cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.fc10f
title: Data from: Higher songs of city birds may not be an individual response to noise

description: It has been observed in many songbird species that populations in noisy
 urban areas sing with a higher minimum frequency than do matched
 populations in quieter, less developed areas. However, why and how this
 divergence occurs is not yet understood. We experimentally tested whether
 chronic noise exposure during vocal learning results in songs with higher
 minimum frequencies in great tits (Parus major), the first species for
 which a correlation between anthropogenic noise and song frequency was
 observed. We also tested vocal plasticity of adult great tits in response
 to changing background noise levels by measuring song frequency and
 amplitude as we changed noise conditions. We show that noise exposure
 during ontogeny did not result in songs with higher minimum frequencies.
 In addition, we found that adult birds did not make any frequency or song
 usage adjustments when their background noise conditions were changed
 after song crystallization. These results challenge the common view of
 vocal adjustments by city birds, as they suggest that either noise itself
 is not the causal force driving the divergence of song frequency between
 urban and forest populations, or that noise induces population-wide
 changes over a time scale of several generations rather than causing
 changes in individual behaviour.
description: Ontogeny Min Freq
 Zollinger et al 2017Mean minimum frequency
 of each song type sung by each bird in the two treatment groups, with mean
 minimum frequencies of the 9 tutor songs.Ontogeny Min Freq
 Zollingeretal2017.xlsxAdult Plasticity 1
 Zollinger et al 2017Minimum frequencies of
 each song type for birds singing in different noise treatments, after
 background noise treatments changed in adulthood.Adult Plasticity 1
 Zollingeretal2017.xlsxAdult Plasticity 2
 Zollinger et al 2017Minimum frequencies of
 all song types sung during 3, randomly selected 5 minute song bouts,
 repeated in both noise treatmentsAdult Plasticity 2
 Zollingeretal2017.xlsxAdult Plasticity 3
 Zollinger et al 2017Peak frequency and song
 amplitude in the presence and absence of noise playback in wild caught
 adults.Adult Plasticity 3 Zollinger
 etal2017.xlsx
DOI: 10.5061/dryad.k9f10
title: Data from: Fully implanted brain-computer interface in a locked-in patient with ALS

description: Options for people with severe paralysis who have lost the ability to
 communicate orally are limited. We describe a method for communication in
 a patient with late-stage amyotrophic lateral sclerosis (ALS), involving a
 fully implanted brain–computer interface that consists of subdural
 electrodes placed over the motor cortex and a transmitter placed
 subcutaneously in the left side of the thorax. By attempting to move the
 hand on the side opposite the implanted electrodes, the patient accurately
 and independently controlled a computer typing program 28 weeks after
 electrode placement, at the equivalent of two letters per minute. The
 brain–computer interface offered autonomous communication that
 supplemented and at times supplanted the patient’s eye-tracking device.
 (Funded by the Government of the Netherlands and the European Union;
 ClinicalTrials.gov number, NCT02224469.)
description: UNP_Target_TaskFile containing ECoG data from the Patient, for one Target Task BCI runRead_me_Target_task.txtUNP_Click_TaskFile containing ECoG data from the Patient, for one Click Task BCI runRead_me_Click_task.txt
DOI: 10.5061/dryad.sp963
title: Data from: Intraspecific trait variation is correlated with establishment success of alien mammals

description: Many studies have aimed to identify common predictors of successful
 introductions of alien species, but the search has had limited success,
 particularly for animals. Past research focused primarily on mean trait
 values even though genetic and phenotypic variation have been shown to
 play a role in establishment success in plants and some animals (mostly
 invertebrates). Using a global database describing 511 introduction events
 representing 97 mammalian species, we show that intraspecific variation in
 morphological traits is associated with establishment success, even when
 controlling for the positive effect of propagule pressure. In particular,
 greater establishment success is associated with more variation in adult
 body size but surprisingly, less variation in neonate body size,
 potentially reflecting distinct trade-offs and constraints that influence
 population dynamics differently. We find no mean trait descriptors
 associated with establishment success, although species occupying wider
 native distribution ranges (which likely have larger niches) are more
 successful. Our results emphasize the importance of explicitly considering
 intraspecific variation to predict establishment success in animal
 species, and generally to understand population dynamics. This
 understanding might improve management of alien species and increase the
 success of intentional releases, e.g. for biocontrol or reintroductions.
description: Gonzalez-Suarez_et_al_Dataset
DOI: 10.5061/dryad.v64q8
title: Data from: Molecular phylogenetics and microsatellite analysis reveals cryptic species of speckled dace (Cyprinidae: Rhinichthys osculus) in Oregon’s Great Basin

description: Speckled dace (Rhinichthys osculus) is a small cyprinid that occurs
 throughout western North America and is the most commonly occurring fish
 in Oregon. Because of the high genetic and morphological variation in this
 species across its range, it has been referred to as a species complex;
 however, no revision to its taxonomy has occurred since 1984. Here, the
 phylogenetics and population genetics of speckled dace are examined
 throughout Oregon’s Great Basin to describe genetic variation and infer
 the geographic boundaries between distinct taxonomic entities and
 populations. We tested the validity of a putative subspecies, Foskett
 Spring speckled dace, that occurs in a single spring within Warner Valley
 in Southeast Oregon and is listed Federally as threatened. Dace were
 collected from Foskett Spring and all surrounding basins containing
 speckled dace (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur),
 as well as Stinking Lake Spring (located within Malheur), created
 phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data,
 and genotyped eight microsatellite loci for population-level analyses.
 Three highly divergent clades warrant species-level status: Malheur stream
 dace, Stinking Lake Spring dace, and dace from the other four basins
 combined. Although Foskett Spring dace were not monophyletic, substantial
 population structure occurs at the basin-level and separates Foskett
 Spring dace from other dace in the surrounding Warner Valley. Thus, we
 recommend ESU status for the isolated population of speckled dace in
 Foskett Spring. The high, previously unrecognized, taxonomic diversity
 within this region indicates a need for a range-wide phylogeographic study
 of speckled dace and an investigation of the morphological distinctiveness
 of the putative new species.
description: S7_alignmentND2 alignment
DOI: 10.5061/dryad.h5f4117
title: Data from: Mean and variance of phylogenetic trees

description: We describe the use of the Fréchet mean and variance in the
 Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the
 diversity of a set of phylogenetic trees. We show that the Fréchet mean is
 comparable to other summary methods, and, despite its stickiness property,
 is more likely to be binary than the majority-rules consensus tree. We
 show that the Fréchet variance is faster and more precise than commonly
 used variance measures. The Fréchet mean and variance are more
 theoretically justified, and more robust, than previous estimates of this
 type, and can be estimated reasonably efficiently, providing a foundation
 for building more advanced statistical methods and leading to applications
 such as mean hypothesis testing and outlier detection.
description: Code for computing
 Frechet mean and varianceSturmMean.zip
DOI: 10.15468/dl.pydgm4
title: Occurrence Download

description: A dataset containing 364597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Belgium",
 "TaxonKey is one of (Aponogeton distachyos, Arthurdendyus triangulatus, Cabomba caroliniana, Callosciurus finlaysonii, Cherax destructor, Corvus splendens, Crassula helmsii, Elodea densa, Eriocheir sinensis, Erythranthe guttata, Faxonius immunis, Faxonius juvenilis, Faxonius rusticus, Faxonius virilis, Gambusia affinis, Heracleum mantegazzianum, Heracleum persicum, Heracleum pubescens, Houttuynia cordata, , Impatiens glandulifera, Koenigia polystachya, Lagarosiphon major, Lepomis gibbosus, Limnoperna fortunei, Ludwigia grandiflora, Ludwigia peploides, Lysichiton americanus, Morone americana, Muntiacus reevesi, Myriophyllum aquaticum, Myriophyllum heterophyllum, Pacifastacus leniusculus, Petasites japonicus, Pontederia cordata, Procambarus acutus, Procambarus clarkii, Procambarus virginalis, Pseudorasbora parva, Pycnonotus cafer, Saururus cernuus, Sciurus carolinensis, Sciurus niger, Solenopsis invicta, Solenopsis richteri, Threskiornis aethiopicus, Vespa velutina, Zizania latifolia)",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 364597 records from 88 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000582-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.8905
title: Data from: Assortative mating counteracts the evolution of dispersal polymorphisms

description: Polymorphic dispersal strategies are found in many plant and animal
 species. An important question is how the genetic variation underlying
 such polymorphisms is maintained. Numerous mechanisms have been discussed,
 including kin competition or frequency-dependent selection. In the context
 of sympatric speciation events genetic and phenotypic variation is often
 assumed to be preserved by assortative mating. Thus, recently, this has
 been advocated as a possible mechanism leading to the evolution of
 dispersal polymorphisms. Here, we examine the role of assortative mating
 for the evolution of trade-off driven dispersal polymorphisms by modelling
 univoltine insect species in a metapopulation. We show that assortative
 mating does not favour the evolution of polymorphisms. On the contrary,
 assortative mating favours the evolution of an intermediate dispersal type
 and a uni-modal distribution of traits within populations. As an
 alternative mechanism dominance may explain the occurrence of two discrete
 morphs.
description: DRYAD_DATAThe files contain the data used to produce the respective figures. The headings are self-expanatory.
DOI: 10.5061/dryad.db18t
title: Data from: Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe

description: The theory of classical and cryptic Pleistocene refugia is based mainly on
 historical changes in temperature, and the refugia are usually defined
 within a latitudinal gradient. However, the gradient of
 oceanic–continental climate (i.e. longitudinal) was also significantly
 variable during glacial cycles with important biotic consequences.
 Range-wide phylogeography of the European ground squirrel (EGS) was used
 to interpret the evolutionary and palaeogeographical history of the
 species in Europe and to shed light on its glacial–interglacial dynamic.
 The EGS is a steppe-inhabiting species and the westernmost member of the
 genus in the Palaearctic region. We have analysed 915 specimens throughout
 the present natural range by employing mitochondrial DNA sequences
 (cytochrome b gene) and 12 nuclear microsatellite markers. The
 reconstructed phylogeography divides the species into two main
 geographical groups, with deep substructuring within both groups. Bulgaria
 is the centre of the ancestral area, and it also has the highest genetic
 diversity within the species. The northernmost group of the EGS survived
 in the southern part of Pannonia throughout several glacial–interglacial
 cycles. Animals from this population probably repeatedly colonized areas
 further to the north and west during the glacial periods, while in the
 interglacial periods, the EGS distribution contracted back to this
 Pannonian refugium. The EGS thus represents a species with a glacial
 expansion/interglacial contraction palaeogeographical dynamics, and the
 Pannonian and southeastern Balkanian steppes are supported as cryptic
 refugia of continental climate during Pleistocene interglacials.
description: Dryad
 alignmentMicrosatellites
 genotypes for all individuals
DOI: 10.5061/dryad.g28rh86
title: Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics

description: Wild specimens are often collected in challenging field conditions, where
 samples may be contaminated with the DNA of conspecific individuals. This
 contamination can result in false genotype calls, which are difficult to
 detect, but may also cause inaccurate estimates of heterozygosity, allele
 frequencies, and genetic differentiation. Marine broadcast spawners are
 especially problematic, because population genetic differentiation is low
 and samples are often collected in bulk and sometimes from active spawning
 aggregations. Here, we used contaminated and clean Pacific herring (Clupea
 pallasi) samples to test (i) the efficacy of bleach decontamination, (ii)
 the effect of decontamination on RAD genotypes, and (iii) the consequences
 of contaminated samples on population genetic analyses. We collected fin
 tissue samples from actively spawning (and thus contaminated) wild herring
 and non-spawning (uncontaminated) herring. Samples were soaked for 10
 minutes in bleach or left untreated, and extracted DNA was used to prepare
 DNA libraries using a restriction-site associated DNA (RAD) approach. Our
 results demonstrate that intraspecific DNA contamination affects patterns
 of individual and population variability, causes an excess of
 heterozygotes, and biases estimates of population structure. Bleach
 decontamination was effective at removing intraspecific DNA contamination
 and compatible with RAD sequencing, producing high-quality sequences,
 reproducible genotypes, and low levels of missing data. Although sperm
 contamination may be specific to broadcast spawners, intraspecific
 contamination of samples may be common and difficult to detect from
 high-throughput sequencing data, and can impact downstream analyses.
description: DataS1File list (files found
 within DataS1.zip): sample_metadata.txt python_calling_genotypes.py
 RAD_genotypes.txt File descriptions: sample_metadata.txt – contains sample
 names and associated metadata (date of sample collection, geographic
 location of sampling, and experimental treatment group).
 python_calling_genotypes.py – python script that takes individual tags.tsv
 files created by pstacks (version 1.29) and uses a minimum sequencing
 depth threshold to designate individual genotypes. RAD_genotypes.txt – a
 dataframe of genotypes (in genepop format) that was used in the final
 analyses of this paper.
DOI: 10.5061/dryad.n7396
title: Data from: Connecting thermal performance curve variation to the genotype: a multivariate QTL approach

description: Thermal performance curves (TPCs) are continuous reaction norms that
 describe the relationship between organismal performance and temperature
 and are useful for understanding trade-offs involved in thermal
 adaptation. While thermal trade-offs such as those between generalists and
 specialists or between hot- and cold-adapted phenotypes are known to be
 genetically variable and evolve during thermal adaptation, little is known
 of the genetic basis to TPCs – specifically, the loci involved and the
 directionality of their effects across different temperatures. To address
 this, we took a multivariate approach, mapping QTL for locomotor activity
 TPCs in the fly, Drosophila serrata using a panel of 76 recombinant inbred
 lines. The distribution of additive genetic (co)variance in the mapping
 population was remarkably similar to the distribution of mutational
 (co)variance for these traits. We detected 11 TPC-QTLs in females and 4 in
 males. Multivariate QTL effects were closely aligned with the major axes
 genetic (co)variation between temperatures; most QTL effects corresponded
 to variation for either overall increases or decreases in activity with a
 smaller number indicating possible trade-offs between activity at high and
 low temperatures. QTLs representing changes in curve shape such as the
 ‘generalist-specialist’ trade-off, thought key to thermal adaptation, were
 poorly represented in the data. We discuss these results in light of
 genetic constraints on thermal adaptation.
description: Locomotor activity for
 D. serrata RILs across 6 temperatures and the 49 QTL
 markers.Parental flies
 originally collected from the field and inbred in the lab. TriKinetic’s
 Drosophilla Activity Monitors (DAMs) used to record fly activity. The 49
 markers consist of microsatelites, dCAPS, and EST derived SNPs. See the
 Readme file for more information.Ril_data.xls
DOI: 10.5061/dryad.1hj46
title: Data from: Global analysis reveals that cryptic diversity is linked with habitat but not mode of life

description: The ubiquity of genetically distinct, cryptic species is limiting any
 attempt to estimate local or global biodiversity as well as impeding
 efforts to conserve species or control pests and diseases. Environmental
 factors or biological traits promoting rapid diversification into
 morphologically similar species remain unclear. Here, using a
 meta-analysis of 1230 studies using DNA sequences to search for cryptic
 diversity in metazoan taxa, we test two hypotheses regarding the frequency
 of cryptic taxa based on mode of life and habitat. First, after correcting
 for study effort and accounting for higher taxonomic affinities and
 biogeographical region of origins, our results do not support the
 hypothesis that cryptic taxa are more frequent among parasitic than
 free-living taxa. Second, in contrast the results support the hypothesis
 that cryptic taxa are more common in certain habitats than others: for a
 given study effort, more cryptic taxa are found in freshwater than in
 terrestrial or marine taxa. These findings suggest that the greater
 heterogeneity and fragmentation of freshwater habitats may promote higher
 rates of genetic differentiation among its inhabitants, a general pattern
 with serious implications for freshwater conservation biology.
description: Cryptic species
 datasetData on the number of
 cryptic species found per study, along with details on focal taxa and
 detection method, from 1230 studies on metazoans.
DOI: 10.5061/dryad.c5j1bb6c
title: Data from: Morphological integration in the hominin dentition: evolutionary, developmental, and functional factors.

description: As the most common and best preserved remains in the fossil record, teeth
 are central to our understanding of evolution. However, many evolutionary
 analyses based on dental traits overlook the constraints that limit dental
 evolution. These constraints are diverse, ranging from developmental
 interactions between the individual elements of a homologous series (the
 whole dentition) to functional constraints related to occlusion. This
 study evaluates morphological integration in the hominin dentition and its
 effect on dental evolution in an extensive sample of Plio- and Pleistocene
 hominin teeth using geometric morphometrics and phylogenetic comparative
 methods. Results reveal that premolars and molars display significant
 levels of covariation; that integration is stronger in the mandibular
 dentition than in the maxillary dentition; and that antagonist teeth,
 especially first molars, are strongly integrated. Results also show an
 association of morphological integration and evolution. Stasis is observed
 in elements with strong functional and/or developmental interactions,
 namely in first molars. Alternatively, directional evolution (and weaker
 integration) occurs in the elements with marginal roles in occlusion and
 mastication, probably in response to other selective pressures. This study
 points to the need to reevaluate hypotheses about hominin evolution based
 on dental characters, given the complex scenario in which teeth evolve.
description: TPS
 filesSee ReadMe
 fileabbreviationsSee ReadMe file
DOI: 10.5061/dryad.90nc6
title: Data from: Mothers may shape the variations in social organization among gorillas

description: When mothers continue to support their offspring beyond infancy, they can
 influence the fitness of those offspring, the strength of social
 relationships within their groups, and the life-history traits of their
 species. Using up to 30 years of demographic data from 58 groups of
 gorillas in two study sites, this study extends such findings by showing
 that mothers may also contribute to differences in social organization
 between closely related species. Female mountain gorillas remained with
 their sons for significantly longer than western gorillas, which may
 explain why male philopatry and multimale groups are more common among
 mountain gorillas. The presence of the putative father and other familiar
 males did not vary significantly between species, and we found only
 limited support for the socio-ecological theory that the distribution of
 adult males is influenced by the distribution of females. Within each
 gorilla species, variations in those distributions may also reflect the
 different stages in the typical life cycle of a group. Collectively, our
 results highlight the potentially far-reaching consequences of maternal
 support that extends beyond infancy, and they illustrate the opportunity
 to incorporate additional factors into phylogenetic analyses of variations
 in social organization, including studies of human evolution.
description: Rout_CoxmePop_FinalMixed effect Cox model to compare the probabilities for male mountain gorillas and western gorillas to reach adulthood in the same group as their mother and other potential relatives.Rout_HaremSizeAverages_FinalAnalysis of variance (ANOVA) to test whether the number of adult females per group is larger for mountain gorillas than western gorillas.Rout_MalesReachAdulthood_FinalGeneralized linear mixed model (GLMM) to compare the probability that males reached adulthood in a breeding group (versus a non-breeding group or solitary).