For soybeans at the
 plot scale, biological and conventional managements produced similar
 yields; at the field scale, biological yielded less than conventional. For
 corn, biological management produced lower yields than conventional in
 both plot- and field-scale experiments. Wheat yields appeared to be less
 affected by the experimental scale than corn and soybean. Conventional
 management was more resilient to field-scale challenges than alternative
 practices, which were more dependent on timely management interventions;
 in particular, mechanical weed control. Results underscore the need for
 much wider adoption of field-scale experimentation when assessing new
 technologies and production-system performance, especially as related to
 closing yield gaps in organic farming and in low-resourced systems typical
 of much of the developing world.
description: kravchenko_2017_pnas_field_scaleThe file “kravchenko_2017_pnas_field_scale.xlsx” consists of six worksheets that contain: the agronomic yields for corn, soybean, and wheat from one field-scale experiment and two plot-scale experiments for the period 2007-2012; precipitation data over the study period; and the analysis of deep soil cores from the field-scale experiment.
DOI: 10.5061/dryad.5002s
title: Data from: Predictions of single-nucleotide polymorphism differentiation between two populations in terms of mutual information

description: Mutual information (I) provides a robust measure of genetic
 differentiation for the purposes of estimating dispersal between
 populations. At present, however, there is little predictive theory for I.
 The growing importance in population biology of analyses of
 single-nucleotide and other single feature polymorphisms (SFPs) is a
 potent reason for developing an analytic theory for I with respect to a
 single locus. This study represents a first step towards such a theory. We
 present theoretical predictions of I between two populations with respect
 to a single haploid biallelic locus. Dynamical and steady-state forecasts
 of I are derived from a Wright-Fisher model with symmetric mutation
 between alleles and symmetric dispersal between populations. Analytical
 predictions of a simple Taylor approximation to I are in good agreement
 with numerical simulations of I and with data on I from SFP analyses of
 dispersal experiments on Drosophila fly populations. The theory presented
 here also provides a basis for the future inclusion of selection effects
 and extension to multi-allelic loci.
description: SNP data for ME
 publication 110519
DOI: 10.5061/dryad.1dh25n9
title: Data from: Snowmelt variation contributes to topoclimatic refugia under montane Mediterranean climate change

description: Improved knowledge of the influence of climate parameters on the
 distribution of plant species is needed to identify potential refugia
 under climate change. Species abundance of trees, mainly conifers, as
 measured by species relative cover, was evaluated on 132 sites in the
 southern Sierra Nevada mountains of California, USA. These mountains
 experience a montane Mediterranean climate characterized by a deep winter
 snowpack and an extended summer drought. The cover data was analyzed in
 terms of the average snowpack water content at its maximum and the average
 date when snow on each site is finally melted. These snow-related
 parameters were calculated from a semi-empirical snow model, taking into
 account site slope and aspect. For the pine, juniper and oak species
 studied these parameters were found to have a much stronger effect on
 species abundance at a site than does elevation. For the conifer species,
 this allows the identification of topographic refugia from climate change.
 This result appears to be related to growth phenology. Elevation was found
 to be more important for the fir species studied. The results on the
 importance of growth phenology should be useful in identifying topographic
 refugia in mountains experiencing a Mediterranean climate worldwide.
description: Snow Model and Cover
 DataSnow model described and
 used in the publication, together with cover data by tree species. See the
 read-me for details.Snow Model and
 Data.zipRoyce_Read-Me.pdf