cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vd7bf
title: Data from: Evolutionary patterns of shape and functional diversification in the skull and jaw musculature of triggerfishes (Teleostei: Balistidae)

description: The robust skull and highly subdivided adductor mandibulae muscles of
 triggerfishes provide an excellent system within which to analyze the
 evolutionary processes underlying phenotypic diversification. We surveyed
 the anatomical diversity of balistid jaws using Procrustes-based geometric
 morphometric analyses and a phylomorphospace approach to quantifying
 morphological transformation through evolution. We hypothesized that
 metrics of interspecific cranial shape would reveal patterns of
 phylogenetic diversification that are congruent with functional and
 ecological transformation. Morphological landmarks outlining skull and
 adductor mandibulae muscle shape were collected from 27 triggerfish
 species. Procrustes-transformed skull shape configurations revealed
 significant phylogenetic and size-influenced structure. Phylomorphospace
 plots of cranial shape diversity reveal groupings of shape between
 different species of triggerfish that are mostly consistent with
 phylogenetic relatedness. Repeated instances of convergence upon similar
 cranial shape by genetically disparate taxa are likely due to the
 functional demands of shared specialized dietary habits. This study shows
 that the diversification of triggerfish skulls occurs via modifications of
 cranial silhouette and the positioning of subdivided jaw adductor muscles.
 Using the morphometric data collected here as input to a biomechanical
 model of triggerfish jaw function, we find that subdivided jaw adductors,
 in conjunction with a unique cranial skeleton, have direct biomechanical
 consequences that are not always congruent with phylomorphospace patterns
 in the triggerfish lineage. The integration of geometric morphometrics
 with biomechanical modeling in a phylogenetic context provides novel
 insight into the evolutionary patterns and ecological role of muscle
 subdivisions in triggerfishes.
description: Maximum posterior
 probability triggerfish treeNexus file for the
 maximum posterior probability triggerfish tree that was used in this study
 for phylogenetic analyses of shape diversification.triggertree.nexCranial shape landmark data.tps file with (x,y) coordinates for 44 cranial landmarks digitized on 79 specimens. Landmarks correspond to those listed in the caption of Figure 1a.triggerlandmarks.tpsTriggerfish jaw biomechanicsSpecies mean measurements of each adductor mandibulae in-levers, out-levers, mechanical advantage (MA), effective mechanical advantage (EMA).Trigger_biomechanics.xlsx
DOI: 10.5061/dryad.1050
title: Data from: Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007

description: Full genome sequencing of 11 Australian and one New Zealand subtype H7
 avian influenza A isolates has enabled the comparison of sequences from
 each of the genome segments to other sequenced subtype H7 avian influenza
 A. The inference of phylogenetic relationships for each segment has been
 used to develop a model of the natural history of these viruses in
 Australia. The Australian H7 hemagglutinins form a monophyletic clade,
 consistent with the long-term, independent evolution due to geographic
 isolation. Based on the analysis of the other available H7 hemagglutinins
 sequences, the three other geographic regions for which similar
 monophyletic clades have been observed were confirmed; these regions are
 Eurasia (Africa, Europe and Asia), North America and South America.
 Analysis of datasets of H7N1, H7N3, H7N7 neuraminidase sequences revealed
 congruent relationships indicating a similar pattern of geographically
 constrained independent evolution for each of the neuraminidase subtype
 datasets. This pattern of evolution in geographic isolation is supported
 by analysis of each of the six remaining segments of the Australian
 isolates. These data in combination with the occurrence of five different
 combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7)
 among the 11 Australian isolates suggests a single maintenance network of
 hosts, probably comprising several avian species, for subtype H7 avian
 influenza A in Australia. A clear time based evolution of the
 hemagglutinins sequences despite the occurrence of multiple neuraminidase
 types suggest a genetic pool from which a variety of reassorants arise
 rather than the presence of a small number of stable viral clones. This
 pattern of evolution is likely to occur in each of the regions mentioned
 above as well as possibly a new region comprising of New Zealand, based on
 the apparent genetic isolation of the isolate analyzed in this study.
description: H7 Australian Avian
 Influenza Supplemental MaterialH7AustralianAvianInfluenza_SupplMaterial.odtH7 Australian Avian Influenza SequencesH7AustralianAvianInfluenza_Sequences.ods
DOI: 10.5061/dryad.cr788
title: Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)

description: The relationship between rates of diversification and of body size change
 (a common proxy for phenotypic evolution) was investigated across
 Elapidae, the largest radiation of highly venomous snakes. Time-calibrated
 phylogenetic trees for 175 species of elapids (more than 50% of known
 taxa) were constructed using seven mitochondrial and nuclear genes.
 Analyses using these trees revealed no evidence for a link between
 speciation rates and changes in body size. Two clades (Hydrophis,
 Micrurus) show anomalously high rates of diversification within Elapidae,
 yet exhibit rates of body size evolution almost identical to the general
 elapid ‘background’ rate. Although correlations between speciation rates
 and rates of body size change exist in certain groups (e.g. ray-finned
 fishes, passerine birds), the two processes appear to be uncoupled in
 elapid snakes. There is also no detectable shift in diversification
 dynamics associated with the colonization of Australasia, which is
 surprising given that elapids appear to be the first clade of venomous
 snakes to reach the continent.
description: File_1 : Molecular
 Alignment in nexus/MrBayes formatThe full molecular
 alignment in nexus format, with all MrBayes commands appended. Plain text
 executable file.File_1_elapids_mrb.txtFile_2: Size data for elapids (Excel)Average and maximum body lengths for elapids, with literature sources, in Excel format.File_2_sizeData.xlsxFile_3: BAMM datafiles (zipped)All datafiles for BAMM analyses of diversification rates and body size, in zipped format. Each analysis has a Tree file, control file, and data file (species diversity and sampling, or body size).File_3_BAMM_files.zipFile_4: BayesTraits files (zipped)Data files for analysis of relationship between rates of speciation and rates of body size evolution, for BayesTraits, in zipped format. Tree file and datafile with speciation and size data for all tips.File_4_BayesTraits_files.zipTables S1-2 and Figs S1-S6 (pdf)Pdf file of Supplementary Tables S1-2 and Supplementary Figures S1-S6.FigsS1-S6_TabS1-2_Final.pdf
DOI: 10.5061/dryad.hr069
title: Data from: Individual variation in whole-animal hypoxia tolerance is associated with cardiac hypoxia tolerance in a marine teleost

description: Hypoxia is a pervasive problem in coastal environments and is predicted to
 have enduring impacts on aquatic ecosystems. Intraspecific variation in
 hypoxia tolerance is well documented in fish; however, the factors
 underlying this variation remain unknown. Here, we investigate the role of
 the heart in individual hypoxia tolerance of the European sea bass
 (Dicentrarchus labrax). We found individual whole-animal hypoxia tolerance
 is a stable trait in sea bass for more than 18 months (duration of study).
 We next examined in vitro cardiac performance and found myocardial muscle
 from hypoxia-tolerant individuals generated greater force, with higher
 rates of contraction and relaxation, than hypoxic-sensitive individuals
 during hypoxic exposure. Thus, whole-animal hypoxia tolerance is
 associated with cardiac hypoxia tolerance. As the occurrence of aquatic
 hypoxia is expected to increase in marine ecosystems, our experimental
 data suggest that cardiac performance may influence fish survival and
 distribution.
description: raw contractile force
 data fish 1Data is recorded as a
 continuous time series using World Precision Instruments Software
 DataTrax.17th dec fish 1
 hypoxia.ild17th dec fish 3
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax18th dec fish 4
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax18th dec fish 5
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax19th dec fish 6
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax19th dec fish 7
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax19th dec fish 8
 hypoxiacontinuous time series
 data for cardiac contraction recorded using World Precision Instruments
 software DataTrax20th dec fish 9
 hypoxia20th dec fish 10
 hypoxia20th dec fish 11
 hypoxiaHCT data
 filesdata files for hypoxia
 Challenge tests
DOI: 10.5061/dryad.5h59j
title: Data from: Environmental optimality, not heterogeneity, drives regional and local species richness in lichen epiphytes

description: Aim: We evaluate the scale dependence of species richness–environment
 relationships with a continent-wide analysis of lichen epiphyte
 communities. Specifically, our goals are to assess: (1) the dependence of
 local richness on regional processes, (2) whether species richness is
 primarily influenced by heterogeneity in environmental conditions or the
 central tendency of those conditions, and (3) whether the relative
 influence of these different aspects of the environment differs between
 local communities and regional species pools. Location: Forests of the
 contiguous United States. Methods: We used variation partitioning and
 model averaging of linear models to relate macrolichen richness at 1923
 forest inventory plots (c. 4000 m2) to measures of environmental
 heterogeneity and mean conditions at local and regional scales. Data
 included 17 local environmental variables and 11 regional-scale variables
 which were obtained from a national forest inventory, herbarium records
 and several climate data sources. Results: Regional-scale variables
 explained more unique variation in local species richness and generally
 had stronger effects than variables measured locally. However, most
 variation in local richness was explained jointly by local and regional
 variables. At both local and regional scales, variables measuring
 environmental heterogeneity explained little variation in species richness
 and had weaker effects than variables characterizing mean environmental
 conditions. Main conclusions: Species richness of epiphytic macrolichens
 is not regulated by environmental heterogeneity locally or regionally and
 instead tracks large-scale climate gradients of water availability and
 temperature. Richness in local communities is influenced by processes
 operating at both regional and local scales, highlighting the importance
 of determining large-scale drivers of lichen richness across the North
 American continent. This research demonstrates a general method for
 comparing the influence of different aspects of the environment on species
 richness across scales and should be applicable to many different
 taxonomic groups.
description: Coyle&Hurlbert_GEBData files and code for conducting analyses described in the associated publication. Includes a README file.
DOI: 10.5061/dryad.t67ng
title: Data from: Novel insights into the map stage of true navigation in non-migratory wild birds (stone curlews, Burhinus oedicnemus)

description: In the map-and-compass model of true navigation, animals in unfamiliar
 sites determine their position relative to a destination site (the map
 stage) before progressing towards it (the compass stage). A major
 challenge in animal navigation research is to understand the still cryptic
 map stage in general, and for free-ranging wild animals in particular. To
 address this challenge, we experimentally translocated wild, non-migratory
 birds (Stone curlews (Burhinus oedicnemus)) far from their nests and
 GPS-tracked their subsequent movements at high resolution and for long
 durations. Homing success was high, and cannot be explained by random
 chance or landmark navigation, implying true navigation. Although highly
 motivated to return home, the homing trajectories of translocated birds
 exhibited a distinct, two-phase pattern resembling the map and compass
 stages: a long, tortuous "wandering phase" without consistent
 approach home, followed by a short and direct "return phase".
 Birds re-translocated to the same site initially repeated the original
 wandering path but switched to the return phase earlier and after covering
 a smaller area; they returned home via a different path but with similar
 movement properties. We thus propose that birds resolve the map by
 acquiring, and potentially learning, the relevant navigation cues during
 the wandering phase.
description: Trajectories all birds
 (n=14)Three files:1. The first
 time each bird was translocated to an unfamiliar area (figure S1). 2. The
 second time each bird was translocated to a familiar area (figure S1).3.
 Home range movements.trajectories
 file.rar
DOI: 10.5061/dryad.pf66v
title: Data from: Using an insect mushroom body circuit to encode route memory in complex natural environments

description: Ants, like many other animals, use visual memory to follow extended routes
 through complex environments, but it is unknown how their small brains
 implement this capability. The mushroom body neuropils have been
 identified as a crucial memory circuit in the insect brain, but their
 function has mostly been explored for simple olfactory association tasks.
 We show that a spiking neural model of this circuit originally developed
 to describe fruitfly (Drosophila melanogaster) olfactory association, can
 also account for the ability of desert ants (Cataglyphis velox) to rapidly
 learn visual routes through complex natural environments. We further
 demonstrate that abstracting the key computational principles of this
 circuit, which include one-shot learning of sparse codes, enables the
 theoretical storage capacity of the ant mushroom body to be estimated at
 hundreds of independent images.
description: Code for mushroom body
 and other modelsCode for running our
 mushroom body model and the other comparative navigation
 models.MB_ant.tar.gz
DOI: 10.5061/dryad.83367
title: Data from: The extinct, giant giraffid Sivatherium giganteum: skeletal reconstruction and body mass estimation

description: Sivatherium giganteum is an extinct giraffid from the Plio–Pleistocene
 boundary of the Himalayan foothills. To date, there has been no rigorous
 skeletal reconstruction of this unusual mammal. Historical and
 contemporary accounts anecdotally state that Sivatherium rivalled the
 African elephant in terms of its body mass, but this statement has never
 been tested. Here, we present a three-dimensional composite skeletal
 reconstruction and calculate a representative body mass estimate for this
 species using a volumetric method. We find that the estimated adult body
 mass of 1246 kg (857—1812 kg range) does not approach that of an African
 elephant, but confirms that Sivatherium was certainly a large giraffid,
 and may have been the largest ruminant mammal that has ever existed. We
 contrast this volumetric estimate with a bivariate scaling estimate
 derived from Sivatherium's humeral circumference and find that there
 is a discrepancy between the two. The difference implies that the humeral
 circumference of Sivatherium is greater than expected for an animal of
 this size, and we speculate this may be linked to a cranial shift in
 centre of mass.
description: Convex hull from initial
 skeletal modelMinimum convex hulls
 from the initial 'preferred' skeletal segments have been
 combined into one 3d model. Model volume is equal to the combined volumes
 of the merged segments.preferred merged
 hull.objConvex hull from
 'minimum' sensitivity analysis modelminumum sensitivity merged
 hull.objConvex hull from
 'maximum' sensitivity analysis modelmaxiumum merged
 hull.obj
DOI: 10.5061/dryad.76735
title: Data from: The trade-off between clutch size and egg mass in tree swallows (Tachycineta bicolor) is modulated by female body mass

description: Egg production is a costly component of reproduction for female birds in
 terms of energy expenditure and maternal investment. Because resources are
 typically limited, clutch size and egg mass are expected to be
 constrained, and this putative trade-off between offspring number and size
 is at the core of life history theory. Nevertheless, empirical evidence
 for this trade-off is equivocal at best, as individual heterogeneity in
 resource acquisition and allocation may hamper the detection of the
 negative correlation between egg number and mass within populations. Here,
 we investigated how female body mass and landscape composition influences
 clutch size, egg mass, and the relationship between these two traits. To
 do so, we fitted linear mixed models using data from tree swallows
 Tachycineta bicolor breeding in a network of 400 nestboxes located along a
 gradient of agricultural intensity between 2004 and 2011. Our dataset
 comprised 1463 broods for clutch size analyses and 4371 eggs (from 847
 broods laid between 2005–2008) for egg mass analyses. Our results showed
 that agricultural intensity negatively impacted clutch size, but not egg
 mass nor the relationship between these two traits. Female mass, on the
 other hand, modulated the trade-off between clutch size and egg mass. For
 heavier females, both traits increased jointly, without evidence of a
 trade-off. However, for lighter females, there was a clear negative
 relationship between clutch size and egg mass. This work shows that
 accounting for individual heterogeneity in body mass allows the detection
 of a clutch size/egg mass trade-off that would have remained undetected
 otherwise. Identifying habitat and individual effects on resource
 allocation towards reproductive traits may help bridging the gap between
 predictions from theory and empirical evidence on life history trade-offs.
description: Clutch Size
 DataDataset for clutch size
 analysesClutchSizeData.txtEgg Mass DataDataset for egg mass analysesEggMassData.txt
DOI: 10.5061/dryad.3q24t
title: Data from: Late-glacial demographic expansion motivates a clock overhaul for population genetics

description: The molecular clock hypothesis is fundamental in evolutionary biology as
 by assuming constancy of the molecular rate it provides a time frame for
 evolution. However, increasing evidence shows time dependence of inferred
 molecular rates with inflated values obtained using recent calibrations.
 As recent demographic calibrations are virtually non-existent in most
 species, older phylogenetic calibration points (&gt;1 Ma) are commonly
 used, which overestimate demographic parameters. To obtain more reliable
 rates of molecular evolution for population studies, I propose the
 Calibration of Demographic Transition (CDT) method, which uses the timing
 of climatic changes over the late glacial warming period to calibrate
 expansions in various species. Simulation approaches and empirical
 datasets from a diversity of species (from mollusk to humans) confirm
 that, when compared to other genealogy-based calibration methods, the CDT
 provides a robust and broadly applicable clock for population genetics.
 The resulting CDT rates of molecular evolution also confirm rate
 heterogeneity over time and among taxa. Comparisons of expansion dates
 with ecological evidence confirm the inaccuracy of phylogenetically
 derived divergence rates when dating population-level events. The CDT
 method opens opportunities for addressing issues such as demographic
 responses to past climate change and the origin of rate heterogeneity
 related to taxa, genes, time and genetic information content.
description: Dryad
 datasetsCDT_example
 file
DOI: 10.5061/dryad.68184
title: Data from: Community-wide changes in inter-taxonomic temporal co-occurrence resulting from phenological shifts

description: Global climate change is known to affect the assembly of ecological
 communities by altering species’ spatial distribution patterns, but little
 is known about how climate change may affect community assembly by
 changing species’ temporal co-occurrence patterns, which is highly likely
 given the widely observed phenological shifts associated with climate
 change. Here we analyzed a 29-year phenological data set comprising
 community-level information on the timing and span of temporal occurrence
 in 11 seasonally occurring animal taxon groups from 329 local
 meteorological observatories across China. We show that widespread shifts
 in phenology have resulted in community-wide changes in the temporal
 overlap between taxa that are dominated by extensions, and that these
 changes are largely due to taxa's altered span of temporal occurrence
 rather than the degree of synchrony in phenological shifts. Importantly,
 our findings also suggest that climate change may have led to less
 phenological mismatch than generally presumed, and that the context under
 which to discuss the ecological consequences of phenological shifts should
 be expanded beyond asynchronous shifts.
description: Hua_et_al-Phenology and
 weather data1. Raw time series on
 the first and last sighting of 50 animal taxa collected from 360
 meteorological observatories between 1981 and 2009. 2. Weather data from
 the same sites where phenological data were collected, including records
 on the daily maximum, minimum, and mean temperature, and daily
 precipitation. In all, weather data for 349 sites within China were
 presented.
DOI: 10.5061/dryad.r4q34
title: Data from: Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns

description: Epidemics of infectious diseases often occur in predictable limit cycles.
 Theory suggests these cycles can be disrupted by high amplitude seasonal
 fluctuations in transmission rates, resulting in deterministic chaos.
 However, persistent deterministic chaos has never been observed, in part
 because sufficiently large oscillations in transmission rates are
 uncommon. Where they do occur, the resulting deep epidemic troughs break
 the chain of transmission, leading to epidemic extinction, even in large
 cities. Here we demonstrate a new path to locally persistent chaotic
 epidemics via subtle shifts in seasonal patterns of transmission, rather
 than through high-amplitude fluctuations in transmission rates. We base
 our analysis on a comparison of measles incidence in 80 major cities in
 the prevaccination era United States and United Kingdom. Unlike the
 regular limit cycles seen in the UK, measles cycles in US cities
 consistently exhibit spontaneous shifts in epidemic periodicity resulting
 in chaotic patterns. We show that these patterns were driven by small
 systematic differences between countries in the duration of the summer
 period of low transmission. This example demonstrates empirically that
 small perturbations in disease transmission patterns can fundamentally
 alter the regularity and spatiotemporal coherence of epidemics.
description: Measles incidence in 80
 cities in the prevaccination US/UKReported measles cases
 in 80 large cities in the prevaccination United States and United Kingdom,
 each biweek for 20 years. US data spans 1920-1940. UK data spans
 1944-1964. Estimated population size of each city, and estimated
 susceptible recruitment over time are also included.measlesUKUS.csv