cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.91rg5
title: Data from: Waterscape genetics of the yellow perch (Perca flavescens): patterns across large connected ecosystems and isolated relict populations

description: Comparisons of a species’ genetic diversity and divergence patterns across
 large connected populations versus isolated relict areas provide important
 data for understanding potential response to global warming, habitat
 alterations, and other perturbations. Aquatic taxa offer ideal case
 studies for interpreting these patterns, because their dispersal and gene
 flow often are constrained through narrow connectivity channels that have
 changed over geological time and/or from contemporary anthropogenic
 perturbations. Our research objective is to better understand the
 interplay between historic influences and modern-day factors (fishery
 exploitation, stocking supplementation, and habitat loss) in shaping
 population genetic patterns of the yellow perch Perca flavescens
 (Percidae: Teleostei) across its native North American range. We employ a
 modified landscape genetics approach, analyzing sequences from the entire
 mitochondrial DNA control region (912 base pairs) and 15 nuclear DNA
 microsatellite loci of 664 spawning adults from 24 populations. Results
 support that perch from three primary glacial refugium areas (Missourian,
 Mississippian, and Atlantic) founded contemporary northern populations.
 Genetic diversity today is highest in southern (never glaciated)
 populations, and also is appreciable in northern areas that were founded
 from multiple refugia. Divergence is greater among isolated populations,
 both north and south; the southern Gulf Coast relict populations are the
 most divergent, reflecting their long history of isolation. Understanding
 the influence of past and current waterway connections on the genetic
 structure of yellow perch populations may help us to assess the roles of
 ongoing climate change and habitat disruptions towards conserving aquatic
 biodiversity.
description: Sepulveda-Villet and
 Stepien 2012 - yellow perch and percid haplotypesNexus formatted input
 file with mtDNA control region sequences for 26 yellow perch haplotypes,
 and reference sequences for Eurasian perch (Perca fluviatilis) and walleye
 (Sander vitreus).MEC Sepulveda Villet and
 Stepien 2012 - yellow perch
 haplotypes.nexusSepulveda-Villet &
 Stepien 2012 - yellow perch broadscale populationsArlequin formatted input
 file including all sampling sites used in study. File includes 664
 individuals with 15 nuclear microsatellite loci.Sepulveda-Villet &
 Stepien 2012 - yellow perch HaplotypesArlequin formatted input
 file with all mtDNA control region haplotypes recovered, sampling sites
 and number of occurrences per haplotype.
DOI: 10.5061/dryad.53dg5
title: Data from: Hiding behavior in Christmas tree worms on different time scales

description: Many animals escape predators by hiding. Hiding decisions are economic in
 that individuals trade off the physiological costs of hiding with the
 benefits of increased security. The number of conspecifics may increase
 competition, security, or attract predators, influencing predation risk.
 We studied hiding time in Christmas tree worms (Spirobranchus giganteus),
 sessile marine invertebrates, which lived with 0–17 other worms within
 20cm. Competition and predation risk reduction both predict a shorter
 latency to re-emerge given the necessity to feed and potential for safety
 in numbers, respectively. In contrast, if grouped worms attract more
 predators, individuals should hide longer. We experimentally induced
 hiding in 174 worms and found a significant, positive relationship between
 hiding time and number of conspecifics. We repeated the test 4 consecutive
 times in 1 day on a subset of 30 worms that were either solitary or lived
 with one other untested worm. We found that worms with longer hiding times
 habituated more quickly than worms with shorter hiding times, and that the
 individual worm explained 55.8% of the variation in hiding time. When we
 conducted the trials for 4 days, we found that the individual worm
 explained 41.75% of the variation, but no evidence of behavioral
 plasticity. Worm antipredator responses were consistently individualistic,
 but behavioral plasticity was only evident over short time scales. For
 sessile marine invertebrates, higher densities may attract predators,
 enhancing rather than diluting predation risk. Worms that cannot move away
 from their neighbors, thus seemingly modify antipredator behavior in
 consistent ways.
description: CTW_IndividualsData from individual analyses.CTW_Repeated_1DayRepeated analysis over 1 day.CTW_Repeated_4DaysRepeated analysis over 4 days.LitReviewData from literature review.
DOI: 10.5061/dryad.f6q5j
title: Data from: The direction of carbon and nitrogen fluxes between ramets changes during ontogeny under simulated competition for light

description: Resource sharing is universal among connected ramets of clonal plants, and
 is driven both by the developmental status of ramets and resource
 gradients. Aboveground competition forms spatial light gradients, but the
 role of resource sharing in such competition is unclear. We examined
 translocation of resources between mother and daughter ramets of Agrostis
 stolonifera under light heterogeneity throughout ramet ontogeny. We
 labelled ramets by 13C and 15N to estimate bidirectional translocation of
 the resources at three developmental stages of daughters. Besides, we
 compared final biomass of integrated and severed ramets to estimate the
 effect of integration on growth. Young developing daughters were supported
 by carbon, whereas nitrogen was only translocated towards daughters at the
 beginning of rooting, regardless of the light conditions. Shading of
 mothers was a major determinant of resource translocation between
 developed ramets, with carbon being preferentially moved to daughters from
 shaded mothers while nitrogen translocation being limited from daughters
 to shaded mothers. Surprisingly, absolute amounts of translocated
 resources did not decline through development. Growth of daughters was
 enhanced by integration regardless of the shading. Apparently, A.
 stolonifera maximizes the resource translocation pattern which enables it
 to spread from unfavourable habitats rather than compensate for light
 heterogeneity among ramets.
description: Labelling and biomass
 dataLabelling data (first
 sheet) - molar stable isotope ratio of nitrogen and carbon in plant
 samples, C and N molar concentration, dry biomass and calculations of
 amounts of 13C and 15N originating form pulse-labelling. Data includes
 only integrated ramet pairs. Biomass data (second sheet) - dry biomass of
 plant samples. Includes both integrated and severed ramet pairs.
 Description of column names is provided in the file.DuchoslavovaJansa_Data.xlsx
DOI: 10.5061/dryad.90p3n019
title: Data from: Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans

description: Pathogen introductions into novel areas can lead to the emergence of new
 fungal diseases of plants. Understanding the origin, introduction
 pathways, possible changes in reproductive system and population size of
 fungal pathogens is essential in devising an integrated strategy for the
 control of these diseases. We used minisatellite markers to infer the
 worldwide invasion history of the fungal plant pathogen Leptosphaeria
 maculans, which causes stem canker (blackleg) of oilseed and vegetable
 brassicas. Clustering analyses partitioned genotypes into distinct
 populations corresponding to major geographic regions, along with two
 differentiated populations in Western Canada. Comparison of invasion
 scenarios using Approximate Bayesian Computation suggested an origin of
 the pathogen in the USA, the region where epidemics were first recorded,
 and independent introductions from there over the last few decades into
 Eastern Canada (Ontario), Europe and Australia. The population in Western
 Canada appeared to be founded from a source in Ontario and the population
 in Chile resulted from an admixture between multiple sources. A bottleneck
 was inferred for the introduction into Western Canada but not into Europe,
 Ontario or Australia. Clonality appeared high in Western Canada, possibly
 because environmental conditions there were less conducive to sexual
 reproduction. Leptosphaeria maculans is a model invasive pathogen with
 contrasting features in different regions: shallow population structure,
 high genetic variability and regular sexual recombination in some regions,
 by comparison with reduced genetic variability, high rates of asexual
 multiplication, strong population structure or admixture in others.
description: minisatellite
 dataMinisatellite data on
 each Leptosphaeria maculans individual [indiv ID, sampling location,
 genotype at the 14 minisatellite loci min 555, min632, mini967, mini1368,
 min1334, min1377, min1721, min1838, min2451, min935-, minLm3, minLm5,
 minLm6 and minLm8mainparams_geogr_priorstructure parameter file used with input file structure_CC_geogr_prior_6grps.txtmainparams_no_geogr_priorstructure parameter file used with input file structure_CC_no_geogr_prior.txtstructure_CC_geogr_prior_6grpsstructure input files for analyses using the region of origin of individuals (six regions) as prior information to assist clusteringstructure_CC_no_geogr_priorstructure input file for analyses making no use of the region of origin of samples as prior information to assist clustering
DOI: 10.5061/dryad.b2q0g
title: Data from: The smell of parents: breeding status influences cuticular hydrocarbon pattern in the burying beetle Nicrophorus vespilloides

description: The waxy layer of the cuticle has been shown to play a fundamental role in
 recognition systems of insects. The biparental burying beetle Nicrophorus
 vespilloides is known to have the ability to discriminate between breeding
 and non-breeding conspecifics and also here cuticular substances could
 function as recognition cue. However, it has not yet been demonstrated
 that the pattern of cuticular lipids can reflect the breeding status of a
 beetle or of any other insect. With chemical analysis using coupled gas
 chromatography–mass spectrometry, we showed that the chemical signature of
 N. vespilloides males and females is highly complex and changes its
 feature with breeding status. Parental beetles were characterized by a
 higher amount of some unusual unsaturated hydrocarbons than beetles which
 are not caring for larvae. The striking correlation between cuticular
 profiles and breeding status suggests that cuticular hydrocarbons inform
 the beetles about parental state and thus enable them to discriminate
 between their breeding partner and a conspecific intruder. Furthermore, we
 found evidence that nutritional conditions also influence the cuticular
 profile and discuss the possibility that the diet provides the precursors
 for the unsaturated hydrocarbons observed in parental beetles. Our study
 underlines the fact that the cuticular pattern is rich of information and
 plays a central role in the burying beetles’ communication systems.
description: Steiger et al 2007
 ProcRSoc DataThis is a Microsoft
 Excel spreadsheet containing the data for Steiger et al (2007) The smell
 of parents: breeding status influences cuticular hydrocarbon pattern in
 the burying beetle Nicrophorus vespilloides. A gas chromatographic
 analysis of the cuticular lipids of different groups of N. vespilloides
 individuals of both sexes was performed. Data represent raw peak areas for
 each of 91 peaks quantified by GC. For compound identity of peaks please
 see publication.
DOI: 10.5061/dryad.kt182
title: Data from: Crop-associated virus infection in a native perennial grass: reduction in plant fitness and dynamic patterns of virus detection

description: To understand the eco-evolutionary significance of plant viruses in
 nature, we must (i) quantify the effects of infection on plant fitness and
 (ii) recognize that native plants are increasingly exposed to
 crop-associated viruses. Studies of perennials are particularly needed:
 most of our knowledge of plant-virus interactions is from annuals, yet
 long-lived species dominate landscapes. Here we used aster models for
 life-history analysis and longitudinal measures of plant virus status to
 evaluate multi-year consequences of crop virus infection in a native
 perennial. We used Barley yellow dwarf virus acquired from wheat to
 inoculate seedlings of Panicum virgatum L. (switchgrass), a North American
 prairie grass. We grew inoculated and mock-inoculated individuals of two
 ecotypes for 3 years in the field. We measured plant size, infection
 status and fitness components. Aster modelling provided integrated
 multi-year measures of fitness. Crop virus inoculation reduced multi-year
 native plant fitness by 30% over 2 years despite generally asymptomatic
 infection and evidence of resistance. This reduction was greater than
 predicted from individual fitness components or most size measures.
 Ecotypes differed in response, with the lowland ecotype experiencing
 higher apparent recovery from infection. Virus treatment in the upland
 ecotype delayed flowering phenology and reduced seed filling. Synthesis.
 Our use of field experimentation, surveys of plant infection status and
 aster modelling demonstrates a rigorous and broadly applicable approach
 for quantifying the effects of viruses and other microbes on multi-year
 plant fitness. We found that a crop virus had negative multi-year effects
 on native plant fitness even after infection was no longer detected.
 Viruses may have substantial effects on native vegetation with
 domestication of landscapes and agricultural expansion.
description: Plant data and virus
 detection in switchgrass experimentSee ReadMe file for
 complete description of columnsSwitchgrass data file
 2012-2014.xls
DOI: 10.5061/dryad.1j6b6
title: Data from: Diet adaptation in dog reflects spread of prehistoric agriculture

description: Adaptations allowing dogs to thrive on a diet rich in starch, including a
 significant AMY2B copy number gain, constituted a crucial step in the
 evolution of the dog from the wolf. It is however not clear if this change
 was associated with the initial domestication or represents a secondary
 shift related to the subsequent development of agriculture. Previous
 efforts to study this process were based on geographically limited data
 sets and low-resolution methods and it is therefore not known to what
 extent the diet adaptations are universal among dogs and whether there are
 regional differences associated with alternative human subsistence
 strategies. Here we use droplet PCR to investigate worldwide AMY2B copy
 number diversity among indigenous as well as breed dogs and wolves to
 elucidate how a change in dog diet was associated with the domestication
 process and subsequent shifts in human subsistence. We find that AMY2B
 copy numbers are bimodally distributed with high copy numbers (median
 2nAMY2B=11) in a majority of dogs but no, or few, duplications (median
 2nAMY2B=3) in a small group of dogs originating mostly in Australia and
 the arctic. We show that this patterns correlates geographically to the
 spread of prehistoric agriculture and conclude that the diet change may
 not have been associated with initial domestication but rather the
 subsequent development and spread of agriculture to most, but not all
 regions of the globe.
description: Supplementary_table_1Summary of all dogs analysed in this study. “AMY2B copy numbers”: Rounded AMY2B copy number of individual; “Name”: name of dog lineage (breed name or name of native dog population if applicable); “Native/Breed”: states whether the individual was analysed as a breed or a native dog; “Country of origin” and “Region of origin”: see Methods section for information on how geographical origin was set,: “Culture”: set to agrarian or non-agrarian depending on whether region of origin overlaps with the approximate spread of pre-historic agriculture.Supplementary_table_2Summary of other canids analysed in this study. “AMY2B copy numbers”: Rounded AMY2B copy number of individual.Supplementary_table_3Summary statistics of AMY2B copy number distribution in dogs. AMY2B copy number distribution in breeds for which at least two individuals were genotyped and in all native dogs grouped into 8 geographical regions (Africa, South West Asia (S. W. Asia), South Asia (S. Asia), East Asia (E. Asia), South East Asia (S. E. Asia), Australia, Arctic America and Arctic Asia). “min” and “max” shows the minimum and maximum copy number observed through out “n” dogs analysed. “sd” shows standard deviation.
DOI: 10.5061/dryad.8509
title: Data from: Ecomorphological diversification among South American spiny rats (Rodentia, Echimyidae): a phylogenetic and chronological approach.

description: The phylogeny of South American spiny rats (Rodentia; Echimyidae) was
 studied using the exon 28 of the von Willebrand Factor nuclear gene (vWF).
 Sequences were analysed separately and in combination with a mitochondrial
 dataset (cyt b, 12S and 16S rRNAs) used in previous publications. The
 basal polytomy of echimyids was partially resolved and unexpected
 intergeneric clades were recovered. Thus, the intimate nested position of
 Myocastor within echimyids is evidenced. A well-supported clade is
 identified, including all the arboreal genera, and a group formed by
 Myocastor, Thrichomys, and Proechimys+Hoplomys. The clustering of
 Euryzygomatomys+Clyomys with Trinomys is also suggested. On the opposite,
 the phylogenetic position of Capromys as well as the relationships among
 arboreal genera remain unclear. Molecular divergence times were estimated
 using a Bayesian relaxed molecular clock and suggest a Middle Miocene
 origin for most of modern genera. The ecomorphological diversification of
 echimyids is discussed in the light of these new results and past
 environmental modifications in South America.
description: Galewski_MolPhylogenetEvol_2005Nucleotide alignment concatenation of 4 mitochondrial and nuclear genes for 37 species of Echymid rodents.Galewski_MolPhylogenetEvol_2005_MLtreeMaximum-likelihood tree inferred from the 4 gene concatenation.
DOI: 10.5061/dryad.5d3s2
title: Data from: Genetic architecture of adaptation to novel environmental conditions in a predominantly selfing allopolyploid plant

description: Genetic architecture of adaptation is traditionally studied in the context
 of local adaptation, viz. spatially varying conditions experienced by the
 species. However, human made changes in the natural environment pose a new
 context to this issue, i.e. adaptation to an environment that is new for
 the species. In this study, we used crossbreeding to analyze genetic
 architecture of adaptation to conditions not currently experienced by the
 species but with high probability of encounter in the near future due to
 the global climate change. We performed targeted inter-population crossing
 using genotypes from two core and two peripheral Triticum dicoccoides
 populations and grew up the parents and three generations of hybrids in a
 greenhouse under simulated desert conditions to analyze the genetic
 architecture of adaptation to these conditions and an effect of gene flow
 from plants having different origin. The observed in allopolyploid T.
 dicoccoides low importance of epistatic gene interactions and low
 probability of hybrid breakdown appear to be the result of permanent
 fixation of heterozygosity and lack of inter-genomic recombination in this
 species. At the same time, predominant but not complete selfing combined
 with an advantage of bivalent pairing of homologous chromosomes appear to
 maintain high genetic variability in T. dicoccoides, greatly enhancing its
 adaptive ability.
description: Data for
 depositing
DOI: 10.5061/dryad.1m3s2
title: Data from: Incomplete lineage sorting in mammalian phylogenomics

description: The impact of incomplete lineage sorting (ILS) on phylogenetic conflicts
 among genes, and the related issue of whether to account for ILS in
 species tree reconstruction, are matters of intense controversy. Here,
 focusing on full-genome data in placental mammals, we empirically test two
 assumptions underlying current usage of tree-building methods that account
 for ILS. We show that in this dataset (i) distinct exons from a common
 gene do not share a common genealogy, and (ii) ILS is only a minor
 determinant of the existing phylogenetic conflict. These results shed new
 light on the relevance and conditions of applicability of ILS-aware
 methods in phylogenomic analyses of protein coding sequences.
description: Scornavacca_SuppFigSupplementary figures, Scornavacca & GaltierScornavacca_SuppMatTrees in newick format, Scornavacca & Galtier
DOI: 10.5061/dryad.056r5
title: Data from: Batch spawning facilitates transfer of an essential nutrient from diet to eggs in a marine fish

description: Fatty acid composition of eggs affects development, growth, and ecological
 performance of fish embryos and larvae, with potential consequences for
 recruitment success. Essential fatty acids in eggs derive from the
 maternal diet, and the time between ingestion and deposition in eggs is
 ecologically important but unknown. We examined the dynamics of diet-egg
 transfer of arachidonic acid (ARA) in the batch-spawning fish, red drum
 (Sciaenops ocellatus), by measuring ARA concentrations in eggs after a
 single diet shift and during a period of irregular variations in diet. ARA
 concentrations in eggs changed within 2-16 days of a diet shift. The rate
 of change was proportional to the magnitude of the shift, with no evidence
 of equilibration. These results are not consistent with eggs being
 assembled entirely from accumulated body stores. The immediate source of
 ARA in eggs appears to be the recent diet. We propose that batch spawning
 produces rapid diet-egg transfer of ARA because it removes large amounts
 of fatty acids from the body and prevents equilibration. The immediacy of
 the diet-egg connection suggests that spawning migration combined with
 short-interval batch spawning may have evolved to take advantage of
 nutrients critical for offspring survival that are available at the
 spawning site.
description: Arachidonic acid content
 of individual spawns of eggs from captive red drum after a
 diet-shift.Data were manually
 entered into a Microsoft Excel spreadsheet then imported into Systat
 statistical software for analysis and graphing. Data extracted from Systat
 to create this file. Variable names and descriptions are provided in
 ReadMe.txt.Diet-shift
 data.xlsRegression statistics
 for changes in arachidonic acid concentration of red drum eggs over time
 after a diet shift. Regression statistics are estimates of initial
 concentration and incorporation rate of arachidonic acid in
 eggs.Data were derived from
 linear regressions computed by Systat statistical software and exported to
 create this file. Variable names and descriptions are provided in
 ReadMe.txt.Diet-shift incorporation
 rates.xlsArachidonic acid content
 of individual spawns of eggs and the diet of captive red drum during
 irregular diet variationsData were manually
 entered into a Microsoft Excel spreadsheet then imported into Systat
 statistical software for analysis and graphing. Data extracted from Systat
 to create this file. Variable names and descriptions are provided in
 ReadMe.txt.Irregular diet
 variations.xls