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Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
No full textThe fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since their initial colonization of land, increasing at most threefold over the last 300 million years. Statistical comparisons support phase-shift models, with most increases in local richness occurring: (1) during the colonization of land by vertebrates, concluding by the late Carboniferous; and (2) across the Cretaceous/Paleogene boundary. Individual groups, such as mammals, lepidosaurs and dinosaurs also experienced early increases followed by periods of stasis often lasting tens of millions of years. Mammal local richness abruptly tripled across the Cretaceous/Paleogene boundary, but did not increase over the next 66 million years. These patterns are consistent with the hypothesis that diversity is constrained at the local-community scale.<br><br><h3>Usage Notes</h3><br>code-for-close-et-al-diversity-dynamics-of-phanerozoic-terrestrial-tetrapods-at-the-local-scaleAll analysis code (R scripts) and data (CSV files downloaded from the Paleobiology Database at www.paleobiodb.org)
Data from: Evaluating the foraging performance of individual honey bees in different environments with automated field RFID systems
No full textMeasuring the individual foraging performances of pollinators is crucial to guide environmental policies that aim at enhancing pollinator health and pollination services. Automated systems have been developed to track the activity of individual honey bees, but their deployment is extremely challenging. This has limited the assessment of individual foraging performances in full-strength bee colonies in the field. Most studies available to date have been constrained to use downsized bee colonies located in urban and suburban areas. Environmental policy-making, on the other hand, needs a more comprehensive assessment of honey bee performances in a broader range of environments, including in remote agricultural and wild areas. Here we detail a new autonomous field method to record high quality data on the flight ontogeny and foraging performance of honey bees, using Radio-Frequency Identification (RFID). We separate bee traffic into returning and exiting tunnels to improve data quality, solving many previous limitations of RFID systems caused by traffic jams and the parasitic coupling of RFID antennae. With this method, we assembled a large RFID dataset made of control bee colonies from experiments conducted in different locations and seasons. We hope our results will be a starting point to understand how ontogenetic and environmental factors affect the individual performances of honey bees, and that our method will enable the large-scale replication of individual pollinator performance studies
Data from: Evidence for a mid-Jurassic adaptive radiation in mammals
No full textA series of spectacular discoveries have transformed our understanding of Mesozoic mammals in recent years. These finds reveal hitherto-unsuspected ecomorphological diversity that suggests that mammals experienced a major adaptive radiation during the Middle to Late Jurassic. Patterns of mammalian macroevolution must be reinterpreted in light of these new discoveries, but only taxonomic diversity and limited aspects of morphological disparity have been quantified. We assess rates of morphological evolution and temporal patterns of disparity using large datasets of discrete characters. Rates of morphological evolution were significantly elevated prior to the Late Jurassic, with a pronounced peak occurring during the Early to Middle Jurassic. This intense burst of phenotypic innovation coincided with a stepwise increase in apparent long-term standing diversity and the attainment of maximum disparity, supporting a “short-fuse” model of early mammalian diversification. Rates then declined sharply, and remained significantly low until the end of the Mesozoic, even among therians. This supports the “long-fuse” model of diversification in Mesozoic therians. Our findings demonstrate that sustained morphological innovation in Triassic stem-group mammals culminated in a global adaptive radiation of crown-group members during the Early to Middle Jurassic.<br><br><h3>Usage Notes</h3><br>Analysis R Code and Full ResultsR scripts and input data for all analyses performed in study, including full output files.Dryad Supplementary Figures for Close et al. Elevated morphological rates and high disparity support a mid-Jurassic adaptive radiation in mammalsDryad supplementary figures, including captions.Close_et_al_Current_Biology_Mesozoic_Mammals_BEAST2BEAST 2 XML file for the morphological-clock/tip-dating analysis conducted using the Zhou et al. (2013) Mesozoic mammal matrix
Data from: Genetics and evidence for balancing selection of a sex-linked colour polymorphism in a songbird
No full textColour polymorphisms play a key role in sexual selection and speciation, yet the mechanisms that generate and maintain them are not fully understood. Here, we use genomic and transcriptomic tools to identify the precise genetic architecture and evolutionary history of a sex-linked colour polymorphism in the Gouldian finch Erythrura gouldiae that is also accompanied by remarkable differences in behaviour and physiology. We find that differences in colour are associated with an ~72-kbp region of the Z chromosome in a putative regulatory region for follistatin, an antagonist of the TGF-β superfamily genes. The region is highly differentiated between morphs, unlike the rest of the genome, yet we find no evidence that an inversion is involved in maintaining the distinct haplotypes. Coalescent simulations confirm that there is elevated nucleotide diversity and an excess of intermediate frequency alleles at this locus. We conclude that this pleiotropic colour polymorphism is most probably maintained by balancing selection.<br><br><h3>Usage Notes</h3><br>Kim et al 2019Source data files used to produce Figures in Kim et al. 201
Data from: Geochemical analyses reveal the importance of environmental history for blue carbon sequestration
No full textCoastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands is known to respond to changes imposed by geomorphic evolution, climatic, sea level and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores – two collected from marine influenced saltmarshes (WAP-M and POR-M) and two from fluvial influenced saltmarshes (WAP-F and POR-F) – highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13C NMR analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C, however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales.<br><br><h3>Usage Notes</h3><br>Kelleway et al - 13CNMR -POR-FThis dataset contains results of continuous sampling down the depth of core profiles (ITRAX and magnetic susceptibility) and results of discrete sampling units (13C NMR and particle size characterisation). Methods of analysis are contained within the methods section of the published article.Kelleway et al - Geochemical analyses reveal the importance of environmental history for blue carbon sequestration.xls
Data from: Landscape context explains changes in the functional diversity of regenerating forests better than climate or species richness
No full textAim<br>A rich literature on forest succession provides general expectations for the steps forests go through while reassembling after disturbance, yet we still have a surprisingly poor understanding of why the outcomes of forest recovery after logging (or other disturbances) vary so extensively. In this paper, we test the hypothesis that regional species pool, system productivity, climate and landscape structure are important drivers of forest reassembly outcomes.<br>Location<br>Transect 1,500 km in length along the east coast of Australia.<br>Time period<br>Survey of 50- to 60-year-old rain forest regrowth and primary forest conducted in 2012 and 2013.<br>Major taxa studied<br>Rain forest plants.<br>Methods<br>In this study, we compare species and functional diversity patterns in pairs of remnant and regrowth (‘secondary’) rain forests spread across a 1,500 km climate and productivity gradient along the east coast of Australia. Our controlled natural experiment was designed to test the importance of regional species pool, system productivity, climate and landscape structure as drivers of species and functional diversity in regenerating forests. Notably, our study design allowed us to hold soil type, general forest type and disturbance history relatively constant in order to test our hypotheses effectively.<br>Results<br>Counter to expectations, few tested factors were strongly related to the recovery of species or functional diversity in regenerating Australian rain forests. The extent of local forest fragmentation was the only factor strongly related to differences between regrowth forests and primary forest remnants, and then only for functional diversity. We found no evidence that species diversity is a reasonable proxy for, or potential driver of, functional diversity patterns.<br>Main conclusions<br>Our findings suggest that forest functional recovery over decades is influenced more by regional landscape context than distinct assembly processes operating across climate and productivity gradients.<br><br><h3>Usage Notes</h3><br>Sams_Mayfield_Rf1_AllThis file contains all of the data used in this paper. The file contains nine Excel sheets. The first is a summary of what is contained in each sheet and the remaining eight are pairs of metadata and raw data files. Each metadata sheet matches the name of the relevant datasheet. Data in this file include trait, climate, abundance and landscape data
Data from: Shoot growth of woody trees and shrubs is predicted by maximum plant height and associated traits
No full text1. The rate of elongation and thickening of individual branches (shoots) varies across plant species. This variation is important for the outcome of competition and other plant-plant interactions. Here we compared rates of shoot growth across 44 species from tropical, warm temperate, and cool temperate forests of eastern Australia. 2. Shoot growth rate was found to correlate with a suite of traits including the potential height of the species, xylem-specific conductivity, leaf size, leaf area per xylem cross-section, twig diameter (at 40 cm length), wood density and modulus of elasticity. 3. Within this suite of traits, maximum plant height was the clearest correlate of growth rates, explaining 50 to 67% of the variation in growth overall (p < 0.0001), and 23 to 32% of the variation (p < 0.05) in growth when holding the influence of the other traits constant. Structural equation models suggest that traits associated with ‘hydraulics’, ‘biomechanics’, and the ‘leaf economics spectrum’ represent three clearly separated axes of variation, with the hydraulic axis exhibiting the strongest alignment with height and largest independent contribution to growth (in the case of branch thickening). However most of the capacity of these axes to predict growth was also associated with maximum height, presumably reflecting coordinated selection on multiple traits that together influence life histories. 4. Growth rates were not strongly correlated with leaf nitrogen or leaf mass per unit leaf area. 5. Correlations between growth and maximum height arose both across latitude (47%, p < 0.0001) and from within-site differences between species (30%, p < 0.0001). Covariation between growth and maximum height was driven in part by variation in irradiance across sites as well as among canopy positions within sites (23%, p < 0.0001). A significant fraction of this shared variation was independent of irradiance (45%, p < 0.0001), reflecting intrinsic differences across species and sites.<br><br><h3>Usage Notes</h3><br>trait_data_Gleason_et_al_2017Leaf, stem, xylem, height, shoot growth data for 44 Australian woody dicotyledon species. Trait descriptions and units are given in the last column.trait_publish.cs
Data from: Signatures of local adaptation along environmental gradients in a range-expanding damselfly (Ischnura elegans)
No full textInsect distributions are shifting rapidly in response to climate change and are undergoing rapid evolutionary change. We investigate the molecular signatures underlying local adaptation in the range-expanding damselfly, Ischnura elegans. Using a landscape genomic approach combined with generalized dissimilarity modelling (GDM), we detect selection signatures on loci via allelic frequency change along environmental gradients. We analyse 13,612 Single Nucleotide Polymorphisms (SNPs), derived from Restriction site-Associated DNA sequencing (RADseq), in 426 individuals from 25 sites spanning the I. elegans distribution in Sweden, including its expanding northern range edge. Environmental association analysis (EAA) and the magnitude of allele frequency change along the range expansion gradient revealed significant signatures of selection in relation to high maximum summer temperature, high mean annual precipitation, and low wind speeds at the range edge. SNP annotations with significant signatures of selection revealed gene functions associated with ongoing range expansion, including heat shock proteins (HSP40 and HSP70), ion transport (V-ATPase) and visual processes (long wavelength-sensitive opsin), which have implications for thermal stress response, salinity tolerance and mate discrimination, respectively. We also identified environmental thresholds where climate-mediated selection is likely to be strong, and indicate that I. elegans is rapidly adapting to the climatic environment during its ongoing range expansion. Our findings empirically validate an integrative approach for detecting spatially explicit signatures of local adaptation along environmental gradients.<br><br><h3>Usage Notes</h3><br>Ischnura elegans draft genome assembly Dec 2015This is a draft assembly of the Ischnura elegans genome produced by Pallavi Chauhan, Bengt Hansson, et al. (unpublished). Production date was December, 2015. An updated and annotated reference genome for Ischnura elegans is scheduled to be available on NCBI in 2018.Ischnura_elegans_draftgenome_assemblyDec2015.fastaCompleteness Report for I.elegans draft genome Dec 15Completeness Report for I.elegans draft genome, Dec 2015Ischnura_elegans_draftgenomeDec2015.output.completeness_reportReport for Ischnura_elegans_draftgenomeDec2015Assembly summary data, coverage and statistics for I.elegans draft genome December 2015Ischnura_elegans_draftgenomeDec2015.reportGDM R code for single SNP-based analysisGDM R code for single SNP-based analysis - data formatting, modelling and outputGDM Upload 20180412.REnvironmental dataEnvironmental data for variables used in GDM and EAAUpload1_EnvData.csvSNP_datafileDatafile for 13612 SNPs in genepop format, generated from Stacks 1.40.PlinkMap_datafilePlink .map datafile for 13612 SNPsGDM_TotalmodelOutput_1758snpsTotal model output for GDM of 1758 candidate SNPsSNPannotations and GDMSNP annotations for all candidate loci and GDM output for SNPs meeting criteria for presentation.SNPannotations.xlsxpopmapPopmap of population site IDs and sample IDsOutlier_EAA_SNPs1758List of SNP IDs for all uniquely identified SNPs from Fst Outlier (Bayescan and OutFlank) and Environmental Association Analysis (LFMM) tests
Data from: Species tree of a recent radiation: the subfamily Delphininae (Cetacea, Mammalia)
No full textLineages undergoing rapid radiations provide exceptional opportunities for studying speciation and adaptation, but also represent a challenge for molecular systematics because retention of ancestral polymorphisms and the occurrence of hybridization can obscure relationships among lineages. Dolphins in the subfamily Delphininae are one such case. Non-monophyly, rapid speciation events, and discordance between morphological and molecular characters have made the inference of phylogenetic relationships within this subfamily very difficult. Here we approach this problem by applying multiple methods intended to estimate species trees using a multi-gene dataset for the Delphininae (Sousa, Sotalia, Stenella, Tursiops, Delphinus and Lagenodelphis). Incongruent gene trees obtained indicate that incomplete lineage sorting and possibly hybridization are confounding the inference of species history in this group. Nonetheless, using coalescent-based methods, we have been able to extract an underlying species-tree signal from divergent histories of independent genes that supports relationships based on morphology. This is the first time a molecular study provides support for such relationships. This study further illustrates how methods of species-tree inference can be very sensitive both to the characteristics of the dataset and the evolutionary processes affecting the evolution of the group under study.<br><br><h3>Usage Notes</h3><br>Amaraletal-DelphininaeSpeciesTree nexus fileNexus file for the concatenation of the 13 nuclear loci and 1 mitochondrial gene that were analyzed in order to estimate a species tree for the subfamily Delphininae
Data from: The loneliness of the long-distance toad: invasion history and social attraction in cane toads (Rhinella marina)
No full textIndividuals at the leading edge of a biological invasion constantly encounter novel environments. These pioneers may benefit from increased social attraction, because low population densities reduce competition and risks of pathogen transfer, and increase benefits of information transfer. In standardised trials, cane toads (Rhinella marina) from invasion-front populations approached conspecifics more often, and spent more time close to them, than did conspecifics from high-density, long-colonised populations.<br><br><h3>Usage Notes</h3><br>Gruber et al. 2017 Social Attraction Dataset doi 10.5061 dryad.g72j