cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1385
title: Data from: Contrasting pattern of natural variation in global Drosophila melanogaster populations

description: Despite the popularity of Drosophila melanogaster in functional and
 evolutionary genetics, the global pattern of natural variation has not yet
 been comprehensively described in this species. For the first time, we
 report a combined survey using neutral microsatellites and mitochondrial
 sequence variation jointly. Thirty-five populations originating from five
 continents were compared. In agreement with previous microsatellite
 studies, sub-Saharan African populations were the most variable ones.
 Consistent with previous reports of a single 'out of Africa'
 habitat expansion, we found that non-African populations contained a
 subset of the African alleles. The pattern of variation detected for the
 mitochondrial sequences differed substantially. The most divergent
 haplotypes were detected in the Mediterranean region while Africa harbored
 most haplotypes, which were all closely related. In the light of the
 well-established African origin of D. melanogaster, our results cast
 severe doubts about the suitability of mtDNA for biogeographic inference
 in this model organism.
description: Microsatellite
 dataGlobalVar08.txtMicrosatellite PrimersThis file lists the primers used to amplify the microsatellite loci. Loci identifier numbers correspond to row 3 of the file "Microsatellite data".
DOI: 10.5061/dryad.rq430
title: Data from: Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle

description: Postcopulatory sperm storage can serve a range of functions, including
 ensuring fertility, allowing delayed fertilization and facilitating sexual
 selection. Sperm storage is likely to be particularly important in
 wide-ranging animals with low population densities, but its prevalence and
 importance in such taxa, and its role in promoting sexual selection, are
 poorly known. Here, we use a powerful microsatellite array and paternal
 genotype reconstruction to assess the prevalence of sperm storage and test
 sexual selection hypotheses of genetic biases to paternity in one such
 species, the critically endangered hawksbill turtle, Eretmochelys
 imbricata. In the majority of females (90.7%, N = 43), all offspring were
 sired by a single male. In the few cases of multiple paternity (9.3%), two
 males fertilized each female. Importantly, the identity and proportional
 fertilization success of males were consistent across all sequential nests
 laid by individual females over the breeding season (up to five nests over
 75 days). No males were identified as having fertilized more than one
 female, suggesting that a large number of males are available to females.
 No evidence for biases to paternity based on heterozygosity or relatedness
 was found. These results indicate that female hawksbill turtles are
 predominantly monogamous within a season, store sperm for the duration of
 the nesting season and do not re-mate between nests. Furthermore, females
 do not appear to be using sperm storage to facilitate sexual selection.
 Consequently, the primary value of storing sperm in marine turtles may be
 to uncouple mating and fertilization in time and avoid costly re-mating.
description: Phillipsetal_MolEcol_hawksbillturtleMicrosoft Excel file with five sheets. Sheet 1: hatchling microsatellite genotypes. Sheet 2: female genotypes. Sheet 3: reconstructed genotypes of males. Sheet 4: list of which female pairs with which male. Sheet 5: nest data - lay dates, numbers of eggs in nests, number of undeveloped eggs.
DOI: 10.5061/dryad.q0fh6734
title: Data from: Phylogenetic plant community structure along elevation is lineage specific

description: The trend of closely related taxa to retain similar environmental
 preferences mediated by inherited traits suggests that several patterns
 observed at the community scale originate from longer evolutionary
 processes. While the effects of phylogenetic relatedness have been
 previously studied within a single genus or family, lineage-specific
 effects on the ecological processes governing community assembly have
 rarely been studied for entire communities or flora. Here, we measured how
 community phylogenetic structure varies across a wide elevation gradient
 for plant lineages represented by 35 families, using a co-occurrence index
 and net relatedness index (NRI). We propose a framework that analyses each
 lineage separately and reveals the trend of ecological assembly at tree
 nodes. We found prevailing phylogenetic clustering for more ancient nodes
 and overdispersion in more recent tree nodes. Closely related species may
 thus rapidly evolve new environmental tolerances to radiate into distinct
 communities, while older lineages likely retain inherent environmental
 tolerances to occupy communities in similar environments, either through
 efficient dispersal mechanisms or the exclusion of older lineages with
 more divergent environmental tolerances. Our study illustrates the
 importance of disentangling the patterns of community assembly among
 lineages to better interpret the ecological role of traits. It also sheds
 light on studies reporting absence of phylogenetic signal, and opens new
 perspectives on the analysis of niche and trait conservatism across
 lineages.
description: Alignment_rbclmatkDNA sequences from plant leaf materials collected in the Diabrelets area. Additional sequences (72) was sourced from GenBank.
DOI: 10.5061/dryad.jh146
title: Data from: Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

description: Effective population size over a generation (Ne) or over a reproductive
 cycle (Nb) and the adult census size (Nc) are important parameters in both
 conservation and evolutionary biology. Ne provides information regarding
 the rate of loss of genetic diversity and can be tracked back in time to
 infer demographic history of populations, whereas Nb may often be more
 easily quantified than Nc for short-term abundance monitoring. In this
 study, we propose (1) an empirical context to Waples et al. (2014) who
 introduced a correction to bias due to overlapping generations, and (2) a
 mathematical relationship between Ne and Nb for direct application in
 Atlantic salmon populations in Québec, Canada. To achieve this, we
 investigate the relationships between Ne, Nb and Nc in 10 Atlantic salmon
 populations, Canada, for which we genotyped 100 randomly sampled
 young-of-the year individuals for 5 consecutive years. The results show a
 positive correlation between Ne, Nb and Nc, suggesting that Nb is an
 indicative parameter for tracking effective population size and abundance
 of Atlantic salmon. However, our model allows predicting Nc from Nb values
 at 27% that can be partly explained by high variance in Nb/Nc both among
 populations (37%) and among years (19%). This result illustrates the need
 for thorough calibration of Nb/Nc before using Nb in monitoring programs,
 as well as a full understanding of the limits of such an approach.
 Finally, we discuss the importance of these results for the management of
 wild populations.
description: genepop_50_atlantic_salmon_popGenepop file of the 50 Atlantic salmon populations:10 rivers (GOD, GPA, LAV, MAL, MAT, PCA, ROC, SJE, SMA, TRI) sampled over 5 consecutive years.
DOI: 10.5061/dryad.1683r1s
title: Data from: Genomic comparisons reveal biogeographic and anthropogenic impacts in the koala (Phascolarctos cinereus); a dietary-specialist species distributed across heterogeneous environments

description: The Australian koala is an iconic marsupial with specific dietary
 requirements distributed across heterogeneous environments, over a large
 geographic range. The distribution and genetic structure of koala
 populations has been heavily influenced by human actions, specifically
 habitat modification, hunting and translocation of koalas. There is
 currently limited information on population diversity and gene-flow at a
 species-wide scale, or with consideration to the potential impacts of
 local adaptation. Using species-wide sampling across heterogeneous
 environments, and high-density genome-wide markers (SNPs and PAVs), we
 show that most koala populations display levels of diversity comparable to
 other outbred species, except for those populations impacted by population
 reductions. Genetic clustering analysis and phylogenetic reconstruction
 reveals a lack of support for taxonomic classification of three koala
 sub-species, with only a single evolutionary significant unit supported.
 Furthermore, ~70% of genetic variance is accounted for at the individual
 level. The Sydney Basin region is highlighted as a unique reservoir of
 genetic diversity, having higher diversity levels (ie. Blue Mountains
 region; AvHecorr=0.20, PL%=68.6). Broad-scale population differentiation
 is primarily driven by an Isolation by Distance genetic structure model
 (49% of genetic variance), with clinal local adaptation corresponding to
 habitat bioregions. Signatures of selection were detected between
 bioregions, with no single region returning evidence of strong selection.
 The results of this study show that although the koala is widely
 considered to be a dietary-specialist species, this apparent
 specialisation has not limited the koala’s ability to maintain gene-flow
 and adapt across divergent environments as long as the required food
 source is available.
description: P. cinereus SNP
 sequencesA fasta file containing
 5,264 short sequences tags from P. cinereus samples collected
 opportunistically across Australia from 2009-2016. Each tag contains an
 allele identifier, along with SNP position and mutation (with the
 dominant/reference SNP being listed first). Eg. 15907811|F|0--48:G&gt;A.
 Produced using the commercial provider, Diversity Arrays Technology
 (DArTseq).For further information, please contact the corresponding
 author.Kjeldsen2018_Pcinereus_SNPs.fasta
DOI: 10.5061/dryad.c744j
title: Data from: Mapping of within-species segregation distortion in D. persimilis and hybrid sterility between D. persimilis and D. pseudoobscura

description: In contrast to the prevailing dogma in the 1990s, recent studies have
 suggested that an evolutionary history of segregation distortion within
 species may contribute to sterility in species hybrids. However, this
 recent work identified segregation distortion exclusively in species
 hybrids which may never have had an evolutionary history of segregation
 distortion in either parent species. We expand on previous work by using a
 strain of Drosophila persimilis exhibiting segregation distortion within
 species to generate QTL maps for segregation distortion and hybrid
 sterility in crosses between D. persimilis and D. pseudoobscura. The maps
 localize regions along the XR contributing to both phenotypes, and they
 indicate one region of overlap between the two maps. This overlap could
 provide preliminary evidence for an association between segregation
 distortion within species and hybrid sterility, but the localizations are
 currently too broad to have confidence in this conclusion. This work is a
 first step towards possibly supporting a genetic conflict model of
 speciation in this system.
description: FalsePositiveEstimationSee ReadMe file.SublineCreationSegDistSee ReadMe file.SterilityREADME
DOI: 10.15468/dl.7hwm5f
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000557-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nd7c8
title: Data from: Light enough to travel or wise enough to stay? Brain size evolution and migratory behaviour in birds

description: Brain size relative to body size is smaller in migratory than in
 non-migratory birds. Two mutually non-exclusive hypotheses had been
 proposed to explain this association. On the one hand, the ‘energetic
 trade-off hypothesis’ claims that migratory species were selected to have
 smaller brains because of the interplay between neural tissue volume and
 migratory flight. In contrast, the ‘behavioural flexibility hypothesis’
 argues that resident species are selected to have higher cognitive
 capacities, and therefore larger brains, to enable survival in harsh
 winters, or to deal with environmental seasonality. Here, I test the
 validity and setting of these two hypotheses using 1,466 globally
 distributed bird species. First, I show that the negative association
 between migration distance and relative brain size is very robust across
 species and phylogeny. Second, I provide strong support for the energetic
 trade-off hypothesis, by showing the validity of the trade-off among
 long-distance migratory species alone. Third, using resident and
 short-distance migratory species, I demonstrate that environmental
 harshness is associated with enlarged relative brain size, therefore
 arguably better cognition. My study provides the strongest comparative
 support to date for both the energetic trade-off and the behavioural
 flexibility hypotheses, and highlights that both mechanisms contribute to
 brain size evolution, but on different ends of the migratory spectrum.
description: Brain size and migration
 distance in birdsThis table contain data
 on 1,475 globally distributed bird species. Data covers: brain mass (g),
 body mass (g), minimum body mass (g), maximum body mass (g), migration
 distance (km), non-breeding range minimum monthly mean temperature (°C),
 breeding range temperature seasonality (°C), mean non-breeding latitude
 (absolute value). Additionally, coordinates of the breeding and wintering
 range geographic centroids (latitude and longitude), and monthly mean
 temperatures for both the breeding and wintering grounds are
 given.SupportingInformation_S4.xls
DOI: 10.5061/dryad.d1jk8
title: Data from: Flexible weighing of olfactory and vector information in the desert ant Cataglyphis fortis

description: Desert ants, Cataglyphis fortis, are equipped with remarkable skills that
 enable them to navigate efficiently. When travelling between the nest and
 a previously visited feeding site, they perform path integration (PI), but
 pinpoint the nest or feeder by following odour plumes. Homing ants respond
 to nest plumes only when the path integrator indicates that they are near
 home. This is crucial, as homing ants often pass through plumes emanating
 from foreign nests and do not discriminate between the plume of their own
 and that of a foreign nest, but should absolutely avoid entering a wrong
 nest. Their behaviour towards food odours differs greatly. Here, we show
 that in ants on the way to food, olfactory information outweighs PI
 information. Although PI guides ants back to a learned feeder, the ants
 respond to food odours independently of whether or not they are close to
 the learned feeding site. This ability is beneficial, as new food
 sources—unlike foreign nests—never pose a threat but enable ants to
 shorten distances travelled while foraging. While it has been shown that
 navigating C. fortis ants rely strongly on PI, we report here that the
 ants retained the necessary flexibility in the use of PI.
description: BuehlmannHanssonKnaden_RawDataThe file provides the raw data (xy coordinates) of foraging ants under different experimental conditions.
DOI: 10.5061/dryad.6jv6vn8
title: Data from: Diving behavior of Cuvier's beaked whales (Ziphius cavirostris) off Cape Hatteras, North Carolina

description: Cuvier’s beaked whales exhibit exceptionally long and deep foraging dives.
 The species is relatively little studied due to their deep-water, offshore
 distribution and limited time spent at the surface. We used LIMPET
 satellite tags to study the diving behavior of Cuvier's beaked whales
 off Cape Hatteras, North Carolina from 2014 to 2016. We deployed 11 tags,
 recording 3,242 hours of behavior data, encompassing 5,926 dives. Dive
 types were highly bimodal; deep dives (&gt;800m, n=1,408) had a median
 depth of 1,456 m and median duration of 58.9 min; shallow dives (50-800m,
 n=4,518) were to median depths of 280 m with a median duration of 18.7
 min. Most surface intervals were very short (median 2.2 min), but all
 animals occasionally performed extended surface intervals. We found no
 diel differences in dive depth or percentage of time spent deep diving,
 but whales spent significantly more time near the surface at night. Other
 populations of this species exhibit similar dive patterns, but with
 regional differences in depth, duration, and inter-dive intervals.
 Satellite-linked tags allow for the collection of long periods of dive
 records, including the occurrence of anomalous behaviors, bringing new
 insights into the lives of these deep divers.
description: Diving behavior of
 Cuvier's beaked whales off Cape Hatteras, North
 CarolinaBehavior data from
 satellite-relayed Wildlife Computers Mk10 Splash tags deployed on
 Cuvier's beaked whales off Cape Hatteras, NC.ZcAllTags-Behavior.xlsx
DOI: 10.5061/dryad.614j89q
title: Data from: Failure modes analysis of electrofluidic display under thermal aging

description: Dielectric failure and optical switching failure in electro-fluidic
 display (EFD) is still a bottleneck for sufficient device lifetime. In
 this study, a dielectric redundancy-designed multilayer insulator of
 ParyleneC/AF1600X was applied in an EFD device. The reliability
 performance was systematically studied by tracking the applied voltage
 dependent leakage current and capacitance changes (I-V & C-V
 curve) with thermal aging time. The multilayer insulator shows a more
 stable performance in leakage current compared to that of single-layer
 insulator. The failure modes during operation underlying the single layer
 and the multilayer dielectric appear to be different as exemplified by
 microscopy images. The single layer AFX shows significant detachment. In
 addition, by quantitatively analyzing the C-V curves with aging time, we
 find that for the single AFX device, the dominant failure mode is
 “no-opening” of the pixels. For the muti-layer device, the dominant
 failure mode is “no-closing” of the pixels. This study provides tools for
 distinguishing the basic failure modes of an EFD device, and demonstrates
 a quantitative method for evaluating the reliability performance of the
 device under thermal aging.
description: Capacitance
 analysis-bilayer devicethe original capacitance
 data of bilayer (ParyleneC+AFX) deviceCapacitance
 analysis-single AFX deviceThe original capacitance
 data of single AFX deviceLeakage current-bilayer
 deviceThe original measured
 current of bilayer (ParyleneC+AFX) deviceLeakage current-single
 AFX deviceThe original measured
 current of single AFX deviceresponse
 uniformityThe slope obtained by
 linearly fitting for the comparison of response uniformity over aging
 time.thickness
 designThe electric field of
 different layer vs dielectric thickness. The theoretical breakdown
 strength of ParyleneC and AFX are also shown.Thickness
 design.opjthe saturation voltage
 testexplore the saturation
 voltage of different dielectric configurationcontact angle
 saturation.opj
DOI: 10.5061/dryad.p8p8q
title: Data from: Recovery linked to life history of sessile epifauna following exclusion of towed mobile fishing gear

description: 1. The use of reserves as conservation tools is widespread. However,
 evaluating the effectiveness of reserve implementation for long-lived
 species has been problematic as it requires sampling programmes over long
 time scales that are appropriate to species’ longevity and recovery rates.
 In the sea, towed bottom fishing gears alter the biodiversity and
 ecosystem services provided by benthic communities and habitats. Marine
 reserves have been used to manage these impacts but our understanding of
 the drivers of their effectiveness for the conservation of temperate reefs
 is incomplete. 2. We examined the effectiveness of marine reserves for
 recovery of temperate reef fauna in relation to their life history. We
 used an underwater video to sample six species with different life
 histories across 60 sites that varied in the duration of protection from
 towed mobile fishing gear at 0, 1, 8 and 10 years. 3. Species with a high
 dispersal potential and less habitat specific requirements such as soft
 corals and king scallops recovered to close to their carrying capacity in
 &lt;3 years. In contrast, the longer-lived Ross coral and pink seafans
 increased in abundance but had not fully recovered; with their projected
 recovery time being 17 to 20 years. 4. Ongoing recovery was evident for
 long-lived species as their mean body -size increased significantly across
 all treatments, whereas shorter-lived species such as queen scallops did
 not change in size and were assumed to have fully recovered. 5. This study
 shows that the recovery rates of biota depend on life history factors,
 such as larval longevity and dispersal potential. Recovery for species
 that had low dispersal potential and specific habitat requirements was
 slow and could take &gt;20 years. This suggests activities such as
 bottom trawling or dredging should be avoided where such species occur if
 their conservation is an objective. In contrast, species with high
 dispersal potential and less habitat specific requirements had shorter
 recovery timescales of ~2-3 years and would be more amenable to managed
 trawl frequencies in areas where activities such as fishing occur.
description: Lyme Bay towed bottom
 fishing impact public dataContains data for the
 abundance and size of nine different species of epifauna sampled across
 Lyme Bay in 2007 and 2016. The data is derived from underwater video
 surveys of the same locations on each sampling date. The surveys are
 distributed across locations within Lyme Bay that were subjected to
 different fishing histories such that we were able to estimate a recovery
 rate for some of the species studied.Online_public_data.xlsx
DOI: 10.5061/dryad.62gj0
title: Data from: TAF4, a subunit of transcription factor II D, directs promoter occupancy of nuclear receptor HNF4A during post-natal hepatocyte differentiation

description: The functions of the TAF subunits of mammalian TFIID in physiological
 processes remain poorly characterised. Here we describe a novel function
 of TAFs in directing genomic occupancy of a transcriptional activator.
 Using liver-specific inactivation in mice, we show that the TAF4 subunit
 of TFIID is required for post-natal hepatocyte maturation. TAF4 promotes
 pre-initiation complex (PIC) formation at post-natal expressed liver
 function genes and down-regulates a subset of embryonic expressed genes by
 increased RNA polymerase II pausing. The TAF4-TAF12 heterodimer interacts
 directly with HNF4A and in vivo TAF4 is necessary to maintain
 HNF4A-directed embryonic gene expression at post-natal stages and promotes
 HNF4A occupancy of functional cis-regulatory elements adjacent to the
 transcription start sites of post-natal expressed genes. Stable HNF4A
 occupancy of these regulatory elements requires TAF4-dependent PIC
 formation highlighting that these are mutually dependent events. Local
 promoter-proximal HNF4A-TFIID interactions therefore act as instructive
 signals for post-natal hepatocyte differentiation.
description: Gene expression changes
 upon inactivation of TFIID subunit TAF4 in neontal mouse
 liverSupplementary File
 1.xlsx