cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.tsey67
title: Occurrence Download

description: A dataset containing 5152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tetragonisca angustula, Puma concolor)",
 "HasCoordinate is true",
 "Country is Brazil"
 ]
}

 The dataset includes 5152 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000612-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.909
title: Data from: Temporally variable multivariate sexual selection on sexually dimorphic traits in a wild insect population

description: A widely held view is that the strength and form of natural selection
 varies in time and space in response to varying ecological forces;
 however, adequate quantitative evaluations of this are relatively scarce.
 In this study, we measured the strength and form of sexual selection
 acting on a suite of male morphological traits in a wild ambush bug
 (Phymata americana) population at 10 sampling dates over 2 years. We
 tested the prediction that the strength and direction of sexual selection
 would be associated with one or more important ecological variables. We
 found that patterns of multivariate selection varied considerably over
 time, and even within a season. Yet, for this population, a sexually
 dimorphic color pattern trait was consistently a target of directional
 selection. The strength of sexual selection on this trait was related to
 both sex ratio and density, which is consistent with the idea that
 ecological factors can play an important role in generating patterns of
 sexual selection. We also demonstrate that the median strength of linear
 selection obtained from replicated cross‐sectional methods was
 qualitatively similar to the estimates obtained from longitudinal methods,
 providing multiple lines of evidence that the evolution of sexual color
 dimorphism in this species is attributable to sexual selection.
description: Mating Success in Ambush
 BugsCross-sectional mating
 success data for Phymata americana in 2003 and 2004. Sampling was
 conducted at the Koffler Scientific Reserve at Joker's Hill (S.
 Ontario, Canada)temporal_rawdata_dryad.xls
DOI: 10.5281/zenodo.8122804
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Mont A. Cazier, http://www.wikidata.org/entity/Q21392418. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
description: http://www.wikidata.org/entity/Q21392418
DOI: 10.5061/dryad.4b3qn
title: Data from: Historical DNA documents long distance natal homing in marine fish

description: The occurrence of natal homing in marine fish remains a fundamental
 question in fish ecology as its unequivocal demonstration requires
 tracking of individuals from fertilization to reproduction. Here, we
 provide evidence of long distance natal homing (&gt; 1000 km) over
 more than sixty years in Atlantic cod (Gadus morhua), through genetic
 analysis of archived samples from marked and recaptured individuals. Using
 a high differentiation Single Nucleotide Polymorphism assay we demonstrate
 that the vast majority of cod tagged in West Greenland and recaptured on
 Icelandic spawning grounds belonged to the Iceland Offshore population,
 strongly supporting a hypothesis of homing. The high degree of natal
 fidelity observed provides the evolutionary settings for development of
 locally adapted populations in marine fish and emphasize the need to
 consider portfolio effects in marine fisheries management strategies.
description: Input
 filesThis excel file contains
 five sheets: SNP information, individual genotypes (baseline populations),
 individual genotypes (to be assigned), an input file for a multinomial
 likelihood ratio test and an input file binomial GLM.
DOI: 10.5061/dryad.12d23
title: Data from: Why migrate during the day: a comparative analysis of North American birds

description: Migration can take place primarily during the day, or at night, or during
 both depending on the species. Why the timing of migration varies among
 species has been the object of much research but the underlying ecological
 processes are still unclear. Proximally, migration timing may be
 influenced by the timing of other activities or may be more prevalent in
 species that migrate over long distances. Adaptive scenarios emphasize the
 reduction in flight costs at night especially in smaller species and the
 advantages of travelling in groups during the day to locate staging sites
 more efficiently. I used phylogenetic independent contrasts to examine
 these hypotheses in all North American nesting birds. I uncovered 24
 evolutionary transitions in migration timing, most of which involved a
 switch from nocturnal to diurnal migration. Few of these transitions
 involved a concomitant change in the timing of foraging habits or
 migration distance. However, species in diurnal clades were larger,
 travelled in larger flocks and were generally more sociable than their
 nocturnal counterparts. The results support the hypotheses that a
 reduction in flight costs and the ability to pool information from
 companions are associated with migration timing in North American bird
 species.
description: appendix_2Raw data concerning the timing of migration in breeding North American birds
DOI: 10.5061/dryad.62p02
title: Data from: Diversification of the monoterpene synthase gene family (TPSb) in Protium, a highly diverse genus of tropical trees

description: Plant monoterpenes are a diverse class of secondary metabolites mediating
 biotic and abiotic interactions with direct effects on plant fitness. To
 evaluate the hypothesis that monoterpene diversity is related to
 functional diversification after gene duplication, we reconstructed the
 evolutionary history of monoterpene synthases (TPSb) – the genes
 underlying monoterpene synthesis – in Protium, a taxonomically and
 chemically diverse genus of tropical trees. We isolated multiple copies of
 TPSb genes from chemically divergent Protium species, reconstructed the
 phylogeny of this gene family, used maximum-likelihood estimation of
 selection coefficients, and inferred residues evolving under positive
 selection. We found evidence for one ancient and multiple more recent
 duplication events giving rise to three, and potentially five, copies of
 TPSb genes currently present in Protium. There was evidence for adaptive
 evolution in one copy with a positively selected residue likely involved
 in protein folding and product specificity. All other copies were inferred
 to be evolving under a combination of stabilizing and/or relaxed
 selection. Although gene copy number is consistent with the extensive
 phenotypic diversity in monoterpenes shown in Protium, selection analyses
 suggest that not all copies are undergoing divergent selection consistent
 with a coevolutionary arms race with enemies, but instead may be under
 stabilizing and relaxed selection consistent with signaling or
 physiological stress functionality.
description: Fragment 1 (N terminal
 domain)Alignment of TPS genes
 for N terminal domain. Alignment is in frame +1Frag1_TPSb.fasFragment 2 (C terminal domain)Alignment of TPS genes for C terminal domain. Alignment is in frame +1Frag2_TPSb.fas
DOI: 10.5061/dryad.7k749
title: Data from: Molecular population genetics of the northern elephant seal Mirounga angustirostris

description: The northern elephant seal, Mirounga angustirostris, was heavily hunted
 and declared extinct in the 19th century. However, a colony remained on
 remote Guadalupe Island, Mexico and the species has since repopulated most
 of its historical distribution. Here, we present a comprehensive
 evaluation of genetic variation in the species. First, we assess the
 effect of the demographic bottleneck on microsatellite variability and
 compare it with that found in other pinnipeds, demonstrating levels of
 variation similar to that in species that continue to be threatened with
 extinction. Next, we use sequence data from these markers to demonstrate
 that some of the limited polymorphism predates the bottleneck. However,
 most contemporary variation appears to have arisen recently and persisted
 due to exponential growth. We also describe how we use the range in allele
 size of microsatellites to estimate ancestral effective population size
 before the bottleneck, demonstrating a large reduction in effective size.
 We then employ a classical method for bacteria to estimate the
 microsatellite mutation rate in the species, deriving an estimate that is
 extremely similar to that estimated for a similar set of loci in humans,
 indicating consistency of microsatellite mutation rates in mammals.
 Finally, we find slight significant structure between some geographically
 separated colonies, although its biological significance is unclear. This
 work demonstrates that genetic analysis can be useful for evaluating the
 population biology of the northern elephant seal, in spite of the
 bottleneck that removed most genetic variation from the species.
description: Microsatellite
 genotypesGenotypes of 22
 microsatellites from 837 northern elephant seals.GenotypeDataforAbadia-CardosoEtAl.xls
DOI: 10.5061/dryad.1920
title: Data from: Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes

description: The genetic diversity and population structure of Arabidopsis thaliana
 populations from Norway were studied and compared to a worldwide sample of
 A. thaliana in order to investigate the demographic history and elucidate
 possible colonization routes of populations at the northernmost species
 limit. We genotyped 282 individuals from 31 local populations using 149
 single nucleotide polymorphism (SNP) markers. A high level of population
 subdivision (FST = 0.85 ± 0.007) was found indicating that A. thaliana is
 highly structured at the regional level. Significant relationships between
 genetic and geographic distances were found, suggesting an isolation by
 distance mode of evolution. Genetic diversity was much lower and the level
 of linkage disequilibrium (LD) higher in populations from the north
 (65–68oN) compared to populations from the south (59–62oN); this is
 consistent with a northward expansion pattern. A neighbor-joining (NJ)
 tree showed that populations from northern Norway form a separate cluster,
 while the remaining populations are distributed over a few minor clusters.
 Minimal gene flow seems to have occurred between populations in different
 regions, especially between the geographically distant northern and
 southern populations. Our data suggest that northern populations represent
 a homogenous group that may have been established from a few founders
 during northward expansions, while populations in the central part of
 Norway constitute an admixed group established by founders of different
 origins, most probably as a result of human-mediated gene flow. Moreover,
 Norwegian populations appeared to be homogenous and isolated compared to a
 worldwide sample of A. thaliana, but they are still grouped with Swedish
 populations, which may indicate common colonization histories.
description: DATApaperMOLECOL
DOI: 10.5061/dryad.420p7
title: Data from: Soil biotic quality lacks spatial structure and is positively associated with fertility in a northern grassland

description: When placing roots in the soil, plants integrate information about soil
 nutrients, plant neighbours and beneficial/detrimental soil organisms.
 While the fine-scale spatial heterogeneity in soil nutrients and plant
 neighbours have been described previously, virtually nothing is known
 about the spatial structure in soil biotic quality (measured here as a
 soil Biota-Induced plant Growth Response, or BIGR), or its correlation
 with nutrients or neighbours. Such correlations could imply trade-offs in
 root placement decisions. Theory would predict that soil BIGR is (1)
 negatively related to soil fertility and (2) associated with plant
 community structure, such that plants influence soil biota (and vice
 versa) through plant-soil feedbacks. We would also expect that since
 plants have species-specific impacts on soil organisms, spatially
 homogeneous plant communities should also homogenize soil BIGR. Here, we
 test these hypotheses in a semiarid grassland by (1) characterizing the
 spatial structure of soil BIGR at a scale experienced by an individual
 plant and (2) correlating it to soil abiotic properties and plant
 community structure. We do so in two types of plant communities: (1)
 low-diversity patches dominated by an invasive grass (Bromus inermis
 Leyss.) and (2) patches covered mostly by native vegetation, with the
 expectation that dominance by Bromus would homogenize soil BIGR. Soil BIGR
 was spatially heterogeneous, but not autocorrelated. This was true in both
 vegetation types (Bromus-invaded vs. native patches). Conversely, soil
 abiotic properties and plant community structure were frequently spatially
 autocorrelated at similar scales. Also, contrary to many studies, we found
 a positive correlation between soil BIGR and soil fertility. Soil BIGR was
 also associated with plant community structure. Synthesis. The positive
 correlation between soil BIGR and some soil nutrient levels suggests that
 plants don't necessarily trade-off between foraging for nutrients vs.
 biotic interactions: nutritional cues could rather indicate the presence
 of beneficial soil biota. Moreover, the spatial structure in plant
 communities, coupled with their correlation with soil BIGR, jointly
 suggest that plant-soil feedbacks operate at local scales in the field:
 this has been identified in modelling studies as an important driver of
 plant coexistence.
description: Greenhouse experiment
 data Greenhouse
 data.xlsx Field data (soil
 nutrients and vegetation) Field data.xlsx
   <strong>Spatial
 distribution of soil cores</strong>   spatial.txt
DOI: 10.15468/dl.wxvt9a
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Portuguese Stag beetles (Coleoptera, Lucanidae)"
 ]
}

 The dataset includes 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000613-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.59h51
title: Data from: Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae)

description: Background The date palm root borer Oryctes agamemnon (Coleoptera:
 Scarabaeidae) is one of the major pests of palms. In Saudi Arabia, both
 larvae and adults of Oryctes are particularly troublesome, especially
 during the establishment of young date palm orchards. Endosymbiotic
 bacteria are known to have a key role in food digestion and insecticide
 resistance mechanisms, and therefore are essential to their host insect.
 Identification of these bacteria in their insect host can lead to
 development of new insect pest control strategies. Results Metagenomic DNA
 from larval midgut of the date palm root borer, O. agamemnon, was analyzed
 for endosymbiotic bacterial communities using denatured gradient gel
 electrophoresis (DGGE) utilizing 16S rRNA genes. The DGGE fingerprints
 with metagenomic DNA showed predominance of eleven major operational
 taxonomic units (OTUs) identified as members of Photobacterium, Vibrio,
 Allomonas, Shewanella, Cellulomonas, and Citrobacter, as well as
 uncultured bacteria, including some uncultured Vibrio members. DGGE
 profiles also showed shifts in the dominant bacterial populations of the
 original soil compared with those that existed in the larval midguts. The
 endosymbiotic bacterial community was dominated by members of the family
 Vibrionaceae (54.5%), followed by uncultured bacteria (18.2%),
 Enterobacteriaceae (9.1%), Shewanellaceae (9.1%), and Cellulomonadaceae
 (9.1%). Phylogenetic studies confirmed the affiliation of the dominant
 OTUs into specified families revealed by clustering of each phylotype to
 its corresponding clade. Relative frequency of each phylotype in larval
 midguts revealed predominance of Vibrio furnisii and Vibrio navarrensis,
 followed by uncultured bacterial spp., then Cellulomonas hominis,
 Shewanella algae, and Citrobacter freundii. Conclusion Analysis of
 metagenomic DNA for endosymbiotic bacterial communities from the midgut of
 Oryctes larvae showed strong selection of specific bacterial populations
 that may have a key role in digestion, as well as other benefits to the
 larvae of O. agamemnon. Determination of the distinct endosymbiotic
 community structure and its possible biological functions within the
 insect could provide us with basic information for future pest control
 research.
description: Phylogenetic alignment
 datasequence data
 codeNJ_Phylogenetic
 tree
DOI: 10.5061/dryad.tq71j
title: Data from: Genetics redraws pelagic biogeography of Calanus

description: Planktonic copepods of the genus Calanus play a central role in North
 Atlantic/Arctic marine food webs. Here, using molecular markers, we redrew
 the distributional ranges of Calanus species inhabiting the North Atlantic
 and Arctic Oceans and revealed much wider and more broadly overlapping
 distributions than previously described. The Arctic shelf species, C.
 glacialis, dominated the zooplankton assemblage of many Norwegian fjords,
 where only C. finmarchicus has been reported previously. In these fjords,
 high occurrences of the Arctic species C. hyperboreus were also found.
 Molecular markers revealed that the most common method of species
 identification, prosome length, cannot reliably discriminate the species
 in Norwegian fjords. Differences in degree of genetic differentiation
 among fjord populations of the two species suggested that C. glacialis is
 a more permanent resident of the fjords than C. finmarchicus. We found no
 evidence of hybridisation between the species. Our results indicate a
 critical need for the wider use of molecular markers to reliably identify
 and discriminate these morphologically-similar copepod species, which
 serve as important indicators of climate responses.
description: Genotypes of
 microsatellites and InDels markers for Calanus spp.Sheet 1: Genotypes of 10
 microsatellites used for population differentiation study of Calanus
 finmarchicus and Calanus glacialis. Sheets 2-3: Genotypes of 6 InDels
 markers used for species identification of Calanus species in the North
 Atlantic and the Arctic Oceans.Genotypes_Microsatellites_InDels_BiologyLetters.xlsx
DOI: 10.5061/dryad.j22k0
title: Data from: Viewing images of snakes accelerates making judgments of their color in humans: red snake effect as an instance of ‘emotional Stroop facilitation’

description: One of the most prevalent current psychobiological notions about human
 behaviour and emotion suggests that prioritization of threatening stimuli
 processing induces deleterious effects on task performance. In order to
 confirm its relevancy, 108 adults and 25 children were required to name
 the colour of images of snakes and flowers, using the pictorial emotional
 Stroop paradigm. When reaction time to answer the colour of each stimulus
 was measured, its value was found to decrease when snake images were
 presented when compared with when flower images were presented. Thus,
 contrary to the expectation from previous emotional Stroop paradigm
 research, emotions evoked by viewing images of snakes as a biologically
 relevant threatening stimulus were found to be likely to exert a
 facilitating rather than interfering effect on making judgements of their
 colour.
description: raw
 data(english)
DOI: 10.5061/dryad.ft71172
title: Data from: Assessing the impacts of imperfect detection on estimates of diversity and community structure through multispecies occupancy modeling

description: Detecting all species in a given survey is challenging, regardless of
 sampling effort. This issue, more commonly known as imperfect detection,
 can have negative impacts on data quality and interpretation, most notably
 leading to false absences for rare or difficult‐to‐detect species. It is
 important that this issue be addressed, as estimates of species richness
 are critical to many areas of ecological research and management. In this
 study, we set out to determine the impacts of imperfect detection, and
 decisions about thresholds for inclusion in occupancy, on estimates of
 species richness and community structure. We collected data from a stream
 fish assemblage in Algonquin Provincial Park to be used as a
 representation of ecological communities. We then used multispecies
 occupancy modeling to estimate species‐specific occurrence probabilities
 while accounting for imperfect detection, thus creating a more informed
 dataset. This dataset was then compared to the original to see where
 differences occurred. In our analyses, we demonstrated that imperfect
 detection can lead to large changes in estimates of species richness at
 the site level and summarized differences in the community structure and
 sampling locations, represented through correspondence analyses.
description: Costello_Species_2009This file contains catch data from Costello Creek in 2009. Each page represents a different species.Costello_Species_2015This file contains catch data from Costello Creek in 2015. Each page represents a different species.
DOI: 10.5061/dryad.51m8c58
title: Data from: Deficit of mitogen-activated protein kinase phosphatase 1 (DUSP1) accelerates progressive hearing loss

description: Mitogen-activated protein kinases (MAPK) p38 and c-Jun N-terminal kinases
 (JNKs) are activated during the cellular response to stress signals. Their
 activity is regulated by the MAPK-phosphatase 1 (DUSP1), a key component
 of the anti-inflammatory response. Stress kinases are well-described
 elements of the response to otic injury and the otoprotective potential of
 JNK inhibitors is being tested in clinical trials. In contrast, there are
 no studies exploring the role of DUSP1 in hearing and hearing loss. Here
 we show that Dusp1 expression is age-regulated in the mouse cochlea. Dusp1
 gene knock-out caused premature progressive hearing loss, as confirmed by
 auditory evoked responses in Dusp1-/- mice. Hearing loss correlated with
 cell death in hair cells, degeneration of spiral neurons and increased
 macrophage infiltration. Dusp1-/- mouse cochleae showed imbalanced redox
 status and deregulated expression of cytokines. These data suggest that
 DUSP1 is essential for cochlear homeostasis in the response to stress
 during ageing.
description: Cochlear gene
 expression, MKPs and MAPKFigure1 - Source Data
 1.xlsxHearing measurements of
 wild type and Mkp1 deficient miceFigure2 - Source Data
 1.xlsxCochlear gene
 expression, cell markersFigure3 - Source Data
 1.xlsxCochlear gene
 expression, oxidative stress markersFigure5 - Source Data
 1.xlsxCochlear gene
 expression, inflammation markersFigure6 - Source Data
 1.xlsx