cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.222vq
title: Data from: Greece: a Balkan subrefuge for a remnant red deer (Cervus elaphus) population

description: A number of phylogeographic studies have revealed the existence of
 multiple ice age refugia within the Balkan Peninsula marking it as a
 biodiversity hotspot. Greece has been reported to harbour genetically
 differentiated lineages from the rest of Balkans for a number of mammal
 species. We therefore searched for distinct red deer lineages in Greece,
 by analysing 78 samples originating from its last population in Parnitha
 Mountain (central Greece). Additionally, we tested the impact of
 human-induced practices on this population. The presence of two discrete
 mtDNA lineages was inferred: i) an abundant one not previously sampled in
 the Balkans and ii) a more restricted one shared with other Balkan
 populations, possibly the result of successful translocations of
 eastern-European individuals. Microsatellite-based analyses of 14 loci
 strongly support the existence of two subpopulations with relative
 frequencies similar to mitochondrial analyses. This study stresses the
 biogeographic importance of central Greece as a separate last Glacial
 Maximun Period (LGM) refugium within the Balkans. It also delineates the
 possible effects that recent translocations of red deer populations had on
 the genetic structuring within Parnitha. We suggest that the Greek red
 deer population of Parnitha is genetically distinct and restocking
 programs should take this genetic evidence into consideration.
description: Karaiskou et
 alMicrosatellite data file
 of Parntitha red deer
DOI: 10.15468/dl.xqhv7z
title: Occurrence Download

description: A dataset containing 34737 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((65.62982 24.69755,75.4089 6.12374,82.2833 9.76704,74.44067 27.22179,65.62982 24.69755))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Squamata"
 ]
}

 The dataset includes 34737 records from 103 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001136-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6f64b
title: Data from: Molecular characterization and population structure of the macaw palm, Acrocomia aculeata (Arecaceae), ex situ germplasm collection using microsatellites markers

description: The Acrocomia aculeata is one of the most promising plants for sustainable
 production of renewable energy. In order to understand patterns of the
 distribution of the allelic diversity of A. aculeata ex situ germplasm
 collection, the present study investigated the hypothesis that the genetic
 variability of the accessions may match their geographical origin. A
 genotypic analysis of 77 A. aculeata accessions was conducted with 6
 simple sequence repeat markers. A high degree of molecular diversity among
 the accessions was found, with an average of 9 alleles per locus and a
 polymorphic information content with a mean of 0.76. A total of 4 clusters
 was identified by the Bayesian analysis of population structure. The
 highest subpopulation diversity was identified in Pop1, mainly formed by
 accessions from State of Mato Grosso do Sul. The populations Pop2A, Pop2B,
 and Pop2C, all from the State of Minas Gerais, showed high genetic
 variability as determined by a higher F st, and a wide genetic variance,
 which were identified within and among the population by analysis of
 molecular variance. Based on our results and on Vavilov’s theory on crop
 origins, one possible diversity center for A. aculeata is proposed to be
 in a region in southeast Brazil.
description: Lanes et al 2014
 Acrocomia aculeata genetic dataExcel file containing
 microsatellite genotypes of accessions A. aculeata. Genetic data of 6
 microsatellite for 77 accessions A. aculeata obtained from the Macaw Palm
 Germoplasm Bank (Brazil). The locus names are listed in the first line.
 The accessions are identified by code of genebank listed in the first
 column of the file. The genotypes of each accessions are from columns 2 to
 13. The allelic description of each accessions was determined by
 informative numerical codes. Missing genetic data are coded as
 "0".
DOI: 10.5061/dryad.p286g
title: Data from: Unified pre- and postsynaptic long-term plasticity enables reliable and flexible learning

description: Although it is well known that long-term synaptic plasticity can be
 expressed both pre- and postsynaptically, the functional consequences of
 this arrangement have remained elusive. We show that
 spike-timing-dependent plasticity with both pre- and postsynaptic
 expression develops receptive fields with reduced variability and improved
 discriminability compared to postsynaptic plasticity alone. These
 long-term modifications in receptive field statistics match recent sensory
 perception experiments. Moreover, learning with this form of plasticity
 leaves a hidden postsynaptic memory trace that enables fast relearning of
 previously stored information, providing a cellular substrate for memory
 savings. Our results reveal essential roles for presynaptic plasticity
 that are missed when only postsynaptic expression of long-term plasticity
 is considered, and suggest an experience-dependent distribution of pre-
 and postsynaptic strength changes.
description: STDP dataset with
 estimated changes in P , q and the mean weightprepostSTDP.xls
DOI: 10.5061/dryad.7t3s4
title: Data from: Direct and indirect effects of early-life environment on lifetime fitness of bighorn ewes

description: Cohort effects, when a common environment affects long-term performance,
 can have a major impact on population dynamics. Very few studies of wild
 animals have obtained the necessary data to study the mechanisms leading
 to cohort effects. We exploited 42 years of individual-based data on
 bighorn sheep to test for causal links between birth density, body mass,
 age at first reproduction, longevity, and lifetime reproductive success
 using path analysis. Specifically, we investigated whether the effect of
 early-life environment on lifetime fitness was the result of indirect
 effects through body mass or direct effects of early-life environment on
 fitness. Additionally, we evaluated whether the effects of early-life
 environment where dependant on the environment experienced during
 adulthood. Contrary to expectation, the effect on lifetime reproductive
 success mediated through body mass was weak compared to the effects found
 via a delay in age at first reproduction, reduced longevity, and the
 direct effect of birth density. Birth density also had an important
 indirect effect on lifetime reproductive success through reduced
 longevity, but only when adult density was high. Our results show that the
 potential long-term consequences of a harsh early-life environment on
 fitness are likely to be underestimated if investigations are limited to
 body mass instead of fitness at several life stages, or if the
 interactions between past and present environment is ignored.
description: dryadDataIndividual information of bighorn sheep ewes used for path analysis.
DOI: 10.5061/dryad.1n1b75b
title: Data from: The effects of experimental design on mating preferences and reproductive isolation in killifish

description: Determining the direction and magnitude of mating preference is
 fundamental to many questions in evolutionary biology. Unlike the
 measurement of traits such as body size, the measurement of mating
 preferences is likely affected by experimental design. Scientists must
 choose both the behavioral assay in which to measure preference and the
 metrics that serve as a proxy for preference. The accuracy of these assays
 and metrics, however, is often unknown and seldom tested. Here, we
 compared the accuracy of 3 assays (dichotomous choice, audience assay, and
 no-choice assay) and 3 metrics (association time, courtship bouts, and
 number of eggs produced) in the bluefin killifish, which possesses strong,
 conspecific mating preferences when in sympatry with rainwater killifish.
 We consistently detected preferences in both males and females when using
 metrics associated with mating (i.e., courting bouts and number of eggs
 spawned). However, we failed to consistently detect preference when using
 time as a metric. We then used all 3 assays and metrics to test for
 cascade reinforcement. Cascade reinforcement predicts that enhanced
 behavioral isolation between sympatric species creates enhanced behavioral
 isolation among populations within species. We tested whether male and
 female bluefin killifish had heightened preference for mates from native
 over foreign populations. We consistently detected female preferences for
 native males, but did not detect male preferences for native females.
 Reproductive isolation values also reflect these preferences. Ultimately,
 we illustrated the importance of using multiple approaches to evaluate and
 legitimize measures of mating preference for males and females choosing
 among mates in different contexts.
description: StJohn&Fuller_2018This file includes six tabs with raw behavioral data. The first two tabs include data measuring mate preference using dichotomous choice assay; tabs three and four include data measuring mate preference using audience assays; and tabs four and five include data measuring mate preference using no choice assays. Further details describing experimental design and measurements are included in each tab.StJohn_Fuller_2018.xlsx
DOI: 10.5061/dryad.vg81t
title: Data from: The impact of digging on craniodental morphology and integration

description: The relationship between the form and function of the skull has been the
 subject of a great deal of research, much of which has concentrated on the
 impact of feeding on skull shape. However, there are a number of other
 behaviours that can influence craniodental morphology. Previous work has
 shown that subterranean rodents that use their incisors to dig
 (chisel-tooth digging) have a constrained cranial shape which is probably
 driven by a necessity to create high bite forces at wide gapes.
 Chisel-tooth digging rodents also have an upper incisor root that is
 displaced further back into the cranium compared with other rodents. This
 study quantified cranial shape and upper incisors of a phylogenetically
 diverse sample of rodents to determine if chisel-tooth digging rodents
 differ in craniodental morphology. The study showed that the crania of
 chisel-tooth digging rodents shared a similar place in morphospace, but a
 strong phylogenetic signal within the sample meant that this grouping was
 non-significant. It was also found that the curvature of the upper incisor
 in chisel-tooth diggers was significantly larger than in other rodents.
 Interestingly, most subterranean rodents in the sample (both chisel-tooth
 and scratch diggers) had upper incisors that were better able to resist
 bending than those of terrestrial rodents, presumably due to their similar
 diets of tough plant materials. Finally, the incisor variables and cranial
 shape were not found to covary consistently in this sample, highlighting
 the complex relationship between a species’ evolutionary history and
 functional morphology.
description: Morphologika file of
 average cranial landmarks procrustes fittedCranial landmarks from
 65 rodent specimens, averaged for each genus and Procrustes fitted, for
 use in GMM analysis (in Morphologika file format).Incisor
 dataIncisor radius of
 curvature, incisor second moment of area and cranial length for 20 genera
 of rodents.Rodent
 phylogenyNexus file of phylogeny
 of rodents, adapted from Fabre et al., 2012.Phylogeny_chapter2.nexus
DOI: 10.5061/dryad.j11fh
title: Data from: The effect of gene flow on coalescent-based species-tree inference

description: Most current methods for inferring species-level phylogenies under the
 coalescent model assume that no gene flow occurs following speciation.
 Several studies have examined the impact of gene flow (e.g., Eckert and
 Carstens (2008); Chung and Ane (2011); Leache et al. (2014); Solis-Lemus
 et al. (2016)) and of ancestral population structure (DeGeorgio and
 Rosenberg, 2016) on the performance of species-level phylogenetic
 inference, and analytic results have been proven for network models of
 gene flow (e.g., Solis-Lemus et al. (2016); Zhu et al. (2016)). However,
 there are few analytic results for a continuous model of gene flow
 following speciation, despite the development of mathematical tools that
 could facilitate such study (e.g., Hobolth et al. (2011); Andersen et al.
 (2014); Tian and Kubatko (2016)). In this paper, we consider a three-taxon
 isolation-with-migration model that allows gene flow between sister taxa
 for a brief period following speciation, as well as variation in the
 effective population sizes across the species tree. We derive the
 probabilities of each of the three gene tree topologies under this model,
 and show that for certain choices of the gene flow and effective
 population size parameters, anomalous gene trees (i.e., gene trees that
 are discordant with the species tree but that have higher probability than
 the gene tree concor- dant with the species tree) exist. We characterize
 the region of parameter space producing anomalous trees, and show that the
 probability of the gene tree that is concordant with the species tree can
 be arbitrarily small. We then show that there is theoretical support for
 using SVDQuartets with an outgroup to infer the rooted three-taxon species
 tree in a model of gene flow between sister taxa. We study the performance
 of SVDQuartets on simulated data and compare it to three other
 commonly-used methods for species tree inference, AS- TRAL, MP-EST, and
 concatenation. The simulations show that ASTRAL, MP-EST, and concatenation
 can be statistically inconsistent when gene flow is present, while
 SVDQuartets performs well, though large sample sizes may be required for
 certain parameter choices.
description: GeneFlowSupplement_MapleThis maple worksheet contains computations and examples to suppement the paper "The Effect of Gene Flow on Coalescent-based Species-tree inference." In particular, the formula for the concordant triple frequency is derived, the formula is shown to agree with the numerical computations from COALGF via an example, and the limits referenced in the section "Analytic Results for the Isolation with Migration Model" are computed explicitly.
DOI: 10.5061/dryad.v3sg2
title: Data from: Producers and scroungers: feeding type composition changes with group size in a socially foraging spider

description: In groups of socially foraging animals, feeding behaviour may change with
 group size in response to varying cost-benefit trade-offs. Numerous
 studies have described group size effects on group-average feeding
 behaviour, particularly emphasizing an increase in scrounging incidence
 for larger groups, where individuals (scroungers) feed from the food
 sources others (producers) discovered. However, individual variation in
 feeding behaviour remains unconsidered in the vast majority of these
 studies even though theoretical models presume individuals to specialize
 in feeding tactic and anticipate higher scrounger-type frequencies in
 larger groups. We combined group-level and individual-level analyses of
 group size effects on social foraging in the subsocial spider
 Australomisidia ergandros. Lending novel experimental support to model
 predictions, we found that individuals specialize in feeding tactic and
 that higher scrounging and lower producing incidence in larger groups were
 mediated through shifts in the ratio of feeding types. Further, feeding
 type specialization was not explained by innate individual differences in
 hunting ability as all feeding types were equally efficient in prey
 capture when foraging alone. Context adaptivity of feeding behaviour might
 allow this subsocial species to succeed under varying socioecological
 conditions.
description: DATA from communal and
 single feeding experimentsThis excel file contains
 the individual feeding parameters obtained from communal feeding trials
 (sheet 1) and single feeding trials (sheet 2). It further contains
 individual descriptive parameters such as group size, group ID, weight and
 weight rank measures that were used as predictors in the statistical
 analyses. The individual feeding parameters are explained in Table 1 as
 well as in the descriptions of the communal and single feeding experiment
 in the "Methods"-section of the manuscript.DATA for MS - Feeding type
 composition changes with group
 size.xlsx
DOI: 10.5061/dryad.p3nt7
title: Data from: Stable isotopes reveal differences in diet among reed bunting subspecies that vary in bill size

description: Reed bunting (Emberiza schoeniclus) subspecies vary considerably in bill
 size and shape and seem to be at an early stage of speciation, in which
 bill might be indirectly causing reproductive isolation. Hence, we
 evaluated whether bill size, as well as age and sex, are associated with
 foraging niche in three West European subspecies of reed bunting: the
 thin-billed schoeniclus, the intermediate-billed lusitanica and the
 thick-billed witherbyi. Blood sampling was undertaken at three sites in
 southwest Europe during the winter (when these subspecies co-occur), and
 stable isotope analyses (carbon and nitrogen) were performed to assess
 their foraging niches. Stable isotope analyses of potential food items
 confirmed uniform baseline isotopic composition among sites. schoeniclus
 showed a significantly broader isotopic niche than lusitanica and
 witherbyi, which seemed otherwise similar despite the fact that witherbyi
 is more divergent in bill traits. Stable isotope ratios were consistent
 with the latter two subspecies feeding on C3-plant-feeding insects,
 whereas schoeniclus diet also included C4 plant material. Despite its
 lower sexual dimorphism, sex and age differences were found only in
 schoeniclus, but these differences vary between locations in a complex
 manner. Our results suggest that bill size and shape differentiated
 between northern, migratory and southern, resident subspecies as a
 consequence of natural selection through competition during the winter,
 which is now reflected in isotopic niche divergence between subspecies.
 The potential roles of sexual selection, reed thickness and summer
 temperature on the difference in bill size (and greater sexual dimorphism)
 between lusitanica and witherbyi are discussed.
description: Bill size and diet in
 reed buntings
DOI: 10.5061/dryad.61n4k
title: Data from: Male and female contributions to behavioral isolation in darters as a function of genetic distance and color distance

description: Determining which reproductive isolating barriers arise first between
 geographically isolated lineages is critical to understanding allopatric
 speciation. We examined behavioral isolation among four recently diverged
 allopatric species in the orangethroat darter clade (Etheostoma: Ceasia).
 We also examined behavioral isolation between each Ceasia species and the
 sympatric rainbow darter Etheostoma caeruleum. We asked (1) is behavioral
 isolation present between allopatric Ceasia species, and how does this
 compare to behavioral isolation with E. caeruleum, (2) does male color
 distance and/or genetic distance predict behavioral isolation between
 species, and (3) what are the relative contributions of female choice,
 male choice, and male competition to behavioral isolation? We found that
 behavioral isolation, genetic differentiation, and male color pattern
 differentiation were present between allopatric Ceasia species. Males, but
 not females, discerned between conspecific and heterospecific mates. Males
 also directed more aggression towards conspecific rival males. The high
 levels of behavioral isolation among Ceasia species showed no obvious
 pattern with genetic distance or male color distance. However, when the E.
 caeruleum was included in the analysis, an association between male
 aggression and male color distance was apparent. We discuss the
 possibility that reinforcement between Ceasia and E. caeruleum is driving
 behavioral isolation among allopatric Ceasia species.
description: Behavioral isolation
 assay dataBehavioral data used to
 measure behavioral isolation between species of Etheostoma darters in the
 laboratory. Data is included for measurements of male aggression, male
 choice, and female choice. Each behavioral trial included a focal male, a
 rival male, and a female.Ceasia BI ms behavioral
 data.xlsx
DOI: 10.5061/dryad.pq373
title: Data from: Cryptic lineages hybridize for worker production in the harvester ant Messor barbarus

description: The reproductive division of labour between queen and worker castes in
 social insects is a defining characteristic of eusociality and a classic
 example of phenotypic plasticity. Whether social insect larvae develop
 into queens or workers has long been thought to be determined by
 environmental cues, i.e. larvae are developmentally totipotent. Contrary
 to this paradigm, several recent studies have revealed that caste is
 determined by genotype in some ant species, but whether this is restricted
 to just a few exceptional species is still unclear. Here, we show that the
 Mediterranean harvester ant Messor barbarus possesses an unusual
 reproductive system, in which the female castes are genetically
 determined. Using both nuclear and mitochondrial data, we show that
 Iberian populations have two distinct, cryptic lineages. Workers are
 always inter-lineage hybrids whereas queens are always produced from
 pure-lineage matings. The results suggest that genetic caste determination
 may be more widespread in ants than previously thought, and that further
 investigation in other species is needed to understand the frequency and
 evolution of this remarkable reproductive system.
description: ESM_Genotypes_Messor_barbarusGenotype data at four microsatellites loci for Iberic populations of Messor barbarusESM_Genotypes.txt
DOI: 10.5061/dryad.4f3f6
title: Data from: Characterization of stress coping style in Senegalese sole (Solea senegalensis) juveniles and breeders for aquaculture

description: The aim of this work was to characterize stress coping styles of
 Senegalese sole (Solea senegalensis) juveniles and breeders and to select
 an operational behavioural screening test (OBST) that can be used by the
 aquaculture industry to classify and select between behavioural phenotypes
 in order to improve production indicators. A total of 61 juveniles and 59
 breeders were subjected to five individual behavioural tests and two
 grouping tests. At the end of the individual tests, all animals were blood
 sampled in order to measure cortisol, glucose and lactate. Three tests
 (restraining, new environment and confinement) characterized the stress
 coping style behaviour of Senegalese sole juveniles and breeders and
 demonstrated inter-individual consistency. Further, the tests when
 incorporated into a principal components analysis (PCA) (i) identified two
 principal axes of personality traits: ‘fearfulness-reactivity’ and
 ‘activity-exploration’, (ii) were representative of the physiological axis
 of stress coping style, and (iii) were validated by established group
 tests. This study proposed for the first time three individual coping
 style tests that reliably represented proactive and reactive personalities
 of Senegalese sole juveniles and breeders. In addition, the three proposed
 tests met some basic operational criteria (rapid testing, no special
 equipment and easy to apply and interpret) that could prove attractive for
 fish farmers to identify fish with a specific behaviour that gives
 advantages in the culture system and that could be used to establish
 selection-based breeding programmes to improve domestication and
 production.
description: Senegalese sole data
 Ibarra-Zatarain et al., 2016Senegalese sole data
 Ibarra-Zatarain etal., 2016.xlsx