cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4m80r
title: Data from: High gene flow across large geographic scales reduces extinction risk for a highly specialised coral feeding butterflyfish

description: The vulnerability of ecologically specialised species to environmental
 fluctuations has been well documented. However, population genetic
 structure can influence vulnerability to environmental change and recent
 studies have indicated that specialised species may have lower genetic
 diversity and greater population structuring compared to their generalist
 counterparts. To examine whether there were differences in population
 genetic structure between a dietary specialist (Chaetodon trifascialis)
 and a dietary generalist (C. lunulatus) we compared the demographic
 history and levels of gene flow of two related coral-feeding
 butterflyfishes. Using allele frequencies of &gt;11 microsatellite
 loci and &gt;350 bases of mitochondrial control region sequence our
 analyses of C. trifascialis and C. lunulatus from five locations across
 the Pacific Ocean revealed contrasting demographic histories and levels of
 genetic structure. Heterozygosity excess tests, neutrality tests and
 mismatch distributions were all highly significant in the dietary
 specialist C. trifascialis (all P&lt;0.01), suggesting genetic
 bottlenecks have occurred in all locations. In contrast, we found little
 evidence of genetic bottlenecks for the dietary generalist C. lunulatus.
 High gene flow and low genetic structuring was detected among locations
 for C. trifascialis. Contrary to our expectations, a greater level of
 genetic structuring between locations was detected for C. lunulatus. These
 results suggest that dietary specialisation may affect demographic history
 through reductions in population size following resource declines, without
 affecting population structure through reductions in gene flow in the same
 way that habitat specialisation appears to. Although C. trifascialis is
 highly vulnerable to coral loss, the high gene flow detected here suggests
 populations will be able to recover from local declines through the
 migration of individuals.
description: C lunulatus
 microsatellite dataAllele frequences for 12
 microsatellite loci. Arelquin format data file. Genomic DNA extracted from
 fin clip tissue samples.Lun data
 final.arp.bakC. trifascialis
 microsatellite dataAllele frequences for 11
 microsatellite loci. Arelquin format data file. Genomic DNA extracted from
 fin clip tissue samples.Tri data
 final.arp.bak
DOI: 10.5061/dryad.54j79463
title: Data from: Environmental and genetic influences on body mass and resting metabolic rates (RMR) in a natural population of weasel Mustela nivalis

description: Body mass (BM) and resting metabolic rates (RMR) are two inexorably linked
 traits strongly related to mammalian life histories. Yet, there have been
 no studies attempting to estimate heritable variation and covariation of
 BM and RMR in natural populations. We used a marker-based approach to
 construct a pedigree and then the ‘animal model’ to estimate narrow sense
 heritability (h^2) of these traits in a free-living population of weasels
 Mustela nivalis – a small carnivore characterised by a wide range of BM
 and extremely high RMR. The most important factors affecting BM of weasels
 were sex and habitat type, whereas RMR was significantly affected only by
 seasonal variation of this trait. All environmental factors had only small
 effect on estimates of additive genetic variance of both BM and RMR. The
 amount of additive genetic variance associated with BM and estimates of
 heritability were high and significant in males (h^2 = 0.61), but low and
 not significant in females (h^2 = 0.32), probably due to small sample size
 for the latter sex. The results from the two-trait model revealed
 significant phenotypic (r_P = 0.62) and genetic correlation (r_A = 0.89)
 between BM and whole body RMR. The estimate of heritability of whole body
 RMR (0.54) and body mass corrected RMR (0.45) were lower than estimates of
 heritability for BM. Both phenotypic and genetic correlations between body
 mass corrected RMR and BM had negative signals (r_P = -0.42 and r_A =
 -0.58). Our results indicate that total energy expenditures of individuals
 can quickly evolve through concerted changes in BM and RMR.
description: Microsatelite data of
 weasels, Bialowieza Forest, PolandMicrosatelites data and
 mean phenotypic data (body mass and RMR) for weasels Mustela nivalis
 captured in Bialowieza Forest, Poland.Weasel_data_genotypes.txtPhenotypic data (body mass and RMR) for multiple captures of weasels, Bialowieza Forest, PolandPhenotypic data (body mass and RMR) for multiple captures of weasels Mustela nivalis, Bialowieza Forest, PolandWeasel_data_phenotypes.txt
DOI: 10.5061/dryad.fq7d1
title: Data from: Testing the depth-differentiation hypothesis in a deepwater octocoral

description: The depth-differentiation hypothesis proposes that the bathyal region is a
 source of genetic diversity and an area where there is a high rate of
 species formation. Genetic differentiation should thus occur over
 relatively small vertical distances, particularly along the upper
 continental slope (200–1000 m) where oceanography varies greatly over
 small differences in depth. To test whether genetic differentiation within
 deepwater octocorals is greater over vertical rather than geographical
 distances, Callogorgia delta was targeted. This species commonly occurs
 throughout the northern Gulf of Mexico at depths ranging from 400 to 900
 m. We found significant genetic differentiation (FST = 0.042) across seven
 sites spanning 400 km of distance and 400 m of depth. A pattern of
 isolation by depth emerged, but geographical distance between sites may
 further limit gene flow. Water mass boundaries may serve to isolate
 populations across depth; however, adaptive divergence with depth is also
 a possible scenario. Microsatellite markers also revealed significant
 genetic differentiation (FST = 0.434) between C. delta and a closely
 related species, Callogorgia americana, demonstrating the utility of
 microsatellites in species delimitation of octocorals. Results provided
 support for the depth-differentiation hypothesis, strengthening the notion
 that factors covarying with depth serve as isolation mechanisms in
 deep-sea populations.
description: Quattrini_etal_Callogorgia_allelecallsTwo worksheets with allele calls for Callogorgia americana and Callogorgia delta. Depth ranges, sites, and unique sample numbers are noted.
DOI: 10.5061/dryad.g8d1v
title: Data from: Male-driven reproductive and agonistic character displacement in darters and its implications for speciation in allopatry

description: Selection against hybridization can cause mating traits to diverge between
 species in sympatry via reproductive character displacement (RCD).
 Additionally, selection against interspecific fighting can cause
 aggressive traits to diverge between sympatric species via agonistic
 character displacement (ACD). By directly affecting conspecific
 recognition traits, RCD and ACD between species can also incidentally
 cause divergence in mating and fighting traits among populations within a
 species (termed cascade RCD and cascade ACD). Here, we demonstrate
 patterns consistent with male-driven RCD and ACD in two groups of darters
 (orangethroat darter clade Ceasia and rainbow darter Etheostoma
 caeruleum). In both groups, males that occur in sympatry (between Ceasia
 and E. caeruleum) have higher levels of preference for mating and fighting
 with conspecifics over heterospecifics than do males from allopatry. This
 is consistent with RCD and ACD. We also found patterns consistent with
 cascade RCD and cascade ACD among species of Ceasia. Ceasia males that are
 sympatric to E. caeruleum (but allopatric to one another) also have
 heightened preferences for mating and fighting with conspecific versus
 heterospecific Ceasia. In contrast, Ceasia males that are allopatric to E.
 caeruleum readily mate and fight with heterospecific Ceasia. We suggest
 that RCD and ACD between Ceasia and E. caeruleum has incidentally led to
 divergence in mating and fighting traits among Ceasia species. This study
 is unique in that male preferences evolve via both RCD (male preference
 for conspecific females) and ACD (male preference to fight conspecific
 males) which leads to subsequent divergence among allopatric lineages.
description: Moran & Fuller 2017
 Current Zoology Dryad dataThe Excel file contains
 two tabs with raw behavioral data. The first tab has data from trials that
 measured male competition and female mate choice and the second tab has
 data from trials that measured male mate choice. Further details on the
 experimental design and interpretation of the variables are provided in
 the document.Moran & Fuller 2017 Dryad
 data .xlsx
DOI: 10.5061/dryad.9t1s9
title: Data from: Understanding the dominant controls on litter decomposition

description: Litter decomposition is a biogeochemical process fundamental to element
 cycling within ecosystems, influencing plant productivity, species
 composition and carbon storage. Climate has long been considered the
 primary broad-scale control on litter decomposition rates, yet recent work
 suggests that plant litter traits may predominate. Both decomposition
 paradigms, however, rely on inferences from cross-biome litter
 decomposition studies that analyse site-level means. We re-analyse data
 from a classical cross-biome study to demonstrate that previous research
 may falsely inflate the regulatory role of climate on decomposition and
 mask the influence of unmeasured local-scale factors. Using the
 re-analysis as a platform, we advocate experimental designs of litter
 decomposition studies that involve high within-site replication,
 measurements of regulatory factors and processes at the same local spatial
 grain, analysis of individual observations and biome-scale gradients.
 Synthesis. We question the assumption that climate is the predominant
 regulator of decomposition rates at broad spatial scales. We propose a
 framework for a new generation of studies focused on factoring local-scale
 variation into the measurement and analysis of soil processes across broad
 scales. Such efforts may suggest a revised decomposition paradigm and
 ultimately improve confidence in the structure, parameter estimates and
 hence projections of biogeochemical models.
description: BergDecompReadMeReadMe file describing the content of the associated data file and R code file for the studyBergDecompDataLitter decomposition data and associated site descriptions and climate data for the 20 sites used in the studyBergDecompCodeStatistical freeware package R code used for analyzing the associated data file in this package and drawing the graphics in the associated manuscript.
DOI: 10.5061/dryad.03v7p
title: Data from: Feed-backs among inbreeding, inbreeding depression in sperm traits and sperm competition can drive evolution of costly polyandry

description: Ongoing ambitions are to understand the evolution of costly polyandry and
 its consequences for species ecology and evolution. Emerging patterns
 could stem from feed-back dynamics between the evolving mating system and
 its genetic environment, defined by interactions among kin including
 inbreeding. However, such feed-backs are rarely considered in non-selfing
 systems. We use a genetically-explicit model to demonstrate a mechanism by
 which inbreeding depression can select for polyandry to mitigate the
 negative consequences of mating with inbred males rather than avoiding
 inbreeding. Specifically, given inbreeding depression in sperm traits,
 costly polyandry evolved to ensure female fertility, without requiring
 explicit inbreeding avoidance. We show the mechanisms behind two main
 feed-backs. First, resulting sperm competition caused evolution of sperm
 traits and further mitigated the negative effect of inbreeding depression
 on female fertility. Second, the evolving mating system fed back to
 decrease population-wide homozygosity, and hence inbreeding. However, net
 overall reduction was small due to compound effects on the variances in
 sex-specific reproductive success and paternity skew. Purging of
 deleterious mutations did not eliminate inbreeding depression in sperm
 traits and hence selection for polyandry. Polyandry evolution, both
 directly and through sperm competition, might consequently facilitate
 evolutionary rescue for populations experiencing sudden increases in
 inbreeding.
description: PolyandryInbreeding
 header filePolyandryInbreeding.hPolyandryInbreeding cpp filePolyandryInbreeding.cppClass Parameters: header fileParameters.hClass Parameters: cpp fileParameters.cppClass Traits: header fileTraits.hClass Traits: cpp fileTraits.cppClass allelic meansa_means.hClass allelic standard deviationsa_std.hClass mutation standard deviationsalpha.hClass Population: header filePopulation.hClass Population: cpp filePopulation.cppClass Individual: header fileIndividual.hClass Individual: cpp fileIndividual.cpp
DOI: 10.5061/dryad.t21kq
title: Data from: Argentine ants (Linepithema humile) use adaptable transportation networks to track changes in resource quality

description: Transportation networks play a crucial role in human and animal societies.
 For a transportation network to be efficient, it must have adequate
 capacity to meet traffic demand. Network design becomes increasingly
 difficult in situations where traffic demand can change unexpectedly. In
 humans, network design is often constrained by path dependency because it
 is difficult to move a road once it is built. A similar issue
 theoretically faces pheromone-trail-laying social insects; once a trail
 has been laid, positive feedback makes re-routing difficult because new
 trails cannot compete with continually reinforced pre-existing trails. In
 the present study, we examined the response of Argentine ant colonies and
 their trail networks to variable environments where resources differ in
 quality and change unexpectedly. We found that Argentine ant colonies
 effectively tracked changes in food quality such that colonies allocated
 the highest proportion of foragers to the most rewarding feeder. Ant
 colonies maximised access to high concentration feeders by building
 additional trails and routes connecting the nest to the feeder. Trail
 networks appeared to form via a pruning process in which lower traffic
 trails were gradually removed from the network. At the same time, we
 observed several instances where new trails appear to have been built to
 accommodate a surge in demand. The combination of trail building when
 traffic demand is high and trail pruning when traffic demand is low
 results in a demand-driven network formation system that allows ants to
 monopolise multiple dynamic resources.
description: Trail networks:
 metricsThis data file contains
 the data from Latty et al 2017. The sheet 'NumAnts Clustered'
 and 'NumAnts Sparse’ gives the number of ants counted on each feeder
 type (1 high, 2 low concentrations) over the experiment (180 mins) on the
 clustered and sparse feeder configurations, respectively. Feeder
 concentration swaps to a new location every 60 mins. 'Trail
 summaries' provides data from analysis of trail networks (composite
 images). Each trail was given a unique designation- the properties of
 trails are given on the sheet entitled "Trail
 details".Latty et al 2017
 Dryad.xlsx
DOI: 10.5061/dryad.5rq71
title: Data from: The effect of foot posture on capacity to apply free moments to the ground: implications for fighting performance in great apes

description: In contrast to most other primates, great apes have feet in which the heel
 supports body weight during standing, walking, and running. One possible
 advantage of this plantigrade foot posture is that it may enhance fighting
 performance by increasing the ability to apply free moments (i.e., force
 couples) to the ground. We tested this possibility by measuring
 performance of human subjects when performing from plantigrade and
 digitigrade (standing on the ball of the foot and toes) postures. We found
 that plantigrade posture substantially increased the capacity to apply
 free moments to the ground and to perform a variety of behaviors that are
 likely to be important to fighting performance in great apes. As
 predicted, performance in maximal effort lateral striking and pushing was
 strongly correlated with free moment magnitude. All else being equal,
 these results suggest species that can adopt plantigrade posture will be
 able to apply larger free moments to the ground than species restricted to
 digitigrade or unguligrade foot posture. Additionally, these results are
 consistent with the suggestion that selection for physical competition may
 have been one of the factors that led to the evolution of the derived
 plantigrade foot posture of great apes.
description: Data (Carrier and
 Cunningham)Each folder of this
 excel file contains subject data for one experiment.
DOI: 10.5061/dryad.1ct82
title: Data from: Development of the annelid axochord: insights into notochord evolution

description: The origin of chordates has been debated for more than a century, with one
 key issue being the emergence of the notochord. In vertebrates, the
 notochord develops by convergence and extension of the chordamesoderm, a
 population of midline cells of unique molecular identity. We identify a
 population of mesodermal cells in a developing invertebrate, the marine
 annelid Platynereis dumerilii, that converges and extends toward the
 midline and expresses a notochord-specific combination of genes. These
 cells differentiate into a longitudinal muscle, the axochord, that is
 positioned between central nervous system and axial blood vessel and
 secretes a strong collagenous extracellular matrix. Ancestral state
 reconstruction suggests that contractile mesodermal midline cells existed
 in bilaterian ancestors. We propose that these cells, via vacuolization
 and stiffening, gave rise to the chordate notochord.
description: Sequence
 alignmentsSequence alignments of
 Platynereis genes encoding actin, colA, foxD, laminin, mhc, mox, paraxis,
 tropomyosin, and twist, with their orthologs from other
 phyla.
DOI: 10.5061/dryad.2p57p
title: Data from: A new promising phylogenetic marker to study the diversity of fungal communities: the Glycoside Hydrolase 63 gene

description: In molecular ecology, the development of efficient molecular markers for
 fungi remains an important research domain. Nuclear ribosomal internal
 transcribed spacer (ITS) region was proposed as universal DNA barcode
 marker for fungi, but this marker was criticized for Indel-induced
 alignment problems and its potential lack of phylogenetic resolution. Our
 main aim was to develop a new phylogenetic gene and a putative functional
 marker, from single-copy gene, to describe fungal diversity. Thus, we
 developed a series of primers to amplify a polymorphic region of the
 Glycoside Hydrolase GH63 gene, encoding exo-acting α-glucosidases, in
 basidiomycetes. These primers were validated on 125 different fungal
 genomic DNAs, and GH63 amplification yield was compared with that of
 already published functional markers targeting genes coding for laccases,
 N-acetylhexosaminidases, cellobiohydrolases and class II peroxidases.
 Specific amplicons were recovered for 95% of the fungal species tested,
 and GH63 amplification success was strikingly higher than rates obtained
 with other functional genes. We downloaded the GH63 sequences from 483
 fungal genomes publicly available at the JGI mycocosm database. GH63 was
 present in 461 fungal genomes belonging to all phyla, except Microsporidia
 and Neocallimastigomycota divisions. Moreover, the phylogenetic trees
 built with both GH63 and Rpb1 protein sequences revealed that GH63 is also
 a promising phylogenetic marker. Finally, a very high proportion of GH63
 proteins was predicted to be secreted. This molecular tool could be a new
 phylogenetic marker of fungal species as well as potential indicator of
 functional diversity of basidiomycetes fungal communities in term of
 secretory capacities.
description: Glycoside Hydrolase
 Family 63 nucleotide sequencesFasta file with
 nucleotide sequences of Glycoside Hydrolase Family 63 protein from
 different fungal strains. In the file the following information of each
 sequence can be found: -organism -mol_type= type of molecule
 -tissue_type=origin of the fungal material -country=country:location
 -clone=name of the strain in the fungal collection The consensus
 assembling of forward and reverse sequences was made using SeqMan
 7v7.0.0GH63_sequences.docx
DOI: 10.5061/dryad.12056m1
title: Data from: DNA methylation as a possible mechanism affecting ability of natural populations to adapt to changing climate

description: Environmentally induced epigenetic variation has been recently recognized
 as a possible mechanism allowing plants to rapidly adapt to novel
 conditions. Despite increasing evidence on the topic, little is known on
 how epigenetic variation affects responses of natural populations to
 changing climate. We studied the effects of experimental demethylation
 (DNA methylation is an important mediator of heritable control of gene
 expression) on performance of a clonal grass, Festuca rubra, coming from
 localities with contrasting temperature and moisture regimes. We compared
 performance of demethylated and control plants from different populations
 under two contrasting climatic scenarios and explored whether the response
 to demethylation depended on genetic relatedness of the plants.
 Demethylation significantly affected plant performance. Its effects
 interacted with population of origin and partly with conditions of
 cultivation. The effects of demethylation also varied between distinct
 genotypes with more closely related genotypes showing more similar
 response to demethylation. For belowground biomass, demethylated plants
 showed signs of adaptation to drought that were not apparent in plants
 that were naturally methylated. The results suggest that DNA methylation
 may modify the response of this species to moisture. DNA methylation may
 thus affect the ability of clonal plants to adapt to novel climatic
 conditions. Whether this variation in DNA methylation may also occur under
 natural conditions, however, remains to be explored. Despite the
 significant interactions between population of origin and demethylation,
 our data do not provide clear evidence that DNA methylation enabled
 adaptation to different environments. In fact, we obtained stronger
 evidence of local adaptation in demethylated than in naturally-methylated
 plants. As changes in DNA methylation may be quite dynamic, it is thus
 possible that epigenetic variation can mask plant adaptations to
 conditions of their origin due to pre-cultivation of the plants under
 standardized conditions. This possibility should be considered in future
 experiments exploring plant adaptations.
description: Epig-dryadData on plant performance in the experiment
DOI: 10.25912/rdf_1769491621416
title: Understanding Australian Adolescents’ Perceptions of Healthy and Sustainable Diets, and Perceptions and Consumption of Pulses