cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.75r59p2
title: Data from: Optical coherence tomography is highly sensitive in detecting prior optic neuritis

description: Objective: To explore sensitivity of optical coherence tomography (OCT) in
 detecting prior unilateral optic neuritis. Methods: Retrospective,
 observational clinical study of all patients who presented from 1/1/14 to
 6/1/17 with unilateral optic neuritis and OCT available at least three
 months after the attack. We compared OCT retinal nerve fiber layer (RNFL)
 and ganglion cell inner plexiform layer (GCIPL) thicknesses between
 affected and unaffected contralateral eyes. We excluded patients with
 concomitant glaucoma or other optic neuropathies. Based on analysis of
 normal controls, thinning was considered significant if RNFL was at least
 9-µm or GCIPL was at least 6-µm less in affected eye compared to
 unaffected eye. Results: Fifty-one patients (18 male and 33 female) were
 included in the study. RNFL and GCIPL thicknesses were significantly lower
 in eyes with optic neuritis compared to unaffected eyes (p&lt;0.001).
 RNFL was thinner by ≥9-µm in 73% of optic neuritis eyes compared to the
 unaffected eye. GCIPL was thinner by ≥6-µm in 96% of optic neuritis eyes.
 The sensitivity of OCT in detecting prior optic neuritis was 96% when
 using both average RNFL and GCIPL thicknesses. When using a threshold ≤1st
 percentile of age-matched controls, sensitivities were 37% for RNFL, 76%
 for GCIPL, and 78% for either GCIPL or RNFL thicknesses, each of which was
 lower than those calculated using the inter-eye difference as the
 threshold (p&lt;0.05). Conclusions: OCT, especially in GCIPL, is a
 highly sensitive modality in detecting prior optic neuritis, which is made
 more robust by using inter-eye differences to approximate change.
description: Supplemental
 FiguresSupplemental Figure 1:
 Sensitivity of OCT calculated by two methods. Sensitivity of OCT in
 detecting prior optic neuritis by using a thickness ≤1st percentile of
 age-matched controls in the Zeiss database (blue bars). Sensitivity of OCT
 in detecting prior optic neuritis by using a 99th percentile intereye
 difference threshold of ≥9 µm in RNFL, ≥6 µm in GCIPL, or either
 thicknesses as a threshold (red bars). Supplemental Figure 2: Comparison
 of intereye RNFL and GCIPL differences. The 99th intereye threshold is
 shown for both RNFL (9µm) and GCIPL (6µm). All eyes that met the 99th
 percentile intereye threshold for RNFL thinning also met the 99th
 percentile intereye threshold for GCIPL, while 12 eyes met the GCIPL 99th
 intereye threshold that did not meet the RNFL
 threshold.
DOI: 10.5061/dryad.pk16b
title: Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis

description: Branching morphogenesis of the epithelial ureteric bud forms the renal
 collecting duct system and is critical for normal nephron number, while
 low nephron number is implicated in hypertension and renal disease.
 Ureteric bud growth and branching requires GDNF signaling from the
 surrounding mesenchyme to cells at the ureteric bud tips, via the Ret
 receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates
 transcription factors Etv4 and Etv5, which are also critical for
 branching. Despite extensive knowledge of the genetic control of these
 events, it is not understood, at the cellular level, how renal branching
 morphogenesis is achieved or how Ret signaling influences epithelial cell
 behaviors to promote this process. Analysis of chimeric embryos previously
 suggested a role for Ret signaling in promoting cell rearrangements in the
 nephric duct, but this method was unsuited to study individual cell
 behaviors during ureteric bud branching. Here, we use Mosaic Analysis with
 Double Markers (MADM), combined with organ culture and time-lapse imaging,
 to trace the movements and divisions of individual ureteric bud tip cells.
 We first examine wild-type clones and then Ret or Etv4 mutant/wild-type
 clones in which the mutant and wild-type sister cells are differentially
 and heritably marked by green and red fluorescent proteins. We find that,
 in normal kidneys, most individual tip cells behave as self-renewing
 progenitors, some of whose progeny remain at the tips while others
 populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type
 cells generated at a UB tip are much more likely to remain at, or move to,
 the new tips during branching and elongation, while their Ret−/− or
 Etv4−/− sister cells tend to lag behind and contribute only to the trunks.
 By tracking successive mitoses in a cell lineage, we find that Ret
 signaling has little effect on proliferation, in contrast to its effects
 on cell movement. Our results show that Ret/Etv4 signaling promotes
 directed cell movements in the ureteric bud tips, and suggest a model in
 which these cell movements mediate branching morphogenesis.
description: Fig 2
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DOI: 10.5061/dryad.n7v81
title: Data from: Environmental heterogeneity and population differences in blue tits personality traits

description: Environmental heterogeneity can result in spatial variation in selection
 pressures that can produce local adaptations. The pace-of-life syndrome
 hypothesis predicts that habitat-specific selective pressures will favor
 the coevolution of personality, physiological, and life-history
 phenotypes. Few studies so far have compared these traits simultaneously
 across different ecological conditions. In this study, we compared 3
 personality traits (handling aggression, exploration speed in a novel
 environment, and nest defense behavior) and 1 physiological trait (heart
 rate during manual restraint) across 3 Corsican blue tit (Cyanistes
 caeruleus) populations. These populations are located in contrasting
 habitats (evergreen vs. deciduous) and are situated in 2 different valleys
 25 km apart. Birds from these populations are known to differ in
 life-history characteristics, with birds from the evergreen habitat
 displaying a slow pace-of-life, and birds from the deciduous habitat a
 comparatively faster pace-of-life. We expected personality to differ
 across populations, in line with the differences in pace-of-life
 documented for life-history traits. As expected, we found behavioral
 differences among populations. Despite considerable temporal variation,
 birds exhibited lower handling aggression in the evergreen populations.
 Exploration speed and male heart rate also differed across populations,
 although our results for exploration speed were more consistent with a
 phenotypic difference between the 2 valleys than between habitats. There
 were no clear differences in nest defense intensity among populations. Our
 study emphasizes the role of environmental heterogeneity in shaping
 population divergence in personality traits at a small spatial scale.
description: Data
 HAData
 HRData Nest
 DefenseData
 Speed
DOI: 10.5061/dryad.d2990
title: Data from: What can multiple phylogenies say about the latitudinal diversity gradient? A new look at the tropical conservatism, out-of-the-tropics, and diversification rate hypotheses

description: We reviewed published phylogenies and selected 111 phylogenetic studies
 representing mammals, birds, insects, and flowering plants. We then mapped
 the latitudinal range of all taxa to test the relative importance of the
 tropical conservatism, out of the tropics, and diversification rate
 hypotheses in generating latitudinal diversity gradients. Most clades
 originated in the tropics, with diversity peaking in the zone of origin.
 Transitions of lineages between latitudinal zones occurred at 16–22% of
 the tree nodes. The most common type of transition was range expansions of
 tropical lineages to encompass also temperate latitudes. Thus, adaptation
 to new climatic conditions may not represent a major obstacle for many
 clades. These results contradict predictions of the tropical conservatism
 hypothesis (i.e., few clades colonizing extratropical latitudes), but
 support the out-of-the-tropics model (i.e., tropical originations and
 subsequent latitudinal range expansions). Our results suggest no
 difference in diversification between tropical and temperate sister
 lineages; thus, diversity of tropical clades was not explained by higher
 diversification rates in this zone. Moreover, lineages with latitudinal
 stasis diversified more compared to sister lineages entering a new
 latitudinal zone. This preserved preexisting diversity differences between
 latitudinal zones and can be considered a new mechanism for why diversity
 tends to peak in the zone of origin.
description: Supplement_selected_phylogeniesFile describing how phylogenies were selected, and a list of all the papers from which phylogenies were selected.Supplement_TableS1File containing the information extracted from the phylogenies in a table (comma delimited format).
DOI: 10.5061/dryad.jp2rm
title: Data from: Genetic variation underlies temperature tolerance of embryos in the sea urchin Heliocidaris erythrogramma armigera

description: Ocean warming can alter natural selection on marine systems, and in many
 cases, the long-term persistence of affected populations will depend on
 genetic adaptation. In this study, we assess the potential for adaptation
 in the sea urchin Heliocidaris erythrogramma armigera, an Australian
 endemic, that is experiencing unprecedented increases in ocean
 temperatures. We used a factorial breeding design to assess the level of
 heritable variation in larval hatching success at two temperatures.
 Fertilized eggs from each full-sibling family were tested at 22 °C
 (current spawning temperature) and 25 °C (upper limit of predicted warming
 this century). Hatching success was significantly lower at higher
 temperatures, confirming that ocean warming is likely to exert selection
 on this life-history stage. Our analyses revealed significant additive
 genetic variance and genotype-by-environment interactions underlying
 hatching success. Consistent with prior work, we detected significant
 nonadditive (sire-by-dam) variance in hatching success, but additionally
 found that these interactions were modified by temperature. Although these
 findings suggest the potential for genetic adaptation, any evolutionary
 responses are likely to be influenced (and possibly constrained) by
 complex genotype-by-environment and sire-by-dam interactions and will
 additionally depend on patterns of genetic covariation with other fitness
 traits.
description: Survival data binary
 formatSurvival data are
 arranged for offspring from each family, with zeros denoting deaths, and
 ones denoting survivors.survbinomial.xlsxFertilisation data in binary formatFertilisation data are arranged in binary format, with zeros denoting unfertilised eggs, and ones denoting fertilised eggs.fertbinomial.xlsx
DOI: 10.5061/dryad.181v0
title: Data from: Individual variation in parental care reaction norms: integration of personality and plasticity

description: Personality (consistent differences between individuals in behavior) and
 plasticity (changes within individuals in behavior) are often viewed as
 separate and opposing phenomena. We tested this idea by analyzing parental
 care reaction norms in a bird that exhibits biparental care. Personality
 in provisioning behavior existed (r ic=0.11) and persisted despite being
 reduced after accounting for individual differences in environment.
 Plasticity was also evident and differed between the sexes. Male visit
 rate was associated with changes in brood size and time of day, but female
 visit rate was associated with changes in nestling age and date. In both
 sexes changes in visit rate were positively correlated with changes in
 their partner’s visit rate. Both sexes also exhibited multidimensional
 reaction norms; interaction terms revealed that within-individual visit
 rates increased more steeply with brood size when nestlings were older,
 and the effect of the partner’s visit rate was sensitive to variation in
 date, precipitation, and the focal bird’s age. Individuals also varied in
 how they responded (reaction norm slope) to changes in nestling age and
 partner visits. Moreover, parental personality was interdependent with
 individual plasticity in several ways. Individuals of both sexes with a
 high visit rate also responded more positively to changes in nestling age,
 and males also showed this pattern with changes in partner visit rate.
 Explicit use of the behavioral reaction norm integrated personality and
 plasticity, revealed that these are not opposing concepts, and stimulated
 new hypotheses about sexual conflict over care and provisioning as a
 life-history trait.
description: PCareFinalSee ReadMe file
DOI: 10.5061/dryad.1tr7p0k
title: Data from: Phylogenetic diversity patterns in Himalayan forests reveal evidence for environmental filtering of distinct lineages

description: Large‐scale environmental gradients have been invaluable for unraveling
 the processes shaping the evolution and maintenance of biodiversity.
 Environmental gradients provide a natural setting to test theories about
 species diversity and distributions within a landscape with changing
 biotic and abiotic interactions. Elevational gradients are particularly
 useful because they often encompass a large climatic range within a small
 geographical extent. Here, we analyzed tree communities in plots located
 throughout Arunachal Pradesh, a province in northeast India located on the
 southern face of the Eastern Himalayas, representing one of the largest
 elevational gradients in the world. Using indices of species and
 phylogenetic diversity, we described shifts in community structure across
 the landscape and explored the putative biotic and abiotic forces
 influencing species assembly. As expected, species richness and
 phylogenetic diversity decreased with increasing elevation; however,
 contrary to predictions of environmental filtering, species relatedness
 did not show any clear trend. Nonetheless, patterns of beta diversity
 (both taxonomic and phylogenetic) strongly suggest lineage filtering along
 the elevational gradient. Our results may be explained if filtering is
 driving the assembly of species from distinct evolutionary lineages. New
 metrics exploring community contributions to regional taxonomic and
 phylogenetic beta diversity provided additional evidence for the
 persistence of unique communities at high elevations. We suggest that
 these patterns may be consistent with filtering on glacial relicts, part
 of once more diverse clades with convergent traits suited to climates at
 the last glacial maximum, resulting in random or over‐dispersed community
 assemblages at high elevations. We propose that these high‐elevation sites
 with evolutionarily distinct species represent possible regions for
 conservation priority that may provide refugia for species threatened by
 current warming trends.
description: Arunachal Pradesh
 Community MatrixThis community matrix
 contains plot and species information for 291 plots in Arunachal Pradesh,
 India. These data were collected in the field by researchers at the North
 Eastern Regional Institute of Science and Technology. The data were
 manipulated using R.AP_CommunityMatrix.csvArunachal Pradesh Plot SummaryThis file contains descriptions of the 291 study plots used in our study, such as location, elevation and climate.AP_PlotSummary.csv
DOI: 10.5061/dryad.320kb06t
title: Data from: High-throughput microsatellite marker development in two sparid species and verification of their transferability in the family Sparidae

description: Recently, 454 sequencing has emerged as a popular method for isolating
 microsatellites owing to cost-effectiveness and time saving. In this
 study, repeat-enriched libraries from two southern African endemic sparids
 (Pachymetopon blochii and Lithognathus lithognathus) were 454 GS-FLX
 sequenced. From these, 7370 sequences containing repeats (SCRs) were
 identified. A brief survey of 23 studies showed a significant difference
 between the number of SCRs when enrichment was performed first before 454
 sequencing. We designed primers for 302 unique fragments containing more
 than five repeat units and suitable flanking regions. A fraction
 (&lt;11%) of these loci were characterized with 18 polymorphic
 microsatellite loci (nine in each of the focal species) being described.
 Sanger sequencing of alleles confirmed that size variation was because of
 differences in the number of tandem repeats. However, a case of homoplasy
 and sequencing errors in the 454 sequencing were identified. These newly
 developed and four previously isolated loci were successfully used to
 identify polymorphic markers in nine other economically important species,
 representative of sparid diversity. The combination of newly developed
 markers with data from previous sparid cross-species studies showed a
 significant negative correlation between genetic divergence to focal
 species and microsatellite transferability. The high level of
 transferability we described (48% amplification success and 32%
 polymorphism) suggests that the 302 microsatellite loci identified
 represent an excellent resource for future studies on sparids.
 Microsatellite marker development should commonly include tests of
 transferability to reduce costs and increase feasibility of population
 genetics studies in nonmodel organisms.
description: DRYAD genotypic data for
 two focal speciesFile 1 Genotypic data
 for two focal species: Excel spreadsheet of genotypic data for 50
 individuals each of two focal sparid species for the developed
 microsatellite markers in these species. There are nine microsatellite
 markers for Pachymetopon blochii and nine for Lithognathus lithognathus.
 The program GeneMarker was used to score the alleles.DRYAD location
 information of speciesFile 2 Location
 information of species: Excel spreadsheet of specimens used and locations
 sampled for the microsatellite marker development and cross-species
 amplification study.DRYAD primers and 454
 sequences for additional sparid lociFile 3 Primers and 454
 sequences for additional sparid loci: Excel spreadsheet of additional
 microsatellite markers identified in two focal sparid species from two
 repeat enrich libraries (using the FIASCO protocol) and a fraction of 454
 sequencing. The table includes repeat type, primers, fragment size and the
 454 sequences in FASTA format.
DOI: 10.5061/dryad.jk183
title: Data from: Geography and past climate changes have shaped the evolution of a widespread lizard from the Chilean hotspot

description: The complex orogenic history and structure of Southern South America,
 coupled with Pleistocene glacial cycles, have generated paleoclimatic and
 environmental changes that influenced the spatial distribution and genetic
 composition of natural populations. Despite the increased number of
 phylogeographic studies in this region and given the frequent
 idiosyncratic phylogeographic patterns, there is still the need to focus
 research especially on species that are currently distributed within a
 wide range of bioclimatic regimes, and that historically have been subject
 to contrasting scenarios. Liolaemus tenuis is a widely distributed lizard
 species inhabiting latitudinally in almost 1,000 km through central and
 southern Chile. Here we describe the geographical patterns of genetic
 variation and lineage diversification within L. tenuis, and their
 association with geography and Pleistocene glaciations, using sequences
 from one mitochondrial and two nuclear genes, and five microsatellite
 loci, and covering most of the species distributional range. Our results
 revealed a high diversity both within and among populations, as well as
 two phylogeographic breaks, which are consistent with two of the larger
 rivers of central Chile, the Maipo and Biobío Rivers. Liolaemus tenuis is
 characterized by several allopatric lineages, especially in its north and
 central range, which suggest a history of multiple vicariance processes.
 Conversely, populations found in the southern range, south of the Biobío
 River, show signatures of recent decreases in effective population sizes,
 coupled with recent range expansions and secondary contact. Niche
 “envelope” data are consistent with patterns of genetic variation; both
 suggest a history of discontinuous areas of relatively stable populations
 throughout all of the distribution of L. tenuis. These data are also
 consistent with higher probabilities of habitat suitability north of the
 Maipo River (ca. 33°S), in both coastal areas and the “Intermediate
 Depression” between 34° - 37°S, as well as in the southern Coastal
 Cordillera between the Biobío and Araucanía regions. Interestingly, both
 molecular and niche envelope modelling data suggest that some populations
 may have persisted in fragmented refugia in Andean valleys, within the
 limits of the ice sheet. Finally, our results suggest that several
 populations of L. tenuis colonized glaciated regions from refugial areas
 in lowlands and coastal regions, and in the southern distribution,
 historic migration events would have occurred from refugial areas within
 the limits of the ice sheet.
description: cytb (80 sequence)
 (2)KIF24withOGLDB5BwithOGMicrosatelliteHaplotype List