cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4gh6tk0
title: Data from: The prevention and detection of human error in ecological stable isotope analysis

description: 1. Stable isotope analysis (SIA) is widely used in ecology, but samples
 are usually analysed in specialist facilities. Like any complex process,
 SIA is susceptible to human error. Despite the best efforts of the SIA
 laboratory, errors may occasionally remain in results released to clients.
 2. We used our experiences as ecologists and laboratory analysts to
 identify human error scenarios to which SIA performed anywhere might be
 susceptible. These scenarios ran from sample selection and submission by
 the ecologist, to the final results report from the SIA laboratory.
 Several scenarios involved errors hard to find by visual examination, by
 either ecologist or analyst. 3. The ecologist can prevent pre-submission
 errors by formalising their sample submission process, and can best
 perform a final results quality check by submitting their own quality
 control material with a matrix similar to that of the samples. Prevention
 of laboratory errors is best accomplished by a comprehensive quality
 management system and a continual-improvement, no-blame laboratory
 culture. 4. We recommend that the ecologist views the entire sample
 selection, submission, and laboratory analysis as an integrated whole,
 establishing their own quality management processes to run alongside those
 of the SIA facility. This recommendation applies to any ecological
 methodology where samples are sent to a specialist facility for analysis.
description: MEE-18-04-284_R1 Hawke
 et al Table S2Stable isotope data in
 analytical sequence, showing the effect of incorrect chromatogram peak
 integration on reported results
DOI: 10.5061/dryad.10h01t1
title: Data from: Purifying selection in the toll-like receptors of song sparrows Melospiza melodia

description: Variation in immune gene sequences is known to influence resistance to
 infectious diseases and parasites, and hence survival and mate choice,
 across animal taxa. Toll-like receptors (TLRs) comprise one essential gene
 family in the vertebrate innate immune system, and recognize
 evolutionarily conserved structures from all major microorganism classes.
 However, the causes and consequences of TLR variation in passerine birds
 remain largely unexplored. We examined seven TLR genes in song sparrows
 (Melospiza melodia), a species that is studied across North America. We
 then examined sequences from four unduplicated TLRs (TLR1LB, TLR3, TLR4
 and TLR15) from birds in two parts of the species’ range (N = 27, N = 6),
 tested for evidence of selection, and conducted pilot analyses of the role
 of TLR heterozygosity in survival. We identified 45 SNPs: 19 caused
 changes in amino acid sequences, and two of these were likely deleterious.
 We found no evidence of codon-level episodic positive selection, but
 detected purifying selection at codons in all TLRs. Contrary to
 expectations we found no strong correlation between heterozygosity at TLRs
 and inbreeding coefficient f (estimate ± se = -0.68 ± 0.37, Radj2 = 0.08,
 F1,25 = 3.38, p = 0.08). In addition, pilot analyses revealed no
 relationship between TLR heterozygosity and survival (β ± SE: 0.09 ± 2.00,
 p = 0.96), possibly due to small sample size. Further analyses of genetic
 diversity in TLRs are likely to advance understanding of the effects of
 innate immune gene diversity on the fitness and persistence of wild
 populations.
description: data for
 dryadThis data was used to
 investigate the effects of TLR heterozygosity on survival of song sparrows
 from Mandarte Island BC, Canada,
DOI: 10.5061/dryad.1032r
title: Data from: Retention of riveted aluminum leg bands by wild turkeys

description: No loss of marks is a critical assumption of mark-recapture models so they
 provide unbiased estimates of population parameters. We double-banded male
 and female wild turkeys with aluminum rivet bands and estimated the
 probability that a bird would be recovered with both bands &lt;1-225
 weeks since banding ( = 51.2 weeks, SD = 44.0). We found that 100% of
 females (n = 37) were recovered with both bands. For males, we recovered 6
 of 188 turkeys missing a rivet band for a retention probability of 0.984
 (95% CI = 0.96-0.99). If male turkeys are double-banded with rivet bands
 the probability of recovering a turkey without any marks is &lt;0.001.
 We failed to detect a change in band retention over time or differences
 between adults and juveniles. Given the low cost and high retention rates
 of rivet aluminum bands, we believe they are an effective marking
 technique for wild turkeys and, for most studies, will minimize any
 concern about the assumption that marks are not lost.
description: R code to analyze
 dataR
 code to read and analyze data to estimate band retention
 rateText
 S1.txtData of band
 lossText file containing
 time between banding and recovery and whether one or both leg bands were
 retained.Text
 S2.txt
DOI: 10.5061/dryad.407j1
title: Data from: A framework for estimating the fixation time of an advantageous allele in stepping-stone models

description: Determining how population subdivision increases the fixation time of an
 advantageous allele is an important problem in evolutionary genetics as
 this influences many processes. Here, I lay out a framework for
 calculating the fixation time of a positively selected allele in a
 subdivided population, as a function of the number of demes present, the
 migration rate between them, and the manner in which they are connected.
 Using this framework it becomes clear that a beneficial allele's
 fixation time is significantly reduced through migration continuously
 introducing copies of the allele into a newly-colonised subpopulation,
 increasing its frequency within these demes. The effect that migration has
 on allele frequency needs to be explicitly taken into account to produce a
 realistic estimate of fixation time. This behaviour is most prominent when
 demes are arranged on a two-dimensional torus, in comparison to
 populations where demes are arranged in a circle. This is because each
 subpopulation is connected to several neighbours over a torus, so that
 there are multiple paths that an allele can take in order to fix. As a
 consequence, some demes experience a greater influx and efflux of migrants
 than others. Analytical results are found to be very accurate when
 compared to stochastic simulations, and are generally robust if there are
 a large number of demes, or if the allele is weakly selected for.
description: Simulations_Hartfield2012_JEBREADME.TXT FOR SIMULATION FILES: These files are the source code for the one-dimensional and two-dimensional population simulations used in the Hartfield 2012 paper "A framework for estimating the fixation time of an advantageous allele in stepping-stone models". Simulations are written in C and need to be compiled prior to execution. See blurb at start of each program for description and how to execute. Please also note that simulations use routines that are part of the GNU Scientific Library (GSL). Since GSL is distributed under the GNU General Public License (http://www.gnu.org/copyleft/gpl.html), you must download it separately from these files. Comments should be sent to Matthew Hartfield (m.hartfield@sms.ed.ac.uk).
DOI: 10.5061/dryad.72n81
title: Data from: Habitat-related variation in the plasticity of a UV sensitive photoreceptor over a small spatial scale in the palmate newt

description: Plastic phenotypes are expected to be favoured in heterogeneous
 environments compared with stable environments. Sensory systems are
 interesting to test this theory because they are costly to produce and
 support, and strong fitness costs are expected if they are not tuned to
 the local environment. Consistently, the visual system of several species
 changes with the conditions experienced during early development. However,
 there is little information on whether the amplitude of the change, i.e.
 the reaction norm, differs between visual environments. Given the rapid
 change of many ecosystems, especially eutrophication for aquatic habitats,
 it is crucial to determine down to which spatial scale change in the
 reaction norm occurs. We addressed this issue by quantifying the
 between-habitat variation in the expression of a UV sensitive opsin in a
 newt. In western France, this species breeds in ponds of small forest
 patches, where water filters out UV, and in agricultural ponds where UV
 transmission is variable. We raised larvae from both habitats with or
 without exposure to UV. Opsin expression was reduced in larvae from
 agricultural habitats when raised without UV, whereas it was low in larvae
 from forest ponds under all lighting conditions. Thus, the variation in
 the reaction norm of opsin expression was lower in stable filtering
 environments and higher in heterogeneous environments. Its variation
 occurred between habitats across a small spatial scale. We discuss the
 hypotheses for this pattern and for the maintenance of residual opsin
 expression in forest populations.
description: Dataset_expression
 of_newt_opsinRelative expression of
 opsins SWS1 and LWS in larvae of Lissotriton helveticus from 2 maternal
 habitats (forest, agricultural). Two ponds (populations) have been sampled
 per habitat. Larvae have been exposed daily to UV for 15 min (UV+), or
 they have not been exposed (UV-).
DOI: 10.5061/dryad.76bn8
title: Data from: Vocal learning via social reinforcement by infant marmoset monkeys

description: For over half a century now, primate vocalizations have been thought to
 undergo little or no experience-dependent acoustic changes during
 development [ 1 ]. If any changes are apparent, then they are routinely
 (and quite reasonably) attributed to the passive consequences of growth.
 Indeed, previous experiments on squirrel monkeys and macaque monkeys
 showed that social isolation [ 2, 3 ], deafness [ 2 ], cross-fostering [ 4
 ] and parental absence [ 5 ] have little or no effect on vocal
 development. Here, we explicitly test in marmoset monkeys—a very vocal and
 cooperatively breeding species [ 6 ]—whether the transformation of
 immature into mature contact calls by infants is influenced by contingent
 parental vocal feedback. Using a closed-loop design, we experimentally
 provided more versus less contingent vocal feedback to twin infant
 marmoset monkeys over their first 2 months of life, the interval during
 which their contact calls transform from noisy, immature calls to tonal
 adult-like “phee” calls [ 7, 8 ]. Infants who received more contingent
 feedback had a faster rate of vocal development, producing mature-sounding
 contact calls earlier than the other twin. The differential rate of vocal
 development was not linked to genetics, perinatal experience, or body
 growth; nor did the amount of contingency influence the overall rate of
 spontaneous vocal production. Thus, we provide the first experimental
 evidence for production-related vocal learning during the development of a
 nonhuman primate.
description: TLG_Vocal_learning_via_social_reinforcementThis file contains the data and MATLAB code used to fit the regression models in "Vocal learning via social reinforcement by infant marmoset monkeys (2017) Takahashi DY, Liao DA, Ghazanfar AA, Current Biology.
DOI: 10.5061/dryad.tc8j2
title: Data from: Marine foraging ecology influences mercury bioaccumulation in deep-diving northern elephant seals

description: Mercury contamination of oceans is prevalent worldwide and methylmercury
 concentrations in the mesopelagic zone (200–1000 m) are increasing more
 rapidly than in surface waters. Yet mercury bioaccumulation in mesopelagic
 predators has been understudied. Northern elephant seals (Mirounga
 angustirostris) biannually travel thousands of kilometres to forage within
 coastal and open-ocean regions of the northeast Pacific Ocean. We coupled
 satellite telemetry, diving behaviour and stable isotopes (carbon and
 nitrogen) from 77 adult females, and showed that variability among
 individuals in foraging location, diving depth and δ13C values were
 correlated with mercury concentrations in blood and muscle. We identified
 three clusters of foraging strategies, and these resulted in substantially
 different mercury concentrations: (i) deeper-diving and offshore-foraging
 seals had the greatest mercury concentrations, (ii) shallower-diving and
 offshore-foraging seals had intermediate levels, and (iii) coastal and
 more northerly foraging seals had the lowest mercury concentrations.
 Additionally, mercury concentrations were lower at the end of the
 seven-month-long foraging trip (n = 31) than after the two-month- long
 post-breeding trip (n = 46). Our results indicate that foraging behaviour
 influences mercury exposure and mesopelagic predators foraging in the
 northeast Pacific Ocean may be at high risk for mercury bioaccumulation.
description: Foraging behavior of
 northern elephant seals and mercury concentrations in blood and
 muscleWe quantified variables
 for the full foraging trip (short and long foraging trip) to describe
 foraging behavior of northern elephant seals, using geography, diving
 behavior, and stable isotopes (carbon and nitrogen). Most seals were
 weighed upon recovery. If not, then RecoveryMassEstimated was recorded as
 1, meaning that the recovery mass was estimated using body composition and
 morphometric measurements. The ToppID is the unique ID for the individual
 and the foraging trip that would link with the full diving and tracking
 file, housed at the University of California, Santa Cruz. The Seal_ID is
 an ID that corresponds to each seal in this study and links with their
 individual histories, also housed at the University of California, Santa
 Cruz.Peterson_et_al_Dataset.csv
DOI: 10.5281/zenodo.17980499
title: SHM_415742_HST_3D

description: Photogrammetric 3D model of a Late Neolithic thick-butted axe with a flared edge collected in Sweden and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=696

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/FAE2971A-DDC1-4421-B1D7-E4720E841C53
DOI: 10.5281/zenodo.17980498
title: SHM_415742_HST_3D

description: Photogrammetric 3D model of a Late Neolithic thick-butted axe with a flared edge collected in Sweden and currently held in the collections of the National Historical Museums in Stockholm.

Link to the Dynamic Collection platform  

https://dyncolldev.ht.lu.se/plus/artifact_view.php?item=696

Link to Sök I Samlingarna  

https://samlingar.shm.se/object/FAE2971A-DDC1-4421-B1D7-E4720E841C53
DOI: 10.5061/dryad.526g0
title: Data from: How does environment influence fighting? The effects of tidal flow on resource value and fighting costs in sea anemones

description: An animal's decision to enter into a fight depends on the interaction
 between perceived resource value (V) and fighting costs (C). Both could be
 altered by predictable environmental fluctuations. For intertidal marine
 animals, such as the sea anemone Actinia equina, exposure to high flow
 during the tidal cycle may increase V by bringing more food. It may also
 increase C via energy expenditure needed to attach to the substrate. We
 asked whether simulated tidal cycles would alter decisions in fighting A.
 equina. We exposed some individuals to still water and others to simulated
 tidal cycles. To gain insights into V, we measured their startle responses
 before and after exposure to the treatments, before staging dyadic fights.
 Individuals exposed to flow present shorter startle responses, suggesting
 that flowing water indicates high V compared with still water. A higher
 probability of winning against no-flow individuals and longer contests
 between flow individuals suggests that increased V increases persistence.
 However, encounters between flow individuals were less likely to escalate,
 suggesting that C is not directly related to V. Therefore, predictable
 environmental cycles alter V and C, but in complex ways.
description: Data from: How does
 environment influence fighting? The effects of tidal flow on resource
 value and fighting costs in sea anemonesData regarding the
 anemone fightsAnemones_FightingData.csvData from: How does environment influence fighting? The effects of tidal flow on resource value and fighting costs in sea anemonesData regarding the startle response of the sea anemonesAnemones_StartleResponse.csv
DOI: 10.5061/dryad.737
title: Data from: Parallel evolution of nonfeeding larvae in echinoids

description: The switch from feeding to nonfeeding larvae is an ecologically important
 transformation that has evolved on several separate occasions within the
 echinoids. In each case, this life history transformation has been
 accompanied by extensive changes in larval morphology. A phylogenetic
 approach is used here to reconstruct these morphological changes, to begin
 asking why they have taken the particular forms observed, and to assess
 the degree of parallel transformation in separate cases. Both traditional
 character mapping and a less usual aggregate analysis indicate massively
 parallel transformations in larval morphology associated with, and only
 with, this particular life history transformation. Some of these parallel
 morphological transformations may be due to relaxed functional constraints
 associated with the ancestral life history mode, but many are probably the
 result of new functional constraints associated with the derived mode. The
 comparative data suggest a simple and testable model for the switch from
 feeding to nonfeeding larvae involving three sequential steps.
description: Wray Data
 SetLarval and embryonic
 morphology data matrixTable1.pdf
DOI: 10.5061/dryad.pc17k
title: Data from: Host species composition influences infection severity among amphibians in the absence of spillover transmission

description: Wildlife epidemiological outcomes can depend strongly on the composition
 of an ecological community, particularly when multiple host species are
 affected by the same pathogen. However, the relationship between host
 species richness and disease risk can vary with community context and with
 the degree of spillover transmission that occurs among co-occurring host
 species. We examined the degree to which host species composition
 influences infection by Batrachochytrium dendrobatidis (Bd), a widespread
 fungal pathogen associated with amphibian population declines around the
 world, and whether transmission occurs from one highly susceptible host
 species to other co-occurring host species. By manipulating larval
 assemblages of three sympatric amphibian species in the laboratory, we
 characterized the relationship between host species richness and infection
 severity, whether infection mediates growth and survivorship differently
 across various combinations of host species, and whether Bd is transmitted
 from experimentally inoculated tadpoles to uninfected tadpoles. We found
 evidence of a dilution effect where Bd infection severity was dramatically
 reduced in the most susceptible of the three host species (Anaxyrus
 boreas). Infection also mediated survival and growth of all three host
 species such that the presence of multiple host species had both positive
 (e.g., infection reduction) and negative (e.g., mortality) effects on
 focal species. However, we found no evidence that Bd infection is
 transmitted by this species. While these results demonstrate that host
 species richness as well as species identity underpin infection dynamics
 in this system, dilution is not the product of reduced transmission via
 fewer infectious individuals of a susceptible host species. We discuss
 various mechanisms, including encounter reduction and antagonistic
 interactions such as competition and opportunistic cannibalism that may
 act in concert to mediate patterns of infection severity, growth, and
 mortality observed in multihost communities.
description: Dryad Han et al. EcoEvo
 Bd diversity dataData collected from an
 experiment to examine dilution effects in larvae of three amphibian
 species experimentally inoculated with Batrachochytrium dendrobatidis
 across various species compositions. Data collected across species
 combinations (combo) for each focal species (species) include growth
 (mass, length), mortality (mean day to death), pathogen treatment (Bd or
 No Bd), mean log(genome equivalents) of Bd in host tissues (quantified
 using real time PCR), the mean proportion of tadpoles that died within
 experimental units, and mean mortality arcsin transformed for statistical
 analyses. Label represents an experimental unit containing 6 tadpoles in
 total at the start of the experiment.
DOI: 10.5061/dryad.kh43b
title: Data from: Floral paedomorphy leads to secondary specialization in pollination of Malagasy Dalechampia (Euphorbiaceae)

description: The traditional evolutionary interpretation of Von Baer’s “laws” of
 embryology is that retention of early developmental forms into adulthood
 (paedomorphosis) leads to the evolution of simpler or more generalized
 morphology and ecology. Here we show that paedomorphosis can also be
 involved in an increase in ecological specialization, in this case of
 plant-pollinator relationships. A paedomorphic transition from generalized
 pollination (by several functional types of pollinators) to specialized
 pollination (by one or a few species in one functional type) occurred in a
 clade of endemic Malagasy vines (Dalechampia spp., Euphorbiaceae). This
 evolutionary transition involved staminate flowers that fail to develop
 “normally,” instead holding mature pollen inside virtually unopened,
 bud-like flowers. This paedomorphic morphology restricts reward access to
 “buzz-pollinating” bees, specifically Xylocopa sp. (carpenter bees), which
 can remove pollen by sonication. This is one of very few reports of
 paedomorphic specialization, and, as far as we are aware, the first
 documented case of a rapid reversal to specialized pollination in a
 lineage of plants that had previously switched from specialized to
 generalized pollination in conjunction with dispersing to a new region.
description: Morphological
 measurements of stamnate flowers and pith cellsMeasurements of lengths
 of staminal columns and pith cells of Dalechampia bernieri and D.
 parvifolia. Measurements made on FAA-preserved material that were
 thin-sectioned, using a compound microscope in the lab.D-p,D-b_cell-lengths.xlsx