cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1492
title: Data from: Does selfing or outcrossing promote local adaptation?

description: The degree to which plants self-fertilize may impact their potential for
 genetic adaptation. Given that the mating system influences genetic
 processes within and among populations, the mating system could limit or
 promote local adaptation. I conducted a literature survey of published
 reciprocal transplant experiments in plant populations to quantify the
 effect of mating system on the magnitude of local adaptation. Mating
 system had no effect on local adaptation. I detected no effect when
 species were categorized as either self-compatible or self-incompatible or
 when accounting for environmental differences between source populations.
 The results suggest that, despite limited genetic variation in selfing
 species and greater potential for gene flow in outcrossing species, mating
 system has little influence on adaptation of populations.
description: File of individual
 observations from published studiesThese data were
 collected from the original publications.Hereford_LA_dataset.xls
DOI: 10.5061/dryad.rf18s
title: Data from: Ecological divergence and sexual selection drive sexual size dimorphism in new world pitvipers (Serpentes: Viperidae)

description: Hypotheses for the origin and maintenance of sexual size dimorphism (SSD)
 fall into three primary categories: (i) sexual selection on male size,
 (ii) fecundity selection on female size and (iii) ecological selection for
 gender-specific niche divergence. We investigate the impact of these
 forces on SSD evolution in New World pitvipers (Crotalinae). We
 constructed a phylogeny from up to eight genes (seven mitochondrial, one
 nuclear) for 104 species of NW crotalines. We gathered morphological and
 ecological data for 82 species for comparative analyses. There is a strong
 signal of sexual selection on male size driving SSD, but less evidence for
 fecundity selection on female size across lineages. No support was found
 for allometric scaling of SSD (Rensch's rule), nor for directional
 selection for increasing male size (the Fairbairn–Preziosi hypothesis) in
 NW crotalines. Interestingly, arboreal lineages experience higher rates of
 SSD evolution and a pronounced shift to female-biased dimorphism. This
 suggests that fecundity selection on arboreal females exaggerates
 ecologically mediated dimorphism, whereas sexual selection drives male
 size in terrestrial lineages. We find that increasing SSD in both
 directions (male- and female-biased) decreases speciation rates. In NW
 crotalines, it appears that increasing magnitudes of ecologically mediated
 SSD reduce rates of speciation, as divergence accumulates within species
 among sexes, reducing adaptive divergence between populations leading to
 speciation.
description: Crotalinae_TreePhylogeny containing 104 ingroup species. Reconstructed using simultaneous tree and date estimation in BEAST. Calibration points are detailed in the Methods section of the paper. Corresponding sequence alignment is included in the Dryad package.Hendry_etal_Crotalinae_Tree.treCrotalinae_Seq_NexusDNA sequence alignment in Nexus format. Up to 8 genes for 104 species. Range = 528bp (8%) - 6342bp (95%) complete. GenBank Accession numbers are provided in online suppl. info Appendix S1.Hendry_etal_Crotalinae_Seq_Nexus.nex
DOI: 10.5061/dryad.1295
title: Data from: Comparison of quantitative and molecular genetic variation of native vs. invasive populations of purple loosestrife (Lythrum salicaria L., Lythraceae)

description: Study of adaptive evolutionary changes in populations of invasive species
 can be advanced through the joint application of quantitative and
 population genetic methods. Using purple loosestrife as a model system, we
 investigated the relative roles of natural selection, genetic drift, and
 gene flow in the invasive process by contrasting phenotypic and neutral
 genetic differentiation among native European and invasive North American
 populations (QST - FST analysis). Our results indicate that invasive and
 native populations harbor comparable levels of AFLP variation, a pattern
 consistent with multiple independent introductions from a diverse European
 gene pool. However, it was observed that the genetic variation reduced
 during subsequent invasion, perhaps by founder effects and genetic drift.
 Comparison of genetically-based quantitative trait differentiation (QST)
 to its expectation under neutrality (FST) revealed no evidence of
 disruptive selection (QST &gt; FST) or stabilizing selection (QST
 &lt; FST). One exception was found for only one trait (the number of
 stems) showing significant sign of stabilizing selection across all
 populations. It suggests that the difficulties in distinguishing the
 effects of non-adaptive population processes and natural selection.
 Multiple introductions of purple loosestrife may have created a genetic
 mixture from diverse source populations and increased population genetic
 diversity, but its link to the adaptive differentiation of invasive North
 American populations needs further research.
description: AFLP data of Lythrum
 salicariaAFLP-data.csvQuantitative trait data of Lythrum salicariaQuantitative-data.csv
DOI: 10.5061/dryad.5p1q0
title: Data from: Intraguild predation leads to genetically based character shifts in the threespine stickleback

description: Intraguild predation is a common ecological interaction that occurs when a
 species preys upon another species with which it competes. The interaction
 is potentially a mechanism of divergence between intraguild prey
 populations, but it is unknown if cases of character shifts in intraguild
 prey are an environmental or evolutionary response. We investigated the
 genetic basis and inducibility of character shifts in threespine
 stickleback from lakes with and without prickly sculpin, a benthic
 intraguild predator. Wild populations of stickleback sympatric with
 sculpin repeatedly show greater defensive armor and water column height
 preference. We lab-raised stickleback from lakes with and without sculpin,
 as well as marine stickleback, and found that differences between
 populations in armor, body shape, and behavior persisted in a common
 garden. Within the common garden, we raised stickleback half-families from
 multiple populations in the presence and absence of sculpin. Although the
 presence of sculpin induced trait changes in the marine stickleback, we
 did not observe an induced response in the freshwater stickleback.
 Behavioral and morphological trait differences between freshwater
 populations thus have a genetic basis and suggest an evolutionary response
 to intraguild predation.
description: Adult_SpinesMeasurements of armor traits from Adult wild-caught stickleback. All measurements are made in mm and are not size corrected. Data from water column assay.Wild_Data.xlsxCommon Garden DataMeasurements of armor traits from common garden experimental stickleback. All measurements are made in mm and are not size corrected. Position of landmarks for body shape. Positional information and distance traveled for water column assay and shoaling assay.Common_Garden_Data.xlsx
DOI: 10.5061/dryad.j7c74
title: Data from: Population genetics provides new insights into biomarker prevalence in dab (Limanda limanda L.): a key marine biomonitoring species

description: Bioindicators are species for which some quantifiable aspect of its
 biology, a biomarker, is assumed to be sensitive to ecosystem health.
 However, there is frequently a lack of information on the underlying
 genetic and environmental drivers shaping the spatiotemporal variance in
 prevalence of the biomarkers employed. Here, we explore the relative role
 of potential variables influencing the spatiotemporal prevalence of
 biomarkers in dab, Limanda limanda, a species used as a bioindicator of
 marine contaminants. Firstly, the spatiotemporal genetic structure of dab
 around UK waters (39 samples across 15 sites for four years: 2005-2008) is
 evaluated with 16 microsatellites. Two temporally stable groups are
 identified corresponding to the North and Irish Seas (average between
 basin G’ST =0.007; G’’ST=0.022). Secondly, we examine the association
 among biomarker prevalence and several variables, including genetic
 structuring, age, and contaminant exposure. Genetic structure had
 significant interactive effects, together with age and some contaminants,
 in the prevalence of some of the biomarkers considered, namely
 hyperpigmentation and liver lesions. The integration of these datasets
 enhanced our understanding of the relationship between biomarker
 prevalence, exposure to contaminants, and population-specific response,
 thereby yielding more informative predictive models of response and
 prospects for environmental remediation.
description: Dab population genetics
 raw data and biomarker modelling infilesThis is a file
 containing raw information on dab, Limanda limanda, population genetic
 structure, contaminant exposure, age and biomarker prevalence around the
 British Isles (dab.popgen.biomonitoring.xlsx). Dab.genotypes:
 microsatellite allele size data in GenAlex format. Further information on
 sex, age, weight, length, inbreeding coefficients (IR and hL values) and
 latitude and longitude is also included where available. Pop.models:
 Information of sample-average age, contaminant exposure (liver
 concentration), prevalence (%) of external biomarkers (HYP, LY, U, EP),
 proxies of populations structure (ca.axis1 and ca.axis3) and sample level
 genetic diversity (Ho) and inbreeding coefficient (Fis). Ind.models:
 Individual information for 451 individuals on population membership
 (ca.axis1, ca.axis3), inbreeding coefficients (IR, hL), length, weight,
 age, sex, age-site average estimated exposure to contaminant, presence or
 absence of external biomarkers, presence or absence of 32 internal
 biomarkers classified by categories (CAT 1: healthy to CAT 5:malignant
 neoplasms) and liver status (lv.sts: highest category of liver damage
 present in an individual). For any questions in the data please contact
 Niklas Tysklind (ntysklind@univ.bangor.ac.uk).dab.popgen.biomonitoring.xlsx
DOI: 10.15482/usda.adc/30233995
title: Data from: Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA

description: This dataset supports the analysis found in Read et al. 2021 "Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA" (DOI: https://doi.org/10.7717/peerj.11959). The data are formatted as truth tables. Each row is one respondent and each column is one condition (i.e. variable) used in the analysis (see Table 2 in the publication for acronym descriptions). Using these data along with the R script appended to the publication, a qualitative comparative analysis can be conducted to distill the necessary and sufficient conditions required for farmers who have not adopted conservation practices to attend an outreach event. There are two datasets, one for crop farmers and one for livestock farmers. Data were collected by the authors via phone interviews with farmers living in Maryland, USA, between September and November 2020.
DOI: 10.15482/usda.adc/30233995.v1
title: Data from: Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA

description: This dataset supports the analysis found in Read et al. 2021 "Exploring private land conservation non-adopters’ attendance at outreach events in the Chesapeake Bay watershed, USA" (DOI: https://doi.org/10.7717/peerj.11959). The data are formatted as truth tables. Each row is one respondent and each column is one condition (i.e. variable) used in the analysis (see Table 2 in the publication for acronym descriptions). Using these data along with the R script appended to the publication, a qualitative comparative analysis can be conducted to distill the necessary and sufficient conditions required for farmers who have not adopted conservation practices to attend an outreach event. There are two datasets, one for crop farmers and one for livestock farmers. Data were collected by the authors via phone interviews with farmers living in Maryland, USA, between September and November 2020.
DOI: 10.5061/dryad.4j5c7
title: Data from: Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model

description: The invariable site plus Γ model is widely used to model rate
 heterogeneity among alignment sites in maximum likelihood and Bayesian
 phylogenetic analyses. The proof that the invariable site plus continuous
 Γ model is identifiable (model parameters can be inferred correctly given
 enough data) has increased the creditability of its application to
 phylogeny reconstruction. However, most phylogenetic software implement
 the invariable site plus discrete Γ model, whose identifiability is likely
 but unproven. How well the parameters of the invariable site plus discrete
 Γ model are estimated is still disputed. Especially the correlation of the
 fraction of invariable sites with the fractions of sites with a slow
 evolutionary rate is discussed as being problematic. We show that
 optimization heuristics as implemented in frequently used phylogenetic
 software cannot always reliably estimate the shape parameter, the
 proportion of invariable sites and the tree length. Here, we propose an
 improved optimization heuristic that accurately estimates the three
 parameters. While research efforts mainly focus on tree search methods,
 our results signify the equal importance of verifying and developing
 effective estimation methods for complex models of sequence evolution.
description: Supplementary
 materialIG-supplement.pdf
DOI: 10.5061/dryad.8rv01
title: Data from: The evolution of growth patterns in mammalian versus non-mammalian cynodonts

description: One of the major evolutionary transitions of the mammaliaform lineage was
 the origin of a typically mammalian pattern of growth. This is
 characterised by rapid juvenile growth followed by abrupt cessation of
 growth at adult size, and may be linked with other important mammaliaform
 apomorphies of dental replacement and morphology. Investigation of growth
 patterns in the tritylodontid cynodont Oligokyphus and the basal
 mammaliaform Morganucodon provides insight into this crucial transition.
 We collected mandibular depth measurements from large samples of
 Morganucodon and Oligokyphus and constructed distributions of mandibular
 depth vs. frequency for each species. These were compared with
 distributions from species from three different growth classes of extant
 amniote: testudines + crocodilians, mammals + birds, and lepidosaurs.
 Discriminant function analysis was used to differentiate between known
 growth classes by using different combinations of three measures of
 mandibular depth distribution shape (skew, kurtosis and coefficient of
 variation), as proxies for different juvenile and adult growth patterns.
 Classification of the fossil species showed that Morganucodon closely
 resembled extant placental mammals in having rapid juvenile growth
 followed by truncated, determinate adult growth. Oligokyphus showed
 intermediate growth patterns, with more extended adult growth patterns
 than Morganucodon, and slightly slower juvenile growth. This suggests a
 gradual evolution of mammalian growth patterns across the cynodont to
 mammaliaform transition, possibly with the origin of rapid juvenile growth
 preceding that of truncated, determinate adult growth. In turn,
 acquisition of both these aspects of mammalian growth was likely necessary
 for the evolution of diphyodont tooth replacement in the mammaliaform
 lineage.
description: O'Meara & Asher
 Supplementary MaterialO'Meara and Asher
 Supplementary Material. Summary statistics for all species, complete
 results from main analysis and all additional discriminant function
 analyses, and life history data and sources. Additional analyses include
 those assessing the position of marsupials, those in which species with
 small sample size are removed, and those assessing the effects of body
 size and life history.O'MearaAsherSuppMat
 .docx
DOI: 10.5061/dryad.62p91
title: Data from: Modulation frequency as a cue for auditory speed perception

description: Unlike vision, the mechanisms underlying auditory motion perception are
 poorly understood. Here we describe an auditory motion illusion revealing
 a novel cue to auditory speed perception: the temporal frequency of
 amplitude modulation (AM-frequency), typical for rattling sounds.
 Naturally, corrugated objects sliding across each other generate rattling
 sounds whose AM-frequency tends to directly correlate with speed. We found
 that AM-frequency modulates auditory speed perception in a highly
 systematic fashion: moving sounds with higher AM-frequency are perceived
 as moving faster than sounds with lower AM-frequency. Even more
 interestingly, sounds with higher AM-frequency also induce stronger motion
 aftereffects. This reveals the existence of specialized neural mechanisms
 for auditory motion perception, which are sensitive to AM-frequency. Thus,
 in spatial hearing, the brain successfully capitalizes on the AM-frequency
 of rattling sounds to estimate the speed of moving objects. This tightly
 parallels previous findings in motion vision, where spatio-temporal
 frequency of moving displays systematically affects both speed perception
 and the magnitude of the motion aftereffects. Such an analogy with vision
 suggests that motion detection may rely on canonical computations, with
 similar neural mechanisms shared across the different modalities.
description: Data_experiment1the file reports subject number, response of the participant, frequency values (expressed as differences from the standard), speed values (expressed as differences from the standard)AMdiff.txtData experiment 2As for experiment 1, the data show subject number, responses, frequency values (as differences from the standard stimulus), speed values (as differences from the standard stimulus)AMdiff2.txtData experiment 2_ after effectthe file presents data of experiment 2 (after effect): subject number, AM frequency, direction of the adapting stimulus, speed and direction of the test stimulus, and participant's responsesdata_AE_exp2.txt
DOI: 10.5061/dryad.0g0fs
title: Data from: A likelihood-based comparison of population histories in a parasitoid guild

description: Little is known about the stability of trophic relationships in complex
 natural communities over evolutionary timescales. Here, we use sequence
 data from 18 nuclear loci to reconstruct and compare the intraspecific
 histories of major Pleistocene refugial populations in the Middle East,
 the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba
 fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all
 attacking Cynipid oak galls. We develop a likelihood method to numerically
 estimate models of divergence between three populations from multilocus
 data. We investigate the power of this framework on simulated data, and -
 using triplet alignments of intronic loci - quantify the support for all
 possible divergence relationships between refugial populations in the four
 parasitoids. Although an East to West order of population divergence has
 highest support in all but one species, we cannot rule out alternative
 population tree topologies. Comparing the estimated times of population
 splits between species, we find that one species, M. amaenus, has a
 significantly older history than the rest of the guild and must have
 arrived in central Europe at least one glacial cycle prior to other guild
 members. This suggests that although all four species may share a common
 origin in the East, they expanded westwards into Europe at different
 times.
description: Lohse_2012_data.tarThe python scripts polarize.py and polarizeSumStat condense a file of multiple alignmnets (fasta format) into either a list of binary alignmnets (O=ancestral, 1=derived state) or a list summary statitsics (for details see Mathematica notebook Lohse_et_al 2012_Analysis). Both are simple text files which use Mathematica's list notation. The archive Lohse_2012_data.tar contains both the python scripts and the data files for each of the four parasitoid species. These are used as input for the likelihood analysis (see in Mathematica notebook Lohse_et_al 2012_Analysis).Lohse_et_al_2012_AnalysisMathematica notebook implementing the likelihood calculation. The summary files provided in Lohse_2012_data.tar are used as input.
DOI: 10.5061/dryad.f0d93
title: Data from: Effects of tree architecture on pollen dispersal and mating patterns in Abies pinsapo Boiss. (Pinaceae)

description: Plant architecture is crucial to pollination and mating in wind pollinated
 species. We investigate the effect of crown architecture on pollen
 dispersal, mating system and offspring quality, combining phenotypic and
 genotypic analyses in a low-density population of the endangered species
 Abies pinsapo. A total of 598 embryos from three relative crown height
 levels (bottom, middle, top) in five mother plants were genotyped using
 eleven nuclear microsatellite markers (nSSRs). Paternity analysis and
 mating system models were used to infer mating and pollen dispersal
 parameters. In addition, seeds were weighed (N = 16,110) and germinated (N
 = 736), and seedling vigour was measured to assess inbreeding depression.
 Overall, A. pinsapo shows a fat-tailed dispersal kernel, with an average
 pollen dispersal distance of 113–227 m, an immigration rate of
 0.84–26.92%, and a number of effective pollen donors ranging between 3.5
 and 11.9. We found an effect of tree height and relative crown height
 levels on mating parameters. A higher proportion of seeds with embryo
 (about 50%) and a higher rate of self-fertilization (about 60%) were found
 at the bottom level in comparison to the top level. Seed weight and
 seedling vigour are positively related. Nevertheless, no differences were
 found in seed weight or in seedling-related variables such as weight and
 length of aerial and subterranean parts among the different relative crown
 height levels, suggesting that seeds from the more strongly inbred bottom
 level are not affected by inbreeding depression. The different relative
 crown height levels also present a similar effective pollen dispersal
 distance and number of effective pollen donors, indicating vertical
 isotropy for outcross pollen. Our results thus suggest that self-pollen
 may compensate for the shortage of outcross pollen in low density
 populations.
description: MEC-13-0531 (source
 data, and variable names and labels)Source data, and
 variable names and labels, used for MEC-13-0531. Separate sheets refer to
 information related to: (1) adult trees, (2) offspring, (3) reproductive
 variables, (4) developed seeds per cone, (5 & 6) seed weight &
 embryo data, (7) germination, and (8) seedling
 variables.MEC-13-0531-data.xlsx
DOI: 10.5061/dryad.435p4
title: Data from: Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots

description: Poaching of elephants is now occurring at rates that threaten African
 populations with extinction. Identifying the number and location of
 Africa’s major poaching hotspots may assist efforts to end poaching and
 facilitate recovery of elephant populations. We genetically assign origin
 to 28 large ivory seizures (≥0.5 tons) made between 1996-2014, also
 testing assignment accuracy. Results suggest that the major poaching
 hotspots in Africa may be currently concentrated in as few as two areas.
 Increasing law enforcement in these two hotspots could help curtail future
 elephant losses across Africa and disrupt this organized transnational
 crime.
description: Reference sample
 location fileProvides location number
 and associated lat/longsfile1.xlsxReference sample genotypes by locationFile contains reference sample genotypes along with a reference location code for each samplefile2.xlsxSample genotypes by seizureFile contains genotypes for each ivory sample, broken down by seizurefile3.xlsx