cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.629sc
title: Data from: Heterogeneous rates of molecular evolution and diversification could explain the Triassic age estimate for angiosperms

description: Dating analyses based on molecular data imply that crown angiosperms
 existed in the Triassic, long before their undisputed appearance in the
 fossil record in the Early Cretaceous. Following a re-analysis of the age
 of angiosperms using updated sequences and fossil calibrations, we use a
 series of simulations to explore the possibility that the older age
 estimates are a consequence of (i) major shifts in the rate of sequence
 evolution near the base of the angiosperms and/or (ii) the representative
 taxon sampling strategy employed in such studies. We show that both of
 these factors do tend to yield substantially older age estimates. These
 analyses do not prove that younger age estimates based on the fossil
 record are correct, but they do suggest caution in accepting the older age
 estimates obtained using current relaxed-clock methods. Although we have
 focused here on the angiosperms, we suspect that these results will shed
 light on dating discrepancies in other major clades.
description: dataThe various data files
 used in the simulation and the empirical reanalysisBeaulieuetalSupplementSupplemental Materials
DOI: 10.5061/dryad.8m65n
title: Data from: Behavioural responses of Atlantic cod to sea temperature changes

description: Understanding responses of marine species to temperature variability is
 essential to predict impacts of future climate change in the oceans. Most
 ectotherms are expected to adjust their behavior to avoid extreme
 temperatures and minimize acute changes in body temperature. However,
 measuring such behavioral plasticity in the wild is challenging. Combining
 4 years of telemetry-derived behavioral data on juvenile and adult (30–80
 cm) Atlantic cod (Gadus morhua), and in situ ocean temperature
 measurements, we found a significant effect of sea temperature on cod
 depth use and activity level in coastal Skagerrak. During summer, cod were
 found in deeper waters when sea surface temperature increased. Further,
 this effect of temperature was stronger on larger cod. Diel vertical
 migration, which consists in a nighttime rise to shallow feeding habitats,
 was stronger among smaller cod. As surface temperature increased beyond
 ~15°C, their vertical migration was limited to deeper waters. In addition
 to larger diel vertical migrations, smaller cod were more active and
 travelled larger distances compared to larger specimens. Cold temperatures
 during winter tended, however, to reduce the magnitude of diel vertical
 migrations, as well as the activity level and distance moved by those
 smaller individuals. Our findings suggest that future and ongoing rises in
 sea surface temperature may increasingly deprive cod in this region from
 shallow feeding areas during summer, which may be detrimental for local
 populations of the species.
description: DataBehaviour metrics
 calculated for each fish for each day, together with environmental data
 (temperature, precipitation and upwelling) for those
 days.
DOI: 10.5061/dryad.05478
title: Data from: Use of elastic stability analysis to explain the stress-dependent nature of soil strength

description: The peak and critical state strengths of sands are linearly related to the
 stress level, just as the frictional resistance to sliding along an
 interface is related to the normal force. The analogy with frictional
 sliding has led to the use of a ‘friction angle’ to describe the
 relationship between strength and stress for soils. The term ‘friction
 angle’ implies that the underlying mechanism is frictional resistance at
 the particle contacts. However, experiments and discrete element
 simulations indicate that the material friction angle is not simply
 related to the friction angle at the particle contacts. Experiments and
 particle-scale simulations of model sands have also revealed the presence
 of strong force chains, aligned with the major principal stress. Buckling
 of these strong force chains has been proposed as an alternative to the
 frictional-sliding failure mechanism. Here, using an idealized abstraction
 of a strong force chain, the resistance is shown to be linearly
 proportional to the magnitude of the lateral forces supporting the force
 chain. Considering a triaxial stress state, and drawing an analogy between
 the lateral forces and the confining pressure in a triaxial test, a linear
 relationship between stress level and strength is seen to emerge from the
 failure-by-buckling hypothesis.
description: Simulation Data and AUTO
 FilesThis .zip archive
 contains an .xlsx spreadsheet of data used to plot Figures 7 and 8 of the
 paper "Use of elastic stability analysis to explain the
 stress-dependent nature of soil strength". This archive also contains
 sets of AUTO input files for these simulations (∗.f and c.∗) and the
 associated AUTO output files (fort.7, fort.8, fort.9).Simulation_Data_and_Files.zip
DOI: 10.5281/zenodo.18015860
title: VSL_BRAND1_10F_1_23C_0k_EDLC_Single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5281/zenodo.18387657
title: VSL_BRAND1_10F_1_23C_0k_EDLC_Single

description: Part of the Variable Temperature DataBase: Temp: 23°C
DOI: 10.5061/dryad.s355k
title: Data from: Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation

description: Background: Antarctic notothenioids are an impressive adaptive radiation.
 While they share recent common ancestry with several species-depauperate
 lineages that exhibit a relictual distribution in areas peripheral to the
 Southern Ocean, an understanding of their evolutionary origins and
 biogeographic history is limited as the sister lineage of notothenioids
 remains unidentified. The phylogenetic placement of notothenioids among
 major lineages of perciform fishes, which include sculpins, rockfishes,
 sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes,
 remains unresolved. We investigate the phylogenetic position of
 notothenioids using DNA sequences of 10 protein coding nuclear genes
 sampled from more than 650 percomorph species. The biogeographic history
 of notothenioids is reconstructed using a maximum likelihood method that
 integrates phylogenetic relationships, estimated divergence times,
 geographic distributions and paleogeographic history. Results: Percophis
 brasiliensis is resolved, with strong node support, as the notothenioid
 sister lineage. The species is endemic to the subtropical and temperate
 Atlantic coast of southern South America. Biogeographic reconstructions
 imply the initial diversification of notothenioids involved the western
 portion of the East Gondwanan Weddellian Province. The geographic
 disjunctions among the major lineages of notothenioids show biogeographic
 and temporal correspondence with the fragmentation of East Gondwana.
 Conclusions: The phylogenetic resolution of Percophis requires a change in
 the classification of percomorph fishes and provides evidence for a
 western Weddellian origin of notothenioids. The biogeographic
 reconstruction highlights the importance of the geographic and climatic
 isolation of Antarctica in driving the radiation of cold-adapted
 notothenioids.
description: DNA sequence alignment
 for phylogeny inferenceDNA sequence alignments
 used for RAxML phylogeny inferencepercophis.phyDivergence time estimateBEAST input file for divergence time analysespercothenA.xmlRAxML bootstrap phylogenypercophis_boottree.tre
DOI: 10.5061/dryad.65fr2
title: Data from: Minimal effects of latitude on present-day speciation rates in New World birds

description: The tropics contain far greater numbers of species than temperate regions,
 suggesting that rates of species formation might differ systematically
 between tropical and non-tropical areas. We tested this hypothesis by
 reconstructing the history of speciation in New World (NW) land birds
 using BAMM, a Bayesian framework for modelling complex evolutionary
 dynamics on phylogenetic trees. We estimated marginal distributions of
 present-day speciation rates for each of 2571 species of birds. The
 present-day rate of speciation varies approximately 30-fold across NW
 birds, but there is no difference in the rate distributions for tropical
 and temperate taxa. Using macroevolutionary cohort analysis, we
 demonstrate that clades with high tropical membership do not produce
 species more rapidly than temperate clades. For nearly any value of
 present-day speciation rate, there are far more species in the tropics
 than the temperate zone. Any effects of latitude on speciation rate are
 marginal in comparison to the dramatic variation in rates among clades.
description: Data and analyses for
 "Minimal effects of latitude on present-day speciation rates in New
 World birds"Includes: BAMM settings,
 BAMM results, raw data (phylogenies + taxonomy + latitude for NW birds),
 and scripts to analyze results in R using the BAMMtools R
 packagerabosky_data.zip
DOI: 10.5061/dryad.4tj59
title: Data from: Association between probable postnatal depression and increased infant mortality and morbidity: findings from the DON population-based cohort study in rural Ghana

description: Objectives: To assess the impact of probable depression in the immediate
 postnatal period on subsequent infant mortality and morbidity. Design:
 Cohort study nested within 4 weekly surveillance of all women of
 reproductive age to identify pregnancies and collect data on births and
 deaths. Setting: Rural/periurban communities within the Kintampo Health
 Research Centre study area of the Brong-Ahafo Region of Ghana.
 Participants: 16 560 mothers who had a live singleton birth reported
 between 24 March 2008 and 11 July 2009, who were screened for probable
 postnatal depression (pPND) between 4 and 12 weeks post partum (some of
 whom had also had depression assessed at pregnancy), and whose infants
 survived to this point. Primary/secondary outcome measures: All-cause
 early infant mortality expressed per 1000 infant-months of follow-up from
 the time of postnatal assessment to 6 months of age. The secondary
 outcomes were (1) all-cause infant mortality from the time of postnatal
 assessment to 12 months of age and (2) reported infant morbidity from the
 time of the postnatal assessment to 12 months of age. Results: 130 infant
 deaths were recorded and singletons were followed for 67 457.4
 infant-months from the time of their mothers’ postnatal depression
 assessment. pPND was associated with an almost threefold increased risk of
 mortality up to 6 months (adjusted rate ratio (RR), 2.86 (1.58 to 5.19);
 p=0.001). The RR up to 12 months was 1.88 (1.09 to 3.24; p=0.023). pPND
 was also associated with increased risk of infant morbidity. Conclusions:
 There is new evidence for the association between maternal pPND and infant
 mortality in low-income and middle-income countries. Implementation of the
 WHO's Mental Health Gap Action Programme (mhGAP) to scale up packages
 of care integrated with maternal health is encouraged as an important
 adjunct to child survival efforts.
description: Don_PP_IMRnotwins_IMRpaperDryad
DOI: 10.5061/dryad.kq1g6
title: Data from: Relationships of diversity, disparity and their evolutionary rates in squirrels (Sciuridae)

description: Several theories predict that rapidly diversifying clades will also
 rapidly diverge phenotypically; yet, there are also reasons for suspecting
 that diversification and divergence might not be correlated. In the widely
 distributed squirrel clade (Sciuridae), we test for correlations between
 per-lineage speciation rates, species richness, disparity and a
 time-invariant measure of disparity that allows for comparing rates when
 evolutionary modes differ, as they do in squirrels. We find that species
 richness and speciation rates are not correlated with clade age or with
 each other. Disparity appears to be positively correlated with clade age
 because young, rapidly diversifying Nearctic grassland clades are strongly
 pulled to a single stable optimum but older, slowly diversifying
 Paleotropical forest clades contain lineages that diverge along multiple
 ecological and morphological lines. That contrast is likely due to both
 the environments they inhabit and their phylogenetic community structure.
 Our results argue against a shared explanation for diversity and disparity
 in favor of geographically mediated modes of speciation and ecologically
 mediated modes of phenotypic evolution.
description: Size And Shape
 Datacentroid size and
 landmark coordinates for individual specimensSizeAndShapeData.xlsxSimulated Disparities of Size and Shaperesults from 1000 trees simulated over 36 myrSimulatedDisparities.xlsx
DOI: 10.5061/dryad.8268
title: Data from: Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome

description: Next-generation sequencing provides a powerful new approach for developing
 functional genomic tools for nonmodel species, helping to narrow the gap
 between studies of model organisms and those of natural populations.
 Consequently, massively parallel 454 sequencing was used to characterize a
 normalized cDNA library derived from skin biopsy samples of twelve
 Antarctic fur seal (Arctocephalus gazella) individuals. Over 412 Mb of
 sequence data were generated, comprising 1.4 million reads of average
 length 286 bp. De novo assembly using Newbler 2.3 yielded 156 contigs plus
 22 869 isotigs, which in turn clustered into 18 576 isogroups. Almost half
 of the assembled transcript sequences showed significant similarity to the
 nr database, revealing a functionally diverse array of genes. Moreover,
 97.9% of these mapped to the dog (Canis lupis familiaris) genome, with a
 strong positive relationship between the number of sequences locating to a
 given chromosome and the length of that chromosome in the dog indicating a
 broad genomic distribution. Average depth of coverage was also almost
 20-fold, sufficient to detect several thousand putative microsatellite
 loci and single nucleotide polymorphisms. This study constitutes an
 important step towards developing genomic resources with which to address
 consequential questions in pinniped ecology and evolution. It also
 supports an earlier but smaller study showing that skin tissue can be a
 rich source of expressed genes, with important implications for studying
 the genomics not only of marine mammals, but also more generally of
 species that cannot be destructively sampled.
description: Sequence
 assemblyMicrosatellite
 listList of contigs /
 isotigs containing microsatellite motifs (perfect di-, tri- and
 tetranucleotide repeats with a minimum length of five repeat
 units).
DOI: 10.5061/dryad.280m5
title: Data from: The evolution of life cycle complexity in aphids: ecological optimization, or historical constraint?

description: For decades, biologists have debated why many parasites have obligate
 multi-host life cycles. Here, we use comparative phylogenetic analyses of
 aphids to evaluate the roles of ecological optimization and historical
 constraint in the evolution of life cycle complexity. If life cycle
 complexity is adaptive, it should be evolutionarily labile, i.e., change
 in response to selection. We provide evidence that this is true in some
 aphids (aphidines), but not others (non-aphidines) – groups that differ in
 the intensity of their relationships with primary hosts. Next, we test
 specific mechanisms by which life cycle complexity could be adaptive or a
 constraint. We find that among aphidines there is a strong association
 between complex life cycles and polyphagy but only a weak correlation
 between life cycle complexity and reproductive mode. In contrast, among
 non-aphidines the relationship between life cycle complexity and host
 breadth is weak but the association between complex life cycles and sexual
 reproduction is strong. Thus, although the adaptiveness of life cycle
 complexity appears to be lineage specific, across aphids, life cycle
 evolution appears to be tightly linked with the evolution of other
 important natural history traits.
description: Hardy_etal_2015_Evolution_ArchiveAn archive containing the phylogenetic trees, trait data and R scripts used in the comparative phylogenetic analyses in Hardy et al. 2015.
DOI: 10.5061/dryad.8274
title: Data from: Cytochrome c oxidase subunit 1 barcode data of fish of the Nayband National Park in the Persian Gulf and analysis using meta-data flag several cryptic species

description: We provide cytochrome c oxidase subunit 1 (COI) barcode sequences of
 fishes of the Nayband National Park, Persian Gulf, Iran. Industrial
 activities, ecological considerations, and goals of The Fish Barcode of
 Life campaign make it crucial that fish species residing in the park be
 identified. To the best of our knowledge, this is the first report of
 barcoding data on fishes of the Persian Gulf. 187 individuals representing
 76 species, 56 genera, and 32 families were examined. The data flagged
 potentially cryptic species of Gerres filamentosus and Plectorhincus
 schotaf. 16S rDNA data on these species are provided. Exclusion of the two
 species resulted in a mean COI intraspecific distance of 0.18%, and a mean
 inter-to intra-specific divergence ratio of 66.7. There was no overlap
 between maximum K2Pdistances among conspecifics (1.66%) and minimum
 distance among congeneric species (6.19%). Barcodes shared among species
 were not observed. Neighbor-joining analysis showed that most species
 formed cohesive sequence units with little variation. Finally, comparison
 of 16 selected species from this study with metadata of conspecifics from
 Australia, India, China and South Africa revealed high inter-region
 divergences and potential existence of six cryptic species. Pairwise
 inter-regional comparisons were more informative than global divergence
 assessments with regard to detection of cryptic variation. Our analysis
 exemplifies optimal use of the expanding barcode data now becoming
 available.
description: MER
 10-0368R1Figures and tables;
 include taxonomical data, divergence values and NJ trees of Nayband fish
 samples as well as a number of comparisons with similar species from other
 seas
DOI: 10.5061/dryad.9mt2v
title: Data from: Poor health is associated with use of anthropogenic resources in an urban carnivore

description: Rates of encounters between humans and wildlife are increasing in cities
 around the world, especially when wildlife overlap with people in time,
 space and resources. Coyotes (Canis latrans) can make use of anthropogenic
 resources and reported rates of conflict have increased in cities across
 North America. This increase may be linked to individual differences in
 the use of human food and developed areas. We compared the relationships
 between coyote age, sex or health and the use of anthropogenic resources,
 which we defined as using developed areas over large home ranges, being
 active during the day, and consuming anthropogenic food. To do so, we
 applied GPS collars to 19 coyotes and sampled hair for stable isotope
 analysis. Eleven coyotes appeared to be healthy and eight were visibly
 infested with sarcoptic mange (Sarcoptes scabiei), a mite that causes hair
 loss. Diseased coyotes used more developed areas, had larger monthly home
 ranges, were more active during the day, and assimilated less protein than
 coyotes that appeared to be healthy. We speculate that anthropogenic food
 provides a low-quality but easily accessible food source for diseased
 coyotes, which in turn may increase reliance on it and other anthropogenic
 resources to promote encounters with people.
description: Murray et al Coyote
 3-hour GPS locations March 14 2015Spreadsheet containing
 GPS location data used in "Poor health is associated with use of
 anthropogenic resources in an urban carnivore". GPS fixes were
 collected from 19 coyotes every 3 hours. Description of column headings
 are found in the spreadsheet.
DOI: 10.5061/dryad.8277
title: Data from: Identifying the critical climatic time window that affects trait expression

description: Identifying the critical time window during which climatic drivers affect
 the expression of phenological, behavioral, and demographic traits is
 crucial for predicting the impact of climate change on trait and
 population dynamics. Two widely used associative methods exist to identify
 critical climatic periods: sliding-window models and recursive operators
 in which the memory of past weather fades over time. Both approaches have
 different strong points, which we combine here into a single method. Our
 method uses flexible functions to differentially weight past weather,
 which can reflect competing hypotheses about time lags and the relative
 importance of recent and past weather for trait expression. Using a
 22-year data set, we illustrate that the climatic window identified by our
 new method explains more of the phenological variation in a sexually
 selected trait than existing approaches. Our new method thus helps to
 better identify the critical time window and the causes of trait response
 to environmental variability.
description: trait (moutling)
 datatrait.txtweather datacontains the weather dataweather.txt
DOI: 10.5061/dryad.h5g85
title: Data from: Phylogenetic uncertainty revisited: implications for ecological analyses

description: Ecologists and biogeographers usually rely on a single phylogenetic tree
 to study evolutionary processes that affect macroecological patterns. This
 approach ignores the fact that each phylogenetic tree is a hypothesis
 about the evolutionary history of a clade, and cannot be directly observed
 in nature. Also, trees often leave out many extant species, or include
 missing species as polytomies because of a lack of information on the
 relationship among taxa. Still, researchers usually do not quantify the
 effects of phylogenetic uncertainty in ecological analyses. We propose
 here a novel analytical strategy to maximizes the use of incomplete
 phylogenetic information, while simultaneously accounting for several
 sources of phylogenetic uncertainty that may distort statistical
 inferences about evolutionary processes. We illustrate the approach using
 a clade-wide analysis of the hummingbirds, evaluating how different
 sources of uncertainty affect several phylogenetic comparative analyses of
 trait evolution and biogeographic patterns. Although no statistical
 approximation can fully substitute for a complete and robust phylogeny,
 the method we describe and illustrate enables researchers to broaden the
 number of clades for which studies informed by evolutionary relationships
 are possible, while allowing the estimation and control of statistical
 error that arises from phylogenetic uncertainty. Software tools to carry
 out the necessary computations are offered.
description: Phylogenetic Uncertain
 TaxaList of missing species
 in the backbone phylogenyHummingbirds Phy - 158
 PUT.txtHummingbirds Phylogeny,
 with Most Derived Consensus Clades for each Phylogenetic Uncertain
 TaxaHummingbirds Phylogeny,
 with Most Derived Consensus Clades for each Phylogenetic Uncertain
 TaxaHummingbirds Phy - MDCC
 Standard.txt25000 Phylogenies of
 McGuire et al. 2007, with MDCCs defined25000 Phylogenies of
 McGuire et al. 2007, with MDCCs definedHummingbirds Phy - 25000 trees
 146spp MDCC.rarGeographic Grid, with
 2868 cells, describing New WorldWH2868 - Geo
 Coords.txtPresence/Absence matrix
 of 304Spp Hummingbird in the Western Hemisphere GridWH2868 - 304Spp Hummingbird
 PresAbsMat.txtBodySize of 304 species
 of HummingbirdsHummingbirds - 304spp
 BodySize.txtElevational range of 304
 species of hummingbirdsHummingbirds - 304spp
 ElevRange.txt