cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4v0d4
title: Data from: The eastern migratory caribou: the role of genetic introgression in ecotype evolution

description: Understanding the evolutionary history of contemporary animal groups is
 essential for conservation and management of endangered species like
 caribou (Rangifer tarandus). In central Canada, the ranges of two caribou
 subspecies (barren-ground/woodland caribou) and two woodland caribou
 ecotypes (boreal/eastern migratory) overlap. Our objectives were to
 reconstruct the evolutionary history of the eastern migratory ecotype and
 to assess the potential role of introgression in ecotype evolution.
 STRUCTURE analyses identified five higher order groups (i.e. three boreal
 caribou populations, eastern migratory ecotype and barren-ground). The
 evolutionary history of the eastern migratory ecotype was best explained
 by an early genetic introgression from barren-ground into a woodland
 caribou lineage during the Late Pleistocene and subsequent divergence of
 the eastern migratory ecotype during the Holocene. These results are
 consistent with the retreat of the Laurentide ice sheet and the
 colonization of the Hudson Bay coastal areas subsequent to the
 establishment of forest tundra vegetation approximately 7000 years ago.
 This historical reconstruction of the eastern migratory ecotype further
 supports its current classification as a conservation unit, specifically a
 Designatable Unit, under Canada’s Species at Risk Act. These findings have
 implications for other sub-specific contact zones for caribou and other
 North American species in conservation unit delineation.
description: microsatellite data for
 Klutschetal 2015This file contains all
 microsatellite genotypes used in the article.Klutschetal_2015-01-08.xlsx
DOI: 10.5061/dryad.vc473
title: Data from: Fine mapping quanitative trait loci affecting murine external ear tissue regeneration in the LG/J by SM/J advanced intercross line

description: External ear hole closure in LG/J mice represents a model of regenerative
 response. It is accompanied by the formation of a blastema-like structure
 and the re-growth of multiple tissues including cartilage. The ability to
 regenerate tissue is heritable. An F34 advanced intercross line of mice
 (Wustl:LG,SM-G34) was generated to identify genomic loci involved in ear
 hole closure over a 30 day healing period. We mapped nineteen quantitative
 trait loci (QTL) for ear hole closure. Individual gene effects are
 relatively small (0.08 mm) and most loci have co-dominant effects with
 phenotypically intermediate heterozygotes. QTL support regions were
 limited to a median size of 2 Mb containing a median of 19 genes.
 Positional candidate genes were evaluated using differential transcript
 expression between LG/J and SM/J healing tissue, function analysis, and
 bioinformatic analysis of SNPs in and around positional candidate genes of
 interest. Analysis of the set of 34 positional candidate genes and those
 displaying expression differences revealed over-representation of genes
 involved in cell cycle regulation/DNA damage, cell migration and adhesion,
 developmentally related genes, and metabolism. This indicates that the
 healing phenotype in LG/J mice involves multiple physiological mechanisms.
description: F34MarkersCIDRThis is the centimorgan map generated by SNP mapping of all members of the LG,SM F34 Advanced Intercross Line. Genotyping was carried out by the Center for Inherited Disease Research (CIDR).
DOI: 10.5061/dryad.cm61n
title: Data from: The effects of competition on the strength and softness of selection

description: Deleterious alleles are constantly introduced into populations due to
 mutation. In subdivided populations, the impact of these mutations depends
 on the strength of selection as well as the softness of selection, i.e.,
 the extent to which fitness is governed by local rather than global
 competition. It is widely appreciated that the intensity and type of
 competition will affect selection on deleterious mutations but most
 empirical work has focused solely on the effects of competition on
 selection strength. However, competition has rarely been studied in the
 context of selection ‘softness’ even though competition is at the
 conceptual root of soft selection. All other things being equal, theory
 predicts that inter- and intraspecific competition have opposing effects
 on the softness of selection. Using Drosophila melanogaster, we estimated
 the strength and softness of selection in a “baseline” competitive
 environment as well as two additional competitive environments
 characterized by either additional intra- or interspecific competitors. We
 found that competitive environment had little effect on the average
 strength of selection. While the softness of selection was affected by the
 type of competition, the direction of change varied across tests of
 different genes, contrary to expectation. Though the “hard/soft” selection
 paradigm implicitly assumes that all individuals are equally sensitive to
 the local competitive environment, we found this not to be the case.
 Wild-type individuals were more sensitive to changes in the genetic
 quality of their local competitors than mutant individuals.
description: InterIntraCompSoftStrSeln-DataShows the number of surviving adults (wild-type and mutants) for each treatment of the experiment.
DOI: 10.5061/dryad.4t3r6
title: Data from: Intraspecific trait variation across multiple scales: the leaf economics spectrum in coffee

description: Understanding species differences in plant functional traits has been
 critical in developing a mechanistic understanding of terrestrial
 ecological processes. Greater attention is now being placed on
 understanding the extent, causes and consequences of intraspecific trait
 variation (ITV). ITV is especially important in governing ecological
 processes in cropping systems, where only a small number of species or
 genotypes exist in high abundances. However, it remains unclear if key
 principles of trait-based ecology – namely the leaf economics spectrum
 (LES) – also describe intraspecific variation in crop functional biology.
 There also remains a need to understand whether ITV within crops is
 random, or structured across environmental, management-related or
 biological levels of organization in agroecosystems. We employed a nested
 design field survey to evaluate ITV in leaf traits in coffee (Coffea
 arabica), one of the world's most widespread tropical crops. We
 evaluated ITV in eight physiological, morphological and chemical leaf
 traits, across five nested categorical levels (sites, management systems,
 spatial location, plant identity, branch identity). We compared patterns
 of LES trait covariation in coffee, to interspecific patterns observed
 across over 700 wild plant species. Patterns of bivariate and multivariate
 ITV in coffee were broadly consistent with, but considerably weaker than,
 interspecific patterns associated with the LES, indicating that crops may
 systematically diverge from global patterns of trait trade-offs observed
 in wild plants. Physiological traits varied most widely (coefficient of
 variation (cv) 42–107%), followed by morphological traits (cv = 15–38%)
 and chemical traits (cv = 3–11%). Physiological ITV was best explained by
 the site in which a coffee plant was growing (17–55% explained), while ITV
 for chemical traits was best explained by management treatments within
 sites (25–36%); morphological ITV was higher even at the individual tree
 level or branch level and remained largely unexplained. Our results
 support the hypothesis that artificial selection and high-resource
 agricultural environments lead crops to systematically deviate from
 patterns of leaf trait covariation observed across wild plants species.
 Coupled with an understanding of how different traits vary systematically
 across multiple levels of biological organization, these findings help
 integrate ITV into future analyses of agroecosystem structure and
 function.
description: Martin et al. Functional
 EcologyFunctional leaf trait
 data for Coffea arabica (var. Caturra).
DOI: 10.5061/dryad.j34g342
title: Data from: Behavioural evolution accompanying host shifts in cactophilic Drosophila larvae

description: For plant utilizing insects, the shift to a novel host is generally
 accompanied by a complex set of phenotypic adaptations. Many such
 adaptations arise in response to differences in plant chemistry,
 competitive environment, or abiotic conditions. One less well-understood
 factor in the evolution of phytophagous insects is the selective
 environment provided by plant shape and volume. Does the physical
 structure of a new plant host favour certain phenotypes? Here, we use
 cactophilic Drosophila, which have colonized the necrotic tissues of cacti
 with dramatically different shapes and volumes, to examine this question.
 Specifically, we analysed two behavioural traits in larvae, pupation
 height and activity, that we predicted might be related to the ability to
 utilise variably shaped hosts. We found that populations of D. mojavensis
 living on lengthy columnar or barrel cactus hosts have greater activity
 and pupate higher in a lab environment than populations living on small
 and flat prickly pear cactus cladodes. Crosses between the most
 phenotypically extreme populations suggest that the genetic architectures
 of these behaviours are distinct. A comparison of activity in additional
 cactophilic species that are specialized on small and large cactus hosts
 shows a consistent trend. Thus, we suggest that greater motility and an
 associated tendency to pupate higher in the lab are potential larval
 adaptations for life on a large plant where space is more abundant and
 resources may be more sparsely distributed.
description: Coleman_etal_E&E_dryaddata
DOI: 10.5061/dryad.5pr61
title: Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection

description: While genetic diversity is hypothesized to be an important factor
 explaining invasion success, there is no consensus yet on how variation in
 source populations or demographic processes affects invasiveness. We used
 mitochondrial DNA haplotypic and microsatellite genotypic data to
 investigate levels of genetic variation and reconstruct the history of
 replicate invasions on three continents in a globally invasive bird, the
 monk parakeet (Myiopsitta monachus). We evaluated whether genetic
 diversity at invasive sites could be explained by (i) the native source
 populations from which they were derived and (ii) demographic bottlenecks
 during introduction. Genetic data indicated a localized source area for
 most sampled invasive populations, with limited evidence for admixing of
 native source populations. This pattern largely coincides with historical
 data on pet trade exports. However, the invasive populations are
 genetically more similar than predicted from the export data alone. The
 extent of bottleneck effects varied among invasive populations. The
 observed low genetic diversity, evidence of demographic contraction and
 restricted source area do not support the hypothesis that invasion is
 favoured by the mixing and recombining of genetic variation from multiple
 source populations. Instead, they suggest that reduced genetic variation
 through random processes may not inhibit successful establishment and
 invasion in this species. However, convergent selection across invasive
 sites could also explain the observed patterns of reduction and similarity
 in genetic variation and/or the restricted source area. In general, the
 alternative explanation of intraspecific variation in invasive potential
 among genotypes or geographic areas is neglected, but warrants more
 attention as it could inform comparative studies and management of
 biological invaders.
description: Dryad microsat data
 Edelaar et al. 2015 monk parakeets Mol EcolIndividual genotypic
 data for 6 microsatellite markers, including information on population,
 geographic area and country of sampling.monk parakeet mtdna
 aligned trimmedAlignment of all
 analysed mtDNA control region haplotypes, trimmed to include only
 overlapping parts, FASTA file format.Dryad haplotype
 frequencies per population Edelaar et al. 2015 monk parakeets mol
 EcolExcel file showing
 haplotype frequenties per population.Dryad haplotypes per
 individual Edelaar et al. 2015 monk parakeets Mol EcolHaplotype of each
 individual, together with population and location data.
DOI: 10.5061/dryad.bc14v
title: Data from: Is the post-disturbance composition of a plant population determined by selection for outcrossed seedlings or by the composition of the seedbank?

description: Seedbanks are expected to buffer populations against disturbances, such as
 fire, that could alter the genetic composition of smaller, ephemeral adult
 populations. However, seedling genotypes may be influenced by the
 spatially heterogeneous nature of both the seedbank and the disturbance
 (for example, germination may vary with local disturbance) and also by
 selection acting on germination and post-germination performance. We used
 microsatellite-DNA surveys of seedlings emerging from the soil-stored
 seedbanks of Grevillea macleayana after wildfire to compare diversity and
 spatial structure in seedlings and adults, and through resampling of the
 seedling data set, to determine whether the resultant adult population
 reflected the effects of selection or random seedling mortality. The large
 post-fire seedling cohorts captured the full allelic diversity of the
 pre-fire adult population. However, we found a mismatch in the genotypic
 structure of adults and seedlings. Seedlings displayed larger heterozygous
 deficits than adults; however, over the ensuing 11 years, seedling
 heterozygosity eventually matched values for the pre-fire adults.
 Increasing heterozygosity among adults has generally been attributed to
 heterosis and/or reduction in Wahlund effects via self-thinning.
 Resampling of early post-fire seedlings to generate samples of equivalent
 size to survivors at 11 years showed that increases in heterozygosity must
 be driven by selection favouring outcrossed seed. This finding is
 important in an evolutionary context but also has implications for the
 restoration of natural or managed populations where a seedbank is a viable
 source of recruits.
description: Grevillea macleayana
 Seedbank Study Microsatellite Genotypes10-locus microsatellite
 genotypes for inter-fire adults and seedlings emerging after fire
 stimulated germination in 2001, for two stands (Lower and Upper) of
 Grevillea macleayana. The post-fire survival of the seedlings was recorded
 in 2007, 2009, and 2012.Grevillea macleayana_Seedbank
 Study_Microsatellite Genotypes.xlsx
DOI: 10.5061/dryad.f082m
title: Data from: Baculovirus infection triggers a positive phototactic response in caterpillars to induce ‘tree-top’ disease

description: Many parasites manipulate host behaviour to enhance parasite transmission
 and survival. A fascinating example is baculoviruses, which often induce
 death in caterpillar hosts at elevated positions (‘tree-top’ disease). To
 date, little is known about the underlying processes leading to this
 adaptive host manipulation. Here, we show that the baculovirus Spodoptera
 exigua multiple nucleopolyhedrovirus (SeMNPV) triggers a positive
 phototactic response in S. exigua larvae prior to death and causes the
 caterpillars to die at elevated positions. This light-dependent climbing
 behaviour is specific for infected larvae, as movement of uninfected
 caterpillars during larval development was light-independent. We
 hypothesize that upon infection, SeMNPV captures a host pathway involved
 in phototaxis and/or light perception to induce this remarkable
 behavioural change.
description: raw_data_Fig1AHeight (mm) at which each individual larva (n=31) was found at time points t=0 hours post-infection (hpi) until 166 hpi. At each time point survival was monitored (alive/dead =A/D).raw_data_Fig1BHeight at death (mm) was measured per individual. Three treatments: 1. Light from above only; 2. Light from below only; 3. Dark conditions only. Two replicate experiments performed for each of the treatments (column replicate #), combined data from these two replicates are used in graph of Fig. 1B.raw_data_Fig2Height (mm) per individual larva measured at different time points after mock-infection, from 0 hours post mock-infection until 214 hpi (light/dark) or 184 hpi (only dark).Two treatments: 1. mock-infected larvae kept under normal light/dark conditions; 2. mock-infected larvae kept under dark conditions.
DOI: 10.5061/dryad.00vg4
title: Data from: Concealed by darkness: interactions between predatory bats and nocturnally migrating songbirds illuminated by DNA sequencing

description: Recently, several species of aerial-hawking bats have been found to prey
 on migrating songbirds, but details on this behaviour and its relevance
 for bird migration are still unclear. We sequenced avian DNA in
 feather-containing scats of the bird-feeding bat Nyctalus lasiopterus from
 Spain collected during bird migration seasons. We found very high prey
 diversity, with 31 bird species from eight families of Passeriformes,
 almost all of which were nocturnally flying sub-Saharan migrants.
 Moreover, species using tree hollows or nest boxes in the study area
 during migration periods were not present in the bats’ diet, indicating
 that birds are solely captured on the wing during night-time passage.
 Additional to a generalist feeding strategy, we found that bats selected
 medium-sized bird species, thereby assumingly optimizing their energetic
 cost-benefit balance and injury risk. Surprisingly, bats preyed upon birds
 half their own body mass. This shows that the 5% prey to predator body
 mass ratio traditionally assumed for aerial hunting bats does not apply to
 this hunting strategy or even underestimates these animals’ behavioural
 and mechanical abilities. Considering the bats’ generalist feeding
 strategy and their large prey size range, we suggest that nocturnal bat
 predation may have influenced the evolution of bird migration strategies
 and behaviour.
description: CytbSPreyPartial Cytochrome b sequences obtained from sequencing of the amplification of the DNA from excrement with specific primers for arthropodes.CytbLPreyPartial Cytochrome b (Part 2) sequences obtained from sequencing of the amplification of the DNA from excrement with specific primers for arthropodesSamples List finalSamples used in the study
DOI: 10.5061/dryad.gv348
title: Data from: The effect of size and sex-ratio experiences on reproductive competition in Nicrophorus vespilloides burying beetles in the wild

description: Male parents face a choice: should they invest more in caring for
 offspring or in attempting to mate with other females? The most profitable
 course depends on the intensity of competition for mates, which is likely
 to vary with the population sex ratio. However, the balance of pay-offs
 may vary among individual males depending on their competitive prowess or
 attractiveness. We tested the prediction that sex ratio and size of the
 resource holding male provide cues regarding the level of mating
 competition prior to breeding and therefore influence the duration of a
 male's biparental caring in association with a female. Male burying
 beetles, Nicrophorus vespilloides were reared, post-eclosion, in groups
 that differed in sex ratio. Experimental males were subsequently
 translocated to the wild, provided with a breeding resource (carcass) and
 filmed. We found no evidence that sex ratio cues prior to breeding
 affected future parental care behaviour but males that experienced
 male-biased sex ratios took longer to attract wild mating partners.
 Smaller males attracted a higher proportion of females than did larger
 males, securing significantly more monogamous breeding associations as a
 result. Smaller males thus avoided competitive male–male encounters more
 often than larger males. This has potential benefits for their female
 partners who avoid both intrasexual competition and direct costs of higher
 mating frequency associated with competing males.
description: Hopwood-etal-male
 reproductive competition in burying beetles
 JEB-2015-00671-dataThese data relate to
 "The effect of size and sex-ratio experiences on reproductive
 competition in Nicrophorus vespilloides burying beetles in the wild."
 Hopwood, Paul E., Moore, Allen J., Tregenza, Tom, Royle, Nick
 J.Hopwood-etal-JEB-2015-00671-data.xlsx
DOI: 10.5061/dryad.rs610
title: Data from: Experimental adaptation to marine conditions by a freshwater alga

description: The marine-freshwater boundary has been suggested as one of the most
 difficult to cross for organisms. Salt is a major ecological factor and
 provides an unequalled range of ecological opportunity because marine
 habitats are much more extensive than freshwater habitats, and because
 salt strongly affects the structure of microbial communities. We exposed
 experimental populations of the freshwater alga Chlamydomonas reinhardtii
 to steadily increasing concentrations of salt. About 98% of the lines went
 extinct. The ones that survived now thrive in growth medium with 36 gL−1
 NaCl, and in seawater. Our results indicate that adaptation to marine
 conditions proceeded first through genetic assimilation of an inducible
 response to relatively low salt concentrations that was present in the
 ancestors, and subsequently by the evolution of an enhanced inducible
 response to high salt concentrations. These changes appear to have evolved
 through reversible and irreversible modifications respectively. The
 evolution of marine from freshwater lineages is an example that clearly
 indicates the possibility of studying certain aspects of major ecological
 transitions in the laboratory.
description: Growth in
 seawaterRate of increase of
 salt-selected lines, the ancestors, wild-type, and marine strain when
 grown in seawater. Data associated with Figure 2.seawater.archive.data.csvAncestor to evolved comparisonRate of increase of ancestors and salt-selected lines in a range of different salt concentrations. Data associated with Figure 3.anc.evolved.archive.data.csvEffect of acclimation on ancestorsRate of increase of ancestors in a range of salt concentrations after acclimation with or without salt, and when grown in the light or in the dark. Data associated with Figure 4.anc.acclimation.archive.data.csvEffect of acclimation on evolved linesRate of increase of salt-selected lines in a range of salt concentrations after acclimation with or without salt. Data associated with Figure 5.evolved.acclim.archive.data.csvCrossing trialRate of increase of salt-selected parents, ancestral parent, F1, and F2 in a range of different salt concentrations after acclimation with or without salt. Data associated with Figure 6.crossing.archive.data.csv